US20180148733A1 - Methods for increasing plant growth and yield by using an ictb sequence - Google Patents

Methods for increasing plant growth and yield by using an ictb sequence Download PDF

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US20180148733A1
US20180148733A1 US15/572,326 US201615572326A US2018148733A1 US 20180148733 A1 US20180148733 A1 US 20180148733A1 US 201615572326 A US201615572326 A US 201615572326A US 2018148733 A1 US2018148733 A1 US 2018148733A1
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plant
ictb
seq
expression
coding sequence
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Benjamin Neil Gray
Matthew Begemann
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Benson Hill Inc
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Benson Hill Biosystems Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • the invention is drawn to compositions and methods for increasing plant growth and yield through expression of an ictB gene in a plant that utilizes C4 photosynthesis and co-expression, in either a C3 or a C4 plant, of an ictB sequence with at least one additional yield-enhancing gene.
  • Traits of interest include plant biomass and yield.
  • Yield is normally defined as the measurable produce of economic value from a crop. This may be defined in terms of quantity and/or quality. Yield is directly dependent on many factors, for example, the number and size of the organs, plant architecture (for example, the number of branches), seed production, leaf senescence, photosynthetic carbon assimilation and more. Root development, nutrient uptake, stress tolerance and early vigor may also be important factors in determining yield. Optimizing the abovementioned factors may therefore contribute to increasing crop yield.
  • Crops such as corn, rice, wheat, canola and soybean account for over half the total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds. They are also a source of sugars, oils and many kinds of metabolites used in industrial processes. Seeds contain an embryo (the source of new shoots and roots) and an endosperm (the source of nutrients for embryo growth during germination and during early growth of seedlings). The development of a seed involves many genes, and requires the transfer of metabolites from the roots, leaves and stems into the growing seed.
  • the endosperm in particular, assimilates the metabolic precursors of carbohydrates, oils and proteins and synthesizes them into storage macromolecules to fill out the grain.
  • An increase in plant biomass is important for forage crops like alfalfa, silage corn and hay.
  • Plants are often characterized by their method of photosynthesis, with most plants using C3, C4, or CAM photosynthesis. While there are a number of plant species that appear to be capable of utilizing one type of photosynthesis under certain environmental conditions and another type of photosynthesis under different environmental conditions, most plants primarily use one of these three classes of photosynthesis. A number of highly productive and economically important crop plants including maize, sugarcane, sorghum, millet, switchgrass, and Miscanthus sp. use C4 photosynthesis. Additionally, a major research effort is ongoing to convert rice ( Oryza sativa ) from a C3 to a C4 plant by using the tools of genetic engineering (http://c4rice.irri.org/).
  • C4 plants are characterized by their cellular specialization, with a ‘C4 carbon shuttle’ used as a way to concentrate CO 2 in bundle sheath cells after it diffuses into mesophyll cells from the atmosphere.
  • CO 2 is first converted into oxaloacetate (C 4 H 2 O 4 2 ⁇ ) in mesophyll cells; the four carbons in oxaloacetate give the C4 photosynthetic pathway its name.
  • This oxaloacetate then undergoes a series of chemical reactions and is transported into bundle sheath cells where it is fixed via the Calvin-Benson cycle into molecules that the plant uses for its growth.
  • C4 plants are more productive than C3 plants in some environments, but methods to improve the productivity of C4 plants are desired.
  • crop yield is a trait that is controlled by many factors.
  • One contributing factor is the rate of photosynthetic carbon assimilation by the plant.
  • rate of photosynthetic carbon assimilation By increasing the rate of carbon assimilation, plant growth and ultimately plant yield may be increased. Therefore, methods for increasing photosynthetic carbon assimilation, particularly C4 photosynthetic carbon assimilation, are desired.
  • compositions and methods for increasing plant growth for higher crop yield involve the expression in a C4 plant of interest of at least one ictB coding sequence. Further provided are compositions and methods for the expression in a plant of interest of at least one ictB coding sequence and increasing the expression of at least one additional coding sequence selected from CO 2 assimilating sequences, such as those sequences involved in the Calvin Benson cycle, starch synthesis, and C4 carbon shuttle.
  • the coding sequences of the invention may be expressed from a single or multiple expression constructs.
  • Compositions comprise DNA constructs comprising an ictB coding sequence or CO 2 elevating sequence optionally linked to a promoter that drives expression in a plant cell.
  • DNA constructs may express both the ictB coding sequence and the CO 2 assimilating sequence operably linked to a promoter or promoters that drive expression in a plant cell.
  • CO 2 assimilating sequences of interest are described elsewhere herein. Plants, seeds, and plant parts expressing the coding sequences of the invention are encompassed by the invention. Additionally, plants expressing an ictB sequence and showing increased expression of a coding sequence selected from CO 2 assimilating sequences, such as those sequences involved in the Calvin Benson cycle, starch synthesis pathway, and C4 carbon shuttle are encompassed by the invention. It is recognized that any method for introduction of the sequences into a plant of interest can be used in the practice of the invention.
  • Such methods include transformation, breeding and the like.
  • the expression of ictB results in yield gains relative to otherwise similar plants that do not express ictB.
  • the co-expression of ictB with an additional gene or genes of interest results in yield gains relative to otherwise similar plants that are greater than would be expected from the expression of either gene on its own.
  • FIG. 1 Amino acid alignment of ictB protein sequences. Fully conserved residues are indicated by an asterisk (*). Positions at which amino acids have certain conserved properties (e.g., hydrophobicity, acidity/alkalinity) are indicated by a colon (:) or period (.) above said residues.
  • compositions and methods for increasing plant yield involve the production of a transformed plant.
  • the transformed plant expresses an ictB sequence or expresses the ictB sequence with increased expression of at least one coding sequence selected from CO 2 assimilating sequences, such as those sequences involved in the Calvin Benson cycle, starch synthesis pathway, and C4 carbon shuttle. While not bound by any theory, it is believed that expression of ictB in higher plants may drive an increased concentration of CO 2 in chloroplasts.
  • ictB expression in C4 plants can provide benefits, as C4 plants utilize the C4 carbon shuttle to transport an increased concentration of CO 2 in bundle sheath cells and it has been proposed previously that the mode-of-action by which ictB expression enhances yield in C3 plants is through a concentration of CO 2 in chloroplasts.
  • a “C4 photosynthetic plant” or a “C4 plant” are photosynthetic plants that use the C4 carbon shuttle to increase CO 2 concentrations in the chloroplasts of bundle sheath cells.
  • a report was published describing negative phenotypic effects of ictB expression in soybean (Piatek N L (2015) MS Thesis, University of Illinois at Urbana-Champaign), thus calling into question whether ictB expression can universally improve growth, even in C3 plants.
  • ictB has been proposed to increase CO 2 concentrations in chloroplasts, thereby improving photosynthetic carbon fixation. Recent studies have called this proposed function of ictB in higher plants into question, with some researchers (Price et al (2012) J Exp Bot 64: 753-768) suggesting that ictB may in fact not act as a bicarbonate transporter in higher plants. Without being bound by any theory, the expression of an ictB gene in higher plants may provide benefits to the plant by modulating the expression of native plant genes or suites of genes. Alternatively, the expression of an ictB gene in higher plants may provide benefits to the plant by causing changes in the plant metabolomic profile.
  • the altered expression of native plant genes or altered metabolomic profile may cause improved growth, seed production, and/or yield in ictB-expressing plants relative to control plants that do not express an ictB gene.
  • the mode of action by which ictB expression improves yield in plants that utilize C3 photosynthesis may differ from the mode of action by which ictB expression improves yield in plants that utilize C4 photosynthesis. Accordingly, the optimal expression strategies for ictB may differ between C3 and C4 plants.
  • Improvement of the function of the Calvin-Benson cycle in such a plant comprises increasing the expression of at least one gene involved in CO 2 assimilation, including genes involved in the Calvin Benson cycle, starch synthesis, and C4 carbon shuttle.
  • genes include SBPase, fructose-1,6-bisphosphatase (FBPase), transketolase, and fructose-1,6-bisphosphate aldolase (FBP aldolase), ADP glucose pyrophosphorylase (AGPase), starch synthase, sucrose phosphate synthase, hc1 (also known as EVE), PHB8 (US20140259220), ATPase, carbonic anhydrase (CA), and the like.
  • AGPase ADP glucose pyrophosphorylase
  • starch synthase starch synthase
  • sucrose phosphate synthase sucrose phosphate synthase
  • hc1 also known as EVE
  • PHB8 US20140259220
  • ATPase carbonic anhydrase (CA), and the like.
  • any method for increasing expression of CO 2 assimilating sequences is encompassed by the present invention. That is, the plant may be manipulated to increase the expression of a native sequence or the plant may be transformed with a construct comprising a promoter that drives expression in the plant operably linked to a CO 2 assimilating sequence.
  • the plant can be transformed with a transcription factor (TF) that regulates the expression of a gene involved in photosynthesis.
  • TF transcription factor
  • the methods of the invention comprise altering the expression of TFs that regulate the expression of genes involved in photosynthesis in plants engineered to express ictB.
  • Additive and/or synergistic benefits for photosynthesis and plant growth and yield may be realized through the co-expression of ictB with genes involved in the Calvin-Benson cycle, the starch or sucrose biosynthetic pathways, water use and hydraulic conductivity, ATP production, CO 2 conversion to HCO 3 ⁇ , or regulation of photosynthetic gene expression.
  • the present invention describes strategies to co-express ictB, a gene derived from a cyanobacterial species and involved in carbon dioxide acquisition, with other genes that may increase plant growth and yield.
  • ictB a gene derived from a cyanobacterial species and involved in carbon dioxide acquisition
  • the co-expression of ictB with these additional genes results in yield gains that are greater than would be realized by the expression of any of these genes alone.
  • Recombinant and heterologous nucleotide sequences encoding the genes of interest are provided. Methods to alter the expression level and/or profile of native plant genes in order to improve plant growth are described.
  • Crop yield is intended the measurement of the amount of a crop that was harvested per unit of land area. Crop yield is the measurement often used for grains or cereals and is typically measured as the amount of plant harvested per unit area for a given time, i.e., metric tons per hectare or kilograms per hectare. Crop yield can also refer to the actual seed or biomass produced or generated by the plant.
  • a “recombinant polynucleotide” comprises a combination of two or more chemically linked nucleic acid segments which are not found directly joined in nature. By “directly joined” is intended the two nucleic acid segments are immediately adjacent and joined to one another by a chemical linkage.
  • the recombinant polynucleotide comprises a polynucleotide of interest or active variant or fragment thereof such that an additional chemically linked nucleic acid segment is located either 5′, 3′ or internal to the polynucleotide of interest.
  • the chemically-linked nucleic acid segment of the recombinant polynucleotide can be formed by deletion of a sequence.
  • the additional chemically linked nucleic acid segment or the sequence deleted to join the linked nucleic acid segments can be of any length, including for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or greater nucleotides.
  • Various methods for making such recombinant polynucleotides are disclosed herein, including, for example, by chemical synthesis or by the manipulation of isolated segments of polynucleotides by genetic engineering techniques.
  • the recombinant polynucleotide can comprise a recombinant DNA sequence or a recombinant RNA sequence.
  • a “fragment of a recombinant polynucleotide” comprises at least one of a combination of two or more chemically linked amino acid segments which are not found directly joined in nature.
  • a “recombinant polynucleotide construct” comprises two or more operably linked nucleic acid segments that are not found operably linked in nature.
  • Non-limiting examples of recombinant polynucleotide constructs include a polynucleotide of interest or active variant or fragment thereof operably linked to heterologous sequences which aid in the expression, autologous replication, and/or genomic insertion of the sequence of interest.
  • heterologous and operably linked sequences include, for example, promoters, termination sequences, enhancers, etc, or any component of an expression cassette; a plasmid, cosmid, virus, autonomously replicating sequence, phage, or linear or circular single-stranded or double-stranded DNA or RNA nucleotide sequence; and/or sequences that encode heterologous polypeptides.
  • a “recombinant polypeptide” comprises a combination of two or more chemically linked amino acid segments which are not found directly joined in nature.
  • the recombinant polypeptide comprises an additional chemically linked amino acid segment that is located either at the N-terminal, C-terminal or internal to the recombinant polypeptide.
  • the chemically-linked amino acid segment of the recombinant polypeptide can be formed by deletion of at least one amino acid.
  • the additional chemically linked amino acid segment or the deleted chemically linked amino acid segment can be of any length, including for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or amino acids.
  • transgenic plants and plant cells are provided in the invention which exhibit increased plant yield.
  • the transgenic plants are C4 plants involving expression of a ictB sequence in the plant.
  • transgenic plants in which an ictB protein is expressed in combination with another gene are encompassed.
  • a “transgenic plant” or “transgenic plant cell” refers to any plant in which one or more, or all, of the cells of the plant include a recombinant or heterologous nucleic acid sequence.
  • a transgenic plant or transgenic plant cell may comprise a transgene integrated within a nuclear genome or organelle genome, or may comprise extra-chromosomally replicating DNA.
  • transgene refers to a nucleic acid that is partly or entirely heterologous, foreign, to a transgenic plant or plant cell into which it is introduced, or a nucleic acid that is present in the plant or plant cell in a genomic or extra-chromosomal position different from that in which the gene is found in nature.
  • heterologous in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.
  • the invention comprises synthetic oligonucleotides or nucleotide sequences.
  • a synthetic sequence is one that is produced or reproduced in a laboratory setting. While the nucleotide sequence may have an altered nucleotide sequence relative to the parent sequence, the synthetic sequence may be identical to the naturally occurring sequence. In both instances, however, the structure of the synthetic sequence is altered or different from that found in the sequence that is directly isolated from its natural setting.
  • altering or “modulating” the expression level of a native plant gene is intended that the expression is upregulated or downregulated relative to the expression level of said gene in a wild-type or control plant. It is recognized that in some instances, plant growth and yield are increased by increasing the expression levels of one or more of the plant genes of the invention, i.e. upregulating expression. Likewise, in some instances, plant growth and yield may be increased by decreasing the expression levels of one or more of the plant genes of the invention, i.e. downregulating expression. Thus, the invention encompasses the upregulation or downregulation of one or more of the genes of the invention.
  • the methods include the upregulation of at least one plant gene and the downregulation of at least one plant gene in a plant of interest that has been engineered to express an ictB gene.
  • concentration and/or activity of at least one of the plant genes of the invention in a transgenic plant is intended that the concentration and/or activity is increased or decreased by at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% relative to a native control plant, plant part, or cell which did not have the sequence of the invention introduced.
  • the expression level of a plant gene may be measured directly, for example, by assaying for the level of the RNA transcript encoded by the plant gene of interest in the plant cells of interest.
  • compositions of the invention are used to alter expression of genes of interest in a plant, particularly genes involved in photosynthesis. Therefore, the expression of a plant gene involved in photosynthetic metabolism may be modulated as compared to a control plant.
  • a “subject plant or plant cell” is one in which genetic alteration, such as transformation, has been effected as to a gene of interest, or is a plant or plant cell which is descended from a plant or cell so altered and which comprises the alteration.
  • a “control” or “control plant” or “control plant cell” provides a reference point for measuring changes in phenotype of the subject plant or plant cell. Thus, the expression levels are higher or lower than those in the control plant depending on the methods of the invention.
  • a control plant or plant cell may comprise, for example: (a) a wild-type plant or cell, i.e., of the same genotype as the starting material for the genetic alteration which resulted in the subject plant or cell; (b) a plant or plant cell of the same genotype as the starting material but which has been transformed with a null construct (i.e.
  • a construct which has no known effect on the trait of interest such as a construct comprising a marker gene
  • a construct comprising a marker gene a construct which has no known effect on the trait of interest, such as a construct comprising a marker gene
  • a plant or plant cell which is a non-transformed segregant among progeny of a subject plant or plant cell
  • a plant or plant cell genetically identical to the subject plant or plant cell but which is not exposed to conditions or stimuli that would induce expression of the gene of interest or (e) the subject plant or plant cell itself, under conditions in which the gene of interest is not expressed.
  • transformed organisms of the invention also include plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
  • the invention encompasses simultaneous modulation of the expression of more than one gene in a plant of interest. Further, the methods and compositions disclosed herein encompass the expression of an ictB protein-encoding gene in a plant of interest that utilizes the C4 photosynthetic pathway.
  • a person skilled in the art will recognize that where more than one gene is being modulated, there are many ways to achieve such simultaneous modulation of expression.
  • a plant cell may be transformed with a vector containing a single, or more than one gene cassette. For example, a full gene cassette comprising at least a plant promoter and an ictB coding sequence may be introduced into a plant. Alternatively, multiple transformation vectors may be used for co-transformation of a plant cell in order to modulate multiple gene targets.
  • transformation approaches or breeding approaches may be used to produce a first plant line wherein the expression of a first gene (e.g., ictB) has been modulated or effected.
  • This plant line may be crossed with a second plant line wherein a second gene of interest has been modulated through a breeding approach or through a transformation approach.
  • the second plant line has certain desirable attributes.
  • the plants resulting from such a cross may be expected to show the desired modulation of both genes of interest or the desired phenotypes as a result of ictB gene expression. Modulation of the genes of interest, such as the ictB gene, is assayed through the use of molecular approaches including RT-PCR, Northern blotting, or quantitative RT-PCR.
  • transformation and breeding approaches to achieve the simultaneous modulation of the expression of two genes may also be used to simultaneously modulate more than two genes through the use of the appropriate transformation and/or breeding techniques and the appropriate screening methods to identify plant lines in which the expression of the genes of interest has been modulated as desired. These approaches may be used to simultaneously modulate the expression of three, four, five, six, seven, eight, or more than eight genes in a plant of interest.
  • the invention encompasses isolated or substantially purified polynucleotide or amino acid compositions.
  • An “isolated” or “purified” polynucleotide or protein, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or protein as found in its naturally occurring environment.
  • an isolated or purified polynucleotide or protein is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived.
  • Fragments and variants of the disclosed polynucleotides and amino acid sequences encoded thereby are also encompassed by the present invention.
  • fragment is intended a portion of the polynucleotide or a portion of the amino acid sequence.
  • variant is intended to mean substantially similar sequences.
  • a variant comprises a polynucleotide having deletions (i.e., truncations) at the 5′ and/or 3′ end; deletion and/or addition of one or more nucleotides at one or more internal sites in the native polynucleotide; and/or substitution of one or more nucleotides at one or more sites in the native polynucleotide.
  • a “native” polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively.
  • variants of a particular polynucleotide of the invention will have at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters as described elsewhere herein.
  • “Variant” amino acid or protein is intended to mean an amino acid or protein derived from the native amino acid or protein by deletion (so-called truncation) of one or more amino acids at the N-terminal and/or C-terminal end of the native protein; deletion and/or addition of one or more amino acids at one or more internal sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein.
  • Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native plant protein.
  • Biologically active variants of a native plant protein of the invention will have at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native sequence as determined by sequence alignment programs and parameters described herein.
  • a biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
  • the plant genes of the invention are modulated, i.e., upregulated or downregulated, in a plant of interest. It may be desirable to upregulate at least one plant gene while simultaneously downregulating at least one different plant gene. In other embodiments, it may be desirable to modulate at least one plant gene while simultaneously expressing an ictB gene in the plant or plant cell of interest. See for example U.S. Provisional Application Nos. 62/158,852 and 62/213,759, herein incorporated by reference. Table 1 lists a number of proteins that are linked with photosynthetic metabolism and may be of particular interest for co-accumulation with an ictB protein of interest.
  • upregulation can be achieved by transforming a plant with an expression cassette comprising a promoter that drives expression in the plant operably linked to at least one plant gene of the invention.
  • Alteration of the expression of one or more genes encoding one or more of the proteins listed in Table 1 may be achieved through the use of precise genome-editing technologies to modulate the expression of the endogenous plant gene sequence. In this manner, a nucleic acid sequence will be inserted proximal to a native plant sequence encoding the TF of interest through the use of methods available in the art.
  • Such methods include, but are not limited to, meganucleases designed against the plant genomic sequence of interest (D'Halluin et al 2013 Plant Biotechnol J 11: 933-941); CRISPR-Cas9, CRISPR-Cpf1, TALENs, and other technologies for precise editing of genomes (Feng, et al. (2013) Cell Research 23:1229-1232, Podevin, et al. (2013) Trends Biotechnology 31: 375-383, Wei et al. (2013) J Gen Genomics 40:281-289, Zhang et al (2013), WO 2013/026740, Zetsche et al. (2015) Cell 163:1-13); Cre-lox site-specific recombination (Dale et al.
  • an ictB gene is expressed in a plant that uses C4 photosynthesis.
  • C4 photosynthesis Based on the high productivity of C4 photosynthesis relative to C3 photosynthesis, efforts are underway to transfer C4 photosynthesis into plant species that use C3 photosynthesis in their native state (http://c4rice.irri.org/).
  • researchers have expressed genes known to be involved in C4 photosynthesis in plants such as rice, tobacco, wheat, Arabidopsis , and potato that use C3 photosynthesis in their native state. Examples include plants engineered to express phosphoenolpyruvate carboxylase (PepC) (Fukayama et al. (2003) Photosynthesis Research 77:227-239, Häusler et al.
  • Enhancers include any molecule capable of enhancing gene expression when inserted into the genome of a plant.
  • an enhancer can be inserted in a region of the genome upstream or downstream of at least one gene of interest to enhance expression
  • Enhancers may be cis-acting, and can be located anywhere within the genome relative to a gene for which expression will be enhanced.
  • an enhancer may be positioned within about 1 Mbp, within about 100 kbp, within about 50 kbp, about 30 kbp, about 20 kbp, about 10 kbp, about 5 kbp, about 3 kbp, or about 1 kbp of a coding sequence for which it enhances expression.
  • Enhancers for use in modulating the expression of an endogenous gene or homolog according to the present invention include classical enhancer elements such as the CaMV 35S enhancer element, cytomegalovirus (CMV) early promoter enhancer element, and the SV40 enhancer element, and also intron-mediated enhancer elements that enhance gene expression such as the maize shrunken-1 enhancer element (Clancy, M. and Hannah, L. C. (2002) Plant Physiol. 130(2):918-29).
  • enhancers which may be introduced into a plant genome to modulate expression include a PetE enhancer (Chua et al. (2003) Plant Cell 15:11468-1479), or a rice ⁇ -amylase enhancer (Chen et al. (2002) J. Biol. Chem. 277:13641-13649), or any enhancer known in the art (Chudalayandi, S. (2011) Methods Mol. Biol. 701:285-300).
  • the present invention comprises a subdomain, fragment, or duplicated enhancer element (Benfrey et al. (1990) EMBO J 9:1677-1684).
  • compositions for modulating gene expression in a plant by inserting a promoter or enhancer into a plant genome such that it modulates expression of an endogenous or exogenous sequence are known in the art.
  • Downregulation or reduction of the activity of a plant gene is also encompassed by the methods of the invention.
  • Many techniques for gene silencing are well known to one of skill in the art, including, but not limited to, antisense technology (see, e.g., Sheehy et al. (1988) Proc. Natl. Acad. Sci. USA 85:8805-8809; and U.S. Pat. Nos. 5,107,065; 5,453,566; and 5,759,829); cosuppression (e.g., Taylor (1997) Plant Cell 9:1245; Jorgensen (1990) Trends Biotech. 8(12):340-344; Flavell (1994) Proc. Natl.
  • oligonucleotide-mediated targeted modification e.g., WO 03/076574 and WO 99/25853
  • Zn-finger targeted molecules e.g., WO 01/52620; WO 03/048345; and WO 00/42219
  • transposon tagging Meissner et al. (2000) Plant J. 22:265-274; Phogat et al. (2000) J. Biosci. 25:57-63; Walbot (2000) Curr. Opin. Plant Biol.
  • antisense constructions complementary to at least a portion of the messenger RNA (mRNA) for the gene sequences can be constructed.
  • Antisense nucleotides are constructed to hybridize with the corresponding mRNA. Modifications of the antisense sequences may be made as long as the sequences hybridize to and interfere with expression of the corresponding mRNA. In this manner, antisense constructions having 70%, optimally 80%, more optimally 85% or greater and up to 100% sequence identity to the corresponding sequences to be silenced may be used. Furthermore, portions of the antisense nucleotides may be used to disrupt the expression of the target gene.
  • the polynucleotides of the present invention may also be used in the sense orientation to suppress the expression of endogenous genes in plants.
  • the methods generally involve transforming plants with a DNA construct comprising a promoter that drives expression in a plant operably linked to at least a portion of a polynucleotide that corresponds to the transcript of the endogenous gene.
  • a nucleotide sequence has substantial sequence identity to the sequence of the transcript of the endogenous gene, optimally greater than about 65% sequence identity, more optimally greater than about 85% sequence identity, most optimally greater than about 95% sequence identity. See, U.S. Pat. Nos. 5,283,184 and 5,034,323, herein incorporated by reference. Such methods may be used to reduce the expression of at least one plant gene.
  • Variant sequences can be isolated by PCR.
  • Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York).
  • Variant sequences may also be identified by analysis of existing databases of sequenced genomes. In this manner, corresponding gene sequences can be identified and used in the methods of the invention.
  • Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys Inc., 9685 Scranton Road, San Diego, Calif., USA). Alignments using these programs can be performed using the default parameters.
  • the CLUSTAL program is well described by Higgins et al. (1988) Gene 73:237-244 (1988); Higgins et al.
  • Gapped BLAST in BLAST 2.0
  • PSI-BLAST in BLAST 2.0
  • PSI-BLAST in BLAST 2.0
  • the polynucleotides of the invention can be provided in expression cassettes for expression in a plant of interest.
  • the cassette will include 5′ and 3′ regulatory sequences operably linked to a polynucleotide of the invention. “Operably linked” is intended to mean a functional linkage between two or more elements.
  • the cassette may additionally contain at least one additional gene to be co-transformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes.
  • Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide to be under the transcriptional regulation of the regulatory regions.
  • the expression cassette may additionally contain selectable marker genes.
  • the expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a polynucleotide of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants.
  • a transcriptional and translational initiation region i.e., a promoter
  • a polynucleotide of the invention i.e., a promoter
  • a transcriptional and translational termination region i.e., termination region
  • promoters may be used in the practice of the invention.
  • Constitutive promoters include the CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026), and the like.
  • Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol.
  • Leaf-preferred promoters are also known in the art. See, for example, Yamamoto et al. (1997) Plant J. 12(2):255-265; Kwon et al. (1994) Plant Physiol. 105:357-67; Yamamoto et al. (1994) Plant Cell Physiol.
  • promoters may be desirable for the expression of some genes of interest. Such promoters may show a peak in expression at a particular developmental stage. Such promoters have been described in the art, e.g., U.S. 62/029,068; Gan and Amasino (1995) Science 270: 1986-1988; Rinehart et al. (1996) Plant Physiol 112: 1331-1341; Gray-Mitsumune et al. (1999) Plant Mol Biol 39: 657-669; Beaudoin and Rothstein (1997) Plant Mol Biol 33: 835-846; Genschik et al. (1994) Gene 148: 195-202, and the like.
  • Promoters that are induced following the application of a particular biotic and/or abiotic stress may be desirable for the expression of some genes of interest.
  • Such promoters have been described in the art, e.g., Yi et al. (2010) Planta 232: 743-754; Yamaguchi-Shinozaki and Shinozaki (1993) Mol Gen Genet 236: 331-340; U.S. Pat. No. 7,674,952; Rerksiri et al. (2013) Sci World J 2013: Article ID 397401; Khurana et al. (2013) PLoS One 8: e54418; Tao et al. (2015) Plant Mol Biol Rep 33: 200-208, and the like.
  • Cell-preferred promoters may be desirable for the expression of some genes of interest. Such promoters may preferentially drive the expression of a downstream gene in a particular cell type such as a mesophyll or a bundle sheath cell. Such cell-preferred promoters have been described in the art, e.g., Viret et al. (1994) Proc Natl Acad USA 91: 8577-8581; U.S. Pat. No. 8,455,718; U.S. Pat. No. 7,642,347; Sattarzadeh et al. (2010) Plant Biotechnol J 8: 112-125; Engelmann et al. (2008) Plant Physiol 146: 1773-1785; Matsuoka et al. (1994) Plant J 6: 311-319, and the like.
  • a specific, non-constitutive expression profile may provide an improved plant phenotype relative to constitutive expression of a gene or genes of interest.
  • many plant genes are regulated by light conditions, the application of particular stresses, the circadian cycle, or the stage of a plant's development. These expression profiles may be highly important for the function of the gene or gene product in planta.
  • One strategy that may be used to provide a desired expression profile is the use of synthetic promoters containing cis-regulatory elements that drive the desired expression levels at the desired time and place in the plant. Cis-regulatory elements that can be used to alter gene expression in planta include (Vandepoele et al.
  • Cis-regulatory elements may also be used to alter promoter expression profiles. See, Venter (2007) Trends Plant Sci 12: 118-124.
  • the rapid development of new technologies for transcriptomic studies and of new methods to analyze such datasets has enabled the discovery of new cis-regulatory elements. It is well understood that microarray datasets used previously did not have the same resolution as transcriptomic data generated using RNA-Seq.
  • the use of these newer technologies to generate transcriptomic data and the development of new software algorithms for the analysis of transcriptomic data has enabled the discovery of novel cis-regulatory elements including those described herein.
  • Plant terminators are known in the art and include those available from the Ti-plasmid of A. tumefaciens , such as the octopine synthase and nopaline synthase termination regions. See, for example, Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res. 15:9627-9639.
  • the genes of interest can be used in expression cassettes to transform plants of interest. As indicated, where more than one gene is being expressed in the transformed, the genes can be present on the same cassette or alternatively, more than one cassette may be used. Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing polypeptides and polynucleotides into plant cells include microinjection (Crossway et al. (1986) Biotechniques 4:320 334), electroporation (Riggs et al. (1986) Proc. Natl.
  • transformed seed also referred to as “transgenic seed” having a polynucleotide of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • the present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots.
  • plant species of interest include, but are not limited to, corn ( Zea mays ), Brassica sp. (e.g., B. napus, B. rapa, B.
  • juncea particularly those Brassica species useful as sources of seed oil, alfalfa ( Medicago sativa ), rice ( Oryza sativa ), rye ( Secale cereale ), sorghum ( Sorghum bicolor, Sorghum vulgare ), millet (e.g., pearl millet ( Pennisetum glaucum ), proso millet ( Panicum miliaceum ), foxtail millet ( Setaria italica ), finger millet ( Eleusine coracana )), sunflower ( Helianthus annuus ), safflower ( Carthamus tinctorius ), wheat ( Triticum aestivum ), soybean ( Glycine max ), tobacco ( Nicotiana tabacum ), potato ( Solanum tuberosum ), peanuts ( Arachis hypogaea ), cotton ( Gossypium barbadense, Gossypium hirsutum ), sweet potato ( Ipomoea batat
  • Example 1 Multigenic Constructs Containing ictB and at Least One Additional Gene of Interest
  • Plant transformation vectors were constructed in plasmid backbones containing sequences for maintenance in both E. coli and Agrobacterium tumefaciens . These transformation vectors contained an ictB expression cassette. Each ictB expression cassette contained an ictB open reading frame (SEQ ID NOs: 1 and 542) encoding an ictB protein (SEQ ID NO: 2). The vectors were designed to target the ictB protein to the cytoplasm in plant tissue in the absence of any signal peptide.
  • Certain transformation vectors were designed to target the ictB protein to the chloroplast envelope in vectors where the ictB open reading frame is flanked at its 5′ terminus by a sequence encoding the signal peptide from the RbcS gene (SEQ ID NOs: 3 and 4), resulting in production of the protein described by SEQ ID NO: 544.
  • Certain transformation vectors were designed to target the ictB protein to the plasma membrane in vectors where the ictB open reading frame is flanked at its 5′ terminus by the PR1a signal peptide (SEQ ID NOs: 5 and 6), resulting in production of the protein described by SEQ ID NO: 546.
  • transformation vectors were designed to target the ictB protein to the endoplasmic reticulum (ER) in vectors where the ictB open reading frame is flanked at its 5′ terminus by the PR1a signal peptide (SEQ ID NOs: 5 and 6) and at its 3′ terminus by a SEKDEL sequence (SEQ ID NOs: 7 and 8), resulting in production of the protein described by SEQ ID NO: 548.
  • the four versions of the ictB protein targeted to different subcellular locations are summarized in Table 2.
  • the ictB open reading frames in the plant transformation vectors were flanked at their 5′ ends by a promoter that is functional in plants and a 5′ untranslated region (5′UTR) to direct transcription and translation, respectively, of the open reading frame.
  • the ictB open reading frames were flanked at their 3′ ends by a functional 3′UTR to stabilize the mRNA.
  • Vectors were designed to express the ictB gene constitutively in vectors containing the maize ubiquitin (ZmUbi) promoter and 5′UTR (SEQ ID NO: 9). These vectors contain the ZmUbi 3′UTR (SEQ ID NO: 12) at the 3′ end of the ictB gene.
  • Vectors were also designed to express the ictB gene preferentially in mesophyll cells in vectors containing the maize PepC (ZmPepC) promoter and 5′UTR (SEQ ID NO: 10). These vectors contain the ZmPepC 3′UTR (SEQ ID NO: 13) at the 3′ end of the ictB gene.
  • Vectors were also designed to express the ictB gene preferentially in bundle sheath cells in vectors containing the maize RbcS (ZmRbcS) promoter and 5′UTR (SEQ ID NO: 11), or a truncated version of the ZmRbcS promoter (SEQ ID NO: 541), or the RbcS7A promoter and 5′UTR (SEQ ID NO: 540), or the GLDC promoter (SEQ ID NO: 539).
  • ZmRbcS maize RbcS
  • SEQ ID NO: 11 the maize RbcS promoter and 5′UTR
  • SEQ ID NO: 541 a truncated version of the ZmRbcS promoter
  • RbcS7A promoter and 5′UTR SEQ ID NO: 540
  • GLDC promoter SEQ ID NO: 539
  • the ictB gene that is expressed may encode an ictB protein other than that found in Synechococcus sp. PCC7942 (SEQ ID NO: 2, encoded by SEQ ID NOs: 1 and 542).
  • the ictB protein sequence that is encoded by the ictB gene may be the protein sequence shown in SEQ ID NO: 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, or 536.
  • Multigenic plant transformation vectors contain one of the ictB expression cassettes described above in addition to an expression cassette for one or more additional genes of interest.
  • Multigenic plant transformation vectors were constructed containing an ictB gene along with one or more genes encoding one or more of the amino acid sequences shown in Table 3.
  • Some of the multigenic plant transformation vectors contained an ictB gene that also included one or more signal peptides (i.e., the RbcS, PR1a, and/or SEKDEL signal peptides, as described above).
  • Multigenic plant transformation vectors contain a functional promoter and 5′UTR upstream of each gene of interest. In some preferred embodiments, a functional 3′UTR is included downstream of these gene(s).
  • the multigenic plant transformation vectors contained the genetic elements listed in Table 4. This table lists the SEQ ID NOs for the promoter and 5′UTR used to drive the expression of each gene listed in the table. Both the DNA sequence and the encoded protein sequence are listed for each gene. In addition to the ictB cassette, the multigenic transformation vectors listed in Table 4 contain an additional one, two, or three functional gene cassettes.
  • the plant transformation vectors listed in Table 4 were transformed into A. tumefaciens for plant transformation.
  • the plant tissue of interest was contacted with A. tumefaciens cells containing the plant transformation vectors. Following contact with the A. tumefaciens cells, the plant tissue was placed on a suitable tissue culture medium for regeneration of fertile plants.
  • the multigenic plant transformation vector is coated onto beads for biolistic bombardment of transformable plant tissue. PCR, Southern blotting, or other suitable molecular assays are performed in order to verify the presence of the ictB gene as well as of the other gene(s) of interest in the genome of the transformed plants.
  • ictB gene and of the other gene(s) of interest are verified through the use of RT-PCR, Northern blotting, or other suitable assays to detect the encoded transcripts.
  • the regenerated plants are grown to maturity. Following the maturation of the plants, above-ground biomass is harvested, dried, and weighed. The seeds are harvested, weighed, and counted.
  • Example 2 Transformation of Zea mays with Multigenic Vectors Containing ictB and at Least One Additional Gene
  • the ictB-containing multigenic vectors shown in Table 5 were used to transform maize ( Zea mays ).
  • the genetic elements contained in each of these constructs are included in Table 4.
  • Each of these vectors was transformed into A. tumefaciens and the A. tumefaciens cells harboring the relevant vector was used to transform embryogenic maize callus.
  • the maize tissue was placed on selective tissue culture medium suitable for regenerating transgenic maize plants.
  • the maize plants were transferred to soil and leaf tissue samples were collected.
  • DNA was extracted from the leaves and PCR and/or Taqman-based assays were performed to confirm the integration of the genes of interest in the maize genome.
  • selected plants were chosen for analysis of gene expression.
  • RNA was extracted from leaf tissue harvested from T0-generation transgenic maize events. The RNA was reverse transcribed and quantitative reverse transcriptase-PCR (qRT-PCR) assays were performed to assess the steady-state levels of transgene-encoded mRNA. Primers were designed for these qRT-PCR assays so that the PCR product amplified was specific to the transgene, without any added signal from wild-type transcripts. For these experiments, the primer pair of SEQ ID NOs: 587 and 588 was used to amplify an 82 bp sequence internal to the ictB coding region.
  • qRT-PCR quantitative reverse transcriptase-PCR
  • the primer pair of SEQ ID NOs: 589 and 590 was used to amplify a 119 bp sequence internal to the SBPase coding region.
  • Transcript levels encoded by the various transgenes were compared with the expression of UBCP, a well-known housekeeping gene in the maize genome (Manoli et al (2012) J Plant Physiol 169:807-815).
  • the primer pair of SEQ ID NOs: 581 and 582 were used to amplify the UBCP transcript in these qRT-PCR assays. Transcript levels were expressed relative to the expression of UBCP; an expression level of 2, for example, would indicate that the expression of the transgene was twice as high as that of UBCP.
  • Table 6 summarizes the results of qRT-PCR assays performed with T0-generation maize transformed with multigenic vectors containing an ictB gene in addition to at least one other gene.
  • Transgenic maize plants containing an ictB cassette and one or more additional transgene cassettes are characterized to assess the effects of the transgenes on plant growth and yield.
  • T0-generation maize events are self-pollinated to produce homozygous events. Homozygous events are identified through the use of Taqman assays to assess zygosity. These homozygous plants are used to pollinate suitable maize varieties to produce hybrid seed containing the transgenes of interest. Alternatively, homozygous plants are pollinated by suitable maize varieties to produce hybrid seed containing the transgenes of interest. The hybrid seed is planted in one or more field environments and cultivated using standard agronomic practices.
  • Yield parameters including the time from planting to reach particular developmental stages (e.g., V1, V2, V3, etc., through R1, R2, R3, etc.), plant height, leaf angle, ear length, ear diameter, number of kernel rows, kernel size, 100 seed weight, kernel number, harvest index, and seed yield are measured for the hybrid plants containing the ictB transgene cassette and other transgene cassette(s).
  • the yield parameters for these transgenic plants are compared with hybrid maize plants with the same genetic background but lacking the transgenes. The effects of transgene integration and expression on maize growth and yield are determined from these measurements and comparisons.
  • Example 3 Transformation of Oryza sativa with Multigenic Vectors Containing ictB and at Least One Additional Gene
  • the ictB-containing multigenic vectors shown in Table 7 were used to transform rice ( Oryza sativa ).
  • the genetic elements contained in each of these constructs are included in Table 4.
  • Each of these vectors was transformed into A. tumefaciens and the A. tumefaciens cells harboring the relevant vector was used to transform embryogenic rice callus.
  • the rice tissue was placed on selective tissue culture medium suitable for regenerating transgenic rice plants.
  • the rice plants were transferred to soil and leaf tissue samples were collected.
  • DNA was extracted from the leaves and PCR and/or Taqman-based assays were performed to confirm the integration of the genes of interest in the rice genome.
  • selected plants were chosen for analysis of gene expression.
  • RNA was extracted from leaf tissue harvested from T0-generation transgenic rice events.
  • the RNA was reverse transcribed and quantitative reverse transcriptase-PCR (qRT-PCR) assays were performed to assess the steady-state levels of transgene-encoded mRNA.
  • Primers were designed for these qRT-PCR assays so that the PCR product amplified was specific to the transgene, without any added signal from wild-type transcripts.
  • the primer pair of SEQ ID NOs: 587 and 588 was used to amplify an 82 bp sequence internal to the ictB coding region.
  • the primer pair of SEQ ID NOs: 591 and 592 was used to amplify a 107 bp region spanning the junction between the ism-2 coding region and the ZmUbi 3′UTR.
  • the primer pair of SEQ ID NOs: 593 and 594 was used to amplify a 110 bp region internal to the Populus sp. hc1 gene.
  • the primer pair of SEQ ID NOs: 595 and 596 was used to amplify a 114 bp region internal to the AGPase large subunit coding region.
  • Transcript levels encoded by the various transgenes were compared with the expression of UBQ5, a well-known housekeeping gene in the rice genome (Jain et al (2006) Biochemical and Biophysical Research Communications 345: 646-651).
  • the primer pair of SEQ ID NOs: 583 and 584 were used to amplify the UBQ5 transcript in these qRT-PCR assays.
  • Transcript levels were expressed relative to the expression of UBQ5; an expression level of 2, for example, would indicate that the expression of the transgene was twice as high as that of UBQ5.
  • Table 8 summarizes the results of qRT-PCR assays performed with T0-generation rice transformed with multigenic vectors containing an ictB gene in addition to at least one other gene.
  • Transgenic rice plants containing an ictB cassette and one or more additional transgene cassettes are characterized to assess the effects of the transgenes on plant growth and yield.
  • T0-generation rice events are self-pollinated to produce homozygous events. Homozygous events are identified through the use of Taqman assays to assess zygosity. These homozygous plants are grown in a greenhouse setting along with wild-type and/or null segregant rice plants of the same genetic background but lacking the transgenes.
  • Yield components including plant height, number of tillers, number of panicles, time from planting to reach various developmental stages of interest, seed number, hundred seed weight, seed size, harvest index, and seed yield are measured.
  • the yield parameters for these transgenic plants are compared with rice plants with the same genetic background but lacking the transgenes. The effects of transgene integration and expression on rice growth and yield are determined from these measurements and comparisons.
  • the ictB-containing multigenic vectors shown in Table 9 were used to transform Setaria viridis.
  • the genetic elements contained in each of these constructs are included in Table 4.
  • Each of these vectors was transformed into A. tumefaciens and the A. tumefaciens cells harboring the relevant vector was used to transform S. viridis callus.
  • the S. viridis tissue was placed on selective tissue culture medium suitable for regenerating transgenic S. viridis plants.
  • the S. viridis plants were transferred to soil and leaf tissue samples were collected. DNA was extracted from the leaves and PCR and/or Taqman-based assays were performed to confirm the integration of the genes of interest in the S. viridis genome. Following confirmation of the integration of the genes of interest in the genome, selected plants were chosen for analysis of gene expression.
  • RNA was extracted from leaf tissue harvested from T0-generation transgenic S. viridis events. The RNA was reverse transcribed and quantitative reverse transcriptase-PCR (qRT-PCR) assays were performed to assess the steady-state levels of transgene-encoded mRNA. Primers were designed for these qRT-PCR assays so that the PCR product amplified was specific to the transgene, without any added signal from wild-type transcripts. For these experiments, the primer pair of SEQ ID NOs: 587 and 588 was used to amplify an 82 bp sequence internal to the ictB coding region.
  • qRT-PCR quantitative reverse transcriptase-PCR
  • the primer pair of SEQ ID NOs: 593 and 594 was used to amplify a 110 bp region internal to the Populus sp. hc1 gene.
  • the primer pair of SEQ ID NOs: 595 and 596 was used to amplify a 114 bp region internal to the AGPase large subunit coding region.
  • the primer pair of SEQ ID NOs: 597 and 598 was used to amplify a 111 bp region internal to the FBP aldolase coding region.
  • Transcript levels encoded by the various transgenes were compared with the expression of GAPDH, a well-known housekeeping gene in the S.
  • Transgenic S. viridis plants containing an ictB cassette and one or more additional transgene cassettes are characterized to assess the effects of the transgenes on plant growth and yield.
  • T0-generation S. viridis events are self-pollinated to produce homozygous events. Hemizygous and homozygous events are identified through the use of Taqman assays to assess zygosity. Hemizygous and homozygous plants are grown in a greenhouse setting along with wild-type and/or null segregant S. viridis plants of the same genetic background but lacking the transgenes.
  • Yield components including plant height, number of tillers, number of panicles, time from planting to reach various developmental stages of interest, seed number, hundred seed weight, seed size, harvest index, and seed yield are measured.
  • the yield parameters for these transgenic plants are compared with S. viridis plants with the same genetic background but lacking the transgenes. The effects of transgene integration and expression on S. viridis growth and yield are determined from these measurements and comparisons.
  • the ictB-containing multigenic vectors shown in Table 11 were used to transform potato ( Solanum tuberosum ).
  • the genetic elements contained in each of these constructs are included in Table 4.
  • Each of these vectors was transformed into A. tumefaciens and the A. tumefaciens cells harboring the relevant vector was used to transform potato cells.
  • the potato tissue was placed on selective tissue culture medium suitable for regenerating transgenic potato plants.
  • the potato plants were transferred to soil and leaf tissue samples were collected.
  • DNA was extracted from the leaves and PCR and/or Taqman-based assays were performed to confirm the integration of the genes of interest in the potato genome.
  • selected plants are chosen for analysis of gene expression.
  • Transgenic potato plants containing an ictB cassette and one or more additional transgene cassettes are characterized to assess the effects of the transgenes on plant growth and yield.
  • Transgenic potato events are cultivated in the greenhouse using cuttings to produce multiple plants that can produce seed potatoes. These seed potatoes are grown in either a greenhouse or a field setting to bulk up the seed potatoes for larger-scale field trials. After this bulking up, the seed potatoes are planted in a field setting along with genetically similar potatoes that lack the transgenes of interest. Yield components including photosynthetic rate, above-ground biomass, tuber biomass, and potato yield in terms of pounds per acre are measured. The yield parameters for these transgenic plants are compared with potato plants with the same genetic background but lacking the transgenes. The effects of transgene integration and expression on potato growth and yield are determined from these measurements and comparisons.
  • Example 6 Co-Transformation of a Plant of Interest with an ictB Vector and at Least One Additional Vector
  • a plant transformation vector containing a functional ictB expression cassette is constructed as described in Example 1.
  • a gene encoding an ictB protein is included in this ictB expression cassette, operably linked to a plant promoter and 5′UTR at its 5′ terminus and a 3′UTR at its 3′ terminus.
  • the plant transformation vector containing the ictB expression cassette also contains one or more additional expression cassettes with a plant promoter and 5′UTR operably linked to an open reading frame which is itself operably linked to a 3′UTR. Whether this transformation vector contains only an ictB expression cassette or contains an ictB expression cassette in addition to one or more additional expression cassettes, this is referred to as the “ictB vector.”
  • a second plant transformation vector is constructed containing a gene expression cassette with a functional promoter and 5′UTR upstream of at least one gene of interest, followed by a 3′UTR downstream of this gene of interest.
  • the open reading frame encodes a protein listed in Table 2.
  • this second vector contains additional gene expression cassettes with functional plant promoters, 5′UTRs, open reading frames, and 3′UTRs so that more than one gene of interest may be included in this second vector.
  • This vector is referred to as the “auxiliary vector.” In certain cases it may be desirable to utilize more than one auxiliary vector for co-transformation with the ictB vector, as described below.
  • the ictB vector is transformed into A. tumefaciens cells while the auxiliary vector(s) is/are transformed into separate A. tumefaciens cells.
  • both the ictB vector and the auxiliary vector(s) are transformed into a single A. tumefaciens cell.
  • the ictB vector and the auxiliary vector(s) are coated onto beads for biolistic bombardment of transformable plant tissue. Following Agrobacterium -mediated transformation or biolistic transformation, the plant tissue is placed onto suitable tissue culture medium for regeneration of fertile plants.
  • PCR, Southern blotting, or other suitable molecular assays are performed in order to verify the presence of the ictB gene as well as of the other gene(s) of interest in the genome of the transformed plants. Expression of the ictB gene and of the other gene(s) of interest is verified through the use of RT-PCR, Northern blotting, or other suitable assays to detect the encoded transcripts.
  • the regenerated plants are grown to maturity. Following the maturation of the plants, above-ground biomass is harvested, dried, and weighed. The seeds are harvested, weighed, and counted.
  • FIG. 1 shows an alignment of thirty-seven ictB protein sequences. This alignment shows at least six regions that are extremely well-conserved among all examined ictB protein sequences. The six regions are located at amino acid residues 209-213, 220-235, 274-279, 341-353, 364-372, and 479-486 based on the numbering shown in FIG. 1 .
  • completely conserved amino acids i.e., residues at which only a single amino acid is found in all of the sequences examined
  • Residues at which there appears to be functional conservation i.e., only amino acids that share certain properties are found at a given position
  • the amino acid sequences shown in FIG. 1 include a conserved region from residues 209-213. As shown in this FIGURE, all of the ictB sequences examined contain the sequence AXWXDXXS (SEQ ID NO: 69), where X is any amino acid. In many of the sequences examined, this region contains the sequence ATWVDPXS (SEQ ID NO: 70). A second conserved region located at amino acid positions 220-235 according to the numbering in FIG. 1 contains the sequence RX(F/Y)(G/S)XLXNPNLXXXYL (SEQ ID NO: 71). In many of the sequences examined, this region contains the sequence RX(F/Y)(G/S)XLGNPNLLAGYL (SEQ ID NO: 72).
  • a third conserved region located at amino acid positions 274-279 according to the numbering in FIG. 1 contains the sequence SRGXWX (SEQ ID NO: 73). In many of the sequences examined, this region contains the sequence SRGGW(I/L) (SEQ ID NO: 74).
  • a fourth conserved region located at amino acid positions 341-353 according to the numbering shown in FIG. 1 contains the amino acid sequence RXD(S/T)SNNFRX(N/T)VW (SEQ ID NO: 75). In many of the sequences examined, this region contains the sequence RXDSSNNFRXNVW (SEQ ID NO: 76).
  • FIG. 1 contains the amino acid sequence PXXGIGPG(N/H) (SEQ ID NO: 77).
  • a sixth conserved region located at amino acid positions 479-486 according to the numbering shown in FIG. 1 contains the amino acid sequence DT(I/V)X(F/Y)RPX (SEQ ID NO: 78). In many of the sequences examined, this region contains the sequence DT(I/V)X(F/Y)RP(E/Q) (SEQ ID NO: 79). Without being limited by theory, it is likely that these six well-conserved regions of the ictB sequences examined are functionally important for the ictB protein. Currently, the precise biochemical function of ictB proteins in vivo is unknown.
  • ictB sequences have been expressed in planta, resulting in elevated rates of photosynthesis and improved growth. Without being limited by theory, it is likely that in planta expression of other putative ictB sequences containing one or more of the conserved amino acid sequences described herein, either singly or in combination with one or more additional gene(s) of interest, will also lead to improved photosynthetic metabolism and plant growth.
  • the plant may be grown from seed, or alternatively may be cultivated clonally, e.g., through the use of tissue culture techniques.
  • Control plants such as null segregants or genetically similar wild-type plants of the same species as the ictB-expressing plant, are grown under identical environmental conditions as the ictB-expressing plant.
  • Plant tissue from different organs including leaves, stems, floral buds, flowers, embryo, endosperm, whole seed, and roots is collected from both ictB-expressing plants and from control plants at the same time. RNA is extracted from these tissues and is used to generate RNA libraries.
  • RNA libraries are analyzed by RNA-Seq or other technologies suitable for obtaining sequence data from RNA samples.
  • the transcriptome of the ictB-expressing plants is compared with the transcriptome of the control plants from the corresponding tissue(s).
  • Transcriptomic analyses are undertaken to determine genes and sets of genes whose expression is altered in ictB-expressing plants relative to control plants.
  • the plant may be grown from seed, or alternatively may be cultivated clonally, e.g., through the use of tissue culture techniques.
  • Control plants such as null segregants or genetically similar wild-type plants of the same species as the ictB-expressing plant, are grown under identical environmental conditions as the ictB-expressing plant.
  • Plant tissue from different organs including leaves, stems, floral buds, flowers, embryo, endosperm, whole seed, and roots is collected from both ictB-expressing plants and from control plants at the same time. Metabolites are extracted from these tissues for downstream analysis.
  • Suitable techniques are applied to generate a metabolite profile from the various tissues collected from ictB-expressing plants and from control plants. Following the generation of this metabolomic data, the metabolome of the ictB-expressing plants is compared with the metabolome of the control plants from the corresponding tissue(s). Metabolomic analyses are undertaken to determine metabolites whose accumulation is altered in ictB-expressing plants relative to control plants.
  • Plant transformation vectors were constructed in plasmid backbones containing sequences for maintenance in both E. coli and Agrobacterium tumefaciens . These transformation vectors contained an ictB expression cassette. Each ictB expression cassette contained an ictB open reading frame (SEQ ID NOs: 1 and 542) encoding an ictB protein (SEQ ID NO: 2). The vectors were designed to target the ictB protein to the cytoplasm in plant tissue in the absence of any signal peptide.
  • Certain transformation vectors were designed to target the ictB protein to the chloroplast envelope in vectors where the ictB open reading frame is flanked at its 5′ terminus by a sequence encoding the signal peptide from the RbcS gene (SEQ ID NOs: 3 and 4), resulting in production of the protein described by SEQ ID NO: 544.
  • Certain transformation vectors were designed to target the ictB protein to the plasma membrane in vectors where the ictB open reading frame is flanked at its 5′ terminus by the PR1a signal peptide (SEQ ID NOs: 5 and 6), resulting in production of the protein described by SEQ ID NO: 546.
  • transformation vectors were designed to target the ictB protein to the endoplasmic reticulum (ER) in vectors where the ictB open reading frame is flanked at its 5′ terminus by the PR1a signal peptide (SEQ ID NOs: 5 and 6) and at its 3′ terminus by a SEKDEL sequence (SEQ ID NOs: 7 and 8), resulting in production of the protein described by SEQ ID NO: 548.
  • the four versions of the ictB protein targeted to different subcellular locations are summarized in Table 2.
  • the ictB open reading frames in the plant transformation vectors were flanked at their 5′ ends by a promoter that is functional in plants and a 5′ untranslated region (5′UTR) to direct transcription and translation, respectively, of the open reading frame.
  • the ictB open reading frames were flanked at their 3′ ends by a functional 3′UTR to stabilize the mRNA.
  • Vectors were designed to express the ictB gene constitutively in vectors containing the maize ubiquitin (ZmUbi) promoter and 5′UTR (SEQ ID NO: 9). These vectors contain the ZmUbi 3′UTR (SEQ ID NO: 12) at the 3′ end of the ictB gene.
  • Vectors were also designed to express the ictB gene preferentially in mesophyll cells in vectors containing the maize PepC (ZmPepC) promoter and 5′UTR (SEQ ID NO: 10). These vectors contain the ZmPepC 3′UTR (SEQ ID NO: 13) at the 3′ end of the ictB gene.
  • Vectors were also designed to express the ictB gene preferentially in bundle sheath cells in vectors containing the maize RbcS (ZmRbcS) promoter and 5′UTR (SEQ ID NO: 11), or a truncated version of the ZmRbcS promoter (SEQ ID NO: 541), or the RbcS7A promoter and 5′UTR (SEQ ID NO: 540), or the GLDC promoter (SEQ ID NO: 539).
  • ZmRbcS maize RbcS
  • SEQ ID NO: 11 the maize RbcS promoter and 5′UTR
  • SEQ ID NO: 541 a truncated version of the ZmRbcS promoter
  • RbcS7A promoter and 5′UTR SEQ ID NO: 540
  • GLDC promoter SEQ ID NO: 539
  • Each of these vectors contain the ZmRbcS 3′UTR (SEQ ID NO: 14) at the 3
  • the ictB gene that is expressed may encode an ictB protein other than that found in Synechococcus sp. PCC7942 (SEQ ID NO: 2, encoded by SEQ ID NOs: 1 and 542).
  • the ictB protein sequence that is encoded by the ictB gene may be the protein sequence shown in SEQ ID NO: 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, or 536.
  • the combination of promoter, 5′UTR, 3′UTR, and signal peptide should determine the cell type(s) in which the ictB gene of interest is expressed as well as the subcellular location in which the encoded ictB protein accumulates.
  • Table 13 summarizes the ictB cassettes in the single-genic vectors used for plant transformation. Although some of the ictB cassettes in the constructs in this table are identical, differences in the transformation vector backbone, such as different selectable markers, exist among these constructs and thus certain vectors are more suitable for transformation of particular species despite identical ictB cassettes.
  • Single-genic plant transformation vectors containing a functional ictB expression cassette were constructed as described in Example 10. These vectors were transformed into A. tumefaciens cells suitable for transformation of plant cells.
  • Table 14 summarizes the single-genic ictB transformation vectors used for transformation of S. viridis.
  • A. tumefaciens cells harboring the transformation vectors shown in Table 14 were brought into contact with S. viridis cells suitable for transformation according to a previously published protocol (PCT/US2015/43989). These S. viridis cells were placed onto selective tissue culture medium containing chemicals suitable for selecting transgenic plants.
  • Table 15 summarizes the number of PCR-positive plants that were recovered from S. viridis transformation with the vectors shown in Table 14.
  • Example 12 Transformation of Maize ( Zea mays ) with Single-Genic ictB Vectors
  • Single-genic plant transformation vectors containing a functional ictB expression cassette were constructed as described in Example 10. These vectors were transformed into A. tumefaciens cells suitable for transformation of plant cells. Table 16 summarizes the constructs that were used to transform maize ( Zea mays cv. B104) cells. A. tumefaciens cells harboring the transformation vector of interest were brought into contact with maize cells suitable for transformation. These maize cells were then placed onto selective tissue culture medium containing chemicals suitable for selecting transgenic plants. PCR-based assays were performed to verify the presence of the ictB gene cassette in the maize cells.
  • Table 17 summarizes the number of PCR-positive plants that were recovered from maize transformation with the vectors shown in Table 16.
  • T0-generation S. viridis plants generated as described above were cultivated and grown to maturity, then allowed to self-pollinate to produce T1-generation seed. This T1 seed was planted and cultivated in a greenhouse setting.
  • Quantitative RT-PCR (qRT-PCR) assays were performed to assess the expression level of the ictB transgenes in S. viridis leaf tissue. Table 18 summarizes the expression data from these assays, with the expression levels of the ictB gene shown relative to the GAPDH gene, a well-known S. viridis housekeeping gene (Lambret-Frotté et al (2015) PLoS One 10: e0135006).
  • the primer pair of SEQ ID NOs: 585 and 586 were used to amplify the GAPDH transcript in these qRT-PCR assays.
  • the primer pair of SEQ ID NOs: 587 and 588 was used to amplify an 82 bp sequence internal to the ictB coding region.
  • Eight to ten individual T1-generation ictB-expressing S. viridis plants derived from selected T0 events were cultivated alongside wild-type and/or null segregant S. viridis plants. The number of days required to reach reproductive development were monitored, and upon maturation of the plants, the total dry weight (DW) of the above-ground biomass and seed weight were measured.
  • Harvest index (HI) was calculated from the ratio of dry seed weight to total above ground biomass dry weight.
  • Table 19 summarizes the data from these T1 experiments, with the data expressed as the percent change relative to null segregant plants grown under identical environmental conditions alongside the transgenic plants.
  • a comparison of the data in Tables 18 and 19 indicates that low to moderate expression of the ictB transgene is generally more beneficial than high expression in the plants examined.
  • Events from the 130950 construct generally showed lower expression levels than those from the 130823 construct, and the 130950 construct showed greater biomass and seed yield improvements than the 130823 construct.
  • 130950.4 showed the highest expression level; this event did not show increased biomass or seed yield relative to null segregant controls.
  • Events 130950.1, 130950.5, and 130950.6 showed low expression of the ictB transgene and these plants accumulated more biomass and seed than null segregant plants.
  • T0-generation transgenic maize plants were generated in the B104 inbred cultivar. Pollen from these T0 events was used to pollinate maize plants of the LH51 inbred cultivar to generate F1 hybrid seed. F1 seed from these LH51 ⁇ B104 was planted in a field environment in two-row plots. Wild-type hybrid LH51 ⁇ B104 plants were grown alongside the transgenic hybrid events in the field, as were null segregant plants. Following maturation of the plants, the ears were harvested and kernels were removed from the ears and dried. The weight of the harvested kernels was used to derive yield data in the units of bushels per acre.
  • Table 20 summarizes this yield data, with yield expressed as percent change relative to control plants (wild-type LH51 ⁇ B104 and null segregants) that were grown at the same field site as the transgenic event.
  • This table also includes ictB transgene expression levels derived from qRT-PCR experiments using RNA extracted from T0-Generation events produced in the B104 inbred cultivar.

Abstract

Compositions and methods for increasing plant growth for higher crop yield are provided. The methods involve the expression of at least one ictB coding sequence in a C4 plant of interest. Further provided are methods for expressing at least one ictB coding sequence and increasing the expression of at least one additional coding sequence of interest selected from CO2 assimilating sequences, such as those sequences involved in the Calvin Benson cycle, starch synthesis pathway, and C4 carbon shuttle in the plant. C4 plants expressing an ictB sequence are encompassed by the invention. Additionally, plants expressing an ictB sequence and those plants showing increased expression of a sequence of interest are encompassed by the invention. The expression of ictB in the C4 plant and the co-expression of ictB with this additional gene or genes results in yield gains.

Description

    FIELD OF THE INVENTION
  • The invention is drawn to compositions and methods for increasing plant growth and yield through expression of an ictB gene in a plant that utilizes C4 photosynthesis and co-expression, in either a C3 or a C4 plant, of an ictB sequence with at least one additional yield-enhancing gene.
    • BACKGROUND OF THE INVENTION
  • The ever-increasing world population and the dwindling supply of arable land available for agriculture fuels research towards developing plants with increased biomass and yield. Conventional means for crop and horticultural improvements utilize selective breeding techniques to identify plants having desirable characteristics. However, such selective breeding techniques have several drawbacks, namely that these techniques are typically labor intensive and result in plants that often contain heterogeneous genetic components that may not always result in the desirable trait being passed on from parent plants. Advances in molecular biology provide means to modify the germplasm of plants. Genetic engineering of plants entails the isolation and manipulation of genetic material (typically in the form of DNA or RNA) and the subsequent introduction of that genetic material into a plant. Such technology has the capacity to deliver crops or plants having various improved economic, agronomic or horticultural traits.
  • Traits of interest include plant biomass and yield. Yield is normally defined as the measurable produce of economic value from a crop. This may be defined in terms of quantity and/or quality. Yield is directly dependent on many factors, for example, the number and size of the organs, plant architecture (for example, the number of branches), seed production, leaf senescence, photosynthetic carbon assimilation and more. Root development, nutrient uptake, stress tolerance and early vigor may also be important factors in determining yield. Optimizing the abovementioned factors may therefore contribute to increasing crop yield.
  • An increase in seed yield is a particularly important trait since the seeds of many plants are important for human and animal consumption. Crops such as corn, rice, wheat, canola and soybean account for over half the total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds. They are also a source of sugars, oils and many kinds of metabolites used in industrial processes. Seeds contain an embryo (the source of new shoots and roots) and an endosperm (the source of nutrients for embryo growth during germination and during early growth of seedlings). The development of a seed involves many genes, and requires the transfer of metabolites from the roots, leaves and stems into the growing seed. The endosperm, in particular, assimilates the metabolic precursors of carbohydrates, oils and proteins and synthesizes them into storage macromolecules to fill out the grain. An increase in plant biomass is important for forage crops like alfalfa, silage corn and hay.
  • Plants are often characterized by their method of photosynthesis, with most plants using C3, C4, or CAM photosynthesis. While there are a number of plant species that appear to be capable of utilizing one type of photosynthesis under certain environmental conditions and another type of photosynthesis under different environmental conditions, most plants primarily use one of these three classes of photosynthesis. A number of highly productive and economically important crop plants including maize, sugarcane, sorghum, millet, switchgrass, and Miscanthus sp. use C4 photosynthesis. Additionally, a major research effort is ongoing to convert rice (Oryza sativa) from a C3 to a C4 plant by using the tools of genetic engineering (http://c4rice.irri.org/). C4 plants are characterized by their cellular specialization, with a ‘C4 carbon shuttle’ used as a way to concentrate CO2 in bundle sheath cells after it diffuses into mesophyll cells from the atmosphere. Typically, in C4 plants, CO2 is first converted into oxaloacetate (C4H2O4 2−) in mesophyll cells; the four carbons in oxaloacetate give the C4 photosynthetic pathway its name. This oxaloacetate then undergoes a series of chemical reactions and is transported into bundle sheath cells where it is fixed via the Calvin-Benson cycle into molecules that the plant uses for its growth. C4 plants are more productive than C3 plants in some environments, but methods to improve the productivity of C4 plants are desired.
  • As described above, crop yield is a trait that is controlled by many factors. One contributing factor is the rate of photosynthetic carbon assimilation by the plant. By increasing the rate of carbon assimilation, plant growth and ultimately plant yield may be increased. Therefore, methods for increasing photosynthetic carbon assimilation, particularly C4 photosynthetic carbon assimilation, are desired.
    • SUMMARY OF THE INVENTION
  • Compositions and methods for increasing plant growth for higher crop yield are provided. The methods involve the expression in a C4 plant of interest of at least one ictB coding sequence. Further provided are compositions and methods for the expression in a plant of interest of at least one ictB coding sequence and increasing the expression of at least one additional coding sequence selected from CO2 assimilating sequences, such as those sequences involved in the Calvin Benson cycle, starch synthesis, and C4 carbon shuttle. The coding sequences of the invention may be expressed from a single or multiple expression constructs. Compositions comprise DNA constructs comprising an ictB coding sequence or CO2 elevating sequence optionally linked to a promoter that drives expression in a plant cell. In some embodiments, DNA constructs may express both the ictB coding sequence and the CO2 assimilating sequence operably linked to a promoter or promoters that drive expression in a plant cell. CO2 assimilating sequences of interest are described elsewhere herein. Plants, seeds, and plant parts expressing the coding sequences of the invention are encompassed by the invention. Additionally, plants expressing an ictB sequence and showing increased expression of a coding sequence selected from CO2 assimilating sequences, such as those sequences involved in the Calvin Benson cycle, starch synthesis pathway, and C4 carbon shuttle are encompassed by the invention. It is recognized that any method for introduction of the sequences into a plant of interest can be used in the practice of the invention. Such methods include transformation, breeding and the like. The expression of ictB results in yield gains relative to otherwise similar plants that do not express ictB. Similarly, the co-expression of ictB with an additional gene or genes of interest results in yield gains relative to otherwise similar plants that are greater than would be expected from the expression of either gene on its own.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIG. 1: Amino acid alignment of ictB protein sequences. Fully conserved residues are indicated by an asterisk (*). Positions at which amino acids have certain conserved properties (e.g., hydrophobicity, acidity/alkalinity) are indicated by a colon (:) or period (.) above said residues.
    •  DETAILED DESCRIPTION OF THE INVENTION
  • Compositions and methods for increasing plant yield are provided. The methods involve the production of a transformed plant. The transformed plant expresses an ictB sequence or expresses the ictB sequence with increased expression of at least one coding sequence selected from CO2 assimilating sequences, such as those sequences involved in the Calvin Benson cycle, starch synthesis pathway, and C4 carbon shuttle. While not bound by any theory, it is believed that expression of ictB in higher plants may drive an increased concentration of CO2 in chloroplasts. In the context of this theory, it is surprising that ictB expression in C4 plants can provide benefits, as C4 plants utilize the C4 carbon shuttle to transport an increased concentration of CO2 in bundle sheath cells and it has been proposed previously that the mode-of-action by which ictB expression enhances yield in C3 plants is through a concentration of CO2 in chloroplasts.
  • Early reports on ictB expression in higher plants utilized C3 plants including Arabidopsis thaliana, tobacco (Nicotiana tabacum), rice (Oryza sativa) and soybean (Glycine max) (Lieman-Hurwitz et al. (2003) Plant Biotechnol J 1:43-50, Lieman-Hurwitz et al. (2005) in Plant Responses to Air Pollution and Global Change, K. Oumasa et al., eds., Yang et al. (2008) in Photosynthesis. Energy From the Sun: 14th International Congress on Photosynthesis, J F Allen et al., eds., Hay W T (2012) Ph.D Thesis, University of Illinois at Urbana-Champaign, Bihmidine S (2012) Ph.D Thesis, University of Nebraska, Simkin et al. (2015) J Exp Bot doi:10.1093/jxb/erv204, Gong et al. (2015) PLoS One 10:e0140928). In these reports, the ictB gene included a chloroplast-targeting signal peptide at the N-terminus of the protein designed to traffic the ictB protein to the chloroplast membrane. These reports also described either neutral or positive phenotypic effects associated with ictB expression. Based on these reports and on the proposed function of the ictB protein in concentrating CO2 its native cyanobacterial host (Bonfil et al. (1998) FEBS Letters 430:236-240), it was proposed that ictB functions to increase CO2 concentrations in the chloroplasts of C3 plants, thereby improving the rate of photosynthetic carbon fixation and leading to improved growth. Based on this proposed mode-of-action, it would be surprising for ictB expression to improve yield in C4 plants, where a carbon concentrating mechanism exists (the “C4 carbon shuttle”) to increase CO2 concentrations in bundle sheath cells and hence ictB would appear to be redundant. Accordingly, as used herein, a “C4 photosynthetic plant” or a “C4 plant” are photosynthetic plants that use the C4 carbon shuttle to increase CO2 concentrations in the chloroplasts of bundle sheath cells. Recently, a report was published describing negative phenotypic effects of ictB expression in soybean (Piatek N L (2015) MS Thesis, University of Illinois at Urbana-Champaign), thus calling into question whether ictB expression can universally improve growth, even in C3 plants. Based on this recent report and the proposed mode-of-action by which ictB has been proposed to improve higher plant growth, it is necessary to elucidate the most effective ways to express ictB to achieve the desired improvements in plant growth and yield.
  • The expression of ictB has been proposed to increase CO2 concentrations in chloroplasts, thereby improving photosynthetic carbon fixation. Recent studies have called this proposed function of ictB in higher plants into question, with some researchers (Price et al (2012) J Exp Bot 64: 753-768) suggesting that ictB may in fact not act as a bicarbonate transporter in higher plants. Without being bound by any theory, the expression of an ictB gene in higher plants may provide benefits to the plant by modulating the expression of native plant genes or suites of genes. Alternatively, the expression of an ictB gene in higher plants may provide benefits to the plant by causing changes in the plant metabolomic profile. The altered expression of native plant genes or altered metabolomic profile may cause improved growth, seed production, and/or yield in ictB-expressing plants relative to control plants that do not express an ictB gene. The mode of action by which ictB expression improves yield in plants that utilize C3 photosynthesis may differ from the mode of action by which ictB expression improves yield in plants that utilize C4 photosynthesis. Accordingly, the optimal expression strategies for ictB may differ between C3 and C4 plants.
  • Further, improving the function of the Calvin-Benson cycle in plants engineered to express ictB has a particularly beneficial effect for photosynthesis and growth (Simkin et al (2015) J Exp Bot 66: 4075-4090; Gong et al (2015) PLoS One 10:e0140928). Improvement of the function of the Calvin-Benson cycle in such a plant comprises increasing the expression of at least one gene involved in CO2 assimilation, including genes involved in the Calvin Benson cycle, starch synthesis, and C4 carbon shuttle. Such genes are described herein and include SBPase, fructose-1,6-bisphosphatase (FBPase), transketolase, and fructose-1,6-bisphosphate aldolase (FBP aldolase), ADP glucose pyrophosphorylase (AGPase), starch synthase, sucrose phosphate synthase, hc1 (also known as EVE), PHB8 (US20140259220), ATPase, carbonic anhydrase (CA), and the like.
  • Therefore for methods involving expression of an ictB sequence in combination with at least one other sequence, it is recognized that any method for increasing expression of CO2 assimilating sequences is encompassed by the present invention. That is, the plant may be manipulated to increase the expression of a native sequence or the plant may be transformed with a construct comprising a promoter that drives expression in the plant operably linked to a CO2 assimilating sequence. In one embodiment the plant can be transformed with a transcription factor (TF) that regulates the expression of a gene involved in photosynthesis. A number of computational approaches may be taken in order to identify such TFs. Thus, the methods of the invention comprise altering the expression of TFs that regulate the expression of genes involved in photosynthesis in plants engineered to express ictB. Additive and/or synergistic benefits for photosynthesis and plant growth and yield may be realized through the co-expression of ictB with genes involved in the Calvin-Benson cycle, the starch or sucrose biosynthetic pathways, water use and hydraulic conductivity, ATP production, CO2 conversion to HCO3 −, or regulation of photosynthetic gene expression.
  • In one embodiment, the present invention describes strategies to co-express ictB, a gene derived from a cyanobacterial species and involved in carbon dioxide acquisition, with other genes that may increase plant growth and yield. The co-expression of ictB with these additional genes results in yield gains that are greater than would be realized by the expression of any of these genes alone. Recombinant and heterologous nucleotide sequences encoding the genes of interest are provided. Methods to alter the expression level and/or profile of native plant genes in order to improve plant growth are described.
  • By “yield” or “crop yield” is intended the measurement of the amount of a crop that was harvested per unit of land area. Crop yield is the measurement often used for grains or cereals and is typically measured as the amount of plant harvested per unit area for a given time, i.e., metric tons per hectare or kilograms per hectare. Crop yield can also refer to the actual seed or biomass produced or generated by the plant.
  • A “recombinant polynucleotide” comprises a combination of two or more chemically linked nucleic acid segments which are not found directly joined in nature. By “directly joined” is intended the two nucleic acid segments are immediately adjacent and joined to one another by a chemical linkage. In specific embodiments, the recombinant polynucleotide comprises a polynucleotide of interest or active variant or fragment thereof such that an additional chemically linked nucleic acid segment is located either 5′, 3′ or internal to the polynucleotide of interest. Alternatively, the chemically-linked nucleic acid segment of the recombinant polynucleotide can be formed by deletion of a sequence. The additional chemically linked nucleic acid segment or the sequence deleted to join the linked nucleic acid segments can be of any length, including for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or greater nucleotides. Various methods for making such recombinant polynucleotides are disclosed herein, including, for example, by chemical synthesis or by the manipulation of isolated segments of polynucleotides by genetic engineering techniques. In specific embodiments, the recombinant polynucleotide can comprise a recombinant DNA sequence or a recombinant RNA sequence. A “fragment of a recombinant polynucleotide” comprises at least one of a combination of two or more chemically linked amino acid segments which are not found directly joined in nature.
  • A “recombinant polynucleotide construct” comprises two or more operably linked nucleic acid segments that are not found operably linked in nature. Non-limiting examples of recombinant polynucleotide constructs include a polynucleotide of interest or active variant or fragment thereof operably linked to heterologous sequences which aid in the expression, autologous replication, and/or genomic insertion of the sequence of interest. Such heterologous and operably linked sequences include, for example, promoters, termination sequences, enhancers, etc, or any component of an expression cassette; a plasmid, cosmid, virus, autonomously replicating sequence, phage, or linear or circular single-stranded or double-stranded DNA or RNA nucleotide sequence; and/or sequences that encode heterologous polypeptides.
  • A “recombinant polypeptide” comprises a combination of two or more chemically linked amino acid segments which are not found directly joined in nature. In specific embodiments, the recombinant polypeptide comprises an additional chemically linked amino acid segment that is located either at the N-terminal, C-terminal or internal to the recombinant polypeptide. Alternatively, the chemically-linked amino acid segment of the recombinant polypeptide can be formed by deletion of at least one amino acid. The additional chemically linked amino acid segment or the deleted chemically linked amino acid segment can be of any length, including for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or amino acids.
  • Transgenic plants and plant cells are provided in the invention which exhibit increased plant yield. In one embodiment, the transgenic plants are C4 plants involving expression of a ictB sequence in the plant. Also, transgenic plants in which an ictB protein is expressed in combination with another gene are encompassed. A “transgenic plant” or “transgenic plant cell” refers to any plant in which one or more, or all, of the cells of the plant include a recombinant or heterologous nucleic acid sequence. For example, a transgenic plant or transgenic plant cell may comprise a transgene integrated within a nuclear genome or organelle genome, or may comprise extra-chromosomally replicating DNA. The term “transgene” refers to a nucleic acid that is partly or entirely heterologous, foreign, to a transgenic plant or plant cell into which it is introduced, or a nucleic acid that is present in the plant or plant cell in a genomic or extra-chromosomal position different from that in which the gene is found in nature. As used herein, “heterologous” in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.
  • The invention comprises synthetic oligonucleotides or nucleotide sequences. A synthetic sequence is one that is produced or reproduced in a laboratory setting. While the nucleotide sequence may have an altered nucleotide sequence relative to the parent sequence, the synthetic sequence may be identical to the naturally occurring sequence. In both instances, however, the structure of the synthetic sequence is altered or different from that found in the sequence that is directly isolated from its natural setting.
  • By “altering” or “modulating” the expression level of a native plant gene is intended that the expression is upregulated or downregulated relative to the expression level of said gene in a wild-type or control plant. It is recognized that in some instances, plant growth and yield are increased by increasing the expression levels of one or more of the plant genes of the invention, i.e. upregulating expression. Likewise, in some instances, plant growth and yield may be increased by decreasing the expression levels of one or more of the plant genes of the invention, i.e. downregulating expression. Thus, the invention encompasses the upregulation or downregulation of one or more of the genes of the invention. Further, the methods include the upregulation of at least one plant gene and the downregulation of at least one plant gene in a plant of interest that has been engineered to express an ictB gene. By modulating the concentration and/or activity of at least one of the plant genes of the invention in a transgenic plant is intended that the concentration and/or activity is increased or decreased by at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% relative to a native control plant, plant part, or cell which did not have the sequence of the invention introduced. The expression level of a plant gene may be measured directly, for example, by assaying for the level of the RNA transcript encoded by the plant gene of interest in the plant cells of interest.
  • The compositions of the invention are used to alter expression of genes of interest in a plant, particularly genes involved in photosynthesis. Therefore, the expression of a plant gene involved in photosynthetic metabolism may be modulated as compared to a control plant. A “subject plant or plant cell” is one in which genetic alteration, such as transformation, has been effected as to a gene of interest, or is a plant or plant cell which is descended from a plant or cell so altered and which comprises the alteration. A “control” or “control plant” or “control plant cell” provides a reference point for measuring changes in phenotype of the subject plant or plant cell. Thus, the expression levels are higher or lower than those in the control plant depending on the methods of the invention.
  • A control plant or plant cell may comprise, for example: (a) a wild-type plant or cell, i.e., of the same genotype as the starting material for the genetic alteration which resulted in the subject plant or cell; (b) a plant or plant cell of the same genotype as the starting material but which has been transformed with a null construct (i.e. with a construct which has no known effect on the trait of interest, such as a construct comprising a marker gene); (c) a plant or plant cell which is a non-transformed segregant among progeny of a subject plant or plant cell; (d) a plant or plant cell genetically identical to the subject plant or plant cell but which is not exposed to conditions or stimuli that would induce expression of the gene of interest; or (e) the subject plant or plant cell itself, under conditions in which the gene of interest is not expressed.
  • While the invention is described in terms of transformed plants, it is recognized that transformed organisms of the invention also include plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
  • The invention encompasses simultaneous modulation of the expression of more than one gene in a plant of interest. Further, the methods and compositions disclosed herein encompass the expression of an ictB protein-encoding gene in a plant of interest that utilizes the C4 photosynthetic pathway. A person skilled in the art will recognize that where more than one gene is being modulated, there are many ways to achieve such simultaneous modulation of expression. A plant cell may be transformed with a vector containing a single, or more than one gene cassette. For example, a full gene cassette comprising at least a plant promoter and an ictB coding sequence may be introduced into a plant. Alternatively, multiple transformation vectors may be used for co-transformation of a plant cell in order to modulate multiple gene targets. Alternatively, transformation approaches or breeding approaches may be used to produce a first plant line wherein the expression of a first gene (e.g., ictB) has been modulated or effected. This plant line may be crossed with a second plant line wherein a second gene of interest has been modulated through a breeding approach or through a transformation approach. In specific embodiments, the second plant line has certain desirable attributes. The plants resulting from such a cross may be expected to show the desired modulation of both genes of interest or the desired phenotypes as a result of ictB gene expression. Modulation of the genes of interest, such as the ictB gene, is assayed through the use of molecular approaches including RT-PCR, Northern blotting, or quantitative RT-PCR. A person skilled in the art will recognize that these transformation and breeding approaches to achieve the simultaneous modulation of the expression of two genes may also be used to simultaneously modulate more than two genes through the use of the appropriate transformation and/or breeding techniques and the appropriate screening methods to identify plant lines in which the expression of the genes of interest has been modulated as desired. These approaches may be used to simultaneously modulate the expression of three, four, five, six, seven, eight, or more than eight genes in a plant of interest.
  • The invention encompasses isolated or substantially purified polynucleotide or amino acid compositions. An “isolated” or “purified” polynucleotide or protein, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or protein as found in its naturally occurring environment. Thus, an isolated or purified polynucleotide or protein is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. Optimally, an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived.
  • Fragments and variants of the disclosed polynucleotides and amino acid sequences encoded thereby are also encompassed by the present invention. By “fragment” is intended a portion of the polynucleotide or a portion of the amino acid sequence. “Variants” is intended to mean substantially similar sequences. For polynucleotides, a variant comprises a polynucleotide having deletions (i.e., truncations) at the 5′ and/or 3′ end; deletion and/or addition of one or more nucleotides at one or more internal sites in the native polynucleotide; and/or substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a “native” polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively. Generally, variants of a particular polynucleotide of the invention will have at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters as described elsewhere herein.
  • “Variant” amino acid or protein is intended to mean an amino acid or protein derived from the native amino acid or protein by deletion (so-called truncation) of one or more amino acids at the N-terminal and/or C-terminal end of the native protein; deletion and/or addition of one or more amino acids at one or more internal sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native plant protein. Biologically active variants of a native plant protein of the invention will have at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native sequence as determined by sequence alignment programs and parameters described herein. A biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
  • As indicated, the plant genes of the invention are modulated, i.e., upregulated or downregulated, in a plant of interest. It may be desirable to upregulate at least one plant gene while simultaneously downregulating at least one different plant gene. In other embodiments, it may be desirable to modulate at least one plant gene while simultaneously expressing an ictB gene in the plant or plant cell of interest. See for example U.S. Provisional Application Nos. 62/158,852 and 62/213,759, herein incorporated by reference. Table 1 lists a number of proteins that are linked with photosynthetic metabolism and may be of particular interest for co-accumulation with an ictB protein of interest. Methods for increasing the expression or upregulating a gene are known in the art and any can be used in the methods of the invention. In one embodiment, upregulation can be achieved by transforming a plant with an expression cassette comprising a promoter that drives expression in the plant operably linked to at least one plant gene of the invention. Alteration of the expression of one or more genes encoding one or more of the proteins listed in Table 1 may be achieved through the use of precise genome-editing technologies to modulate the expression of the endogenous plant gene sequence. In this manner, a nucleic acid sequence will be inserted proximal to a native plant sequence encoding the TF of interest through the use of methods available in the art. Such methods include, but are not limited to, meganucleases designed against the plant genomic sequence of interest (D'Halluin et al 2013 Plant Biotechnol J 11: 933-941); CRISPR-Cas9, CRISPR-Cpf1, TALENs, and other technologies for precise editing of genomes (Feng, et al. (2013) Cell Research 23:1229-1232, Podevin, et al. (2013) Trends Biotechnology 31: 375-383, Wei et al. (2013) J Gen Genomics 40:281-289, Zhang et al (2013), WO 2013/026740, Zetsche et al. (2015) Cell 163:1-13); Cre-lox site-specific recombination (Dale et al. (1995) Plant J 7:649-659; Lyznik, et al. (2007) Transgenic Plant J 1:1-9; FLP-FRT recombination (Li et al. (2009) Plant Physiol 151:1087-1095); Bxb1-mediated integration (Yau et al. Plant J (2011) 701:147-166); zinc-finger mediated integration (Wright et al. (2005) Plant J 44:693-705); Cai et al. (2009) Plant Mol Biol 69:699-709); and homologous recombination (Lieberman-Lazarovich and Levy (2011) Methods Mol Biol 701: 51-65); Puchta, H. (2002) Plant Mol Biol 48:173-182). The insertion of said nucleic acid sequences will be used to achieve the desired result of overexpression of one or more of the genes encoding one or more of the proteins listed in Table 1.
  • TABLE 1
    Photosynthetic proteins that may be of interest for co-accumulation
    with ictB
    Gene SEQ ID(s)
    SBPase 15, 25, 179-200
    FBPase 16, 201-221
    FBP aldolase 17, 26, 222-250
    AGPase (small subunit) 18, 251-272
    AGPase (large subunit) 19, 273-316
    AGPase (Sh2-ism2 mutant) 20
    Sucrose phosphate synthase 27, 28, 29, 30,
    318-358
    Starch synthase 31, 32, 33, 359-390
  • In specific embodiments, an ictB gene is expressed in a plant that uses C4 photosynthesis. Based on the high productivity of C4 photosynthesis relative to C3 photosynthesis, efforts are underway to transfer C4 photosynthesis into plant species that use C3 photosynthesis in their native state (http://c4rice.irri.org/). To reach this goal, researchers have expressed genes known to be involved in C4 photosynthesis in plants such as rice, tobacco, wheat, Arabidopsis, and potato that use C3 photosynthesis in their native state. Examples include plants engineered to express phosphoenolpyruvate carboxylase (PepC) (Fukayama et al. (2003) Photosynthesis Research 77:227-239, Häusler et al. (1999) J Exp Bot 50:1231-1242, Häusler et al. (2001) J Exp Bot 52:1785-1803, Kandoi et al. (2016) Photosynth Res DOI 10.1007/s11120-016-0224-3, Ku et al. (1999) Nat Biotechnol 17:76-80, Qin et al. (2015) Protoplasma DOI 10.1007/s00709-015-0906-2), phosphoenolpyruvate carboxykinase (PepCK) (Suzuki et al. (2000) Plant Physiol 124:163-172), pyruvate-phosphate dikinase (PPDK) (Sheriff et al. (1998) Plant Sci 136:43-57, Ishimaru et al. (1998) Physiologia Plantarum 103:340-346), and NADP malic enzyme (Gallardo et al. (1995) Planta 197:324-332, Tsuchida et al. (2001) Plant Cell Physiol 42:138-145). Co-expression of ictB along with one or more genes designed to provide C4 photosynthesis or C4-like photosynthesis in a plant that uses C3 photosynthesis in its native state may provide additional benefits for the photosynthetic metabolism of said plant.
  • Enhancers include any molecule capable of enhancing gene expression when inserted into the genome of a plant. Thus, an enhancer can be inserted in a region of the genome upstream or downstream of at least one gene of interest to enhance expression Enhancers may be cis-acting, and can be located anywhere within the genome relative to a gene for which expression will be enhanced. For example, an enhancer may be positioned within about 1 Mbp, within about 100 kbp, within about 50 kbp, about 30 kbp, about 20 kbp, about 10 kbp, about 5 kbp, about 3 kbp, or about 1 kbp of a coding sequence for which it enhances expression. An enhancer may also be located within about 1500 bp of a gene for which it enhances expression, or may be directly proximal to or located within an intron of a gene for which it enhances expression Enhancers for use in modulating the expression of an endogenous gene or homolog according to the present invention include classical enhancer elements such as the CaMV 35S enhancer element, cytomegalovirus (CMV) early promoter enhancer element, and the SV40 enhancer element, and also intron-mediated enhancer elements that enhance gene expression such as the maize shrunken-1 enhancer element (Clancy, M. and Hannah, L. C. (2002) Plant Physiol. 130(2):918-29). Further examples of enhancers which may be introduced into a plant genome to modulate expression include a PetE enhancer (Chua et al. (2003) Plant Cell 15:11468-1479), or a rice α-amylase enhancer (Chen et al. (2002) J. Biol. Chem. 277:13641-13649), or any enhancer known in the art (Chudalayandi, S. (2011) Methods Mol. Biol. 701:285-300). In some embodiments, the present invention comprises a subdomain, fragment, or duplicated enhancer element (Benfrey et al. (1990) EMBO J 9:1677-1684).
  • Further provided herein are methods and compositions for modulating gene expression in a plant by inserting a promoter or enhancer into a plant genome such that it modulates expression of an endogenous or exogenous sequence. As indicated above, methods for determining an insertion site for a promoter or enhancer using the sequences provided herein and methods for inserting a promoter or enhancer sequence into a plant genome at a given insertion site are known in the art.
  • Downregulation or reduction of the activity of a plant gene (also known as gene silencing or gene suppression) is also encompassed by the methods of the invention. Many techniques for gene silencing are well known to one of skill in the art, including, but not limited to, antisense technology (see, e.g., Sheehy et al. (1988) Proc. Natl. Acad. Sci. USA 85:8805-8809; and U.S. Pat. Nos. 5,107,065; 5,453,566; and 5,759,829); cosuppression (e.g., Taylor (1997) Plant Cell 9:1245; Jorgensen (1990) Trends Biotech. 8(12):340-344; Flavell (1994) Proc. Natl. Acad. Sci. USA 91:3490-3496; Finnegan et al. (1994) Bio/Technology 12:883-888; and Neuhuber et al. (1994) Mol. Gen. Genet. 244:230-241); RNA interference (Napoli et al. (1990) Plant Cell 2:279-289; U.S. Pat. No. 5,034,323; Sharp (1999) Genes Dev. 13:139-141; Zamore et al. (2000) Cell 101:25-33; and Montgomery et al. (1998) Proc. Natl. Acad. Sci. USA 95:15502-15507), virus-induced gene silencing (Burton et al. (2000) Plant Cell 12:691-705; and Baulcombe (1999) Curr. Op. Plant Bio. 2:109-113); target-RNA-specific ribozymes (Haseloff et al. (1988) Nature 334: 585-591); hairpin structures (Smith et al. (2000) Nature 407:319-320; WO 99/53050; WO 02/00904; WO 98/53083; Chuang and Meyerowitz (2000) Proc. Natl. Acad. Sci. USA 97:4985-4990; Stoutjesdijk et al. (2002) Plant Physiol. 129:1723-1731; Waterhouse and Helliwell (2003) Nat. Rev. Genet. 4:29-38; Pandolfini et at (2003) BMC Biotechnology 3:7, U.S. Patent Publication No. 20030175965; Panstruga et al. (2003) Mol. Biol. Rep. 30:135-140; Wesley et al. (2001) Plant J. 27:581-590; Wang and Waterhouse (2001) Curr. Opin. Plant Biol. 5:146-150; U.S. Patent Publication No. 20030180945; and, WO 02/00904, all of which are herein incorporated by reference); ribozymes (Steinecke et al. (1992) EMBO J. 11:1525; and Perriman et al. (1993) Antisense Res. Dev. 3:253); oligonucleotide-mediated targeted modification (e.g., WO 03/076574 and WO 99/25853); Zn-finger targeted molecules (e.g., WO 01/52620; WO 03/048345; and WO 00/42219); transposon tagging (Maes et al. (1999) Trends Plant Sci. 4:90-96; Dharmapuri and Sonti (1999) FEMS Microbiol. Lett. 179:53-59; Meissner et al. (2000) Plant J. 22:265-274; Phogat et al. (2000) J. Biosci. 25:57-63; Walbot (2000) Curr. Opin. Plant Biol. 2:103-107; Gai et al. (2000) Nucleic Acids Res. 28:94-96; Fitzmaurice et al. (1999) Genetics 153:1919-1928; Bensen et al. (1995) Plant Cell 7:75-84; Mena et al. (1996) Science 274:1537-1540; and U.S. Pat. No. 5,962,764); each of which is herein incorporated by reference; and other methods or combinations of the above methods known to those of skill in the art.
  • It is recognized that with the polynucleotides of the invention, antisense constructions, complementary to at least a portion of the messenger RNA (mRNA) for the gene sequences can be constructed. Antisense nucleotides are constructed to hybridize with the corresponding mRNA. Modifications of the antisense sequences may be made as long as the sequences hybridize to and interfere with expression of the corresponding mRNA. In this manner, antisense constructions having 70%, optimally 80%, more optimally 85% or greater and up to 100% sequence identity to the corresponding sequences to be silenced may be used. Furthermore, portions of the antisense nucleotides may be used to disrupt the expression of the target gene.
  • The polynucleotides of the present invention may also be used in the sense orientation to suppress the expression of endogenous genes in plants. The methods generally involve transforming plants with a DNA construct comprising a promoter that drives expression in a plant operably linked to at least a portion of a polynucleotide that corresponds to the transcript of the endogenous gene. Typically, such a nucleotide sequence has substantial sequence identity to the sequence of the transcript of the endogenous gene, optimally greater than about 65% sequence identity, more optimally greater than about 85% sequence identity, most optimally greater than about 95% sequence identity. See, U.S. Pat. Nos. 5,283,184 and 5,034,323, herein incorporated by reference. Such methods may be used to reduce the expression of at least one plant gene.
  • Variant sequences can be isolated by PCR. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York).
  • Variant sequences may also be identified by analysis of existing databases of sequenced genomes. In this manner, corresponding gene sequences can be identified and used in the methods of the invention.
  • Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent sequence identity between any two sequences can be accomplished using a mathematical algorithm. Non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller (1988) CABIOS 4:11-17; the local alignment algorithm of Smith et al. (1981) Adv. Appl. Math. 2:482; the global alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453; the search-for-local alignment method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 872264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
  • Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys Inc., 9685 Scranton Road, San Diego, Calif., USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. (1988) Gene 73:237-244 (1988); Higgins et al. (1989) CABIOS 5:151-153; Corpet et al. (1988) Nucleic Acids Res. 16:10881-90; Huang et al. (1992) CABIOS 8:155-165; and Pearson et al. (1994) Meth. Mol. Biol. 24:307-331. The ALIGN program is based on the algorithm of Myers and Miller (1988) supra. A PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used with the ALIGN program when comparing amino acid sequences. The BLAST programs of Altschul et al (1990) J. Mol. Biol. 215:403 are based on the algorithm of Karlin and Altschul (1990) supra. BLAST nucleotide searches can be performed with the BLASTN program, score=100, wordlength=12, to obtain nucleotide sequences homologous to a nucleotide sequence encoding a protein of the invention. BLAST protein searches can be performed with the BLASTX program, score=50, wordlength=3, to obtain amino acid sequences homologous to a protein or polypeptide of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g., BLASTN for nucleotide sequences, BLASTX for proteins) can be used. See www.ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection.
  • The polynucleotides of the invention can be provided in expression cassettes for expression in a plant of interest. The cassette will include 5′ and 3′ regulatory sequences operably linked to a polynucleotide of the invention. “Operably linked” is intended to mean a functional linkage between two or more elements. The cassette may additionally contain at least one additional gene to be co-transformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
  • The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a polynucleotide of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants.
  • A number of promoters may be used in the practice of the invention. Constitutive promoters include the CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026), and the like.
  • Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-196; Orozco et al. (1993) Plant Mol Biol. 23(6):1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al. (1993) Plant J. 4(3):495-505. Leaf-preferred promoters are also known in the art. See, for example, Yamamoto et al. (1997) Plant J. 12(2):255-265; Kwon et al. (1994) Plant Physiol. 105:357-67; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Gotor et al. (1993) Plant J. 3:509-18; Orozco et al. (1993) Plant Mol. Biol. 23(6):1129-1138; and Matsuoka et al. (1993) Proc. Natl. Acad. Sci. USA 90(20):9586-9590.
  • Developmentally-regulated promoters may be desirable for the expression of some genes of interest. Such promoters may show a peak in expression at a particular developmental stage. Such promoters have been described in the art, e.g., U.S. 62/029,068; Gan and Amasino (1995) Science 270: 1986-1988; Rinehart et al. (1996) Plant Physiol 112: 1331-1341; Gray-Mitsumune et al. (1999) Plant Mol Biol 39: 657-669; Beaudoin and Rothstein (1997) Plant Mol Biol 33: 835-846; Genschik et al. (1994) Gene 148: 195-202, and the like.
  • Promoters that are induced following the application of a particular biotic and/or abiotic stress may be desirable for the expression of some genes of interest. Such promoters have been described in the art, e.g., Yi et al. (2010) Planta 232: 743-754; Yamaguchi-Shinozaki and Shinozaki (1993) Mol Gen Genet 236: 331-340; U.S. Pat. No. 7,674,952; Rerksiri et al. (2013) Sci World J 2013: Article ID 397401; Khurana et al. (2013) PLoS One 8: e54418; Tao et al. (2015) Plant Mol Biol Rep 33: 200-208, and the like.
  • Cell-preferred promoters may be desirable for the expression of some genes of interest. Such promoters may preferentially drive the expression of a downstream gene in a particular cell type such as a mesophyll or a bundle sheath cell. Such cell-preferred promoters have been described in the art, e.g., Viret et al. (1994) Proc Natl Acad USA 91: 8577-8581; U.S. Pat. No. 8,455,718; U.S. Pat. No. 7,642,347; Sattarzadeh et al. (2010) Plant Biotechnol J 8: 112-125; Engelmann et al. (2008) Plant Physiol 146: 1773-1785; Matsuoka et al. (1994) Plant J 6: 311-319, and the like.
  • It is recognized that a specific, non-constitutive expression profile may provide an improved plant phenotype relative to constitutive expression of a gene or genes of interest. For instance, many plant genes are regulated by light conditions, the application of particular stresses, the circadian cycle, or the stage of a plant's development. These expression profiles may be highly important for the function of the gene or gene product in planta. One strategy that may be used to provide a desired expression profile is the use of synthetic promoters containing cis-regulatory elements that drive the desired expression levels at the desired time and place in the plant. Cis-regulatory elements that can be used to alter gene expression in planta include (Vandepoele et al. (2009) Plant Physiol 150: 535-546; Rushton et al. (2002) Plant Cell 14: 749-762). Cis-regulatory elements may also be used to alter promoter expression profiles. See, Venter (2007) Trends Plant Sci 12: 118-124. The rapid development of new technologies for transcriptomic studies and of new methods to analyze such datasets has enabled the discovery of new cis-regulatory elements. It is well understood that microarray datasets used previously did not have the same resolution as transcriptomic data generated using RNA-Seq. The use of these newer technologies to generate transcriptomic data and the development of new software algorithms for the analysis of transcriptomic data has enabled the discovery of novel cis-regulatory elements including those described herein.
  • Plant terminators are known in the art and include those available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See, for example, Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res. 15:9627-9639.
  • As indicated, the genes of interest, including an ictB gene, can be used in expression cassettes to transform plants of interest. As indicated, where more than one gene is being expressed in the transformed, the genes can be present on the same cassette or alternatively, more than one cassette may be used. Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing polypeptides and polynucleotides into plant cells include microinjection (Crossway et al. (1986) Biotechniques 4:320 334), electroporation (Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-mediated transformation (U.S. Pat. No. 5,563,055 and U.S. Pat. No. 5,981,840), direct gene transfer (Paszkowski et al. (1984) EMBO J. 3:2717-2722), and ballistic particle acceleration (see, for example, U.S. Pat. No. 4,945,050; U.S. Pat. No. 5,879,918; U.S. Pat. Nos. 5,886,244; and, 5,932,782; Tomes et al. (1995) in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); McCabe et al. (1988) Biotechnology 6:923-926); and Lec1 transformation (WO 00/28058). Also see Weissinger et al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987) Particulate Science and Technology 5:27 37 (onion); Christou et al. (1988) Plant Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio/Technology 6:923-926 (soybean); Finer and McMullen (1991) In Vitro Cell Dev. Biol. 27P:175-182 (soybean); Singh et al. (1998) Theor. Appl. Genet. 96:319-324 (soybean); Datta et al. (1990) Biotechnology 8:736 740 (rice); Klein et al. (1988) Proc. Natl. Acad. Sci. USA 85:4305 4309 (maize); Klein et al. (1988) Biotechnology 6:559 563 (maize); U.S. Pat. Nos. 5,240,855; 5,322,783; and, 5,324,646; Klein et al. (1988) Plant Physiol. 91:440 444 (maize); Fromm et al. (1990) Biotechnology 8:833 839 (maize); Hooykaas-Van Slogteren et al. (1984) Nature (London) 311:763-764; U.S. Pat. No. 5,736,369 (cereals); Bytebier et al. (1987) Proc. Natl. Acad. Sci. USA 84:5345-5349 (Liliaceae); De Wet et al. (1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman et al. (Longman, New York), pp. 197-209 (pollen); Kaeppler et al. (1990) Plant Cell Reports 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet. 84:560-566 (whisker-mediated transformation); D'Halluin et al. (1992) Plant Cell 4:1495-1505 (electroporation); Li et al. (1993) Plant Cell Reports 12:250-255 and Christou and Ford (1995) Annals of Botany 75:407-413 (rice); Osjoda et al. (1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium tumefaciens); all of which are herein incorporated by reference. “Stable transformation” is intended to mean that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by the progeny thereof.
  • The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a polynucleotide of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • The present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plant species of interest include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley, vegetables, ornamentals, and conifers.
  • Embodiments of the invention include:
      • 1. A method for increasing crop yield comprising transforming a plant that utilizes C4 photosynthesis with at least one ictB coding sequence.
      • 2. The method of embodiment 1, wherein said ictB coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 2, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 536, 544, 546, and 548.
      • 3. The method of embodiment 1, wherein said ictB coding sequence encodes a protein with at least 50% sequence identity to SEQ ID NO: 2 and contains the sequence motifs set forth in SEQ ID NOs: 69, 71, 73, 75, 77, and 78.
      • 4. A plant having stably incorporated into its genome a construct comprising a promoter that drives expression in a plant operably linked to an ictB coding sequence, wherein said plant utilizes C4 photosynthesis.
      • 5. The plant of embodiment 4, wherein said ictB coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 2, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 536, 544, 546, and 548.
      • 6. The plant of embodiment 4, wherein said ictB coding sequence encodes a protein with at least 50% sequence identity to SEQ ID NO: 2 and contains the sequence motifs set forth in SEQ ID NOs: 69, 71, 73, 75, 77, and 78.
      • 7. Transformed seed of any one of the plants of embodiment 4.
      • 8. The plant of embodiment 4 wherein said plant is a monocot.
      • 9. The plant of embodiment 8 wherein said plant is from the genus Zea.
      • 10. The plant of embodiment 8 wherein said plant is from the genus Sorghum.
      • 11. The plant of embodiment 8 wherein said plant is from the genus Setaria.
      • 12. The plant of embodiment 8 wherein said plant is from the genus Saccharum.
      • 13. The plant of embodiment 8 wherein said plant is from the genus Miscanthus.
      • 14. The plant of embodiment 8 wherein said plant is from the genus Panicum.
      • 15. The plant of embodiment 8 wherein said plant is from the genus Pennisetum.
      • 16. The plant of embodiment 8 wherein said plant is from the genus Megathyrsus.
      • 17. The plant of embodiment 4 wherein said plant is a dicot.
      • 18. A plant having stably incorporated into its genome a construct comprising a promoter that drives expression in a plant operably linked to an ictB coding sequence, wherein said plant utilizes C3 photosynthesis in its native state but has been engineered to exhibit partially or completely certain aspects of C4 photosynthesis.
      • 19. The plant of embodiment 18 wherein said plant that utilizes C3 photosynthesis in its native state but has been engineered to exhibit partially or completely certain aspects of C4 photosynthesis expresses a gene encoding a phosphoenolpyruvate carboxylase (PepC), phosphoenolpyruvate carboxykinase (PepCK), carbonic anhydrase (CA), NADP malic enzyme, malate dehydrogenase, or pyruvate-phosphate dikinase (PPDK) protein.
      • 20. The plant of embodiment 4 wherein said plant exhibits increased growth relative to a control plant that does not comprise an ictB coding sequence.
      • 21. The plant of embodiment 4 wherein said plant exhibits increased biomass yield relative to a control plant that does not comprise an ictB coding sequence.
      • 22. The plant of embodiment 4 wherein said plant exhibits increased seed yield relative to a control plant that does not comprise an ictB coding sequence.
      • 23. The method of embodiment 1, wherein said ictB coding sequence is selected from the group of SEQ ID NOs: 1, 542, 543, 545, 547, and 580.
      • 24. The method of embodiment 1, wherein said ictB coding sequence is expressed from a constitutive promoter.
      • 25. The method of embodiment 24, wherein said constitutive promoter is selected from the group of SEQ ID NOs: 9 and 537.
      • 26. The method of embodiment 1, wherein said ictB coding sequence is expressed from a bundle sheath-preferred promoter.
      • 27. The method of embodiment 26, wherein said bundle sheath-preferred promoter is selected from the group of SEQ ID NOs: 11, 539, 540, and 541.
      • 28. The method of embodiment 1, wherein said ictB coding sequence is expressed from a mesophyll-preferred promoter.
      • 29. The method of embodiment 28, wherein said mesophyll-preferred promoter comprises SEQ ID NO: 10.
      • 30. The plant of embodiment 4, wherein said ictB coding sequence is selected from the group of SEQ ID NOs: 1, 542, 543, 545, 547, and 580.
      • 31. The plant of embodiment 4, wherein said ictB coding sequence is expressed from a constitutive promoter.
      • 32. The plant of embodiment 31, wherein said constitutive promoter is selected from the group of SEQ ID NOs: 9 and 537.
      • 33. The plant of embodiment 4, wherein said ictB coding sequence is expressed from a bundle sheath-preferred promoter.
      • 34. The plant of embodiment 33, wherein said bundle sheath-preferred promoter is selected from the group of SEQ ID NOs: 11, 539, 540, and 541.
      • 35. The plant of embodiment 4, wherein said ictB coding sequence is expressed from a mesophyll-preferred promoter.
      • 36. The plant of embodiment 35, wherein said mesophyll-preferred promoter comprises SEQ ID NO: 10.
      • 37. The plant of embodiment 18, wherein said ictB coding sequence is selected from the group of SEQ ID NOs: 1, 542, 543, 545, and 547.
      • 38. The plant of embodiment 18, wherein said ictB coding sequence is expressed from a constitutive promoter.
      • 39. The plant of embodiment 38, wherein said constitutive promoter is selected from the group of SEQ ID NOs: 9 and 537.
      • 40. The plant of embodiment 18, wherein said ictB coding sequence is expressed from a bundle sheath-preferred promoter.
      • 41. The plant of embodiment 40, wherein said bundle sheath-preferred promoter is selected from the group of SEQ ID NOs: 11, 539, 540, and 541.
      • 42. The plant of embodiment 18, wherein said ictB coding sequence is expressed from a mesophyll-preferred promoter.
      • 43. The plant of embodiment 42, wherein said mesophyll-preferred promoter comprises SEQ ID NO: 10.
      • 44. The method of embodiment 1, wherein said ictB coding sequence is fused in-frame with a sequence encoding a signal peptide.
      • 45. The method of embodiment 44, wherein said sequence encoding a signal peptide is selected from the group consisting of SEQ ID NOs: 3, 5, and 7.
      • 46. The method of embodiment 44, wherein said sequence encoding a signal peptide encodes an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 6, and 8.
      • 47. The plant of embodiment 4, wherein said ictB coding sequence is fused in-frame with a sequence encoding a signal peptide.
      • 48. The plant of embodiment 47, wherein said sequence encoding a signal peptide is selected from the group consisting of SEQ ID NOs: 3, 5, and 7.
      • 49. The plant of embodiment 47, wherein said sequence encoding a signal peptide encodes an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 6, and 8.
      • 50. The plant of embodiment 18, wherein said ictB coding sequence is fused in-frame with a sequence encoding a signal peptide.
      • 51. The plant of embodiment 50, wherein said sequence encoding a signal peptide is selected from the group consisting of SEQ ID NOs: 3, 5, and 7.
      • 52. The plant of embodiment 50, wherein said sequence encoding a signal peptide encodes an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 6, and 8.
      • 53. The method of embodiment 44, wherein said ictB coding sequence fused in-frame with a sequence encoding a signal peptide comprises SEQ ID NO: 543, 545, or 547.
      • 54. The plant of embodiment 47, wherein said ictB coding sequence fused in-frame with a sequence encoding a signal peptide comprises SEQ ID NO: 543, 545, or 547.
      • 55. The plant of embodiment 50, wherein said ictB coding sequence fused in-frame with a sequence encoding a signal peptide comprises SEQ ID NO: 543, 545, or 547.
      • 56. A method for increasing crop yield comprising transforming a plant with at least one ictB coding sequence and increasing expression of at least one CO2 assimilating coding sequence.
      • 57. The method of embodiment 56, wherein said CO2 assimilating coding sequence is selected from coding sequences involved in the Calvin Benson cycle, starch synthesis pathway, and C4 carbon shuttle.
      • 58. The method of embodiment 57, wherein the at least one CO2 assimilating coding sequence is selected from the group consisting of SBPase, FBPase, FBPaldolase, AGPase small subunit, AGPase large subunit, sucrose phosphate synthase, starch synthase, PHB, carbonic anhydrase, and hc1.
      • 59. The method of any one of embodiments 56-58, wherein said additional coding sequence is selected from SBPase, FBPase, FBP aldolase, the large AGPase subunit, the small AGPase subunit, and starch synthase.
      • 60. The method of any one of embodiments 56-60, wherein said ictB coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 2, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, or 68.
      • 61. The method of embodiment 56, wherein said ictB coding sequence encodes a protein with at least 50% sequence identity to SEQ ID NO: 2 and contains the sequence motifs set forth in SEQ ID NOs: 69, 71, 73, 75, 77, and 78.
      • 62. The method of embodiment 60, wherein said ictB coding sequence encodes a protein with at least 50% sequence identity to SEQ ID NO: 2 and contains the sequence motifs set forth in SEQ ID NOs: 70, 72, 74, 75, 77, and 79.
      • 63. The method of embodiment 56, wherein one additional coding sequence encodes a protein selected from the group consisting of SBPase, FBPase, or FBP aldolase, and a second additional coding sequence is selected from the large AGPase subunit, the small AGPase subunit, and starch synthase.
      • 64. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 23, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, and 178.
      • 65. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 15, 25, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, and 200.
      • 66. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 16, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, and 221.
      • 67. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 17, 26, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, and 250.
      • 68. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 18, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, and 272.
      • 69. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 19, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, and 316.
      • 70. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 27, 28, 29, 30, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, and 358.
      • 71. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 31, 32, 33, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, and 390.
      • 72. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 21, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, and, 488.
      • 73. The method of embodiment 56, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 22, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, and 535.
      • 74. A plant having stably incorporated into its genome a construct comprising a promoter that drives expression in a plant operably linked to an ictB coding sequence, wherein said plant has increased expression of at least one CO2 assimilating coding sequence.
      • 75. The plant of embodiment 74, wherein said CO2 assimilating coding sequence is selected from coding sequences encoding proteins involved in the Calvin Benson cycle, starch synthesis, and C4 carbon shuttle.
      • 76. The plant of embodiment 75, wherein the at least one CO2 assimilating coding sequence encodes a protein selected from the group consisting of SBPase, FBPase, FBPaldolase, AGPase small subunit, AGPase large subunit, sucrose phosphate synthase, starch synthase, PHB, carbonic anhydrase, and hc1.
      • 77. The plant of any one of embodiments 74-76, wherein said CO2 assimilating coding sequence encodes a protein selected from SBPase, FBPase, FBP aldolase, the large AGPase subunit, the small AGPase subunit, and starch synthase.
      • 78. The plant of any one of embodiments 74-77, wherein said ictB coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 2, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, or 68.
      • 79. The plant of embodiment 74, wherein said ictB coding sequence encodes a protein with at least 50% sequence identity to SEQ ID NO: 2 and contains the sequence motifs set forth in SEQ ID NOs: 69, 71, 73, 75, 77, and 78.
      • 80. The plant of embodiment 74, wherein said ictB coding sequence encodes a protein with at least 50% sequence identity to SEQ ID NO: 2 and contains the sequence motifs set forth in SEQ ID NOs: 70, 72, 74, 75, 77, and 79.
      • 81. The plant of embodiment 74, wherein one CO2 assimilating coding sequence encodes a protein selected from the group consisting of SBPase, FBPase, or FBP aldolase, and a second CO2 assimilating coding sequence encodes a protein selected from the large AGPase subunit, the small AGPase subunit, and starch synthase.
      • 82. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 23, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, and 178.
      • 83. The plant of embodiment 74, wherein said additional CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 15, 25, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, and 200.
      • 84. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 16, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, and 221.
      • 85. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 17, 26, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, and 250.
      • 86. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 18, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, and 272.
      • 87. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 19, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, and 316.
      • 88. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 27, 28, 29, 30, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, and 358.
      • 89. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 31, 32, 33, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, and 390.
      • 90. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 21, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, and, 488.
      • 91. The plant of embodiment 74, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 22, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, and 535.
      • 92. Transformed seed of any one of the plants of embodiments 74-91.
      • 93. The transformed plant of any one of embodiments 74-91 wherein said plant is a monocot.
      • 94. The transformed plant of any one of embodiments 74-91 wherein said plant is a dicot.
  • The following examples are offered by way of illustration and not by way of limitation. All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
  • Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.
    • EXPERIMENTAL Example 1: Multigenic Constructs Containing ictB and at Least One Additional Gene of Interest
  • Plant transformation vectors were constructed in plasmid backbones containing sequences for maintenance in both E. coli and Agrobacterium tumefaciens. These transformation vectors contained an ictB expression cassette. Each ictB expression cassette contained an ictB open reading frame (SEQ ID NOs: 1 and 542) encoding an ictB protein (SEQ ID NO: 2). The vectors were designed to target the ictB protein to the cytoplasm in plant tissue in the absence of any signal peptide. Certain transformation vectors were designed to target the ictB protein to the chloroplast envelope in vectors where the ictB open reading frame is flanked at its 5′ terminus by a sequence encoding the signal peptide from the RbcS gene (SEQ ID NOs: 3 and 4), resulting in production of the protein described by SEQ ID NO: 544. Certain transformation vectors were designed to target the ictB protein to the plasma membrane in vectors where the ictB open reading frame is flanked at its 5′ terminus by the PR1a signal peptide (SEQ ID NOs: 5 and 6), resulting in production of the protein described by SEQ ID NO: 546. Certain transformation vectors were designed to target the ictB protein to the endoplasmic reticulum (ER) in vectors where the ictB open reading frame is flanked at its 5′ terminus by the PR1a signal peptide (SEQ ID NOs: 5 and 6) and at its 3′ terminus by a SEKDEL sequence (SEQ ID NOs: 7 and 8), resulting in production of the protein described by SEQ ID NO: 548. The four versions of the ictB protein targeted to different subcellular locations are summarized in Table 2.
  • TABLE 2
    ictB proteins containing signal peptides
    5′ signal 3′ signal Protein Subcellular
    peptide ictB protein peptide Produced location
    None ictB (SEQ None ictB (SEQ ID Cytoplasm
    ID NO: 2) NO: 2)
    RbcS (SEQ ID ictB (SEQ None RbcS-ictB Chloroplast
    NO: 4) ID NO: 2) (SEQ ID NO: Envelope
    544)
    PR1a (SEQ ID ictB (SEQ None PR1a-ictB Plasma
    NO: 6) ID NO: 2) (SEQ ID NO: Membrane
    546)
    PR1a (SEQ ID ictB (SEQ SEKDEL PR1a-ictB- ER
    NO: 6) ID NO: 2) (SEQ ID SEKDEL
    NO: 8) (SEQ ID NO:
    548)
  • The ictB open reading frames in the plant transformation vectors were flanked at their 5′ ends by a promoter that is functional in plants and a 5′ untranslated region (5′UTR) to direct transcription and translation, respectively, of the open reading frame. The ictB open reading frames were flanked at their 3′ ends by a functional 3′UTR to stabilize the mRNA. Vectors were designed to express the ictB gene constitutively in vectors containing the maize ubiquitin (ZmUbi) promoter and 5′UTR (SEQ ID NO: 9). These vectors contain the ZmUbi 3′UTR (SEQ ID NO: 12) at the 3′ end of the ictB gene. Vectors were also designed to express the ictB gene preferentially in mesophyll cells in vectors containing the maize PepC (ZmPepC) promoter and 5′UTR (SEQ ID NO: 10). These vectors contain the ZmPepC 3′UTR (SEQ ID NO: 13) at the 3′ end of the ictB gene. Vectors were also designed to express the ictB gene preferentially in bundle sheath cells in vectors containing the maize RbcS (ZmRbcS) promoter and 5′UTR (SEQ ID NO: 11), or a truncated version of the ZmRbcS promoter (SEQ ID NO: 541), or the RbcS7A promoter and 5′UTR (SEQ ID NO: 540), or the GLDC promoter (SEQ ID NO: 539). Each of these vectors contain the ZmRbcS 3′UTR (SEQ ID NO: 14) at the 3′ end of the ictB gene.
  • In some instances, the ictB gene that is expressed may encode an ictB protein other than that found in Synechococcus sp. PCC7942 (SEQ ID NO: 2, encoded by SEQ ID NOs: 1 and 542). In some cases, the ictB protein sequence that is encoded by the ictB gene may be the protein sequence shown in SEQ ID NO: 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, or 536.
  • Multigenic plant transformation vectors contain one of the ictB expression cassettes described above in addition to an expression cassette for one or more additional genes of interest. Multigenic plant transformation vectors were constructed containing an ictB gene along with one or more genes encoding one or more of the amino acid sequences shown in Table 3. Some of the multigenic plant transformation vectors contained an ictB gene that also included one or more signal peptides (i.e., the RbcS, PR1a, and/or SEKDEL signal peptides, as described above).
  • TABLE 3
    Proteins of interest for co-expression with ictB
    Protein SEQ ID(s)
    SBPase 15, 25, 179-200
    FBPase 16, 201-221
    FBP aldolase 17, 26, 222-250
    AGPase (small subunit) 18, 251-272
    AGPase (large subunit) 19, 273-316
    AGPase (Sh2-ism2 mutant) 20
    Sucrose phosphate synthase 27, 28, 29, 30,
    318-358
    Starch synthase 31, 32, 33, 359-390
    PHB 21, 391-488
    Carbonic Anhydrase 22, 489-535
    hc1/EVE 23, 80-178
    BRADI3G31600.1 24
    MYB Transcription Factor 559 
  • Multigenic plant transformation vectors contain a functional promoter and 5′UTR upstream of each gene of interest. In some preferred embodiments, a functional 3′UTR is included downstream of these gene(s). In some preferred embodiments, the multigenic plant transformation vectors contained the genetic elements listed in Table 4. This table lists the SEQ ID NOs for the promoter and 5′UTR used to drive the expression of each gene listed in the table. Both the DNA sequence and the encoded protein sequence are listed for each gene. In addition to the ictB cassette, the multigenic transformation vectors listed in Table 4 contain an additional one, two, or three functional gene cassettes.
  • TABLE 4
    Multigenic Plant Transformation Vectors Containing an ictB Gene
    Gene 2 Gene 3 Gene 4
    Promoter ictB (DNA/ Promoter (DNA/ Promoter (DNA/ Promoter (DNA/
    Construct 1 Protein) 2 Protein) 3 Protein) 4 Protein)
    130234 541 561/544 549 562/24
    130259 9 561/544 541 563/15
    130260 9 561/544 541  564/204
    130261 9 561/544 541 574/19
    130262 9 561/544 541 565/18
    130287 541 561/544 9 563/15
    130288 541 561/544 9  564/204
    130289 541 561/544 9 574/19
    130290 541 561/544 9 565/18
    130293 541 561/544 10 566/22
    130294 541 561/544 9 566/22
    130296 541 561/544 9 567/21
    130416 541 561/544 9 568/17
    130470 537 580/544 556 573/25
    130472 537 580/544 557 575/26
    130475 537 580/544 537  576/411
    130477 537 580/544 537 577/80
    130624 541 561/544 550 563/15
    130625 541 561/544 558 568/17
    130850 11 542/2  554 569/20
    130851 11 561/544 554 569/20
    130852 9 561/544 554 569/20
    130865 11 561/544 537 570/23
    130866 11 561/544 537  571/113
    130867 11 542/2  537 570/23
    130868 11 542/2  537  571/113
    130873 11 561/544 537 570/23
    130874 11 561/544 537  571/113
    130875 11 542/2  537 570/23
    130876 11 542/2  537  571/113
    130887 11 561/544 549 562/24
    130888 11 542/2  549 562/24
    130889 9 561/544 549 562/24
    130893 9 561/544 549 562/24
    130916 11 561/544 558  560/559
    130947 9 561/544 537 570/23
    130948 9 561/544 537  571/113
    130967 11 561/544 537  571/113
    130968 11 561/544 537 570/23
    130969 11 561/544 539 568/17
    130978 537 561/544 11 565/18
    131075 537 561/544 11 568/17
    131076 537 561/544 539 568/17
    131127 9 561/544 553 569/20
    131190 9 561/544 550 563/15
    131192 9 561/544 553 569/20
    131405 537 561/544 552 572/28
    131406 537 561/544 550 563/15
    131459 9 561/544 552 572/28
    131478 9 561/544 553 569/20
    130237 9 561/544 541 563/15 541  564/204
    130243 541 561/544 10 566/22 541 565/18
    130244 541 561/544 10 566/22 541 574/19
    130419 541 561/544 541 563/15 541 568/17
    130471 537 580/544 537 578/19 555 579/18
    130627 541 561/544 551 565/18 541 574/19
    130965 537 561/544 537 574/19 11 565/18
    130971 11 561/544 539 568/17 537 570/23
    130980 11 561/544 537 574/19 537 570/23
    130981 11 561/544 537 574/19 537  571/113
    131150 9 561/544 550 563/15 553 569/20
    131193 9 561/544 550 563/15 553 569/20
    131460 9 561/544 552 572/28 550 563/15
    131479 9 561/544 553 569/20 550 563/15
    130966 537 561/544 537 574/19 539 568/17 11 565/18
    130973 11 561/544 537 574/19 539 568/17 537 570/23
  • The plant transformation vectors listed in Table 4 were transformed into A. tumefaciens for plant transformation. The plant tissue of interest was contacted with A. tumefaciens cells containing the plant transformation vectors. Following contact with the A. tumefaciens cells, the plant tissue was placed on a suitable tissue culture medium for regeneration of fertile plants. Alternatively, the multigenic plant transformation vector is coated onto beads for biolistic bombardment of transformable plant tissue. PCR, Southern blotting, or other suitable molecular assays are performed in order to verify the presence of the ictB gene as well as of the other gene(s) of interest in the genome of the transformed plants. Expression of the ictB gene and of the other gene(s) of interest is verified through the use of RT-PCR, Northern blotting, or other suitable assays to detect the encoded transcripts. The regenerated plants are grown to maturity. Following the maturation of the plants, above-ground biomass is harvested, dried, and weighed. The seeds are harvested, weighed, and counted.
    • Example 2: Transformation of Zea mays with Multigenic Vectors Containing ictB and at Least One Additional Gene
  • The ictB-containing multigenic vectors shown in Table 5 were used to transform maize (Zea mays). The genetic elements contained in each of these constructs are included in Table 4. Each of these vectors was transformed into A. tumefaciens and the A. tumefaciens cells harboring the relevant vector was used to transform embryogenic maize callus.
  • TABLE 5
    Multigenic ictB-containing vectors used for maize transformation
    Construct
    130234 130889 130289 130865
    130624 130851 130290 130887
    130287 131190 130293 130916
    130888 130237 130294 131192
    131127 130243 130296 131193
    130852 130244 130416 131478
    130259 130260 130419 131459
    130850 130261 130866 131479
    131150 130262 130867 131460
    130868 130288
  • Following the Agrobacterium-mediated transformation, the maize tissue was placed on selective tissue culture medium suitable for regenerating transgenic maize plants. The maize plants were transferred to soil and leaf tissue samples were collected. DNA was extracted from the leaves and PCR and/or Taqman-based assays were performed to confirm the integration of the genes of interest in the maize genome. Following confirmation of the integration of the genes of interest in the genome, selected plants were chosen for analysis of gene expression.
  • For gene expression assays, total RNA was extracted from leaf tissue harvested from T0-generation transgenic maize events. The RNA was reverse transcribed and quantitative reverse transcriptase-PCR (qRT-PCR) assays were performed to assess the steady-state levels of transgene-encoded mRNA. Primers were designed for these qRT-PCR assays so that the PCR product amplified was specific to the transgene, without any added signal from wild-type transcripts. For these experiments, the primer pair of SEQ ID NOs: 587 and 588 was used to amplify an 82 bp sequence internal to the ictB coding region. The primer pair of SEQ ID NOs: 589 and 590 was used to amplify a 119 bp sequence internal to the SBPase coding region. Transcript levels encoded by the various transgenes were compared with the expression of UBCP, a well-known housekeeping gene in the maize genome (Manoli et al (2012) J Plant Physiol 169:807-815). The primer pair of SEQ ID NOs: 581 and 582 were used to amplify the UBCP transcript in these qRT-PCR assays. Transcript levels were expressed relative to the expression of UBCP; an expression level of 2, for example, would indicate that the expression of the transgene was twice as high as that of UBCP. Table 6 summarizes the results of qRT-PCR assays performed with T0-generation maize transformed with multigenic vectors containing an ictB gene in addition to at least one other gene.
  • TABLE 6
    Expression levels relative to the maize UBCP gene of transgenes
    in T0-generation maize transformed with the 131150 Vector
    Event ictB ism-2 SBPase
    131150-1 nd 2 not tested 1 nd 2
    131150-2 0.44 not tested 1 0.03
    131150-3 3.23 not tested 1 0.20
    131150-6 9.10 not tested 1 0.34
    1 Expression of the ism-2 gene was not tested in these samples because its expression was driven by a promoter that is not active in leaf tissue
    2 Expression of this gene was not detected in the leaf sample used for these assays
  • Transgenic maize plants containing an ictB cassette and one or more additional transgene cassettes are characterized to assess the effects of the transgenes on plant growth and yield. T0-generation maize events are self-pollinated to produce homozygous events. Homozygous events are identified through the use of Taqman assays to assess zygosity. These homozygous plants are used to pollinate suitable maize varieties to produce hybrid seed containing the transgenes of interest. Alternatively, homozygous plants are pollinated by suitable maize varieties to produce hybrid seed containing the transgenes of interest. The hybrid seed is planted in one or more field environments and cultivated using standard agronomic practices. Yield parameters including the time from planting to reach particular developmental stages (e.g., V1, V2, V3, etc., through R1, R2, R3, etc.), plant height, leaf angle, ear length, ear diameter, number of kernel rows, kernel size, 100 seed weight, kernel number, harvest index, and seed yield are measured for the hybrid plants containing the ictB transgene cassette and other transgene cassette(s). The yield parameters for these transgenic plants are compared with hybrid maize plants with the same genetic background but lacking the transgenes. The effects of transgene integration and expression on maize growth and yield are determined from these measurements and comparisons.
    • Example 3: Transformation of Oryza sativa with Multigenic Vectors Containing ictB and at Least One Additional Gene
  • The ictB-containing multigenic vectors shown in Table 7 were used to transform rice (Oryza sativa). The genetic elements contained in each of these constructs are included in Table 4. Each of these vectors was transformed into A. tumefaciens and the A. tumefaciens cells harboring the relevant vector was used to transform embryogenic rice callus.
  • TABLE 7
    Multigenic ictB-containing vectors used for rice transformation
    Construct
    130234 130868
    130296 130965
    130625 130980
    130624 130981
    130627 131075
    130866 130969
    130867 130971
    130850 130973
    130851 130966
    130852 131405
    130865 131406
  • Following the Agrobacterium-mediated transformation, the rice tissue was placed on selective tissue culture medium suitable for regenerating transgenic rice plants. The rice plants were transferred to soil and leaf tissue samples were collected. DNA was extracted from the leaves and PCR and/or Taqman-based assays were performed to confirm the integration of the genes of interest in the rice genome. Following confirmation of the integration of the genes of interest in the genome, selected plants were chosen for analysis of gene expression.
  • For gene expression assays, total RNA was extracted from leaf tissue harvested from T0-generation transgenic rice events. The RNA was reverse transcribed and quantitative reverse transcriptase-PCR (qRT-PCR) assays were performed to assess the steady-state levels of transgene-encoded mRNA. Primers were designed for these qRT-PCR assays so that the PCR product amplified was specific to the transgene, without any added signal from wild-type transcripts. For these experiments, the primer pair of SEQ ID NOs: 587 and 588 was used to amplify an 82 bp sequence internal to the ictB coding region. The primer pair of SEQ ID NOs: 591 and 592 was used to amplify a 107 bp region spanning the junction between the ism-2 coding region and the ZmUbi 3′UTR. The primer pair of SEQ ID NOs: 593 and 594 was used to amplify a 110 bp region internal to the Populus sp. hc1 gene. The primer pair of SEQ ID NOs: 595 and 596 was used to amplify a 114 bp region internal to the AGPase large subunit coding region. Transcript levels encoded by the various transgenes were compared with the expression of UBQ5, a well-known housekeeping gene in the rice genome (Jain et al (2006) Biochemical and Biophysical Research Communications 345: 646-651). The primer pair of SEQ ID NOs: 583 and 584 were used to amplify the UBQ5 transcript in these qRT-PCR assays. Transcript levels were expressed relative to the expression of UBQ5; an expression level of 2, for example, would indicate that the expression of the transgene was twice as high as that of UBQ5. Table 8 summarizes the results of qRT-PCR assays performed with T0-generation rice transformed with multigenic vectors containing an ictB gene in addition to at least one other gene.
  • TABLE 8
    Expression levels relative to the rice UBQ5 gene of transgenes
    in T0-generation rice transformed with multigenic vectors
    Event Gene 2 ID Gene 3 ID ictB Gene 2 Gene 3
    130852-1 ism-2 7.31 0.53
    130852-2 ism-2 20.92 0.29
    130852-3 ism-2 23.25 0.22
    130868-1 hc1 (Sorghum 3.97 not
    bicolor) tested 1
    130980-2 hc1 (Populus sp.) AGPase (large 68.78 11.37 0.80
    subunit)
    130980-3 hc1 (Populus sp.) AGPase (large 6.96 5.84 0.18
    subunit)
    130980-4 hc1 (Populus sp.) AGPase (large nd 2 nd 2 nd 2
    subunit)
    130980-6 hc1 (Populus sp.) AGPase (large 44.22 0.02 0.10
    subunit)
    130980-7 hc1 (Populus sp.) AGPase (large 14.32 12.07 0.35
    subunit)
    130980-8 hc1 (Populus sp.) AGPase (large 7.91 4.85 0.27
    subunit)
    130980-9 hc1 (Populus sp.) AGPase (large 16.44 14.59 0.46
    subunit)
    130980-10 hc1 (Populus sp.) AGPase (large 14.43 13.49 0.45
    subunit)
    130980-11 hc1 (Populus sp.) AGPase (large 9.89 11.56 0.23
    subunit)
    130980-12 hc1 (Populus sp.) AGPase (large 34.44 0.01 0.07
    subunit)
    130981-2 hc1 (Sorghum AGPase (large nd 2 not nd 2
    bicolor) subunit) tested 1
    130981-3 hc1 (Sorghum AGPase (large nd 2 not nd 2
    bicolor) subunit) tested 1
    130981-4 hc1 (Sorghum AGPase (large 0.85 not 0.13
    bicolor) subunit) tested 1
    130981-5 hc1 (Sorghum AGPase (large nd 2 not 0.37
    bicolor) subunit) tested 1
    130981-6 hc1 (Sorghum AGPase (large 17.49 not 0.25
    bicolor) subunit) tested 1
    130981-10 hc1 (Sorghum AGPase (large 1.90 not 0.07
    bicolor) subunit) tested 1
    130981-11 hc1 (Sorghum AGPase (large 1.03 not 0.29
    bicolor) subunit) tested 1
    130981-13 hc1 (Sorghum AGPase (large 2.58 not 0.03
    bicolor) subunit) tested 1
    130981-14 hc1 (Sorghum AGPase (large 3.46 not nd 2
    bicolor) subunit) tested 1
    130981-15 hc1 (Sorghum AGPase (large 1.21 not 0.28
    bicolor) subunit) tested 1
    1 Expression of the S. bicolor hc1 gene was not tested in these samples
    2 Expression of this gene was not detected in the leaf sample used for these assays
  • Transgenic rice plants containing an ictB cassette and one or more additional transgene cassettes are characterized to assess the effects of the transgenes on plant growth and yield. T0-generation rice events are self-pollinated to produce homozygous events. Homozygous events are identified through the use of Taqman assays to assess zygosity. These homozygous plants are grown in a greenhouse setting along with wild-type and/or null segregant rice plants of the same genetic background but lacking the transgenes. Yield components including plant height, number of tillers, number of panicles, time from planting to reach various developmental stages of interest, seed number, hundred seed weight, seed size, harvest index, and seed yield are measured. The yield parameters for these transgenic plants are compared with rice plants with the same genetic background but lacking the transgenes. The effects of transgene integration and expression on rice growth and yield are determined from these measurements and comparisons.
    • Example 4: Transformation of Setaria viridis with Multigenic Vectors Containing ictB and at Least One Additional Gene
  • The ictB-containing multigenic vectors shown in Table 9 were used to transform Setaria viridis. The genetic elements contained in each of these constructs are included in Table 4. Each of these vectors was transformed into A. tumefaciens and the A. tumefaciens cells harboring the relevant vector was used to transform S. viridis callus.
  • TABLE 9
    Multigenic ictB-containing vectors used for S. viridis transformation
    Construct
    130965 130973
    130947 130969
    130978 130876
    130967 130874
    130948 130966
    130980 130875
    130971 130893
    131076 131405
    130968 131406
    130873
  • Following the Agrobacterium-mediated transformation, the S. viridis tissue was placed on selective tissue culture medium suitable for regenerating transgenic S. viridis plants. The S. viridis plants were transferred to soil and leaf tissue samples were collected. DNA was extracted from the leaves and PCR and/or Taqman-based assays were performed to confirm the integration of the genes of interest in the S. viridis genome. Following confirmation of the integration of the genes of interest in the genome, selected plants were chosen for analysis of gene expression.
  • For gene expression assays, total RNA was extracted from leaf tissue harvested from T0-generation transgenic S. viridis events. The RNA was reverse transcribed and quantitative reverse transcriptase-PCR (qRT-PCR) assays were performed to assess the steady-state levels of transgene-encoded mRNA. Primers were designed for these qRT-PCR assays so that the PCR product amplified was specific to the transgene, without any added signal from wild-type transcripts. For these experiments, the primer pair of SEQ ID NOs: 587 and 588 was used to amplify an 82 bp sequence internal to the ictB coding region. The primer pair of SEQ ID NOs: 593 and 594 was used to amplify a 110 bp region internal to the Populus sp. hc1 gene. The primer pair of SEQ ID NOs: 595 and 596 was used to amplify a 114 bp region internal to the AGPase large subunit coding region. The primer pair of SEQ ID NOs: 597 and 598 was used to amplify a 111 bp region internal to the FBP aldolase coding region. Transcript levels encoded by the various transgenes were compared with the expression of GAPDH, a well-known housekeeping gene in the S. viridis genome (Lambret-Frotté et al (2015) PLoS One 10: e0135006). The primer pair of SEQ ID NOs: 585 and 586 were used to amplify the GAPDH transcript in these qRT-PCR assays. Transcript levels were expressed relative to the expression of GAPDH; an expression level of 2, for example, would indicate that the expression of the transgene was twice as high as that of GAPDH. Table 10 summarizes the results of qRT-PCR assays performed with T0-generation S. viridis transformed with multigenic vectors containing an ictB gene in addition to at least one other gene.
  • TABLE 10
    Expression levels relative to the S. viridis GAPDH gene of transgenes
    in T0-generation S. viridis transformed with multigenic vectors
    Event Gene 2 ID Gene 3 ID Gene 4 ID ictB Gene 2 Gene 3 Gene 4
    130971-12B FBP aldolase hc1 (Populus sp.) 0.04 0.002 0.13
    130973-1B FBP aldolase hc1 (Populus sp.) AGPase (large 0.07 0.02 0.33 0.01
    subunit)
    130973-2 FBP aldolase hc1 (Populus sp.) AGPase (large 0.54 0.07 0.52 0.02
    subunit)
    130973-3 FBP aldolase hc1 (Populus sp.) AGPase (large 0.37 0.04 0.58 0.01
    subunit)
    130973-4 FBP aldolase hc1 (Populus sp.) AGPase (large 0.05 0.01 0.12 0.02
    subunit)
    130973-5A FBP aldolase hc1 (Populus sp.) AGPase (large 0.13 0.04 0.30 0.03
    subunit)
    130973-6A FBP aldolase hc1 (Populus sp.) AGPase (large 0.09 0.02 0.19 0.01
    subunit)
    130947-2 hc1 (Populus sp.) 0.18 0.11
    130947-3 hc1 (Populus sp.) 0.20 0.10
    130947-4A hc1 (Populus sp.) 0.17 0.09
    130947-5A hc1 (Populus sp.) 0.36 0.06
    130947-9 hc1 (Populus sp.) 0.34 0.01
    130947-10A hc1 (Populus sp.) 0.57 0.02
    130947-11 hc1 (Populus sp.) 0.29 0.38
    130947-12 hc1 (Populus sp.) 1.87 0.02
    130947-13 hc1 (Populus sp.) 1.18 0.09
    130947-14 hc1 (Populus sp.) 0.69 0.03
    130947-15A hc1 (Populus sp.) 0.50 0.01
    130947-18B hc1 (Populus sp.) 0.86 0.01
    130947-19A hc1 (Populus sp.) 0.31 0.01
    130947-20B hc1 (Populus sp.) 0.10 0.04
    130947-21B hc1 (Populus sp.) 0.17 0.03
    130947-22 hc1 (Populus sp.) 0.64 0.05
    130947-23A hc1 (Populus sp.) nd 1 0.004
    1 Expression of this gene was not detected in the leaf sample used for these assays
  • Transgenic S. viridis plants containing an ictB cassette and one or more additional transgene cassettes are characterized to assess the effects of the transgenes on plant growth and yield. T0-generation S. viridis events are self-pollinated to produce homozygous events. Hemizygous and homozygous events are identified through the use of Taqman assays to assess zygosity. Hemizygous and homozygous plants are grown in a greenhouse setting along with wild-type and/or null segregant S. viridis plants of the same genetic background but lacking the transgenes. Yield components including plant height, number of tillers, number of panicles, time from planting to reach various developmental stages of interest, seed number, hundred seed weight, seed size, harvest index, and seed yield are measured. The yield parameters for these transgenic plants are compared with S. viridis plants with the same genetic background but lacking the transgenes. The effects of transgene integration and expression on S. viridis growth and yield are determined from these measurements and comparisons.
    • Example 5: Transformation of Solanum tuberosum with Multigenic Vectors Containing ictB and at Least One Additional Gene
  • The ictB-containing multigenic vectors shown in Table 11 were used to transform potato (Solanum tuberosum). The genetic elements contained in each of these constructs are included in Table 4. Each of these vectors was transformed into A. tumefaciens and the A. tumefaciens cells harboring the relevant vector was used to transform potato cells.
  • TABLE 11
    Multigenic ictB-containing vectors used for S. tuberosum transformation
    Construct
    130470
    130471
    130472
    130475
    130477
  • Following the Agrobacterium-mediated transformation, the potato tissue was placed on selective tissue culture medium suitable for regenerating transgenic potato plants. The potato plants were transferred to soil and leaf tissue samples were collected. DNA was extracted from the leaves and PCR and/or Taqman-based assays were performed to confirm the integration of the genes of interest in the potato genome. Following confirmation of the integration of the genes of interest in the genome, selected plants are chosen for analysis of gene expression.
  • Expression of the transgenes in potato tissue is confirmed through the use of qRT-PCR, RT-PCR, Northern blotting, or other suitable assays. Leaf tissue is harvested from transgenic potato leaves and RNA is extracted. This RNA is assayed for the presence of the transcripts encoded by the transgenes in the constructs listed in Table 11.
  • Transgenic potato plants containing an ictB cassette and one or more additional transgene cassettes are characterized to assess the effects of the transgenes on plant growth and yield. Transgenic potato events are cultivated in the greenhouse using cuttings to produce multiple plants that can produce seed potatoes. These seed potatoes are grown in either a greenhouse or a field setting to bulk up the seed potatoes for larger-scale field trials. After this bulking up, the seed potatoes are planted in a field setting along with genetically similar potatoes that lack the transgenes of interest. Yield components including photosynthetic rate, above-ground biomass, tuber biomass, and potato yield in terms of pounds per acre are measured. The yield parameters for these transgenic plants are compared with potato plants with the same genetic background but lacking the transgenes. The effects of transgene integration and expression on potato growth and yield are determined from these measurements and comparisons.
    • Example 6: Co-Transformation of a Plant of Interest with an ictB Vector and at Least One Additional Vector
  • A plant transformation vector containing a functional ictB expression cassette is constructed as described in Example 1. A gene encoding an ictB protein is included in this ictB expression cassette, operably linked to a plant promoter and 5′UTR at its 5′ terminus and a 3′UTR at its 3′ terminus. In some cases the plant transformation vector containing the ictB expression cassette also contains one or more additional expression cassettes with a plant promoter and 5′UTR operably linked to an open reading frame which is itself operably linked to a 3′UTR. Whether this transformation vector contains only an ictB expression cassette or contains an ictB expression cassette in addition to one or more additional expression cassettes, this is referred to as the “ictB vector.”
  • In addition to the ictB vector, a second plant transformation vector is constructed containing a gene expression cassette with a functional promoter and 5′UTR upstream of at least one gene of interest, followed by a 3′UTR downstream of this gene of interest. In some cases the open reading frame encodes a protein listed in Table 2. In some cases this second vector contains additional gene expression cassettes with functional plant promoters, 5′UTRs, open reading frames, and 3′UTRs so that more than one gene of interest may be included in this second vector. This vector is referred to as the “auxiliary vector.” In certain cases it may be desirable to utilize more than one auxiliary vector for co-transformation with the ictB vector, as described below.
  • The ictB vector is transformed into A. tumefaciens cells while the auxiliary vector(s) is/are transformed into separate A. tumefaciens cells. Alternatively, both the ictB vector and the auxiliary vector(s) are transformed into a single A. tumefaciens cell. Alternatively, the ictB vector and the auxiliary vector(s) are coated onto beads for biolistic bombardment of transformable plant tissue. Following Agrobacterium-mediated transformation or biolistic transformation, the plant tissue is placed onto suitable tissue culture medium for regeneration of fertile plants. PCR, Southern blotting, or other suitable molecular assays are performed in order to verify the presence of the ictB gene as well as of the other gene(s) of interest in the genome of the transformed plants. Expression of the ictB gene and of the other gene(s) of interest is verified through the use of RT-PCR, Northern blotting, or other suitable assays to detect the encoded transcripts. The regenerated plants are grown to maturity. Following the maturation of the plants, above-ground biomass is harvested, dried, and weighed. The seeds are harvested, weighed, and counted.
    • Example 7: Identification of ictB Proteins
  • FIG. 1 shows an alignment of thirty-seven ictB protein sequences. This alignment shows at least six regions that are extremely well-conserved among all examined ictB protein sequences. The six regions are located at amino acid residues 209-213, 220-235, 274-279, 341-353, 364-372, and 479-486 based on the numbering shown in FIG. 1. In this FIGURE, completely conserved amino acids (i.e., residues at which only a single amino acid is found in all of the sequences examined) are indicated by an asterisk (*). Residues at which there appears to be functional conservation (i.e., only amino acids that share certain properties are found at a given position) are indicated by a period (.) or a colon (:).
  • The amino acid sequences shown in FIG. 1 include a conserved region from residues 209-213. As shown in this FIGURE, all of the ictB sequences examined contain the sequence AXWXDXXS (SEQ ID NO: 69), where X is any amino acid. In many of the sequences examined, this region contains the sequence ATWVDPXS (SEQ ID NO: 70). A second conserved region located at amino acid positions 220-235 according to the numbering in FIG. 1 contains the sequence RX(F/Y)(G/S)XLXNPNLXXXYL (SEQ ID NO: 71). In many of the sequences examined, this region contains the sequence RX(F/Y)(G/S)XLGNPNLLAGYL (SEQ ID NO: 72). A third conserved region located at amino acid positions 274-279 according to the numbering in FIG. 1 contains the sequence SRGXWX (SEQ ID NO: 73). In many of the sequences examined, this region contains the sequence SRGGW(I/L) (SEQ ID NO: 74). A fourth conserved region located at amino acid positions 341-353 according to the numbering shown in FIG. 1 contains the amino acid sequence RXD(S/T)SNNFRX(N/T)VW (SEQ ID NO: 75). In many of the sequences examined, this region contains the sequence RXDSSNNFRXNVW (SEQ ID NO: 76). A fifth conserved region located at amino acid positions 364-372 according to the numbering shown in FIG. 1 contains the amino acid sequence PXXGIGPG(N/H) (SEQ ID NO: 77). A sixth conserved region located at amino acid positions 479-486 according to the numbering shown in FIG. 1 contains the amino acid sequence DT(I/V)X(F/Y)RPX (SEQ ID NO: 78). In many of the sequences examined, this region contains the sequence DT(I/V)X(F/Y)RP(E/Q) (SEQ ID NO: 79). Without being limited by theory, it is likely that these six well-conserved regions of the ictB sequences examined are functionally important for the ictB protein. Currently, the precise biochemical function of ictB proteins in vivo is unknown. Multiple ictB sequences have been expressed in planta, resulting in elevated rates of photosynthesis and improved growth. Without being limited by theory, it is likely that in planta expression of other putative ictB sequences containing one or more of the conserved amino acid sequences described herein, either singly or in combination with one or more additional gene(s) of interest, will also lead to improved photosynthetic metabolism and plant growth.
    • Example 8: RNA-Seq to Determine Effects of ictB Expression on the Plant Transcriptome
  • A plant that has been transformed to contain a functional ictB cassette in its genome, and that has been shown to express the ictB gene, is cultivated. The plant may be grown from seed, or alternatively may be cultivated clonally, e.g., through the use of tissue culture techniques. Control plants such as null segregants or genetically similar wild-type plants of the same species as the ictB-expressing plant, are grown under identical environmental conditions as the ictB-expressing plant. Plant tissue from different organs including leaves, stems, floral buds, flowers, embryo, endosperm, whole seed, and roots is collected from both ictB-expressing plants and from control plants at the same time. RNA is extracted from these tissues and is used to generate RNA libraries. These RNA libraries are analyzed by RNA-Seq or other technologies suitable for obtaining sequence data from RNA samples. Following the generation of RNA-Seq data, the transcriptome of the ictB-expressing plants is compared with the transcriptome of the control plants from the corresponding tissue(s). Transcriptomic analyses are undertaken to determine genes and sets of genes whose expression is altered in ictB-expressing plants relative to control plants.
    • Example 9: Metabolic Profiling to Determine Effects of ictB Expression on the Plant Metabolome
  • A plant that has been transformed to contain a functional ictB cassette in its genome, and that has been shown to express the ictB gene, is cultivated. The plant may be grown from seed, or alternatively may be cultivated clonally, e.g., through the use of tissue culture techniques. Control plants such as null segregants or genetically similar wild-type plants of the same species as the ictB-expressing plant, are grown under identical environmental conditions as the ictB-expressing plant. Plant tissue from different organs including leaves, stems, floral buds, flowers, embryo, endosperm, whole seed, and roots is collected from both ictB-expressing plants and from control plants at the same time. Metabolites are extracted from these tissues for downstream analysis. Suitable techniques are applied to generate a metabolite profile from the various tissues collected from ictB-expressing plants and from control plants. Following the generation of this metabolomic data, the metabolome of the ictB-expressing plants is compared with the metabolome of the control plants from the corresponding tissue(s). Metabolomic analyses are undertaken to determine metabolites whose accumulation is altered in ictB-expressing plants relative to control plants.
    • Example 10: Single-Gene Transformation Constructs Containing ictB
  • Plant transformation vectors were constructed in plasmid backbones containing sequences for maintenance in both E. coli and Agrobacterium tumefaciens. These transformation vectors contained an ictB expression cassette. Each ictB expression cassette contained an ictB open reading frame (SEQ ID NOs: 1 and 542) encoding an ictB protein (SEQ ID NO: 2). The vectors were designed to target the ictB protein to the cytoplasm in plant tissue in the absence of any signal peptide. Certain transformation vectors were designed to target the ictB protein to the chloroplast envelope in vectors where the ictB open reading frame is flanked at its 5′ terminus by a sequence encoding the signal peptide from the RbcS gene (SEQ ID NOs: 3 and 4), resulting in production of the protein described by SEQ ID NO: 544. Certain transformation vectors were designed to target the ictB protein to the plasma membrane in vectors where the ictB open reading frame is flanked at its 5′ terminus by the PR1a signal peptide (SEQ ID NOs: 5 and 6), resulting in production of the protein described by SEQ ID NO: 546. Certain transformation vectors were designed to target the ictB protein to the endoplasmic reticulum (ER) in vectors where the ictB open reading frame is flanked at its 5′ terminus by the PR1a signal peptide (SEQ ID NOs: 5 and 6) and at its 3′ terminus by a SEKDEL sequence (SEQ ID NOs: 7 and 8), resulting in production of the protein described by SEQ ID NO: 548. The four versions of the ictB protein targeted to different subcellular locations are summarized in Table 2.
  • The ictB open reading frames in the plant transformation vectors were flanked at their 5′ ends by a promoter that is functional in plants and a 5′ untranslated region (5′UTR) to direct transcription and translation, respectively, of the open reading frame. The ictB open reading frames were flanked at their 3′ ends by a functional 3′UTR to stabilize the mRNA. Vectors were designed to express the ictB gene constitutively in vectors containing the maize ubiquitin (ZmUbi) promoter and 5′UTR (SEQ ID NO: 9). These vectors contain the ZmUbi 3′UTR (SEQ ID NO: 12) at the 3′ end of the ictB gene. Vectors were also designed to express the ictB gene preferentially in mesophyll cells in vectors containing the maize PepC (ZmPepC) promoter and 5′UTR (SEQ ID NO: 10). These vectors contain the ZmPepC 3′UTR (SEQ ID NO: 13) at the 3′ end of the ictB gene. Vectors were also designed to express the ictB gene preferentially in bundle sheath cells in vectors containing the maize RbcS (ZmRbcS) promoter and 5′UTR (SEQ ID NO: 11), or a truncated version of the ZmRbcS promoter (SEQ ID NO: 541), or the RbcS7A promoter and 5′UTR (SEQ ID NO: 540), or the GLDC promoter (SEQ ID NO: 539). Each of these vectors contain the ZmRbcS 3′UTR (SEQ ID NO: 14) at the 3′ end of the ictB gene. Table 12 summarizes the genetic elements used to regulate expression of the ictB gene.
  • TABLE 12
    Promoters, 5′UTRs, and 3′UTRs used
    to regulate ictB gene expression
    Predicted
    Expression
    Promoter and 5′UTR 3′UTR Profile
    ZmUbi (SEQ ID NO: 9) ZmUbi (SEQ ID NO: 12) Constitutive
    2X35S (SEQ ID NO: 537) 35S polyA (SEQ ID NO: Constitutive
    538)
    ZmPepC (SEQ ID NO: 10) ZmPepC (SEQ ID NO: 13) Mesophyll-
    Preferred
    ZmRbcS (SEQ ID NO: 11) ZmRbcS (SEQ ID NO: 14) BS-Preferred
    ZmRbcS_truncated (SEQ ID ZmRbcS (SEQ ID NO: 14) BS-Preferred
    NO: 541)
    GLDC (SEQ ID NO: 539) ZmRbcS (SEQ ID NO: 14) BS-Preferred
    RbcS7A (SEQ ID NO: 540) ZmRbcS (SEQ ID NO: 14) BS-Preferred
  • In some instances, the ictB gene that is expressed may encode an ictB protein other than that found in Synechococcus sp. PCC7942 (SEQ ID NO: 2, encoded by SEQ ID NOs: 1 and 542). In some cases, the ictB protein sequence that is encoded by the ictB gene may be the protein sequence shown in SEQ ID NO: 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, or 536.
  • As shown in Tables 2 and 12 above, the combination of promoter, 5′UTR, 3′UTR, and signal peptide should determine the cell type(s) in which the ictB gene of interest is expressed as well as the subcellular location in which the encoded ictB protein accumulates. Table 13 summarizes the ictB cassettes in the single-genic vectors used for plant transformation. Although some of the ictB cassettes in the constructs in this table are identical, differences in the transformation vector backbone, such as different selectable markers, exist among these constructs and thus certain vectors are more suitable for transformation of particular species despite identical ictB cassettes.
  • TABLE 13
    Summary of Single-Genic ictB Plant Transformation
    Vector ictB Cassettes
    Predicted Predicted
    Promoter + Signal Cell Subcellular
    Vector 5′UTR Peptide 3′UTR Type(s) Location
    130265 ZmUbi RbcS ZmUbi All Chloroplast
    130268 ZmUbi None ZmUbi All Cytoplasm
    130269 ZmPepC RbcS ZmPepC Mesophyll Chloroplast
    130273 ZmRbcS RbcS ZmRbcS BS Chloroplast
    (truncated)
    130276 ZmRbcS None ZmRbcS BS Cytoplasm
    (truncated)
    130781 ZmUbi RbcS ZmUbi All Chloroplast
    130782 ZmPepC RbcS ZmPepC Mesophyll Chloroplast
    130793 ZmUbi None ZmUbi All Cytoplasm
    130807 ZmPepC None ZmPepC Mesophyll Cytoplasm
    130808 ZmPepC PR1a ZmPepC Mesophyll Plasma
    Membrane
    130809 ZmPepC PR1a- ZmPepC Mesophyll ER
    SEKDEL
    130810 ZmUbi PR1a ZmUbi All Plasma
    Membrane
    130811 ZmUbi PR1a- ZmUbi All ER
    SEKDEL
    130822 ZmRbcS RbcS ZmRbcS BS Chloroplast
    130823 ZmRbcS None ZmRbcS BS Cytoplasm
    130885 ZmRbcS RbcS ZmRbcS BS Chloroplast
    130886 ZmRbcS None ZmRbcS BS Cytoplasm
    130950 ZmRbcS RbcS ZmRbcS BS Chloroplast
    130964 2X35S RbcS 35S polyA All Chloroplast
    131054 ZmRbcS None ZmRbcS BS Cytoplasm
    131055 ZmRbcS RbcS ZmRbcS BS Chloroplast
    131056 ZmUbi RbcS ZmUbi All Chloroplast
    131180 GLDC None ZmRbcS BS Cytoplasm
    131181 GLDC RbcS ZmRbcS BS Chloroplast
    131203 RbcS7A None ZmRbcS BS Cytoplasm
    131204 RbcS7A RbcS ZmRbcS BS Chloroplast
    • Example 11: Transformation of Setaria viridis with Single-Genic ictB Constructs
  • Single-genic plant transformation vectors containing a functional ictB expression cassette were constructed as described in Example 10. These vectors were transformed into A. tumefaciens cells suitable for transformation of plant cells. Table 14 summarizes the single-genic ictB transformation vectors used for transformation of S. viridis. A. tumefaciens cells harboring the transformation vectors shown in Table 14 were brought into contact with S. viridis cells suitable for transformation according to a previously published protocol (PCT/US2015/43989). These S. viridis cells were placed onto selective tissue culture medium containing chemicals suitable for selecting transgenic plants.
  • TABLE 14
    Vectors used for S. viridis Transformation
    Predicted Predicted
    Promoter + Signal Cell Subcellular
    Vector 5′UTR Peptide 3′UTR Type(s) Location
    130265 ZmUbi RbcS ZmUbi All Chloroplast
    130269 ZmPepC RbcS ZmPepC Mesophyll Chloroplast
    130273 ZmRbcS RbcS ZmRbcS BS Chloroplast
    (truncated)
    130276 ZmRbcS None ZmRbcS BS Cytoplasm
    (truncated)
    130781 ZmUbi RbcS ZmUbi All Chloroplast
    130782 ZmPepC RbcS ZmPepC Mesophyll Chloroplast
    130793 ZmUbi None ZmUbi All Cytoplasm
    130807 ZmPepC None ZmPepC Mesophyll Cytoplasm
    130808 ZmPepC PR1a ZmPepC Mesophyll Plasma
    Membrane
    130809 ZmPepC PR1a- ZmPepC Mesophyll ER
    SEKDEL
    130810 ZmUbi PR1a ZmUbi All Plasma
    Membrane
    130811 ZmUbi PR1a- ZmUbi All ER
    SEKDEL
    130822 ZmRbcS RbcS ZmRbcS BS Chloroplast
    130823 ZmRbcS None ZmRbcS BS Cytoplasm
    130950 ZmRbcS RbcS ZmRbcS BS Chloroplast
    130964 2X35S RbcS 35S polyA All Chloroplast
    131180 GLDC None ZmRbcS BS Cytoplasm
    131181 GLDC RbcS ZmRbcS BS Chloroplast
    131203 RbcS7A None ZmRbcS BS Cytoplasm
    131204 RbcS7A RbcS ZmRbcS BS Chloroplast
  • PCR-based assays were used to determine whether the ictB cassette was successfully integrated into the S. viridis genome. Table 15 summarizes the number of PCR-positive plants that were recovered from S. viridis transformation with the vectors shown in Table 14.
  • TABLE 15
    Number of Transgenic Events Recovered from S. viridis
    Transformation with Single-Genic ictB Vectors
    Number of
    Vector Events
    130265 5
    130269 6
    130273 3
    130276 5
    130781 1
    130782 1
    130793 2
    130807 5
    130808 30
    130809 0
    130810 38
    130811 26
    130822 34
    130823 36
    130950 9
    130964 29
    131180 33
    131181 31
    131203 46
    131204 17
  • Transformation was successful in many cases, but some of the vectors shown in Tables 14 and 15 produced few PCR-positive transgenic S. viridis events. Work is ongoing to understand whether this is a result of toxicity of the ictB gene cassette in these vectors or due to other unrelated causes.
    • Example 12: Transformation of Maize (Zea mays) with Single-Genic ictB Vectors
  • Single-genic plant transformation vectors containing a functional ictB expression cassette were constructed as described in Example 10. These vectors were transformed into A. tumefaciens cells suitable for transformation of plant cells. Table 16 summarizes the constructs that were used to transform maize (Zea mays cv. B104) cells. A. tumefaciens cells harboring the transformation vector of interest were brought into contact with maize cells suitable for transformation. These maize cells were then placed onto selective tissue culture medium containing chemicals suitable for selecting transgenic plants. PCR-based assays were performed to verify the presence of the ictB gene cassette in the maize cells.
  • TABLE 16
    Vectors used for Maize Transformation
    Predicted Predicted
    Promoter + Signal Cell Subcellular
    Vector 5′UTR Peptide 3′UTR Type(s) Location
    130265 ZmUbi RbcS ZmUbi All Chloroplast
    130268 ZmUbi None ZmUbi All Cytoplasm
    130269 ZmPepC RbcS ZmPepC Mesophyll Chloroplast
    130273 ZmRbcS RbcS ZmRbcS BS Chloroplast
    (truncated)
    130276 ZmRbcS None ZmRbcS BS Cytoplasm
    (truncated)
    130885 ZmRbcS RbcS ZmRbcS BS Chloroplast
    130886 ZmRbcS None ZmRbcS BS Cytoplasm
    131054 ZmRbcS None ZmRbcS BS Cytoplasm
    131055 ZmRbcS RbcS ZmRbcS BS Chloroplast
    131056 ZmUbi RbcS ZmUbi All Chloroplast
  • PCR-based assays were used to determine whether the ictB cassette was successfully integrated into the maize genome. Table 17 summarizes the number of PCR-positive plants that were recovered from maize transformation with the vectors shown in Table 16.
  • TABLE 17
    Vectors used for Maize Transformation
    Number of
    Vector Events
    130265 91
    130268 12
    130269 0
    130273 83
    130276 63
    130885 0
    130886 0
    131054 0
    131055 0
    131056 0
  • Transformation was successful in a number of cases, but some of the vectors shown in Tables 16 and 17 failed to produce any PCR-positive transgenic maize events. Work is ongoing to understand whether this is a result of toxicity of the ictB gene cassette in these vectors or due to other unrelated causes.
    • Example 13: Characterization of ictB-Expressing Setaria viridis
  • T0-generation S. viridis plants generated as described above were cultivated and grown to maturity, then allowed to self-pollinate to produce T1-generation seed. This T1 seed was planted and cultivated in a greenhouse setting. Quantitative RT-PCR (qRT-PCR) assays were performed to assess the expression level of the ictB transgenes in S. viridis leaf tissue. Table 18 summarizes the expression data from these assays, with the expression levels of the ictB gene shown relative to the GAPDH gene, a well-known S. viridis housekeeping gene (Lambret-Frotté et al (2015) PLoS One 10: e0135006). The primer pair of SEQ ID NOs: 585 and 586 were used to amplify the GAPDH transcript in these qRT-PCR assays. For these experiments, the primer pair of SEQ ID NOs: 587 and 588 was used to amplify an 82 bp sequence internal to the ictB coding region. Eight to ten individual T1-generation ictB-expressing S. viridis plants derived from selected T0 events were cultivated alongside wild-type and/or null segregant S. viridis plants. The number of days required to reach reproductive development were monitored, and upon maturation of the plants, the total dry weight (DW) of the above-ground biomass and seed weight were measured. Harvest index (HI) was calculated from the ratio of dry seed weight to total above ground biomass dry weight. Table 19 summarizes the data from these T1 experiments, with the data expressed as the percent change relative to null segregant plants grown under identical environmental conditions alongside the transgenic plants.
  • TABLE 18
    ictB Expression Levels in selected
    S. viridis events relative to GAPDH
    Expression
    Event Level
    130823.1 0.09 ± 0.03
    130823.2 0.12 ± 0.12
    130823.3 0.32 ± 0.28
    130823.5 0.18 ± 0.23
    130950.1 0.07 ± 0.04
    130950.2 0.07 ± 0.06
    130950.4 0.16 ± 0.07
    130950.5 0.06 ± 0.06
    130950.6 0.06 ± 0.06
  • TABLE 19
    T1-Generation Data from ictB-expressing S. viridis, Expressed
    as Percent Change Relative to Null Segregant Plants
    Seed
    DW Yield HI
    130808.02 −16%  −8%  8%
    130808.04a −27% −26%  0%
    130808.05a −38% −38% −4%
    130808.06 −36% −49% −23% 
    130808.1 −11% −29% −19% 
    130808.2  −6% −23% −16% 
    130808.3  −5% −17% −10% 
    130808.4  3%  −1%  0%
    130808.6  −9%  −9%  0%
    130811.03  −3%  19% 19%
    130811.04a  9%  34% 23%
    130811.05 −20% −15%  4%
    130811.08  5%  26% 19%
    130823.1 −13%  0% 21%
    130823.2 −13%  −5% 11%
    130823.3 −13% −19% −5%
    130823.5 −19% −24% −11% 
    130950.1  18%  43% 21%
    130950.2 −22% −29% −16% 
    130950.4 −13%  0% 16%
    130950.5  16%  43% 26%
    130950.6  10%  21% 11%
    130964.1  −7%  −2% 11%
    130964.2 −13% −14% −5%
    130964.3  5%  2%  0%
    130964.4 −10% −12%  0%
    130964.6 −13% −14% −5%
    130810.1 −37% −50% −16% 
    130810.13A −29% −42% −19% 
    130810.14A −10% −13% −6%
    130810.16B −37% −56% −32% 
    130810.5A  −7% −26% −19% 
  • As Table 19 shows, three of five events from the 130950 construct had higher DW and higher seed yield than null segregants, indicating positive effects resulting from ictB expression in this construct. Four of four events from the 130823 construct caused a decrease in biomass accumulation and seed yield relative to null segregant plants, indicating negative effects resulting from ictB expression in this construct. The events from the 130964 construct showed neither an increase nor a decrease in biomass accumulation and seed yield relative to null segregants. The 130808 events generally showed a decrease in biomass accumulation and seed yield relative to null segregants. Three of the five 130810 events tested showed a decrease in biomass accumulation and seed yield relative to null segregants, indicating negative effects resulting from ictB expression in this construct. Three of the four 130811 events tested showed no change in biomass accumulation but increased seed production, leading to an increased harvest index (HI) relative to null segregant plants. No significant changes in the time required for the plants to reach reproductive growth stages were seen among the events from any of these constructs (data not shown). The results of these experiments indicated that ictB expression in S. viridis was most beneficial when the gene was expressed primarily in bundle sheath cells and the protein was targeted to the chloroplast. Increased seed production was observed when the gene was expressed constitutively and the protein was targeted to the ER. Conversely, ictB expression was detrimental to S. viridis when the gene was expressed constitutively and targeted to the chloroplast as well as when the gene was expressed preferentially in mesophyll cells and targeted to the plasma membrane.
  • A comparison of the data in Tables 18 and 19 indicates that low to moderate expression of the ictB transgene is generally more beneficial than high expression in the plants examined. Events from the 130950 construct generally showed lower expression levels than those from the 130823 construct, and the 130950 construct showed greater biomass and seed yield improvements than the 130823 construct. Within the 130950 construct, 130950.4 showed the highest expression level; this event did not show increased biomass or seed yield relative to null segregant controls. Events 130950.1, 130950.5, and 130950.6 showed low expression of the ictB transgene and these plants accumulated more biomass and seed than null segregant plants.
    • Example 14: Characterization of ictB-Expressing Zea mays
  • T0-generation transgenic maize plants were generated in the B104 inbred cultivar. Pollen from these T0 events was used to pollinate maize plants of the LH51 inbred cultivar to generate F1 hybrid seed. F1 seed from these LH51×B104 was planted in a field environment in two-row plots. Wild-type hybrid LH51×B104 plants were grown alongside the transgenic hybrid events in the field, as were null segregant plants. Following maturation of the plants, the ears were harvested and kernels were removed from the ears and dried. The weight of the harvested kernels was used to derive yield data in the units of bushels per acre. Table 20 summarizes this yield data, with yield expressed as percent change relative to control plants (wild-type LH51×B104 and null segregants) that were grown at the same field site as the transgenic event. This table also includes ictB transgene expression levels derived from qRT-PCR experiments using RNA extracted from T0-Generation events produced in the B104 inbred cultivar.
  • TABLE 20
    F1-Generation Hybrid ictB-Expressing Maize Data,
    Expressed as Percent Yield Change Relative to
    Control Plants and ictB Expression Levels
    Event % Change Expression Level
    130265.16B 10.8% 0.04
    130265.9B 10.7% 0.10
    130265.10C 9.4% 0.11
    130265-17D 11.2% 0.31
    130265.9A 2.9% 0.12
    130265.15I 2.9% 0.10
    130265.1 2.8% Not Detected
    130265-17B 8.6% 0.13
    130265.4B 0.3% 0.06
    130265.7 −0.2% 0.11
    130265.15A −4.7% 0.15
    130265.15G −10.1% 0.09
    130273.17F 20.7% Not Tested
    130273.17G 6.7% Not Tested
    130273.12B 3.3% 0.014
    130273.17E 1.6% Not Tested
    130273.10A 0.8% 0.04
    130273.13A 0.2% 0.27
    130273-11B 7.6% 0.04
    130273.11A −0.3% 0.03
    130273.15F −1.9% 0.07
    130273.10C −3.8% 0.05
    130273.10D −4.3% 0.01
    130273-17H 0.5% Not Tested
    130273.14B −7.8% 0.23
    130273.2B −11.3% 0.02
    130273-13D −11.2% 0.28
    130276.4A 10.3% 0.04
    130276.5A 7.5% 0.03
    130276-11 13.5% 0.04
    130276-17 12.1%  0.0001
    130276-20D 9.7% 0.01
    130276-20E 9.2%  0.001
    130276-3B 2.1% 0.06
  • As Table 20 shows, seven out of seven 130276 events had increased yield relative to control plants, with yield changes ranging from 2.1% to 13.5% higher than controls. Eight out of fifteen 130273 events had increased yield relative to control plants, with yield changes ranging from 11.3% lower than controls to 20.7% higher than controls. Nine out of twelve 130265 events had increased yield relative to control plants, with yield changes ranging from 10.1% lower than controls to 11.2% higher than controls.

Claims (33)

We claim:
1. A method for increasing crop yield comprising transforming a plant that utilizes C4 photosynthesis with at least one ictB coding sequence.
2. The method of claim 1, wherein said ictB coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 2 and 544.
3. A plant having stably incorporated into its genome a construct comprising a promoter that drives expression in a plant operably linked to an ictB coding sequence, wherein said plant utilizes C4 photosynthesis.
4. The plant of claim 3, wherein said ictB coding sequence encodes a protein selected from the group of SEQ ID NOs: 2 and 544.
5. Seed of any one of the plants of claim 3.
6. The plant of claim 3 wherein said plant is a monocot.
7. The plant of claim 6 wherein said plant is from the genus Zea.
8. The plant of claim 3 wherein said plant is a dicot.
9. The method of claim 1, wherein said ictB coding sequence is selected from the group of SEQ ID NOs: 1, 542, 543, and 580.
10. The plant of claim 3, wherein said ictB coding sequence is selected from the group of SEQ ID NOs: 1, 542, 543, and 580.
11. A method for increasing crop yield comprising transforming a plant with an ictB coding sequence and increasing the expression of at least one additional coding sequence involved in CO2 assimilation, and wherein said additional coding sequence is at least one of SBPase, FBPase, and FBP aldolase.
12. The method of claim 11, wherein said ictB coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 2, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 536, 544, 546, and 548.
13. The method of claim 11, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 23, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, and 178.
14. The method of claim 11, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 15, 25, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, and 200.
15. The method of claim 11, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 16, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, and 221.
16. The method of claim 11, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 17, 26, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, and 250.
17. The method of claim 11, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 27, 28, 29, 30, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, and 358.
18. The method of claim 11, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 31, 32, 33, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, and 390.
19. The method of claim 11, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 21, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, and, 488.
20. The method of claim 11, wherein said additional coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 22, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, and 535.
21. A plant having stably incorporated into its genome a construct comprising a promoter that drives expression in a plant operably linked to an ictB coding sequence, wherein said plant has increased expression of at least one CO2 assimilating coding sequence wherein said CO2 assimilating coding sequence is at least one of SBPase, FBPase, and FBP aldolase.
22. The plant of claim 21, wherein said ictB coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 2, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 536, 544, 546, and 548.
23. The plant of claim 21, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 23, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, and 178.
24. The plant of claim 21, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 15, 25, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, and 200.
25. The plant of claim 21, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 16, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, and 221.
26. The plant of claim 21, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 17, 26, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, and 250.
27. The plant of claim 21, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 27, 28, 29, 30, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, and 358.
28. The plant of claim 21, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 31, 32, 33, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, and 390.
29. The plant of claim 21, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 21, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, and, 488.
30. The plant of claim 21, wherein said CO2 assimilating coding sequence encodes a protein selected from the group consisting of SEQ ID NOs: 22, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, and 535.
31. Transformed seed of any one of the plants of claims 21-30.
32. The transformed plant of any one of claims 21-30 wherein said plant is a monocot.
33. The transformed plant of any one of claims 21-30 wherein said plant is a dicot.
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