OA19673A - Plant regulatory elements and uses thereof. - Google Patents
Plant regulatory elements and uses thereof. Download PDFInfo
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- OA19673A OA19673A OA1201900290 OA19673A OA 19673 A OA19673 A OA 19673A OA 1201900290 OA1201900290 OA 1201900290 OA 19673 A OA19673 A OA 19673A
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Abstract
The invention provides recombinant DNA molecules and constructs, as well as their nucleotide sequences, useful for modulating gene expression in plants. The invention also provides transgenic plants, plant cells, plant parts, and seeds comprising the recombinant DNA molecules operably linked to heterologous transcribable DNA molecules, as are methods of their use.
Description
PLANT REGULATORY ELEMENTS AND USES THEREOF
REFERENCE TO RELATED APPLICATION
[0001] This application claims the benefit of United States Provisional Application No. 62/448,019, filed January 19, 2017, which is herein incorporated by reference in its entirety.
INCORPORATION OF SEQUENCE LISTING
[0002] The computer readable form of the sequence listing that is contained in the file named “MONS436WO-sequence_listing.txt” is 59,917 bytes (as measured in Microsoft Windows®) and was created on January 12, 2018, is filed by electronic submission concurrently with this application and is herein incorporated by reference in its entirety.
FIELD OF THE INVENTION
[0003] The invention relates to the field of plant molecular biology and plant genetic engineering. More specifically, the invention relates to DNA molécules useful for modulating gene expression in plants.
BACKGROUND
[0004] Regulatory éléments are genetic éléments that regulate gene activity by modulating the transcription of an operably linked transcribable DNA molécule. Such éléments may include promoters, leaders, introns, and 3' untranslated régions and are useful in the field of plant molecular biology and plant genetic engineering.
SUMMARY OF THE INVENTION
[0005] The invention provides novel synthetic gene regulatory éléments for use in plants. The invention also provides recombinant DNA molécules and constructs comprising the regulatory éléments. The présent invention also provides transgenic plant cells, plants, and seeds comprising the synthetic regulatory éléments. In one embodiment, the synthetic regulatory éléments are operably linked to a heterologous transcribable DNA molécule. The présent invention also provides methods of using the synthetic regulatory éléments and methods of making and using the recombinant DNA molécules comprising the synthetic regulatory éléments and transgenic plant cells, plants, and seeds comprising the synthetic regulatory éléments operably linked to a transcribable DNA molécule.
[0006] Thus, in one aspect, the invention provides a recombinant DNA molécule comprising a DNA sequence selected from the group consisting of: (a) a sequence with at least 85 percent sequence identity to any of SEQ ID NOs:l-29 and 43-45; (b) a sequence comprising any of SEQ ID NOs:l-29 and 43-45; and (c) a fragment of any of SEQ ID NOs:l-29 and 43-45, wherein the fragment has gene-regulatory activity; wherein the sequence is operably linked to a heterologous transcribable DNA molécule. By “heterologous transcribable DNA molécule,” it is meant that the transcribable DNA molécule is heterologous with respect to the polynucleotide sequence to which it is operably linked. In spécifie embodiments, the recombinant DNA molécule comprises a DNA sequence having at least about 90 percent, at least 91 percent, at least 92 percent, at least 93 percent, at least 94 percent, at least 95 percent, at least 96 percent, at least 97 percent, at least 98 percent, or at least 99 percent sequence identity to the DNA sequence of any of SEQ ID NOs:l-29 and 43-45. In particular embodiments, the DNA sequence comprises a regulatory element. In some embodiments the regulatory element comprises a promoter. In still other embodiments, the heterologous transcribable DNA molécule comprises a gene of agronomie interest, such as a gene capable of providing herbicide résistance in plants, or a gene capable of providing plant pest résistance in plants. In still other embodiments, the invention provides a construct comprising a recombinant DNA molécule as provided herein.
[0007] In another aspect, provided herein are transgenic plant cells comprising a recombinant DNA molécule comprising a DNA sequence selected from the group consisting of: (a) a sequence with at least about 85 percent sequence identity to any of SEQ ID NOs:l-29 and 43-45; (b) a sequence comprising any of SEQ ID NOs:l-29 and 43-45; and (c) a fragment of any of SEQ ID NOs:l-29 and 43-45, wherein the fragment has gene-regulatory activity; wherein the DNA sequence is operably linked to a heterologous transcribable DNA molécule. In certain embodiments, the transgenic plant cell is a monocotyledonous plant cell. In other embodiments, the transgenic plant cell is a dicotyledonous plant cell.
[0008] In still yet another aspect, further provided herein is a transgenic plant, or part thereof, comprising a recombinant DNA molécule comprising a DNA sequence selected from the group consisting of: a) a sequence with at least 85 percent sequence identity to any of SEQ ID NOs:l and 43-45; b) a sequence comprising any of SEQ ID NOs:l-29 and 43-45; and c) a fragment of any of SEQ ID NOs:l-29 and 43-45, wherein the fragment has gene-regulatory activity; wherein the sequence is operably linked to a heterologous transcribable DNA molécule. In spécifie embodiments, the transgenic plant is a progeny plant of any génération that comprises the recombinant DNA molécule. A transgenic seed comprising the recombinant DNA molécule that produces such a transgenic plant when grown is also provided herein.
[0009] In another aspect, the invention provides a method of producing a commodity product comprising obtaining a transgenic plant or part thereof containing a recombinant DNA molécule of the invention and producing the commodity product therefrom. In one embodiment, the commodity product is processed seeds, grains, plant parts, oils and meal.
[0010] In still yet another aspect, the invention provides a method of producing a transgenic plant comprising a recombinant DNA molécule of the invention comprising transforming a plant cell with the recombinant DNA molécule of the invention to produce a transformed plant cell and regenerating a transgenic plant from the transformed plant cell.
BRIEF DESCRIPTION OF THE SEQUENCES
[0011] SEQ ID NO:1 is a DNA sequence of a synthetic regulatory expression éléments group (EXP), EXP-At.GSP442.nno+At.Cyco:3 comprising a synthetic promoter (P-At.GSP442.nno:2), operably linked 5' to a synthetic leader (L-At.GSP442.nno:l), operably linked 5' to an intron (IAt.Cyco:2).
[0012] SEQ ID NO:2 is a synthetic promoter sequence, P-At.GSP442.nno:2.
[0013] SEQ ID NO:3 is a synthetic leader sequence, L-At.GSP442.nno:l.
[0014] SEQ ID NO:4 is a DNA sequence of a synthetic EXP, EXP-At.GSP571 comprising a synthetic promoter (P-At.GSP571.nno:5), operably linked 5' to a synthetic leader (LAt.GSP571.nno:l).
[0015] SEQ ID NO:5 is a synthetic promoter sequence, P-At.GSP571.nno:5.
[0016] SEQ ID NO:6 is a synthetic leader sequence, L-At.GSP571.nno:l.
[0017] SEQ ID NO:7 is a DNA sequence of a synthetic regulatory expression éléments group (EXP), .EXP-At.GSP571.nno+At.Cyco:2 comprising a synthetic promoter (P-At.GSP571.nno:5), operably linked 5' to a synthetic leader (L-At.GSP571.nno:l), operably linked 5' to an intron (IAt.Cyco:2).
[0018] SEQ ID NO:8 is a DNA sequence of a synthetic regulatory expression éléments group (EXP), EXP-At.GSP571.nno+At.GSI21.nno:10 comprising a synthetic promoter (PAt.GSP571.nno:5), operably linked 5' to a synthetic leader (L-At.GSP571.nno:l), operably linked 5' to a synthetic intron (I-At.GSI21.nno:2).
[0019] SEQ ID NO:9 is a synthetic intron sequence, I-At.GSI21.nno:2.
[0020] SEQ ID NO: 10 is a DNA sequence of a synthetic EXP, EXPAt.GSP571.nno+At.GSI102.nno:l comprising a synthetic promoter (P-At.GSP571.nno:5), operably linked 5' to a synthetic leader (L-At.GSP571.nno:l), operably linked 5' to a synthetic intron (I-At.GSI102.nno:l).
[0021] SEQ ID NO:11 is a synthetic intron sequence, I-At.GSI102.nno:l.
[0022] SEQ ID NO: 12 is a DNA sequence of a synthetic EXP, EXP-ALGSP564 comprising a synthetic promoter (P-At.GSP564.nno:3), operably linked 5' to a synthetic leader (LAt.GSP564.nno:l).
[0023] SEQ ID NO:13 is a synthetic promoter sequence, P-At.GSP564.nno:3.
[0024] SEQ ID NO:14 is a synthetic leader sequence, L-At.GSP564.nno:l.
[0025] SEQ ID NO: 15 is a DNA sequence of a synthetic EXP, EXP-At.GSP564.nno+At.Cyco:2 comprising a synthetic promoter (P-At.GSP564.nno:3), operably linked 5' to a synthetic leader (L-At.GSP564.nno:l), operably linked 5' to an intron (I-At.Cyco:2).
[0026] SEQ ID NO: 16 is a DNA sequence of a synthetic EXP, EXPAt.GSP564.nno+At.GSI17.nno:2 comprising a synthetic promoter (P-At.GSP564.nno:3), operably linked 5' to a synthetic leader (L-At.GSP564.nno:l), operably linked 5' to a synthetic intron (I-At.GSI17.nno:l).
[0027] SEQ ID NO: 17 is a synthetic intron sequence, I-At.GSI17.nno:l.
[0028] SEQ ID NO: 18 is a DNA sequence of a synthetic EXP, EXPAt.GSP564.nno+At.GSI102.nno:l comprising a synthetic promoter (P-At.GSP564.nno:3), operably linked 5' to a synthetic leader (L-At.GSP564.nno:l), operably linked 5' to a synthetic intron (I-At.GSI102.nno:l).
[0029] SEQ ID NO: 19 is a DNA sequence of a synthetic EXP, EXP-At.GSP579 comprising a synthetic promoter (P-At.GSP579.nno:2), operably linked 5' to a synthetic leader (LAt.GSP579.nno:l).
[0030] SEQ ID NO:20 is a synthetic promoter sequence, P-At.GSP579.nno:2.
[0031] SEQ ID NO:21 is a synthetic leader sequence, L-At.GSP579.nno:l.
[0032] SEQ ID NO:22 is a DNA sequence of a synthetic EXP, EXPAt.GSP579.nno+At.GSI102.nno:3 comprising a synthetic promoter (P-At.GSP579.nno:2), operably linked 5' to a synthetic leader (L-At.GSP579.nno:l), operably linked 5' to synthetic intron (I-At.GSI102.nno:l).
[0033] SEQ ID NO:23 is a DNA sequence of a synthetic EXP, EXPAt.GSP571.nno+At.GSP442.nno+At.Cyco:l comprising a synthetic chimeric promoter (PAt.GSP571/442, which is comprised of a synthetic enhancer (E-At.GSP571.nno:l) operably linked 5' to a synthetic promoter (P-At.GSP442.nno:2)), operably linked 5' to a synthetic leader (L-At.GSP442.nno:l), operably linked 5' to a leader (L-At.Cyco-1:1:2), operably linked 5' to an intron (I-At.Cyco:2).
[0034] SEQ ID NO:24 is a synthetic enhancer sequence, E-At.GSP571.nno:l.
[0035] SEQ ID NO:25 is a DNA sequence of a synthetic chimeric promoter, P-At.GSP571/442 comprised of a synthetic enhancer (E-At.GSP571.nno:l) operably linked 5' to a synthetic promoter (P-At.GSP442.nno:2).
[0036] SEQ ID NO:26 is a DNA sequence of a synthetic EXP, EXPAt.GSP576.nno+At.GSI17.nno:3 comprising a synthetic promoter (P-At.GSP576.nno:4), operably linked 5' to a synthetic leader (L-At.GSP576.nno:2), operably linked 5' to synthetic intron (I-At.GSI17.nno:l).
[0037] SEQ ID NO:27 is a synthetic promoter sequence, P-At.GSP576.nno:4.
[0038] SEQ ID NO:28 is a synthetic leader sequence, L-At.GSP576.nno:2.
[0039] SEQ ID NO:29 is a synthetic 3' UTR, T-Zm.GST59.nno:l.
[0040] SEQ ID NO:30 is a DNA sequence of a synthetic EXP, EXP-At.GSP221+At.Cyco:3 comprising a synthetic promoter (P-At.GSP221:3), operably linked 5' to a synthetic leader (LAt.GSP221:l), operably linked 5' to an intron (I-At.Cyco:2).
[0041] SEQIDNO:31 is a synthetic promoter sequence, P-At.GSP221:3.
[0042] SEQ ID NO:32 is a synthetic leader sequence, L-At.GSP221:l.
[0043] SEQ ID NO:33 is an intron sequence, I-At.Cyco:2 derived from a Cytochrome c oxidase subunit Via gene from Arabidopsis.
[0044] SEQ ID NO:34 is a 3' UTR sequence, T-Mt.Sali3-2-l:2:l derived from the Sali3 gene of Medicago truncatula.
[0045] SEQ ID NO:35 is a 3' UTR sequence, T-Mt.Oxr-1:2:1 derived from a putative oxidoreductase (OXR) protein gene from Medicago truncatula.
[0046] SEQ ID NO:36 is a 3' UTR sequence, T-Gb.FbL2:l derived from the Gossypium barbadense FbLate-2 gene.
[0047] SEQ ID NO:37 is a 3' UTR sequence, T-Mt.RD22-1:2:1 derived from a dehydrationresponsive protein RD22 gene from Medicago truncatula.
[0048] SEQ ID NO:38 is a DNA sequence of an EXP derived from a Cytochrome c oxidase subunit Via gene from Arabïdopsis, EXP-At.Cyco:l:l comprising a promoter (P-At.Cyco-1:1:2), operably linked 5' to a leader (L-At.Cyco-1:1:2), operably linked 5' to intron (I-At.Cyco-l:l:l).
[0049] SEQ ID NO:39 is a promoter sequence, P-At.Cyco-1:1:2 derived from a Cytochrome c oxidase subunit Via gene from Arabïdopsis.
[0050] SEQ ID NO:40 is a leader sequence, L-At.Cyco-1:1:2 derived from a Cytochrome c oxidase subunit Via gene from Arabidopsis.
[0051] SEQ ID NO:41 is an intron sequence, I-At.Cyco-l:l:l derived from a Cytochrome c oxidase subunit Via gene from Arabidopsis.
[0052] SEQ ID NO:42 is a coding sequence for β-glucuronidase (GUS) with a processable intron derived from the potato light-inducible tissue-specific ST-LS1 gene (Genbank Accession: X04753).
[0053] SEQ ID NO:43 is a DNA sequence of an EXP, EXP-At.GSP442+L-I-At.Cyco comprising the synthetic promoter, P-At.GSP442.nno:2, operably linked 5' to the synthetic leader, L-At.GSP442.nno:l, operably linked 5' to the leader, L-At.Cyco-l:l:2, which is operably linked 5' to the intron, I-At.Cyco:2.
[0054] SEQ ID NO:44 is a DNA sequence of the synthetic 3' UTR, T-Zm.GST7.nno:2.
[0055] SEQ ID NO:45 is a DNA sequence of an EXP, EXP-At.GSP576.nno+At.Cyco:l comprising the synthetic promoter, P-At.GSP564.nno:3, operably linked 5' to the synthetic leader, L-At.GSP564.nno:l, which is operably linked 5' to the intron, I-At.Cyco:2.
[0056] SEQ ID NO:46 is a DNA sequence of the EXP, EXP-CaMV.35S comprising the 35S promoter and leader derived from the Cauliflower mosaic virus.
[0057] SEQ ID NO:47 is a DNA sequence of the intron, I-Zm.DnaK:l, derived from the heat shock protein 70 (Hsp70) gene (DnaK) from Zea mays.
[0058] SEQ ID NO:48 is a DNA sequence of the 3' UTR, T-Os.LTP:l, derived from the Lipid Transfer Protein-like gene (LTP) from Oryza sativa.
[0059] SEQ ID NO:49 is a coding sequence for the NanoLuc® luciferase fluorescent protein (Promega, Madison, WI 53711), Nluc which was engineered by directed évolution from a deepsea shrimp (Qplophorus gacilirostris) luciferase.
[0060] SEQ ID NO:50 is a DNA sequence of the EXP, EXP-At.Bglu21+At.Cyco:2 comprising the promoter and leader of a beta-glucuronidase 21 gene from Arabidopsis thaliana, operably linked 5' to the intron, I-At.Cyco-l:l:l.
[0061] SEQ ID NO:51 is a DNA sequence of the EXP, EXP-CaMV.35S-enh+Ph.DnaK:l:3 comprising an enhanced Cauliflower mosaic virus 35S promoter, operably linked 5' to the leader of the heat shock protein 70 (HSP70) gene from Pétunia x hybrid.
[0062] SEQ ID NO:52 is a DNA sequence of the EXP, EXP-Gm.Sphasl:l:l comprising the promoter and leader of the 7S alpha prime gene of soybean.
[0063] SEQ ID NO:53 is a DNA sequence of the EXP, EXP-CaMV.35S-enh+Zm.DnaK:l:l comprising an enhanced Cauliflower mosaic virus 35S promoter, operably linked 5' to the intron, I-Zm.DnaK:l.
[0064] SEQ ID NO:54 is a DNA sequence encoding a luciferase protein (LUCIFERASE:1:3) derived from Photinuspyralis (Firefly).
[0065] SEQ ID NO:55 is a DNA sequence of the 3' UTR, T-AGRtu.nos-1:1:13 derived from the Agrobacterium tumefaciens nopaline synthase gene.
[0066] SEQ ID NO:56 is a DNA sequence of the EXP, EXP-CaMV.35S-enh-Lhcbl comprising an enhanced Cauliflower mosaic virus 35S promoter, operably linked 5' to the leader of a chlorophyll a/b-binding gene of the light-harvesting complex of Triticum aestivum (Wheat).
[0067] SEQ ID NO:57 is a DNA sequence encoding a luciferase protein (CR-Ren.hRenilla Lucife-0:0:1) derived from Renilla reniformis (Sea Pansy).
DETAILED DESCRIPTION OF THE INVENTION
[0068] The invention provides synthetic regulatory éléments having gene-regulatory activity in plants. The nucléotide sequences of these synthetic regulatory éléments are provided as SEQ ID NOs:l-32 and SEQ ID NOs:43-45. These synthetic regulatory éléments are capable of affecting the expression of an operably linked transcribable DNA molécule in plant tissues, and therefore regulating gene expression of an operably linked transgene in transgenic plants. The invention also provides methods of modifying, producing, and using recombinant DNA molécules which contain the provided synthetic regulatory éléments. The invention also provides compositions that include transgenic plant cells, plants, plant parts, and seeds containing the recombinant DNA molécules of the invention, and methods for preparing and using the same.
[0069] The following définitions and methods are provided to better define the présent invention and to guide those of ordinary skill in the art in the practice of the présent invention. Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art.
DNA Molécules
[0070] As used herein, the term “DNA” or “DNA molécule” refers to a double-stranded DNA molécule of genomic or synthetic origin, i.e., a polymer of deoxyribonucleotide bases or a DNA molécule, read from the 5' (upstream) end to the 3' (downstream) end. As used herein, the term “DNA sequence” refers to the nucléotide sequence of a DNA molécule. The nomenclature used herein corresponds to that of Title 37 ofthe United States Code of Fédéral Régulations § 1.822, and set forth in the tables in WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3.
[0071] As used herein, a “recombinant DNA molécule” is a DNA molécule comprising a combination of DNA molécules that would not naturally occur together without human intervention. For instance, a recombinant DNA molécule may be a DNA molécule that is comprised of at least two DNA molécules heterologous with respect to each other, a DNA molécule that comprises a DNA sequence that deviates from DNA sequences that exist in nature, a DNA molécule that comprises a synthetic DNA sequence or a DNA molécule that has been incorporated into a host cell’s DNA by genetic transformation or gene editing.
[0072] As used herein, a synthetic nucléotide sequence or “artificial nucléotide sequence” is a nucléotide sequence that is not known to occur in nature, that is not naturally occurring, or that does not occur without human intervention. The gene-regulatory éléments of the présent invention comprise synthetic nucléotide sequences. Preferably, synthetic nucléotide sequences share little or no extended homology to natural sequences. Extended homology in this context generally refers to 100% sequence identity extending beyond about 25 nucléotides of contiguous sequence.
[0073] Reference in this application to an “isolated DNA molécule,” or an équivalent term or phrase, is intended to mean that the DNA molécule is one that is présent alone or in combination with other compositions, but not within its natural environment. For example, nucleic acid éléments such as a coding sequence, intron sequence, untranslated leader sequence, promoter sequence, transcriptional termination sequence, and the like, that are naturally found within the DNA of the genome of an organism are not considered to be “isolated” so long as the element is within the genome of the organism and at the location within the genome in which it is naturally found. However, each of these éléments, and subparts of these éléments, would be “isolated” within the scope of this disclosure so long as the element is not within the genome of the organism and at the location within the genome in which it is naturally found. In one embodiment, the term “isolated” refers to a DNA molécule that is at least partially separated from some of the nucleic acids which normally flank the DNA molécule in its native or natural State. Thus, DNA molécules fused to regulatory or coding sequences with which they are not normally associated, for example as the resuit of recombinant techniques, are considered isolated herein. Such molécules are considered isolated when integrated into the chromosome of a host cell or présent in a nucleic acid solution with other DNA molécules, in that they are not in their native State. For the purposes of this disclosure, any transgenic nucléotide sequence, Le., the nucléotide sequence of the DNA inserted into the genome of the cells of a plant or bacterium, or présent in an extrachromosomal vector, would be considered to be an isolated nucléotide sequence whether it is présent within the plasmid or similar structure used to transform the cells, within the genome of the plant or bacterium, or présent in détectable amounts in tissues, progeny, biological samples or commodity products derived from the plant or bacterium.
[0074] As used herein, the term “sequence identity” refers to the extent to which two optimally aligned polynucleotide sequences or two optimally aligned polypeptide sequences are identical. An optimal sequence alignment is created by manually aligning two sequences, e.g., a reference sequence and another sequence, to maximize the number of nucléotide matches in the sequence alignment with appropriate internai nucléotide insertions, délétions, or gaps. As used herein, the term “reference sequence” refers to a DNA sequence provided as SEQ ID NOs:l-32 and SEQ ID NOs:43-45.
[0075] As used herein, the term “percent sequence identity” or “percent identity” or “% identity” is the identity fraction multiplied by 100. The “identity fraction” for a sequence optimally aligned with a reference sequence is the number of nucléotide matches in the optimal alignment, divided by the total number of nucléotides in the reference sequence, e.g., the total number of nucléotides in the full length of the entire reference sequence. Thus, one embodiment of the invention provides a DNA molécule comprising a sequence that, when optimally aligned to a reference sequence, provided herein as any ofSEQ ID NOs:l-32 and SEQ ID NOs:43-45, has at least about 85 percent identity, at least about 86 percent identity, at least about 87 percent identity, at least about 88 percent identity, at least about 89 percent identity, at least about 90 percent identity, at least about 91 percent identity, at least about 92 percent identity, at least about 93 percent identity, at least about 94 percent identity, at least about 95 percent identity, at least about 96 percent identity, at least about 97 percent identity, at least about 98 percent identity, at least about 99 percent identity, or at least about 100 percent identity to the reference sequence. In still further spécifie embodiments, a sequence having a percent identity to any of SEQ ID NOs:l-32 and SEQ ID NOs:43-45 may be defined as exhibiting promoter activity possessed by the starting sequence from which it is derived. A sequence having a percent identity to any of SEQ ID NOs:l-32 and SEQ ID NOs:43-45 may further comprise a “minimal promoter” which provides a basal level of transcription and is comprised of a TATA box or équivalent sequence for récognition and binding of the RNA polymerase II complex for initiation of transcription.
Regulatory Eléments
[0076] Regulatory éléments such as promoters, leaders (also known as 5’ UTRs), enhancers, introns, and transcription termination régions (or 3 ' UTRs) play an intégral part in the overall expression of genes in living cells. The term “regulatory element,” as used herein, refers to a DNA molécule having gene-regulatory activity. The term “gene-regulatory activity,” as used herein, refers to the ability to affect the expression of an operably linked transcribable DNA molécule, for instance by affecting the transcription and/or translation of the operably linked transcribable DNA molécule. Regulatory éléments, such as promoters, leaders, enhancers, introns and 3' UTRs that function in plants are useful for modifying plant phenotypes through genetic engineering.
[0077] As used herein, a “regulatory expression element group” or “EXP” sequence may refer to a group of operably linked regulatory éléments, such as enhancers, promoters, leaders, and introns. For example, a regulatory expression element group may be comprised, for instance, of a promoter operably linked 5' to a leader sequence. EXP’s useful in practicing the présent invention include SEQ IDNOs:l, 4, 7, 8,10, 12, 15, 16, 18, 19, 22, 23, 26, 30,43 and 45.
[0078] Regulatory éléments may be characterized by their gene expression pattern, e.g., positive and/or négative effects such as constitutive expression or temporal, spatial, developmental, tissue, environmental, physiological, pathological, cell cycle, and/or chemically responsive expression, and any combination thereof, as well as by quantitative or qualitative indications. As used herein, a “gene expression pattern” is any pattern of transcription of an operably linked DNA molécule into a transcribed RNA molécule. The transcribed RNA molécule may be translated to produce a protein molécule or may provide an antisense or other regulatory RNA molécule, such as a double-stranded RNA (dsRNA), a transfer RNA (tRNA), a ribosomal RNA (rRNA), a microRNA (miRNA), and the like.
[0079] As used herein, the term “protein expression” is any pattern of translation of a transcribed RNA molécule into a protein molécule. Protein expression may be characterized by its temporal, spatial, developmental, or morphological qualities, as well as by quantitative or qualitative indications.
[0080] A promoter is useful as a regulatory element for modulating the expression of an operably linked transcribable DNA molécule. As used herein, the term “promoter” refers generally to a DNA molécule that is involved in récognition and binding of RNA polymerase II and other proteins, such as trans-acting transcription factors, to initiate transcription. A promoter may be initially isolated from the 5' untranslated région (5' UTR) of a genomic copy of a gene. Altemately, promoters may be synthetically produced or manipulated DNA molécules. Promoters may also be chimeric. Chimeric promoters are produced through the fusion of two or more heterologous DNA molécules. Promoters useful in practicing the présent invention include promoter éléments comprised within any of SEQ ID NOs:2, 5, 13, 20, 25, 27, 31 and 39 or fragments or variants thereof. In spécifie embodiments of the invention, the claimed DNA molécules and any variants or dérivatives thereof as described herein, are further defined as comprising promoter activity, i.e., are capable of acting as a promoter in a host cell, such as in a transgenic plant. In still further spécifie embodiments, a fragment may be defined as exhibiting promoter activity possessed by the starting promoter molécule from which it is derived, or a fragment may comprise a “minimal promoter” which provides a basal level of transcription and is comprised of a TATA box or équivalent DNA sequence for récognition and binding of the RNA polymerase II complex for initiation of transcription.
[0081] In one embodiment, fragments of a promoter sequence disclosed herein are provided. Promoter fragments may comprise promoter activity, as described above, and may be useful alone or in combination with other promoters and promoter fragments, such as in constructing chimeric promoters, or in combination with other expression éléments and expression element fragments. In spécifie embodiments, fragments of a promoter are provided comprising at least about 50, at least about 75, at least about 95, at least about 100, at least about 125, at least about 150, at least about 175, at least about 200, at least about 225, at least about 250, at least about 275, at least about 300, at least about 500, at least about 600, at least about 700, at least about 750, at least about 800, at least about 900, or at least about 1000 contiguous nucléotides, or longer, of a DNA molécule having promoter activity as disclosed herein. In certain embodiments, the invention provides fragments of a promoter provided herein, having the activity of the full length sequence. Methods for producing such fragments from a starting promoter molécule are well known in the art.
[0082] Compositions derived from any of the promoter éléments comprised within any of SEQ ID NOs:2, 5, 13, 20, 25, 27, 31 and 39, such as internai or 5' délétions, for example, can be produced using methods known in the art to improve or alter expression, including by removing éléments that hâve either positive or négative effects on expression; duplicating éléments that hâve positive or négative effects on expression; and/or duplicating or removing éléments that hâve tissue- or cell-specific effects on expression. Compositions derived from any of the promoter éléments comprised within any of SEQ ID NOs:2, 5, 13, 20, 25, 27, 31 and 39 comprised of 3' délétions in which the TATA box element or équivalent sequence thereof and downstream sequence is removed can be used, for example, to make enhancer éléments. Further délétions can be made to remove any éléments that hâve positive or négative; tissue-specific; cell-specific; or timing-specific (such as, but not limited to, circadian rhythm) effects on expression. Any of the promoter éléments comprised within any of SEQ ID NOs:2, 5, 13, 20, 25, 27, 31 and 39 and fragments or enhancers derived therefrom can be used to make chimeric transcriptional regulatory element compositions.
[0083] In accordance with the invention, a promoter or promoter fragment may be analyzed for the presence of known promoter éléments, i.e., DNA sequence characteristics, such as a TATA box and other known transcription factor binding site motifs. Identification of such known promoter éléments may be used by one of skill in the art to design variants of the promoter having a similar expression pattern to the original promoter.
[0084] As used herein, the term “leader” refers to a DNA molécule isolated from the untranslated 5' région (5' UTR) a gene and defined generally as a nucléotide segment between the transcription start site (TSS) and the protein coding sequence start site. Altemately, leaders may be synthetically produced or manipulated DNA éléments. A leader can be used as a 5' regulatory element for modulating expression of an operably linked transcribable DNA molécule. Leader molécules may be used with a heterologous promoter or with their native promoter. Leaders useful in practicing the présent invention include SEQ ID NOs:3, 6, 14, 21, 28, 32 and 40; or any of the leader éléments comprised within any of SEQ ID NOs:l, 4, 7, 8, 10, 12, 15, 16, 18, 19, 22, 23, 26, 30, 43 and 45 or fragments or variants thereof. In spécifie embodiments, such DNA sequences may be defined as being capable of acting as a leader in a host cell, including, for example, a transgenic plant cell. In one embodiment, such sequences are decoded as comprising leader activity.
[0085] The leader sequences (also referred to as 5' UTRs) presented as SEQ ID NOs:3, 6, 14, 21, 28, 32 and 40 or any of the leader éléments comprised within any of SEQ ID NOs:l, 4, 7, 8, 10, 12, 15, 16, 18, 19, 22, 23, 26, 30 and 43 may be comprised of regulatory éléments, or may adopt secondary structures that can hâve an effect on transcription or translation of an operably linked transcribable DNA molécule. The leader sequences presented as SEQ ID NOs:3, 6, 14, 21, 28, 32 and 40 or any of the leader éléments comprised within any of SEQ ID NOs:l, 4, 7, 8, 10, 12, 15, 16, 18, 19, 22, 23, 26, 30, 43 and 45 can be used in accordance with the invention to make chimeric regulatory éléments that affect transcription or translation of a an operably linked transcribable DNA molécule.
[0086] As used herein, the term “intron” refers to a DNA molécule that may be isolated or identified from a gene and may be defined generally as a région spliced out during messenger RNA (mRNA) processing prior to translation. Altemately, an intron may be a synthetically produced or manipulated DNA element. An intron may contain enhancer éléments that effect the transcription of operably linked genes. An intron may be used as a regulatory element for modulating expression of an operably linked transcribable DNA molécule. A construct may comprise an intron, and the intron may or may not be heterologous with respect to the transcribable DNA molécule. Examples of introns known in the art include the rice actin intron and the corn HSP70 intron.
[0087] In plants, the inclusion of some introns in gene constructs leads to increased mRNA and protein accumulation relative to constructs lacking the intron. This effect has been termed “intron mediated enhancement” (IME) of gene expression. Introns known to stimulate expression in plants hâve been identified in maize genes (e.g., tubAl, Adhl, Shl, and Ubil), in rice genes (e.g., tpi) and in dicotyledonous plant genes like those from pétunia (e.g., rbcS), potato (e.g., st-lsl) and from Arabidopsis thaliana (e.g., ubq3 and patl). It has been shown that délétions or mutations within the splice sites of an intron reduce gene expression, indicating that splicing might be needed for IME. However, IME in dicotyledonous plants has been shown by point mutations within the splice sites of the patl gene from A. thaliana. Multiple uses of the same intron in one plant hâve been shown to exhibit disadvantages. In those cases, it is necessary to hâve a collection of basic control éléments for the construction of appropriate recombinant DNA éléments. Exemplary introns useful in practicing the présent invention are presented as SEQ ID NOs:9,11,17,33 and 41.
[0088] As used herein, the terms “3' transcription termination molécule,” “3' untranslated région” or “3' UTR” refer to a DNA molécule that is used during transcription to the untranslated région of the 3' portion of an mRNA molécule. The 3' untranslated région of an mRNA molécule may be generated by spécifie cleavage and 3' polyadenylation, also known as a polyA tail. A 3' UTR may be operably linked to and located downstream of a transcribable DNA molécule and may include a polyadenylation signal and other regulatory signais capable of affecting transcription, mRNA processing, or gene expression. PolyA tails are thought to function in mRNA stability and in initiation of translation. Examples of 3' transcription termination molécules in the art are the nopaline synthase 3' région; wheat hspl7 3' région, pea rubisco small subunit 3' région, cotton E6 3' région, and the coixin 3' UTR.
[0089] 3' UTRs typically find bénéficiai use for the recombinant expression of spécifie DNA molécules. A weak 3' UTR has the potential to generate read-through, which may affect the expression of the DNA molécule located in the neighboring expression cassettes. Appropriate control of transcription termination can prevent read-through into DNA sequences (e.g., other expression cassettes) localized downstream and can further allow efficient recycling of RNA polymerase to improve gene expression. Efficient termination of transcription (release of RNA Polymerase II from the DNA) is prerequisite for re-initiation of transcription and thereby directly affects the overall transcript level. Subséquent to transcription termination, the mature mRNA is released from the site of synthesis and template transported to the cytoplasm. Eukaryotic mRNAs are accumulated as poly(A) forms in vivo, making it difficult to detect transcriptional termination sites by conventional methods. However, prédiction of functional and efficient 3' UTRs by bioinformatics methods is difficult in that there are no conserved DNA sequences that would allow easy prédiction of an effective 3 ' UTR.
[0090] From a practical standpoint, it is typically bénéficiai that a 3 ' UTR used in an expression cassette possesses the following characteristics. First, the 3' UTR should be able to efficiently and effectively terminate transcription of the transgene and prevent read-through of the transcript into any neighboring DNA sequence, which can be comprised of another expression cassette as in the case of multiple expression cassettes residing in one transfer DNA (T-DNA), or the neighboring chromosomal DNA into which the T-DNA has inserted. Second, the 3' UTR should not cause a réduction in the transcriptional activity imparted by the promoter, leader, enhancers, and introns that are used to drive expression of the DNA molécule. Finally, in plant biotechnology, the 3' UTR is often used for priming of amplification reactions of reverse transcribed RNA extracted from the transformed plant and used to: (1) assess the transcriptional activity or expression of the expression cassette once integrated into the plant chromosome; (2) assess the copy number of insertions within the plant DNA; and (3) assess zygosity of the resulting seed after breeding. The 3' UTR is also used in amplification reactions of DNA extracted from the transformed plant to characterize the intactness of the inserted cassette. A 3 ' UTR useful in practicing the présent invention is presented as SEQ ID NOs:29, 34, 35, 36, 37, and 44.
[0091] As used herein, the term “enhancer” or “enhancer element” refers to a cri-acting regulatory element, a.k.a. c/s-element, which confers an aspect of the overall expression pattern, but is usually insufïïcient alone to drive transcription, of an operably linked transcribable DNA molécule. Unlike promoters, enhancer éléments do not usually include a transcription start site (TSS) or TATA box or équivalent DNA sequence. A promoter or promoter fragment may naturally comprise one or more enhancer éléments that affect the transcription of an operably linked DNA sequence. An enhancer element may also be fused to a promoter to produce a chimeric promoter cfr-element, which confers an aspect of the overall modulation of gene expression. An example of an enhancer element derived from the synthetic promoter, PAt.GSP571.nno:5 (SEQ ID NO:5) is provided as SEQ ID NO:24 (E-At.GSP571.nno:l).
[0092] Many promoter enhancer éléments are believed to bind DNA-binding proteins and/or affect DNA topology, producing local conformations that selectively allow or restrict access of RNA polymerase to the DNA template or that facilitate sélective opening of the double hélix at the site of transcriptional initiation. An enhancer element may function to bind transcription factors that regulate transcription. Some enhancer éléments bind more than one transcription factor, and transcription factors may interact with different afïïnities with more than one enhancer domain. Enhancer éléments can be identified by a number of techniques, including délétion analysis, i.e., deleting one or more nucléotides from the 5' end or internai to a promoter;
DNA binding protein analysis using DNase I footprinting; méthylation interférence; electrophoresis mobility-shift assays; in vivo genomic footprinting by ligation-mediated polymerase chain reaction (PCR); and other conventional assays or by DNA sequence similarity analysis using known c/s-element motifs or enhancer éléments as a target sequence or target motif with conventional DNA sequence comparison methods, such as BLAST. The fine structure of an enhancer domain can be further studied by mutagenesis (or substitution) of one or more nucléotides or by other conventional methods known in the art. Enhancer éléments can be obtained by Chemical synthesis or by isolation from regulatory éléments that include such éléments, and they can be synthesized with additional flanking nucléotides that contain useful restriction enzyme sites to facilitate subsequence manipulation. Thus, the design, construction, and use of enhancer éléments according to the methods disclosed herein for modulating the expression of operably linked transcribable DNA molécules are encompassed by the invention. An exemplary enhancer useful in practicing this invention is presented as SEQ ID NO:24.
[0093] As used herein, the term “chimeric” refers to a single DNA molécule produced by fusing a first DNA molécule to a second DNA molécule, where neither the first nor the second DNA molécule would normally be found in that configuration, i.e. fused to the other. The chimeric DNA molécule is thus a new DNA molécule not otherwise normally found in nature. As used herein, the term “chimeric promoter” refers to a promoter produced through such manipulation of DNA molécules. A chimeric promoter may combine two or more DNA fragments for example, the fusion of a promoter to an enhancer element. Thus, the design, construction, and use of chimeric promoters according to the methods disclosed herein for modulating the expression of operably linked transcribable DNA molécules are encompassed by the présent invention. An exemplary chimeric promoter is presented herein as SEQ ID NO:25 (PAt.GSP571/442).
[0094] Chimeric regulatory éléments can be designed to comprise various constituent éléments which may be operatively linked by various methods known in the art, such as restriction enzyme digestion and ligation, ligation independent cloning, modular assembly of PCR products during amplification, or direct Chemical synthesis of the regulatory element, as well as other methods known in the art. The resulting various chimeric regulatory éléments can be comprised of the same, or variants of the same, constituent éléments but differ in the DNA sequence or DNA sequences that comprise the linking DNA sequence or sequences that allow the constituent parts to be operatively linked. In the invention, the DNA sequences provided as SEQ ID NOs:l32 and SEQ ID NOs:43-45 may provide regulatory element reference sequences, wherein the constituent éléments that comprise the reference sequence may be joined by methods known in the art and may comprise substitutions, délétions, and/or insertions of one or more nucléotides or mutations that naturally occur in bacterial and plant cell transformation.
[0095] As used herein, the term “variant” refers to a second DNA molécule, such as a regulatory element, that is in composition similar, but not identical to, a first DNA molécule, and wherein the second DNA molécule still maintains the general functionality, i.e. the same or similar expression pattern, for instance through more or less équivalent transcriptional activity, of the first DNA molécule. A variant may be a shorter or truncated version of the first DNA molécule or an altered version of the sequence of the first DNA molécule, such as one with different restriction enzyme sites and/or internai délétions, substitutions, or insertions. A “variant” can also encompass a regulatory element having a nucléotide sequence comprising a substitution, délétion, or insertion of one or more nucléotides of a reference sequence, wherein the dérivative regulatory element has more or less or équivalent transcriptional or translational activity than the corresponding parent regulatory molécule. In the présent invention, a polynucleotide sequence provided as SEQ ID NOs:l-32 and SEQ ID NOs:43-45 may be used to create variants that are in similar in composition, but not identical to, the DNA sequence of the original regulatory element, while still maintaining the general functionality, i.e., the same or similar expression pattern, of the original regulatory element. Production of such variants of the invention is well within the ordinary skill of the art in light of the disclosure and is encompassed within the scope of the invention.
[0096] The effïcacy of the modifications, duplications, or délétions described herein on the desired expression aspects of a particular transgene may be tested empirically in stable and transient plant assays, such as those described in the working examples, so as to validate the results, which may vary depending upon the changes made and the goal of the change in the starting DNA molécule.
Constructs
[0097] As used herein, the term “construct” means any recombinant DNA molécule such as a plasmid, cosmid, virus, phage, or linear or circular DNA or RNA molécule, derived from any source, capable of genomic intégration or autonomous réplication, comprising a DNA molécule where at least one DNA molécule has been linked to another DNA molécule in a functionally opérative manner, i.e. operably linked. As used herein, the term “vector” means any construct that may be used for the purpose of transformation, i.e., the introduction of heterologous DNA or RNA into a host cell. A construct typically includes one or more expression cassettes. As used herein, an “expression cassette” refers to a DNA molécule comprising at least a transcribable DNA molécule operably linked to one or more regulatory éléments, typically at least a promoter and a 3' UTR.
[0098] As used herein, the term “operably linked” refers to a first DNA molécule joined to a second DNA molécule, wherein the first and second DNA molécules are so arranged that the first DNA molécule affects the function of the second DNA molécule. The two DNA molécules may or may not be part of a single contiguous DNA molécule and may or may not be adjacent. For example, a promoter is operably linked to a transcribable DNA molécule if the promoter modulâtes transcription of the transcribable DNA molécule of interest in a cell. A leader, for example, is operably linked to DNA sequence when it is capable of affecting the transcription or translation of the DNA sequence.
[0099] The constructs of the invention may be provided, in one embodiment, as double tumorinducing (Ti) plasmid border constructs that hâve the right border (RB or AGRtu.RB) and left border (LB or AGRtu.LB) régions of the Ti plasmid isolated from Agrobacterium tumefaciens comprising a T-DNA that, along with transfer molécules provided by the A. tumefaciens cells, permit the intégration of the T-DNA into the genome of a plant cell (see, e.g., U.S. Patent 6,603,061). The constructs may also contain the plasmid backbone DNA segments that provide réplication function and antibiotic sélection in bacterial cells, e.g., an Escherichia coli origin of réplication such as ori322, a broad host range origin of réplication such as oriV or oriRi, and a coding région for a selectable marker such as Spec/Strp that encodes for Tn7 aminoglycoside adenyltransferase (aadA) conferring résistance to spectinomycin or streptomycin, or a gentamicin (Gm, Gent) selectable marker gene. For plant transformation, the host bacterial strain is often A. tumefaciens ABI, C58, or LBA4404, however other strains known to those skilled in the art of plant transformation can function in the invention.
[00100] Methods are known in the art for assembling and introducing constructs into a cell in such a manner that the transcribable DNA molécule is transcribed into a functional mRNA molécule that is translated and expressed as a protein. For the practice of the invention, conventional compositions and methods for preparing and using constructs and host cells are well known to one skilled in the art. Typical vectors useful for expression of nucleic acids in higher plants are well known in the art and include vectors derived from the Ti plasmid of Agrobacterium tumefaciens and the pCaMVCN transfer control vector.
[00101] Various regulatory éléments may be included in a construct, including any of those provided herein. Any such regulatory éléments may be provided in combination with other regulatory éléments. Such combinations can be designed or modified to produce désirable regulatory features. In one embodiment, constructs of the invention comprise at least one regulatory element operably linked to a transcribable DNA molécule operably linked to a 3' UTR.
[00102] Constructs of the invention may include any promoter or leader provided herein or known in the art. For example, a promoter of the invention may be operably linked to a heterologous non-translated 5' leader such as one derived from a heat shock protein gene. Alternatively, a leader of the invention may be operably linked to a heterologous promoter such as the Cauliflower Mosaic Virus 35S transcript promoter.
[00103] Expression cassettes may also include a transit peptide coding sequence that encodes a peptide that is useful for sub-cellular targeting of an operably linked protein, particularly to a chloroplast, leucoplast, or other plastid organelle; mitochondria; peroxisome; vacuole; or an extracellular location. Many chloroplast-localized proteins are expressed from nuclear genes as precursors and are targeted to the chloroplast by a chloroplast transit peptide (CTP). Examples of such isolated chloroplast proteins include, but are not limited to, those associated with the small subunit (SSU) of ribulose-l,5,-bisphosphate carboxylase, ferredoxin, ferredoxin oxidoreductase, the light-harvesting complex protein I and protein II, thioredoxin F, and enolpyruvyl shikimate phosphate synthase (EPSPS). Chloroplast transit peptides are described, for example, in U.S. Patent No. 7,193,133. It has been demonstrated that non-chloroplast proteins may be targeted to the chloroplast by the expression of a heterologous CTP operably linked to the transgene encoding a non-chloroplast proteins.
Transcribable DNA molécules
[00104] As used herein, the term “transcribable DNA molécule” refers to any DNA molécule capable of being transcribed into a RNA molécule, including, but not limited to, those having protein coding sequences and those producing RNA molécules having sequences useful for gene suppression. The type of DNA molécule can include, but is not limited to, a DNA molécule from the same plant, a DNA molécule from another plant, a DNA molécule from a different organism, or a synthetic DNA molécule, such as a DNA molécule containing an antisense message of a gene, or a DNA molécule encoding an artificial, synthetic, or otherwise modified version of a transgene. Exemplary transcribable DNA molécules for incorporation into constructs of the invention include, e.g., DNA molécules or genes from a species other than the species into which the DNA molécule is incorporated or genes that originale from, or are présent in, the same species, but are incorporated into récipient cells by genetic engineering methods rather than classical breeding techniques.
[00105] A “transgene” refers to a transcribable DNA molécule heterologous to a host cell at least with respect to its location in the host cell genome and/or a transcribable DNA molécule artificially incorporated into a host cell’s genome in the current or any prior génération of the cell.
[00106] A regulatory element, such as a synthetic promoter of the invention, may be operably linked to a heterologous transcribable DNA molécule. As used herein, the term “heterologous” refers to the combination of two or more DNA molécules when such a combination is not normally found in nature. For example, the two DNA molécules may be derived from different species and/or the two DNA molécules may be derived from different genes, e.g., different genes from the same species or the same genes from different species, or one of the DNA molécules might be synthetic and not found in nature. A regulatory element is heterologous with respect to an operably linked transcribable DNA molécule if such a combination is not normally found in nature, i.e., the transcribable DNA molécule does not naturally occur operably linked to the regulatory element.
[00107] The transcribable DNA molécule may generally be any DNA molécule for which expression of a transcript is desired. Such expression of a transcript may resuit in translation of the resulting mRNA molécule, and thus protein expression. Altematively, for example, a transcribable DNA molécule may be designed to ultimately cause decreased expression of a spécifie gene or protein. In one embodiment, this may be accomplished by using a transcribable DNA molécule that is oriented in the antisense direction. One of ordinary skill in the art is familiar with using such antisense technology. Any gene may be negatively regulated in this manner, and, in one embodiment, a transcribable DNA molécule may be designed for suppression of a spécifie gene through expression of a dsRNA, siRNA or miRNA molécule.
[00108] Thus, one embodiment of the invention is a recombinant DNA molécule comprising a regulatory element of the invention, such as those provided as SEQ ID NOs:l-32 and SEQ ID NOs:43-45, operably linked to a heterologous transcribable DNA molécule so as to modulate transcription of the transcribable DNA molécule at a desired level or in a desired pattern when the construct is integrated in the genome of a transgenic plant cell. In one embodiment, the transcribable DNA molécule comprises a protein-coding région of a gene and in another embodiment the transcribable DNA molécule comprises an antisense région of a gene.
Genes of Agronomie Interest
[00109] A transcribable DNA molécule may be a gene of agronomie interest. As used herein, the term “gene of agronomie interest” refers to a transcribable DNA molécule that, when expressed in a particular plant tissue, cell, or cell type, confers a désirable characteristic. The product of a gene of agronomie interest may act within the plant in order to cause an effect upon the plant morphology, physiology, growth, development, yield, grain composition, nutritional profile, disease or pest résistance, and/or environmental or Chemical tolérance or may act as a pesticidal agent in the diet of a pest that feeds on the plant. In one embodiment of the invention, a regulatory element of the invention is incorporated into a construct such that the regulatory element is operably linked to a transcribable DNA molécule that is a gene of agronomie interest. In a transgenic plant containing such a construct, the expression of the gene of agronomie interest can confer a bénéficiai agronomie trait. A bénéficiai agronomie trait may include, for example, but is not limited to, herbicide tolérance, insect control, modified yield, disease résistance, pathogen résistance, modified plant growth and development, modified starch content, modified oil content, modified fatty acid content, modified protein content, modified fruit ripening, enhanced animal and human nutrition, biopolymer productions, environmental stress résistance, pharmaceutical peptides, improved processing qualities, improved flavor, hybrid seed production utility, improved fiber production, and désirable biofuel production.
[00110] Examples of genes of agronomie interest known in the art include, but are not limited to, those for herbicide résistance (U.S. Patent Nos. 6,803,501; 6,448,476; 6,248,876; 6,225,114; 6,107,549; 5,866,775; 5,804,425; 5,633,435; and 5,463,175), increased yield (U.S. Patent Nos. USRE38,446; 6,716,474; 6,663,906; 6,476,295; 6,441,277; 6,423,828; 6,399,330; 6,372,211; 6,235,971; 6,222,098; and 5,716,837), insect control (U.S. Patent Nos. 6,809,078; 6,713,063; 6,686,452; 6,657,046; 6,645,497; 6,642,030; 6,639,054; 6,620,988; 6,593,293; 6,555,655;
6,538,109; 6,537,756; 6,521,442; 6,501,009; 6,468,523; 6,326,351; 6,313,378; 6,284,949;
6,281,016; 6,248,536; 6,242,241; 6,221,649; 6,177,615; 6,156,573; 6,153,814; 6,110,464;
6,093,695; 6,063,756; 6,063,597; 6,023,013; 5,959,091; 5,942,664; 5,942,658, 5,880,275;
5,763,245; and 5,763,241), fungal disease résistance (U.S. Patent Nos. 6,653,280; 6,573,361; 6,506,962; 6,316,407; 6,215,048; 5,516,671; 5,773,696; 6,121,436; 6,316,407; and 6,506,962), virus résistance (U.S. Patent Nos. 6,617,496; 6,608,241; 6,015,940; 6,013,864; 5,850,023; and 5,304,730), nematode résistance (U.S. Patent No. 6,228,992), bacterial disease résistance (U.S. Patent No. 5,516,671), plant growth and development (U.S. Patent Nos. 6,723,897 and 6,518,488), starch production (U.S. Patent Nos. 6,538,181; 6,538,179; 6,538,178; 5,750,876; 6,476,295), modified oils production (U.S. Patent Nos. 6,444,876; 6,426,447; and 6,380,462), high oil production (U.S. Patent Nos. 6,495,739; 5,608,149; 6,483,008; and 6,476,295), modified fatty acid content (U.S. Patent Nos. 6,828,475; 6,822,141; 6,770,465; 6,706,950; 6,660,849; 6,596,538; 6,589,767; 6,537,750; 6,489,461; and 6,459,018), high protein production (U.S. Patent No. 6,380,466), fruit ripening (U.S. Patent No. 5,512,466), enhanced animal and human nutrition (U.S. Patent Nos. 6,723,837; 6,653,530; 6,5412,59; 5,985,605; and 6,171,640), biopolymers (U.S. Patent Nos. USRE37,543; 6,228,623; and 5,958,745, and 6,946,588), environmental stress résistance (U.S. Patent No. 6,072,103), pharmaceutical peptides and secretable peptides (U.S. Patent Nos. 6,812,379; 6,774,283; 6,140,075; and 6,080,560), improved Processing traits (U.S. Patent No. 6,476,295), improved digestibility (U.S. Patent No. 6,531,648) low raffinose (U.S. Patent No. 6,166,292), industrial enzyme production (U.S. Patent No. 5,543,576), improved flavor (U.S. Patent No. 6,011,199), nitrogen fixation (U.S. Patent No. 5,229,114), hybrid seed production (U.S. Patent No. 5,689,041), fiber production (U.S. Patent
Nos. 6,576,818; 6,271,443; 5,981,834; and 5,869,720) and biofuel production (U.S. Patent No. 5,998,700).
[00111] Alternatively, a gene of agronomie interest can affect the above mentioned plant characteristics or phenotypes by encoding a RNA molécule that causes the targeted modulation of gene expression of an endogenous gene, for example by antisense (see, e.g. U.S. Patent 5,107,065); inhibitory RNA (“RNAi,” including modulation of gene expression by miRNA-, siRNA-, trans-acting siRNA-, and phased sRNA-mediated mechanisms, e.g., as described in published applications U.S. 2006/0200878 and U.S. 2008/0066206, and in U.S. patent application 11/974,469); or cosuppression-mediated mechanisms. The RNA could also be a catalytic RNA molécule (e.g., a ribozyme or a riboswitch; see, e.g., U.S. 2006/0200878) engineered to cleave a desired endogenous mRNA product. Methods are known in the art for constructing and introducing constructs into a cell in such a manner that the transcribable DNA molécule is transcribed into a molécule that is capable of causing gene suppression.
Selectable Markers
[00112] Selectable marker transgenes may also be used with the regulatory éléments of the invention. As used herein the term “selectable marker transgene” refers to any transcribable DNA molécule whose expression in a transgenic plant, tissue or cell, or lack thereof, can be screened for or scored in some way. Selectable marker genes, and their associated sélection and screening techniques, for use in the practice of the invention are known in the art and include, but are not limited to, transcribable DNA molécules encoding B-glucuronidase (GUS), green fluorescent protein (GFP), proteins that confer antibiotic résistance, and proteins that confer herbicide tolérance. An example of a selectable marker transgene is provided as SEQ ID NO:42.
Cell Transformation
[00113] The invention is also directed to a method of producing transformed cells and plants that comprise one or more regulatory éléments operably linked to a transcribable DNA molécule.
[00114] The term “transformation” refers to the introduction of a DNA molécule into a récipient host. As used herein, the term “host” refers to bacteria, fungi, or plants, including any cells, tissues, organs, or progeny of the bacteria, fungi, or plants. Plant tissues and cells of particular interest include protoplasts, calli, roots, tubers, seeds, stems, leaves, seedlings, embryos, and pollen.
[00115] As used herein, the term “transformed” refers to a cell, tissue, organ, or organism into which a foreign DNA molécule, such as a construct, has been introduced. The introduced DNA molécule may be integrated into the genomic DNA of the récipient cell, tissue, organ, or organism such that the introduced DNA molécule is inherited by subséquent progeny. A “transgenic” or “transformed” cell or organism may also include progeny of the cell or organism and progeny produced from a breeding program employing such a transgenic organism as a parent in a cross and exhibiting an altered phenotype resulting from the presence of a foreign DNA molécule. The introduced DNA molécule may also be transiently introduced into the récipient cell such that the introduced DNA molécule is not inherited by subséquent progeny. The term “transgenic” refers to a bacterium, fungus, or plant containing one or more heterologous DNA molécules.
[00116] There are many methods well known to those of skill in the art for introducing DNA molécules into plant cells. The process generally comprises the steps of selecting a suitable host cell, transforming the host cell with a vector, and obtaining the transformed host cell. Methods and materials for transforming plant cells by introducing a plant construct into a plant genome in the practice of this invention can include any of the well-known and demonstrated methods. Suitable methods include, but are not limited to, bacterial infection (e.g., Agrobacterium), binary BAC vectors, direct delivery of DNA (e.g., by PEG-mediated transformation, desiccation/inhibition-mediated DNA uptake, electroporation, agitation with Silicon carbide fibers, and accélération of DNA coated particles), and gene editing (e.g., CRISPR-Cas Systems), among others.
[00117] This disclosure further contemplâtes that the disclosed synthetic expression éléments can be engineered in planta by using various gene editing methods known in the art. Such technologies used for genome editing include, but are not limited to, ZFN (zinc-finger nuclease), meganucleases, TALEN (Transcription activator-like effector nucleases), and CRISPR (Clustered Regularly Interspaced Short Palindromie Repeats)/Cas (CRISPR-associated) Systems. These genome editing methods can be used to alter the expression element sequence within a plant cell to a different sequence.
100118] Host cells may be any cell or organism, such as a plant cell, algal cell, algae, fungal cell, fungi, bacterial cell, or insect cell. In spécifie embodiments, the host cells and transformed cells may include cells from crop plants.
[00119] A transgenic plant subsequently may be regenerated from a transgenic plant cell of the invention. Using conventional breeding techniques or self-pollination, seed may be produced from this transgenic plant. Such seed, and the resulting progeny plant grown from such seed, will contain the recombinant DNA molécule of the invention, and therefore will be transgenic.
[00120] Transgenic plants of the invention can be self-pollinated to provide seed for homozygous transgenic plants of the invention (homozygous for the recombinant DNA molécule) or crossed with non-transgenic plants or different transgenic plants to provide seed for heterozygous transgenic plants of the invention (heterozygous for the recombinant DNA molécule). Both such homozygous and heterozygous transgenic plants are referred to herein as “progeny plants.” Progeny plants are transgenic plants descended from the original transgenic plant and containing the recombinant DNA molécule of the invention. Seeds produced using a transgenic plant of the invention can be harvested and used to grow générations of transgenic plants, i.e., progeny plants of the invention, comprising the construct of this invention and expressing a gene of agronomie interest. Descriptions of breeding methods that are commonly used for different crops can be found in one of several reference books, see, e.g., Allard, Principles of Plant Breeding, John Wiley & Sons, NY, U. of CA, Davis, CA, 50-98 (1960); Simmonds, Principles of Crop Improvement, Longman, Inc., NY, 369-399 (1979); Sneep and Hendriksen, Plant breeding Perspectives, Wageningen (ed), Center for Agricultural Publishing and Documentation (1979); Fehr, Soybeans: Improvement, Production and Uses, 2nd Edition, Monograph, 16:249 (1987); Fehr, Principles of Variety Development, Theory and Technique, (Vol. 1) and Crop Species Soybean (Vol. 2), lowa State Univ., Macmillan Pub. Co., NY, 360376 (1987).
[00121] The transformed plants may be analyzed for the presence of the gene or genes of interest and the expression level and/or profile conferred by the regulatory éléments of the invention. Those of skill in the art are aware of the numerous methods available for the analysis of transformed plants. For example, methods for plant analysis include, but are not limited to, Southern blots or northem blots, PCR-based approaches, biochemical analyses, phenotypic screening methods, field évaluations, and immunodiagnostic assays. The expression of a transcribable DNA molécule can be measured using TaqMan® (Applied Biosystems, Foster City, CA) reagents and methods as described by the manufacturer and PCR cycle times determined using the TaqMan® Testing Matrix. Alternatively, the Invader® (Third Wave Technologies, Madison, WI) reagents and methods as described by the manufacturer can be used to evaluate transgene expression.
[00122] The invention also provides for parts of a plant of the invention. Plant parts include, but are not limited to, leaves, stems, roots, tubers, seeds, endosperm, ovule, and pollen. Plant parts of the invention may be viable, nonviable, regenerable, and/or non-regenerable. The invention also includes and provides transformed plant cells comprising a DNA molécule of the invention. The transformed or transgenic plant cells of the invention include regenerable and/or non-regenerable plant cells.
[00123] The invention also provides a commodity product that is produced from a transgenic plant or part thereof containing the recombinant DNA molécule of the invention. Commodity products of the invention contain a détectable amount of DNA comprising a DNA sequence selected from the group consisting of SEQ ID NOs:l-32 and SEQ ID NOs:43-45. As used herein, a “commodity product” refers to any composition or product which is comprised of material derived from a transgenic plant, seed, plant cell, or plant part containing the recombinant DNA molécule of the invention. Commodity products include but are not limited to processed seeds, grains, plant parts, and meal. A commodity product of the invention will contain a détectable amount of DNA corresponding to the recombinant DNA molécule of the invention. Détection of one or more of this DNA in a sample may be used for determining the content or the source of the commodity product. Any standard method of détection for DNA molécules may be used, including methods of détection disclosed herein.
[00124] The invention may be more readily understood through reference to the following examples, which are provided by way of illustration, and are not intended to be limiting of the invention, unless specified. It should be appreciated by those of skill in the art that the techniques disclosed in the following examples represent techniques discovered by the inventors to function well in the practice of the invention. However, those of skill in the art should, in light ofthe présent disclosure, appreciate that many changes can be made in the spécifie embodiments that are disclosed and still obtain a like or similar resuit without departing from the spirit and scope of the invention, therefore ail matter set forth or shown in the accompanying drawings is to be interpreted as illustrative and not in a limiting sense.
EXAMPLES Example 1 Design, Synthesis, and Cloning of Synthetic Regulatory Eléments
[00125] The regulatory éléments provided in Table 1 are novel synthetic expression éléments designed through algorithmic methods. These computationally-designed synthetic regulatory éléments were chemically synthesized and cloned to make synthetic regulatory expression element groups (EXPs). Well over 1,000 synthetic regulatory éléments were designed and assayed in soybean protoplasts and stably transformed soybean plants to identify those synthetic regulatory éléments that provided desired characteristics, such as protein expression levels and patterns of expression. The synthetic regulatory éléments described in Table 1 provide various patterns of expression useful in driving expression of many different coding sequences and interfering RNAs of agronomie interest.
[00126] The computationally-designed synthetic regulatory éléments do not hâve extended homology to any known nucleic acid sequences that exist in nature. The synthetic EXPs and the corresponding promoters, leaders, introns and 3' UTRs are presented in Table 1. The synthetic EXPs were cloned using methods known in the art into binary plant transformation vectors, operably linked to a B-glucuronidase (GUS) coding sequence, and the vectors were used to evaluate the levels and patterns of expression provided by the synthetic EXPs in stably transformed soybean, cotton and corn plants.
[00127] Analysis of the synthetic regulatory element transcription start site (TSS) and intron/exon splice junctions can be performed using transformed plant tissue. Briefly, the plants are transformed with the plant expression vectors comprising the cloned DNA fragments operably linked to a heterologous transcribable DNA molécule. Next, the 5' RACE System for Rapid Amplification of cDNA Ends, Version 2.0 (Invitrogen, Carlsbad, California 92008) is used to confirm the synthetic regulatory element TSS and intron/exon splice junctions by analyzing the DNA sequence of the produced mRNA transcripts.
Table 1. Synthetic transcriptional regulatory expression element groups, promoters, leaders, introns, and 3' UTRs.
| Annotation | SEQ ID NO: | Size (bp) | Description and/or regulatory éléments of EXP linked in 5’ —* 3’ direction (SEQ ID NOs): |
| EXP-At.GSP442.nno+At.Cyco:3 | 1 | 855 | EXP: P-At.GSP442.nno:2 (SEQ ID NO:2), L- At.GSP442.nno:l (SEQ ID NO:3), I-At.Cyco:2 (SEQ ID NO:33) |
| P-At.GSP442.nno:2 | 2 | 480 | Promoter |
| L-At.GSP442.nno:l | 3 | 20 | Leader |
| EXP-At.GSP571 | 4 | 500 | EXP: P-At.GSP571.nno:5 (SEQ ID NO:5), L- At.GSP571.nno:l (SEQ ID NO:6) |
| P-At.GSP571.nno:5 | 5 | 451 | Promoter |
| L-At.GSP571.nno:l | 6 | 49 | Leader |
| EXP-At.GSP571 .nno+At.Cyco:2 | Ί | 855 | EXP: P-At.GSP571.nno:5 (SEQ ID NO:5), L- At.GSP571.nno:l (SEQ ID NO:6), I-At.Cyco:2 (SEQ ID NO:33) |
| EXP-At.GSP571 .nno+At.GSI21 .nno: 10 | 8 | 816 | EXP: P-At.GSP571.nno:5 (SEQ ID NO:5), LAt.GSP571.nno:l (SEQ IDNO:6), I-At.GSI21.nno:2 (SEQ IDNO:9) |
| I-At.GSI21.nno:2 | 9 | 309 | Intron |
| EXP-At.GSP571 .nno+At.GSI 102.nno: 1 | 10 | 810 | EXP: P-At.GSP571.nno:5 (SEQ ID NO:5), LAt.GSP571.nno:l (SEQ IDNO:6), I-At.GSI102.nno:l (SEQ |
| Annotation | SEQ ID NO: | Size (bp) | Description and/or regulatory éléments of EXP linked in 5’ —» 3’ direction (SEQ ID NOs): |
| IDNO:11) | |||
| I-At.GSI102.nno:l | 11 | 310 | Intron |
| EXP-At.GSP564 | 12 | 500 | EXP: P-At.GSP564.nno:3 (SEQ ID NO: 13), L- At.GSP564.nno:l (SEQ IDNO:14) |
| P-At.GSP564.nno:3 | 13 | 461 | Promoter |
| L-At.GSP564.nno: 1 | 14 | 39 | Leader |
| EXP-At.GSP564.nno+At.Cyco:2 | 15 | 855 | EXP: P-At.GSP564.nno:3 (SEQ ID NO: 13), L- At.GSP564.nno:l (SEQ ID NO: 14), I-At.Cyco:2 (SEQ ID NO:33) |
| EXP-At.GSP564.nno+At.GSI 17.nno:2 | 16 | 807 | EXP: P-At.GSP564.nno:3 (SEQ IDNO:13), LAt.GSP564.nno:l (SEQ IDNO:14), I-At.GSI17.nno:l (SEQ IDNO:17) |
| I-At.GSI17.nno:l | 17 | 300 | Intron |
| EXP-At.GSP564.nno+At.GSI102.nno:l | 18 | 810 | EXP: P-At.GSP564.nno:3 (SEQ ID NO: 13), LAt.GSP564.nno:l (SEQ IDNO:14), I-At.GSI102.nno:l (SEQ IDNO:11) |
| EXP-At.GSP579 | 19 | 500 | EXP: P-At.GSP579.nno:2 (SEQ ID NO:20), L- At.GSP579.nno:l (SEQ IDNO:21) |
| P-At.GSP579.nno:2 | 20 | 449 | Promoter |
| L-At.GSP579.nno:l | 21 | 51 | Leader |
| Annotation | SEQID NO: | Size (bp) | Description and/or regulatory éléments of EXP linked in 5’ -> 3’ direction (SEQ ID NOs): |
| EXP-At.GSP579.nno+At.GSI 102.nno:3 | 22 | 810 | EXP: P-At.GSP579.nno:2 (SEQ ID NO:20), LAt.GSP579.nno:l (SEQ IDNO:21), I-At.GSI102.nno:l (SEQID NO: 11) |
| EXP- At.GSP571 .nno+At.GSP442.nno+At.Cyco: 1 | 23 | 1350 | EXP: E-At.GSP571.nno:l (SEQ ID NO:24), PAt.GSP442.nno:2 (SEQ IDNO:2), L-At.GSP442.nno:l (SEQ ID NO:3), L-At.Cyco-1:1:2 (SEQ ID NO:40), IAt.Cyco:2 (SEQ IDNO:33) |
| E-At.GSP571.nno:l | 24 | 422 | Enhancer |
| P-At.GSP571/442 | 25 | 902 | Chimeric Promoter: E-At.GSP571.nno:l (SEQ ID NO:24), P-At.GSP442.nno:2 (SEQ ID NO:2) |
| EXP-At.GSP576.nno+At.GSI17.nno:3 | 26 | 800 | EXP: P-At.GSP576.nno:4 (SEQ ID NO:27), LAt.GSP576.nno:2 (SEQ IDNO:28), I-At.GSI17.nno:l (SEQ IDNO:17) |
| P-At.GSP576.nno:4 | 27 | 458 | Promoter |
| L-At.GSP576.nno:2 | 28 | 42 | Leader |
| T-Zm.GST59.nno:l | 29 | 400 | 3'UTR |
| EXP-At.GSP221+At.Cyco:3 | 30 | 947 | EXP: P-At.GSP221:3 (SEQ IDNO:31), L-At.GSP221:l (SEQ ID NO:32), I-At.Cyco:2 (SEQ ID NO:33) |
| P-At.GSP221:3 | 31 | 370 | Promoter |
| L-At.GSP221:l | 32 | 229 | Leader |
| Annotation | SEQ ID NO: | Size (bp) | Description and/or regulatory éléments of EXP linked in 5’ -► 3’ direction (SEQ ID NOs): |
| EXP-At.GSP442+L-I-At.Cyco | 43 | 928 | EXP: P-At.GSP442.nno:2 (SEQ ID NO:2), LAt.GSP442.nno:l (SEQ IDNO:3), L-At.Cyco-l:l:2 (SEQ ID NO:40), I-At.Cyco:2 (SEQ ID NO:33) |
| T-Zm.GST7.nno:2 | 44 | 300 | 3'UTR |
| EXP-At.GSP576.nno+At.Cyco: 1 | 45 | 855 | EXP: P-At.GSP576.nno:4 (SEQ ID NO:27), LAt.GSP576.nno:2 (SEQ ID NO:28), I-At.Cyco:2 (SEQ ID NO:33) |
Example 2
Analysis of the Synthetic EXPs, EXP-At.GSP442.nno+At.Cyco:3 and EXPAt.GSP221+At.Cyco:3, Driving GUS Expression in Stably Transformed Soybean Plants
[00128] Soybean plants were transformed with vectors, specifically plant expression vectors containing regulatory element groups driving expression of the β-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the selected regulatory element groups on expression.
[00129] Soybean plants were transformed with plant GUS expression constructs comprising the endogenous EXP, EXP-At.Cyco:l:l (SEQ ID NO:38), and two synthetic EXPs, EXPAt.GSP442.nno+At.Cyco:3 (SEQ ID NO:1) and EXP-At.GSP221+At.Cyco:3 (SEQ ID NO:30). EXP-At.Cyco:l:l (SEQ ID NO:38) is derived from a Cytochrome c oxidase subunit Via gene from Arabidopsïs and is comprised of the promoter, P-At.Cyco-l:l:2 (SEQ ID NO:39), operably linked 5' to the leader, L-At.Cyco-l:l:2 (SEQ ID NO:40), which is operably linked 5' to an intron, I-AtCyco-l:l:l (SEQ IDN0:41). EXP-At.GSP442.nno+At.Cyco:3 (SEQ IDNO:1) and EXP-At.GSP221+At.Cyco:3 (SEQ ID NO:30) each comprised a synthetic promoter and leader operably linked 5' to the intron, I-At.Cyco:2 (SEQ ID NO:33). The sequence of I-At.Cyco:2 (SEQ ID NO:33) is identical to the sequence of I-At.Cyco-l:l:l (SEQ ID NO:41), with the exception that there are two nucléotides after the intron splice site included in the sequence of IAt.Cyco-l:l:l. Both I-At.Cyco introns splice the same.
[00130] The regulatory éléments were cloned into base plant expression vectors using standard methods known in the art. The resulting plant expression vectors contained a right border région from Agrobacterium tumefaciens (B-AGRtu.right border), a first transgene sélection cassette used for sélection of transformed plant cells that confers résistance to the antibiotic, spectinomycin; a second transgene cassette to assess the activity of the regulatory element, which comprised an EXP sequence operably linked 5' to a coding sequence for β-glucuronidase (GUS, GOI-Ec.uidA+St.LSl:l:l, SEQ ID NO:42) containing a processable intron derived from the potato light-inducible tissue-specific ST-LS1 gene (Genbank Accession: X04753), operably linked 5' to a 3' UTR from the Gossypium barbadense FbLate-2 gene (T-Gb.FbL2:l, SEQ ID NO:36); and a left border région from Agrobacterium tumefaciens (B-AGRtu.left border).
[00131] Soybean plant cells were transformed by Agrobacterium-mediated transformation using these binary transformation vector constructs, as is well known in the art. The resulting transformed plant cells were induced to form whole soybean plants.
[00132] Histochemical GUS analysis was used for qualitative and quantitative expression analysis of the transformed plants. Whole tissue sections were incubated with GUS staining solution X-Gluc (5-bromo-4-chloro-3-indolyl-b-glucuronide) (1 milligram/milliliter) for an appropriate length of time, rinsed, and visually inspected for blue coloration. GUS activity was qualitatively determined by direct visual inspection or inspection under a microscope using selected plant organs and tissues.
[00133] For quantitative analysis of GUS expression, total protein was extracted from selected tissues of transformed soybean plants. One microgram of total protein was used with the fluorogenic substrate 4-methyleumbelliferyl-P-D-glucuronide (MUG) in a total reaction volume of 50 microliters. The reaction product, 4-methlyumbelliferone (4-MU), is maximally fluorescent at high pH, where the hydroxyl group is ionized. Addition of a basic solution of sodium carbonate simultaneously stops the assay and adjusts the pH for quantifying the fluorescent product. Fluorescence was measured with excitation at 365 nm, émission at 445 nm using a Fluoromax-3 with Micromax Reader, with slit width set at excitation 2 nm and émission 3nm. Values are provided in units of nmol GUS/hour/mg total protein.
[00134] The following tissues were sampled for GUS expression in the Ro génération; V5 stage root, leaf-sink, and source-leaf; RI stage root, leaf-petiole, leaf-source, and flowers; R3 stage seed-immature and pod; R5 stage seed-cotyledon; and R8 stage seed-embryo and seedcotyledon. Table 2 shows the mean quantitative GUS expression for each of the sampled tissues driven by the tested EXP regulatory element groups wherein “ND” indicates the expression in a particular tissue was not determined.
Table 2. Mean quantitative GUS expression in stably transformed soybean plants driven by synthetic regulatory element groups and the endogenous EXP, EXP-At.Cyco:l:l.
| Developmental Stage | Organ | EXPAt.Cyco:l:l (SEQ ID NO:38) | EXPAt.GSP442.nno+At.Cyco:3 (SEQIDNO:1) | EXP- At.GSP221+At.Cyco:3 (SEQIDNO:30) |
| V5 | Root | 151 | 399 | 928 |
| Leaf-Sink | 39 | 65 | 59 | |
| Leaf-Source | 52 | 109 | 100 | |
| RI | Root | ND | 616 | 1893 |
| Leaf-Petiole | 97 | 470 | 136 | |
| Leaf-Source | 46 | 177 | 240 | |
| Flowers | 71 | 277 | 140 | |
| R3 | Seed- Immature | 64 | 477 | ND |
| Pod | 84 | 575 | 702 | |
| R5 | Seed- Cotyledon | 91 | 564 | 58 |
| R8 | Seed- Embryo | 57 | 149 | 301 |
| Seed- Cotyledon | 100 | 1118 | 414 |
[00135] As can be seen in Table 2, each of the synthetic regulatory element groups has a unique pattern of expression in the tissues sampled compared to the endogenous EXP. For example, the synthetic At.GSP442 promoter, P-At.GSP442.nno:2 (SEQ ID NO:2), and leader, LAt.GSP442.nno:l (SEQ ID NO:3), of EXP-At.GSP442.nno+At.Cyco:3 (SEQ ID NO:1) provides 10 greater levels of GUS expression in ail of the assayed organs relative to the endogenous EXPAt.Cyco:l:l (SEQ ID NO:38), which comprises an identical intron sequence. Analysis of the TSS demonstrated a consistent TSS. The intron was properly excised in the resulting mRNA as expected. Further, the synthetic At.GSP221 promoter, P-AT.GSP221:3 (SEQ ID NO:31), and leader, L-At.GSP221:l (SEQ ID NO:32), of EXP-At.GSP221+At.Cyco:3 (SEQ ID NO:30) also provides higher levels of constitutive expression in most organs assayed relative to the endogenous EXP-At.Cyco:l:l, and demonstrates a consistent TSS. However, the TSS of EXPAt.GSP221+At.Cyco:3 was not located in the predicted location - there were multiple potential TATA éléments. This croates potential concems for multiple transcripts, which could produce multiple coding sequences. As such, EXP-At.GSP221+At.Cyco:3 was not considered acceptable for use in driving transgene expression in stably transformed dicot plants. This demonstrates one of the complexities in designing synthetic expression éléments. Numerous synthetic éléments were assayed in the development and identification of synthetic expression éléments, but only a small subset provided désirable characteristics and regulatory activity, illustrating the complexity in designing effective synthetic transcriptional regulatory éléments.
[00136] As can be seen in Table 2, the synthetic promoter, P-At.GSP442.nno:2 (SEQ ID NO:2) and L-At.GSP442.nno:l (SEQ ID NO:3) comprised within EXP-At.GSP442.nno+At.Cyco:3 (SEQ ID NO:1) is able to drive constitutive transgene expression of an operably linked transgene in a stably transformed soybean plant.
Example 3
Analysis of the Synthetic ALGSP571 Promoter and Leader, and the Synthetic At.GSI21 and At.GSI102 Introns, Driving GUS Expression in Stably Transformed Soybean Plants
[00137] Soybean plants were transformed with vectors, specifically plant expression vectors containing regulatory element groups driving expression of the β-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the selected regulatory element groups on expression.
[00138] Soybean plants were transformed with plant GUS expression constructs, comprising the synthetic EXPs, EXP-At.GSP571 (SEQ ID NO:4), EXP-At.GSP571.nno+At.Cyco:2 (SEQ ID NO:7), EXP-At.GSP571.nno+At.GSI21.nno:10 (SEQ ID NO:8), and EXPAt.GSP571.nno+At.GSI102.nno:l (SEQ ID NO: 10). Each of the synthetic EXPs comprised the synthetic At.GSP571 promoter (SEQ ID NO:5) and leader (SEQ ID NO:6). EXP36
At.GSP571.nno+At.Cyco:2 comprised the endogenous Arabidopsis intron, I-At.Cyco:2 (SEQ ID NO:33). EXP-At.GSP571.nno+At.GSI21.nno:10 and EXP-At.GSP571.nno+At.GSI102.nno:l comprised the synthetic introns, I-At.GSI21.nno:2 (SEQ ID NO:9) and I-At.GSI102.nno:l (SEQ ID NO: 11), respectively. The binary plant transformation vectors were similar to those 5 described in Example 2 with the exception that each of the At.GSP571 EXP vectors comprised the 3' UTR, T-Mt.Sali3-2-l:2:l (SEQ ID NO:34), derived from the Sali3 gene of Medicago truncatula.
[00139] Quantitative and qualitative GUS expression analysis was performed as described in Example 2. Tissue samples used for analysis were the same as that described in Example 2. 10 Table 3 shows the mean quantitative GUS expression for each of the sampled tissues driven by the tested synthetic EXP regulatory éléments, wherein “ND” indicates the expression in a particular tissue was not determined.
Table 3. Mean quantitative GUS expression in stably transformed soybean plants driven by synthetic regulatory éléments.
| Developmental Stage | Organ | EXPAt.GSP571 (SEQ ID NO:4) | EXPAt.GSP571.nno+ At.Cyco:2 (SEQ IDNO:7) | EXPAt.GSP571.nno+ At.GSI21.nno:10 (SEQ IDNO:8) | EXPAt.GSP571.nno+ At.GSI102.nno:l (SEQ IDNO:10) |
| V5 | Root | 40 | 57 | 165 | 579 |
| Leaf-Sink | 650 | 612 | 792 | 1683 | |
| Leaf-Source | 1379 | 1090 | 1475 | 2128 | |
| RI | Root | 110 | ND | 457 | 645 |
| Leaf-Petiole | 951 | 1091 | 1267 | 1167 | |
| Leaf-Source | 1995 | 3538 | 2094 | 2129 | |
| Flowers | 703 | 830 | 1408 | 350 | |
| R3 | Seed- Immature | 75 | 609 | 495 | 232 |
| Pod | 852 | 2228 | 4014 | 1535 | |
| R5 | Seed- Cotyledon | 650 | 474 | 540 | 1433 |
| R8 | Seed-Embryo | 1153 | 1004 | 603 | 1122 |
| Seed- Cotyledon | 2449 | 4524 | 2533 | 2648 |
[00140] As can be seen in Table 3, the synthetic At.GSP571 promoter and leader provide constitutive expression in ail the organs assayed. Expression was highest in the leaf and seeds. Analysis of the TSS demonstrated a consistent TSS. Operably linking an intron sequence altered expression in many of the organs, providing a means to “fine-tune” the constitutive expression. Différences in expression were observed when operably linking the synthetic introns, IAt.GSI21.nno:2 (SEQ ID NO:9) and I-At.GSI102.nno:l (SEQ ID NO:11). The synthetic introns enhanced expression in some tissues, but differed in the level of enhancement for each organ. For example, enhancement using the synthetic intron I-At.GSI21.nno:2 in R3 pod was higher than the enhancement seen using the synthetic intron I-At.GSI102.nno:l and the endogenous intron I-At.Cyco:2 relative to EXP-At.GSP571. Expression was only slightly enhanced by the three operably linked introns in RI petiole. In RI flowers, I-At.GSI21.nno:2 and I-At.Cyco:2 enhanced expression, with I-At.GSI21.nno:2 providing a high level of expression enhancement and I-At.Cyco:2 providing a moderate level of enhancement. Interestingly, I-At.GSI102.nno:l reduced expression in RI flowers.
[00141] Analysis of the resulting mRNAs showed proper and consistent processing of the intron éléments.
[00142] The synthetic promoter, P-At.GSP571.nno:5 (SEQ ID NO:5) and leader LAt.GSP571.nno:l (SEQ ID NO:6) comprised within EXP-At.GSP571 (SEQ ID NO:4) provide constitutive expression of an operably linked transgene in stably transformed soybean plants. The synthetic EXPs, EXP-At.GSP571.nno+At.Cyco:2 (SEQ ID NO:7), which comprises the Arabidopsis intron I-At.Cyco:2 (SEQ ID NO:33), and EXP-At.GSP571.nno+At.GSI21.nno:10 (SEQ ID NO:8) and EXP-At.GSP571.nno+At.GSI102.nno:l (SEQ ID NO:10), which comprise the synthetic introns I-At.GSI21.nno:2 (SEQ ID NO:9) and I-At.GSI102.nno:l (SEQ ID NO:11), respectively, provide unique patterns of constitutive expression in stably transformed soybean plants. The synthetic introns, I-At.GSI21.nno:2 (SEQ ID NO:9) and I-At.GSI102.nno:l (SEQ ID NO:11), provide enhanced or modulated expression in many of the plant organs when operably linked to EXP-At.GSP571 (SEQ ID NO:4). These unique expression patterns can be used to drive spécifie transgenes in which the spécifie expression pattern of one of the four At.GSP571 EXPs is most désirable.
Example 4
Analysis of the Synthetic At.GSP564 Promoter and Leader, and the Synthetic At.GSI17 and At.GSI102 Introns, Driving GUS Expression in Stably Transformed Soybean Plants
[00143] Soybean plants were transformed with vectors, specifically plant expression vectors containing regulatory element groups driving expression of the B-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the selected regulatory element groups on expression.
[00144] Soybean plants were transformed with plant GUS expression constructs, comprising the synthetic EXPs, EXP-At.GSP564 (SEQ ID NO: 12), EXP-At.GSP564.nno+At.Cyco:2 (SEQ ID NO:15), EXP-At.GSP564.nno+At.GSI17.nno:2 (SEQ ID NO:16), and EXPAt.GSP564.nno+At.GSI102.nno:l (SEQ ID NO: 18). Each of the synthetic EXPs comprised the synthetic P-At.GSP564.nno:3 promoter (SEQ ID NO: 13) and synthetic L-At.GSP564.nno.l leader (SEQ ID NO: 14). EXP-At.GSP564.nno+At.Cyco:2 comprised the Arabidopsis intron, IAt.Cyco:2 (SEQ ID NO:33). EXP-At.GSP564.nno+At.GSI17.nno:2 and EXPAt.GSP564.nno+At.GSI102.nno:l comprised the synthetic introns, I-At.GSI17.nno:l (SEQ ID NO: 17) and I-At.GSI102.nno:l (SEQ ID NO:11), respectively. The binary plant transformation vectors were similar to those described in Example 2, with the exception that each of the At.GSP564 EXP vectors comprised the 3' UTR, T-Mt.Oxr-1:2:1 (SEQ ID NO:35), derived from a putative oxidoreductase (OXR) protein gene from Medicago truncatula.
[00145] Quantitative and qualitative GUS expression analysis was performed as described in Example 2. Tissue samples used for analysis were the same as that described in Example 2. Table 4 shows the mean quantitative GUS expression for each of the sampled tissues driven by the tested synthetic EXP regulatory éléments, wherein “ND” indicates the expression in a particular tissue was not determined.
Table 4. Mean quantitative GUS expression in stably transformed soybean plants driven by synthetic regulatory éléments.
| Developmental Stage | Organ | EXP-At.GSP564 (SEQ IDNO: 12) | EXPAt.GSP564.nno+ At.Cyco:2 (SEQ IDNO: 15) | EXPAt.GSP564.nno+ At.GSI17.nno:2 (SEQ IDNO: 16) | EXPAt.GSP564.nno+ At.GSI102.nno:l (SEQ IDNO: 18) |
| V5 | Root | 61 | 108 | 54 | 145 |
| Leaf-Sink | 38 | 220 | 89 | 259 | |
| Leaf-Source | 74 | 421 | 209 | 1229 | |
| RI | Root | 118 | 165 | 2348 | 627 |
| Leaf-Petiole | 90 | 235 | 273 | 148 | |
| Leaf-Source | 140 | 205 | 436 | 917 | |
| Flowers | 66 | 91 | ND | 305 | |
| R3 | Seed- Immature | 26 | ND | 101 | ND |
| Pod | 40 | ND | 749 | ND | |
| R5 | Seed- Cotyledon | 25 | 88 | 78 | 61 |
| R8 | Seed-Embryo | 38 | 97 | 137 | 70 |
| Seed- Cotyledon | 79 | 288 | 655 | 572 |
[00146] As can be seen in Table 4, the synthetic At.GSP564 promoter and leader provide constitutive expression in ail the organs assayed. Expression was highest in the leaf and seeds. Analysis ofthe TSS demonstrated a consistent TSS. Operably linking an intron sequence altered expression in many of the organs, providing a means to “fine-tune” the constitutive expression. Différences in expression were observed when operably linking the synthetic introns, IAt.GSI17.nno:l (SEQ ID NO:17) and I-At.GSI102.nno:l (SEQ ID NO:11). The synthetic introns enhanced expression in some tissues relative to EXP-At.GSP564, but differed in the level of enhancement for each organ. For example, enhancement using the synthetic intron IAt.GSI102.nno:l in V5 source leaf was higher than the enhancement seen using the synthetic intron I-At.GSI17.nno:l. In RI root, enhancement using the synthetic intron I-At.GSI17.nno:l was higher than the enhancement conferred by the synthetic intron I-At.GSI102.nno:l. Both synthetic introns provided greater enhancement of expression in RI source leaf than the endogenous intron, I-At.Cyco:2.
[00147] Analysis of the resulting mRNAs showed proper and consistent processing of the intron éléments.
[00148] The synthetic At.GSP564 promoter, P-At.GSP564.nno.3 (SEQ ID NO: 13) and leader, L-At.GSP564.nno:l (SEQ ID NO: 14) comprising EXP-At.GSP564 (SEQ ID NO: 12) provide constitutive expression of an operably linked transgene in stably transformed soybean plants. The synthetic EXPs, EXP-At.GSP564.nno+At.Cyco:2 (SEQ ID NO:15), which comprises the Arahidopsis intron I-At.Cyco:2 (SEQ ID NO:33), and EXP-At.GSP564.nno+At.GSI17.nno:2 (SEQ ID NO:16) and EXP-At.GSP564.nno+At.GSI102.nno:l (SEQ ID NO:18), which comprise the synthetic introns, I-At.GSI17.nno:l (SEQ ID NO:17) and I-At.GSI102.nno:l (SEQ ID NO: 11), respectively, provide unique patterns of constitutive expression in stably transformed soybean plants. The synthetic introns, I-At.GSI17.nno:l (SEQ ID NO: 17) and IAt.GSI102.nno:l (SEQ ID NO:11), provide enhanced or modulated transgene expression in many of the plant organs when operably linked to EXP-At.GSP564 (SEQ ID NO: 12). These unique expression patterns can be used to drive spécifie transgenes in which the spécifie expression pattern of one of the four At.GS564 EXPs is most désirable.
Example 5
Analysis of the Synthetic EXP, EXP-At.GSP579.nno+At.GSI102.nno:3, Driving GUS Expression in Stably Transformed Soybean Plants
[00149] Soybean plants were transformed with vectors, specifically plant expression vectors containing a synthetic regulatory element group driving expression of the β-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the selected synthetic regulatory element group on expression.
[00150] Soybean plants were transformed with a plant GUS expression construct, comprising the synthetic EXP, EXP-At.GSP579.nno+At.GSI102.nno:3 (SEQ ID NO:22). EXPAt.GSP579.nno+At.GSI102.nno:3 comprises EXP-At.GSP579 (SEQ ID NO: 19) consisting of the At.GSP promoter and leader (SEQ ID NOs:20 and 21, respectively), operably linked 5' to the synthetic intron, I-At.GSI102.nno:l (SEQ ID NO: 11). The GUS transgene cassette also comprises the 3' UTR, T-Mt.RD22-1:2:1 (SEQ ID NO:37) derived from a dehydrationresponsive protein RD22 gene from Medicago truncatula.
[00151] Quantitative and qualitative GUS expression analysis was performed as described in Example 2. Tissue samples used for analysis were the same as that described in Example 2. Table 5 shows the mean quantitative GUS expression for each of the sampled tissues driven by the synthetic EXP, EXP-At.GSP579.nno+At.GSI102.nno:3, wherein “ND” indicates the expression in a particular tissue was not determined.
Table 5. Mean quantitative GUS expression in stably transformed soybean plants driven by EXP-At.GSP579.nno+At.GSI102.nno:3.
| Developmental Stage | Organ | EXP- At.GSP579.nno+At.GSI102.nno:3 (SEQ IDNO:22) |
| V5 | Root | 187 |
| Leaf-Sink | 311 | |
| Leaf- Source | 458 | |
| RI | Root | 148 |
| Leaf- Petiole | 118 | |
| Leaf- Source | 425 | |
| Flowers | 130 | |
| R3 | Seed- Immature | ND |
| Pod | ND | |
| R5 | Seed- Cotyledon | ND |
| R8 | Seed- Embryo | 127 |
| Seed- Cotyledon | 266 |
[00152] As can be seen in Table 5, EXP-At.GSP579.nno+At.GSI102.nno:3 (SEQ ID NO:22) provides constitutive expression in stably transformed soybean plants. The synthetic promoter P-At.GSP579.nno:2 (SEQ ID NO:20) and leader L-At.GSP579.nno:l (SEQ ID NO:21) comprised within EXP-At.GSP579 (SEQ ID NO: 19) drive constitutive expression of an operably linked transgene. It can be inferred by the previous Examples in which the synthetic intron, I44
At.GSI102.nno: 1 (SEQ ID NO:11), was operably linked to other constitutive synthetic promoters that I-At.GSI102.nno:l enhanced or modulated the constitutive expression imparted by EXPAt.GSP579 in at least some of the organs sampled.
Example 6
Analysis of the Synthetic EXP, EXP-At.GSP571.nno+At.Cyco:2, Driving GUS Expression in Stably Transformed Cotton Plants
[00153] Cotton plants were transformed with a vector, specifically a plant expression vector containing a synthetic regulatory element group driving expression of the β-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the synthetic regulatory element group on expression.
[00154] A plant binary vector comprising the synthetic EXP, EXP-At.GSP571.nno+At.Cyco:2 (SEQ ID NO:7), similar to that described in Example 3, was used to stably transform cotton plants. The GUS transgene cassette comprised EXP-At.GSP571.nno+At.Cyco:2 operably linked 5' to a coding sequence for β-glucuronidase (GUS, GOI-Ec.uidA+St.LSl:l:l, SEQ ID NO:42) containing a processable intron derived from the potato light-inducible tissue-specific ST-LS1 gene (Genbank Accession: X04753), operably linked 5' to a 3' UTR from the Gossypium barbadense FbLate-2 gene (T-Gb.FbL2:l, SEQ ID NO:36). The resulting transformed cotton events were grown and tissue samples were derived from 4Node Leaf; 8Node Petiole, Sink Leaf, and Source Leaf; Pre-fertilization Square Bracts and Square Bud; Flowering Anther and Flower Ovary; and 8 Days After Pollination (DAP) Boll Wall were sampled and assayed for qualitative and quantitative GUS expression.
[00155] Table 6 shows the mean quantitative GUS expression for each of the sampled tissues driven by the synthetic EXP, EXP-At.GSP571.nno+At.Cyco:2.
Table 6. Mean quantitative GUS expression in stably transformed cotton plants driven by EXP-At.GSP571.nno+At.Cyco:2.
| Stage | Organ | Mean |
| 4Node | Leaf | 1232.57 |
| 8Node | Leaf, Petiole | 223.68 |
| Leaf, Sink | 612.14 | |
| Leaf, Source | 618.9 | |
| Pre-fertilization | Square Bracts | 381.69 |
| Square Bud | 347.22 | |
| Flowering | Anther | 64.66 |
| Flower, Ovary | 210.92 | |
| 8DAP | Boll Wall | 835.94 |
[00156] As can be seen in Table 6, EXP-At.GSP571.nno+At.Cyco:2 expressed in ail the tissues sampled. Expression was highest in 4Node Leaf and lowest in the Flowering Anther. Expression in 8Node Sink and Source Leaf were relatively the same and about half that of the 4Node Leaf. Expression was also high in the Boll Wall. Table 6 demonstrates that the promoter, P-At.GSP571.nno:5 (SEQ ID NO:5), is able to drive constitutive expression in stably transformed cotton plants. The intron, I-At.Cyco:2 (SEQ ID NO:33), within EXP-
At.GSP571.nno+At.Cyco:2 enhanced expression of the P-At.GSP57Lnno:5 promoter in stably transformed soybean plants, as shown in Example 3.
Example 7
Analysis of the Synthetic Chimeric Promoter P-ALGSP571/442 Driving GUS Expression in Stably Transformed Soybean Plants
[00157] Soybean plants were transformed with vectors, specifically plant expression vectors containing regulatory element groups driving expression of the β-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the selected synthetic regulatory element groups on expression.
[00158] Soybean plants were transformée! with a plant binary vector comprising the synthetic EXP, EXP-At.GSP571.nno+At.GSP442.nno+At.Cyco:l (SEQ IDNO:23), which is comprised of the synthetic chimeric promoter P-At.GSP571/442 (SEQ ID NO:25) comprising a synthetic enhancer E-At.GSP571.nno:l (SEQ ID NO:24) derived from the synthetic promoter PAt.GSP571.nno:5 (SEQ ID NO:5) which is operably linked 5' to the synthetic promoter PAt.GSP442.nno:2 (SEQ ID NO:2) and is operably linked 5' with the synthetic leader, LAt.GSP442.nno:l (SEQ ID NO:3), operably linked 5' to the leader, L-AtCyco-l:l:2 (SEQ ID NO:40), which is operably linked 5' to the intron, I-At.Cyco:2 (SEQ ID NO:33). The GUS transgene cassette comprised EXP-At.GSP571.nno+At.GSP442.nno+At.Cyco:l operably linked 5' to a coding sequence for B-glucuronidase (GUS, GOI-Ec.uidA+St.LSl:l:l, SEQ ID NO:42) containing a processable intron derived from the potato light-inducible tissue-specific ST-LS1 gene (Genbank Accession: X04753), operably linked 5' to the synthetic 3' UTR, TZm.GST59.nno:l (SEQ ID NO:29).
[00159] A plant binary vector used to compare the activity of the chimeric promoter was also constructed. The vector comprised an EXP, EXP-At.GSP442+L-I-At.Cyco (SEQ ID NO:43), which is comprised of the synthetic promoter, P-At.GSP442.nno:2 (SEQ ID NO:2), operably linked 5' to the synthetic leader, L-At.GSP442.nno: 1 (SEQ ID NO:3), operably linked 5' to the leader, L-At.Cyco-l:l:2 (SEQ ID NO:40), which is operably linked 5’ to the intron, I-At.Cyco:2 (SEQ ID NO:33). The binary vectors are similar to those described in Examples 2-6, with the exception that each GUS transgene cassette has the synthetic 3' UTR, T-Zm.GST59.nno:l (SEQ IDNO:29) operably linked 3' to the GUS coding sequence.
[00160] Soybean plants were transformed with the two binary vectors. Tissue samples were taken of selected organs at spécifie developmental stages and assayed for qualitative and quantitative GUS expression. Table 7 shows the mean quantitative GUS expression for each of the sampled tissues driven by the synthetic EXPs, EXPAt.GSP571 .nno+At.GSP442.nno+At.Cyco: 1 and EXP-At.GSP442+L-I-At.Cyco.
Table 7. Mean quantitative GUS expression in stably transformed soybean plants driven by EXP-At.GSP571.nno+At.GSP442.nno+At.Cyco:l and EXP-At.GSP442+L-I-At.Cyco.
| EXP-At.GSP442+L-IAt.Cyco (SEQ ID NO:43) | EXPAt.GSP571.nno+At.GSP442.nno+At.Cyco:l (SEQ ID NO:23) | ||
| Stage | Organ | Mean | Mean |
| V5 | Leaf, Sink | 69.61 | 72.12 |
| Leaf, Source | 88.22 | 96.06 | |
| Root | 74.67 | 102.9 | |
| RI | Flowers | 79.16 | 62.01 |
| Leaf, Petiole | 77.07 | 87 | |
| Leaf, Source | 66.59 | 114.33 | |
| Root | 76.88 | 123.12 | |
| R3 | Pod | 93.19 | 102.54 |
| Seed, Immature | 71.15 | 61.62 | |
| R5 | Seed, Cotylédon | 78.72 | 92.83 |
| R8 | Seed, Cotylédon | 65.55 | 72.15 |
| Seed, Embryo | 129.95 | 107.66 |
[00161] As can be seen in Table 7, the addition of the synthetic enhancer E-At.GSP571.nno:l enhanced expression in many of the tissues sampled. Both EXPs provided constitutive expression in the stably transformed soybean plants. The synthetic 3' UTR, T-Zm.GST59.nno:l, functioned in a similar manner as a native 3' UTR in providing proper termination and polyadenylation of the transcript.
Example 8
Analysis of the Synthetic Chimeric Promoter P-At.GSP571/442 Driving GUS Expression in Stably Transformed Cotton Plants
[00162] Cotton plants were transformed with a vector, specifically a plant expression vector containing a synthetic regulatory element group driving expression of the B-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the selected synthetic regulatory element group on expression.
[00163] Cotton plants were transformed with a plant binary vector comprising the synthetic EXP, EXP-At.GSP571.nno+At.GSP442.nno+At.Cyco:l (SEQ ID NO:23), which is comprised of the synthetic chimeric promoter P-At.GSP571/442 (SEQ ID NO:25) comprising a synthetic enhancer E-At.GSP571.nno:l (SEQ ID NO:24) derived from the synthetic promoter PAt.GSP571.nno:5 (SEQ ID NO:5) which is operably linked 5' to the synthetic promoter PAt.GSP442.nno:2 (SEQ ID NO:2) and is operably linked 5' to the synthetic leader, LAt.GSP442.nno:l (SEQ ID NO:3), operably linked 5' to the leader, L-At.Cyco-l:l:2 (SEQ ID NO:40), which is operably linked 5' to the intron, I-At.Cyco:2 (SEQ ID NO:33). The GUS transgene cassette comprised EXP-At.GSP571.nno+At.GSP442.nno+At.Cyco:l operably linked 5' to a coding sequence for B-glucuronidase (GUS, GOI-Ec.uidA+St.LSl:l:l, SEQ ID NO:42) containing a processable intron derived from the potato light-inducible tissue-specific ST-LS1 gene (Genbank Accession: X04753), operably linked 5' to the synthetic 3' UTR, TZm.GST59.nno:l (SEQ ID NO:29). The resulting transformed cotton events were grown and tissue samples derived from 4Node Leaf; 8Node Petiole, Sink Leaf, and Source Leaf; Prefertilization Square Bracts and Square Bud; Flowering Anther and Flower Ovary; and 8 Days After Pollination (DAP) Boll Wall were sampled and assayed for qualitative and quantitative GUS expression.
[00164] Table 8 shows the mean quantitative GUS expression for each of the sampled tissues driven by the synthetic EXP, EXP-At.GSP571.nno+At.GSP442.nno+At.Cyco:l wherein “bdl” means below détection limit.
Table 8. Mean quantitative GUS expression in stably transformed cotton plants driven by EXP-At.GSP571.nno+At.GSP442.nno+At.Cyco:l.
| Stage | Organ | Mean |
| 4Node | Leaf | 177.74 |
| 8Node | Leaf, Petiole | bdl |
| Leaf, Sink | 108.39 | |
| Leaf, Source | 294.99 | |
| Pre-fertilization | Square Bracts | 78.84 |
| Square Bud | 118.21 | |
| Flowering | Anther | 69.19 |
| Flower, Ovary | 69.78 | |
| 8DAP | Boll Wall | 159.58 |
[00165] As can be seen in Table 8, EXP-At.GSP571.nno+At.GSP442.nno+At.Cyco:l (SEQ ID 5 NO:23) was able to drive constitutive GUS expression in the tissues sampled. Expression in the
Petiole was determined to be below détection limits. Expression was highest in 8Node Source Leaf. Expression was relatively equal in the Flowering Anther and Flower Ovary. In addition, the synthetic 3' UTR, T-Zm.GST59.nno:l (SEQ ID NO:29) functioned in a similar manner as a native 3' UTR in providing proper termination and polyadenylation of the transcript.
Example 9
Analysis of the Synthetic EXP, EXP-At.GSP576.nno+At.Cyco:l, Driving GUS Expression in Stably Transformed Soybean Plants
[00166] Soybean plants were transformed with a vector, specifically a plant expression vector containing a synthetic regulatory element group driving expression of the B-glucuronidase (GUS) 15 transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the selected synthetic regulatory element group on expression.
[00167] Soybean plants were transformed with a plant binary vector comprising the synthetic EXP, EXP-At.GSP576.nno+At.Cyco:l (SEQ ID NO:45). The GUS transgene cassette also comprised the 3' UTR from the Gossypium barbadense FbLate-2 gene (T-Gb.FbL2:l, SEQ ID NO:36), operably linked 3' to the GUS coding sequence. The resulting transformed soybean events were grown and tissue samples of selected organs from several developmental stages were sampled and assayed for qualitative and quantitative GUS expression. Expression of GUS in the stably transformed soybean plants, driven by EXP-At.GSP576.nno+At.Cyco:l, is presented in Table 9.
Table 9. Mean quantitative GUS expression in stably transformed soybean plants driven by EXP-At.GSP576.nno+At.Cyco:l.
| Developmental Stage | Organ | Mean |
| V5 | Root | 60.95 |
| Leaf-Sink | 97.43 | |
| Leaf-Source | 181.64 | |
| RI | Root | 82.4 |
| Leaf-Petiole | 208.28 | |
| Leaf-Source | 214 | |
| Flowers | 123.37 | |
| R3 | Seed-Immature | 95.29 |
| Pod | 158.24 | |
| R5 | Seed-Cotyledon | 85.97 |
| R8 | Seed-Embryo | 67.4 |
| Seed-Cotyledon | 52.92 |
[00168] As can be seen in Table 9, EXP-At.GSP576.nno+At.Cyco:l (SEQ ID NO:45) provided constitutive expression in stably transformed soybean plants. The synthetic promoter PAt.GSP576.nno:4 (SEQ ID NO:27) and leader L-At.GSP576.nno:2 (SEQ ID NO:28) drive constitutive expression of an operably linked transgene. It can be inferred by the previous Examples in which the intron, I-At.Cyco:2 (SEQ ID NO:33), was operably linked to other constitutive synthetic promoters, that I-At.Cyco:2 enhanced or modulated the constitutive expression imparted by P-At.GSP576.nno:4 in at least some of the organs sampled.
Example 10
Analysis of the Synthetic EXP, EXP-At.GSP576.nno+At.GSI17.nno:3, Driving GUS Expression in Stably Transformed Soybean Plants
[00169] Soybean plants are transformed with vectors, specifically plant expression vectors containing regulatory element groups driving expression of the B-glucuronidase (GUS) transgene. The resulting plants are analyzed for GUS protein expression to assess the effect of the selected regulatory element groups on expression.
[00170] Soybean plants are transformed with plant binary vectors comprising either the synthetic EXP, EXP-At.GSP576.nno+At.GSI17.nno:3 (SEQ ID NO:26), or the EXP, EXPAt.Cyco:l:l (SEQ ID NO:38). The GUS transgene cassettes also comprise the 3’ UTR from the Gossypium barbadense FbLate-2 gene (T-Gb.FbL2:l, SEQ ID NO:36) operably linked 3’ to the GUS coding sequence. The resulting transformed soybean events are grown and tissue samples of selected organs from several developmental stages are sampled and assayed for qualitative and quantitative GUS expression. Expression of GUS in the stably transformed soybean plants, driven by EXP-At.GSP576.nno+At.GSI17.nno:3, is compared to the expression driven by EXPAtCyco:l:l. Expression of GUS in stably transformed soybean plants driven by EXPAt.GSP576.nno+At.GSI17.nno:3 is démonstrative of the ability of the synthetic promoter PAt.GSP576.nno:4 (SEQ ID NO:27) and leader L-At.GSP576.nno:2 (SEQ ID NO:28) to drive constitutive expression of an operably linked transgene.
[00171] As demonstrated in Examples 9 and 11, the synthetic promoter P-At.GSP576.nno:4 (SEQ ID NO:27) and leader L-At.GSP576.nno:2 (SEQ ID NO:28) drive constitutive expression of an operably linked transgene. As was demonstrated in Example 4, the synthetic intron, IAt.GSI17.nno:l (SEQ ID NO.T7) enhanced or modulated transgene expression in many of the plant organs when operably linked to EXP-At.GSP564 (SEQ ID NO: 12). Likewise, it can be reasonably expected that expression of the synthetic promoter P-At.GSP576.nno:4 and leader LAt.GSP576.nno:2 would be enhanced or modulated in a similar manner.
Example 11
Analysis of the Synthetic EXP, EXP-At.GSP576.nno+At.GSI17.nno:3, Driving GUS Expression in Stably Transformed Cotton Plants
[00172] Cotton plants were transformed with a vector, specifically a plant expression vector containing a synthetic regulatory element group driving expression of the B-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of the selected synthetic regulatory element group on expression.
[00173] Cotton plants were transformed with a binary vector comprising the synthetic EXP, EXP-At.GSP576.nno+At.GSI17.nno:3 (SEQ ID NO:26), as previously described in Example 10.
The GUS transgene cassettes also comprised the 3' UTR from the Gossypium barbadense FbLate-2 gene (T-Gb.FbL2:l, SEQ ID NO:36) operably linked 3' to the GUS coding sequence. The resulting transformed cotton events were grown and tissue samples derived from 4Node Leaf; 8Node Petiole, Sink Leaf, and Source Leaf; Pre-fertilization Square Bracts and Square Bud; Flowering Anther and Flower Ovary; and 8 Days After Pollination (DAP) Boll Wall were sampled and assayed for qualitative and quantitative GUS expression.
[00174] Table 10 shows the mean quantitative GUS expression for each of the sampled tissues driven by the synthetic EXP-At.GSP576.nno+At.GSI17.nno:3.
Table 10. Mean quantitative GUS expression in stably transformed cotton plants driven by EXP-At.GSP576.nno+At.GSI17.nno:3.
| Stage | Organ | Mean |
| 4Node | Leaf | 579.03 |
| 8Node | Leaf, Petiole | 301.57 |
| Leaf, Sink | 159.4 | |
| Leaf, Source | 577.11 | |
| Pre-fertilization | Square Bracts | 262.66 |
| Square Bud | 223.59 | |
| Flowering | Anther | 171.2 |
| Flower, Ovary | 109 | |
| 8DAP | Boll Wall | 433.64 |
[00175] As can be seen in Table 10, EXP-At.GSP576.nno+At.GSI17.nno:3 (SEQ ID NO: 26) drove constitutive expression of the GUS transgene in stably transformed cotton plants. Expression was highest in 4Node Leaf, 8Node Source Leaf, and 8DAP Boll Wall. The synthetic promoter P-At.GSP576.nno:4 (SEQ ID NO:27) and leader L-At.GSP576.nno:2 (SEQ ID NO:28) are able to drive constitutive expression of an operably linked transgene in stably transformed cotton plants. As was demonstrated in Example 4, the synthetic intron, I-At.GSI17.nno:l (SEQ
ID NO: 17), enhanced or modulated transgene expression in many of the plant organs when operably linked to EXP-At.GSP564 (SEQ ID NO: 12). Likewise, it can be reasonably expected that expression of the synthetic promoter, P-At.GSP576.nno:4 and leader, L-At.GSP576.nno:2, would be enhanced or modulated in a similar manner in stably transformed cotton plants.
Example 12
Enhancer Eléments derived from the Regulatory Element
[00176] Enhancers are derived from the promoter éléments presented as SEQ ID NOs: 2, 5, 13, 20, 25, 27, 31, and 39. The enhancer element may be comprised of one or more cis regulatory éléments that when operably linked 5' or 3' to a promoter element, or operably linked 5' or 3' to additional enhancer éléments that are operably linked to a promoter, can enhance or modulate expression levels of a transcribable DNA molécule, or provide expression of a transcribable DNA molécule in a spécifie cell type or plant organ or at a particular time point in development or circadian rhythm. Enhancers are made by removing the TATA box or functionally similar éléments and any downstream sequence from the promoters that allow transcription to be initiated from the promoters presented as SEQ ID NOs: 2, 5, 13, 20, 25, 27, 31, and 39 or fragments thereof. For example, the synthetic enhancer, E-At.GSP571.nno:l (SEQ ID NO:24) was derived from the synthetic promoter, P-At.GSP571.nno:5 (SEQ ID NO:5) and consists of nucléotides 1 through 422 of P-At.GSP571.nno:5, eliminating the 3' downstream sequence which also contains the TATA box of the synthetic promoter.
[00177] Further refinement of the enhancer element may be required and is validated empirically. In addition, position of the enhancer element relative to other éléments within a chimeric regulatory element group is also empirically determined, since the order of each element within the chimeric regulatory element group may impart different effects, depending upon the relative positions of each element. Some promoter éléments will hâve multiple TATA box or TATA box-like éléments and potentially multiple transcription start sites. Under those circumstances, it may be necessary to first identify where the first TSS is located and then begin designing enhancers using the first TSS to prevent the potential initiation of transcription from occurring within a putative enhancer element.
[00178] Enhancer éléments, derived from the synthetic promoter éléments presented as SEQ ID NOs: 2, 5, 13, 20, 25, 27, 31, and 39 are cloned using methods known in the art to be operably linked 5' or 3' to a promoter element, or operably linked 5' or 3' to additional enhancer éléments that are operably linked to a promoter. Altematively, enhancer éléments can be cloned, using methods known in the art, to provide a larger enhancer element that is comprised of two or more copies of the enhancer and cloned using methods known in the art to be operably linked 5 ' or 3 ' to a promoter element, or operably linked 5' or 3' to additional enhancer éléments that are operably linked to a promoter producing a chimeric transcriptional regulatory element. Enhancer éléments can also be cloned using methods known in the art to be operably linked 5' to a promoter element derived from a different genus organism, or operably linked 5' or 3' to additional enhancer éléments derived from other genus organisms that are operably linked to a promoter derived from either the same or different genus organism, resulting in a chimeric regulatory element. A GUS expression plant transformation vector may be constructed using methods known in the art similar to the constructs described in Example 2 in which the resulting plant expression vectors contain a right border région from Agrobacterium tumefaciens (BAGRtu.right border), a first transgene sélection cassette used for sélection of transformed plant cells that confers résistance to the antibiotic, spectinomycin; and a second transgene cassette to test the enhancer element comprised of, the enhancer element operably linked 5' or 3' to a promoter element or operably linked 5' or 3' to additional enhancer éléments that are in tum operably linked to a promoter which is operably linked 5' to a leader element, operably linked to a coding sequence for B-glucuronidase (GUS, GOI-Ec.uidA+St.LS 1:1:1, SEQ ID NO:42) containing a processable intron derived from the potato light-inducible tissue-specific ST-LS1 gene (Genbank Accession: X04753), operably linked to a 3' termination région, and a left border région from A. tumefaciens (B-AGRtu.left border). The resulting plasmids are used to transform soybean plants or other genus plants by the methods described in the Examples. Altematively, protoplast cells derived from soybean or other genus plants are transformed using methods known in the art to perform transient assays.
[00179] GUS expression driven by a regulatory element comprising one or more enhancers is evaluated in stable or transient plant assays to détermine the effects of the enhancer element on expression of a transcribable DNA molécule. Modifications to one or more enhancer éléments or duplication of one or more enhancer éléments may be performed based upon empirical expérimentation and the resulting gene expression régulation that is observed using each regulatory element composition. Altering the relative positions of one or more enhancers in the resulting regulatory or chimeric regulatory éléments may affect the transcriptional activity or specificity of the regulatory or chimeric regulatory element and is determined empirically to identify the best enhancers for the desired transgene expression profile within the soybean plant or other genus plant.
Example 13
Analysis of the Effect upon GUS Expression Imparted by the Synthetic 3' UTR, TZm.GST7.nno:2, in Stably Transformed Soybean Plants
[00180] Soybean plants were transformed with a vector, specifically plant expression vectors containing regulatory element groups driving expression of the β-glucuronidase (GUS) transgene. The resulting plants were analyzed for GUS protein expression to assess the effect of selected regulatory éléments on expression.
[00181] Soybean plants were transformed with two binary vectors comprising EXP-At.GSP571 (SEQ ID NO:4) driving GUS expression. The GUS transgene cassettes also comprised either the endogenous 3' UTR T-Mt.Sali3-2-l:2:l (SEQ ID NO:34) or the synthetic 3' UTR, TZm.GST7.nno:2 (SEQ ID NO:44). GUS protein expression was quantitatively measured in the organs of stably transformed soybean plants transformed with the two constructs. Expression of GUS was compared between the constructs. Table 11 below shows the mean GUS expression modulated by the synthetic 3' UTR, T-Zm.GST7.nno:2, relative to the endogenous 3' UTR, T-
Mt.Sali3-2-l :2:1, wherein “nd” mean not determined and “bdl” means below détection limit.
Table 11. Mean quantitative GUS expression in stab y transformed soybean plants.
| Developmental Stage | Organ | T-MtSali3-2- 1:2:1 (SEQ ID NO:34) | TZm.GST7.nno:2 (SEQID NO:44) | Fold Atténuation |
| V5 | Root | 40 | bdl | |
| Leaf-Sink | 650 | 88 | 7.4 | |
| Leaf-Source | 1379 | 278 | 5.0 | |
| RI | Root | 110 | 72 | 1.5 |
| Leaf-Petiole | 951 | 199 | 4.8 | |
| Leaf-Source | 1995 | 642 | 3.1 | |
| Flowers | 703 | 139 | 5.1 | |
| R3 | Seed- Immature | 75 | bdl | |
| Pod | 852 | 386 | 2.2 | |
| R5 | Seed- Cotyledon | 650 | 174 | 3.7 |
| R8 | Seed- Embryo | 1153 | nd | |
| Seed- Cotyledon | 2449 | nd |
[00182] As can be seen in Table 11, the synthetic 3' UTR, T-Zm.GST7.nno:2 attenuated expression relative to the 3' UTR, T-Mt.Sali3-2-l:2:l in ail tissues assayed. The degree of atténuation varied for each tissue from 1.5 fold in RI Roots to 7.4 fold in V5 Sink Leaf. The use of a 3' UTR to attenuate expression in stably transformed plants has great utility. For example, a 3' UTR can be used in combination with other regulatory éléments such as promoters, leaders, and introns to fine tune expression of a transgene, particularly those wherein high expression may lead to off-phenotypic effects that are deleterious to the transformed plant. Analysis of the resulting GUS transcript confirmed proper termination of the transcript imparted by the synthetic
3' UTR, T-Zm.GST7.nno:2. The synthetic 3' UTR, T-Zm.GST7.nno:2, is able to modulate expression and properly terminate transcription in stably transformed soybean plants.
Example 14
Analysis of the Synthetic 3' UTRs, T-Zm.GST7.nno:2 and T-Zm.GST59.nno:l, on GUS Expression in Corn Protoplast Cells
[00183] Corn leaf protoplasts were transformed with vectors, specifically expression vectors containing test regulatory éléments driving expression of the β-glucuronidase (GUS) transgene. The resulting transformed corn leaf protoplasts were analyzed for GUS protein expression to assess the effect of the selected regulatory éléments on expression.
[00184] Corn protoplasts, derived from leaf tissue, were transformed with expression vectors comprising synthetic expression éléments and compared to expression éléments known in the art. Two expression vectors were constructed to assess the activity of the synthetic 3' UTRs, TZm.GST7.nno:2 (SEQ ID NO:44) and T-Zm.GST59.nno:l (SEQ ID NO:29) and two construct expression vectors were also constructed. Each of the four constructs comprised a transgene cassette comprising the constitutive promoter and leader, EXP-CaMV.35S (SEQ ID NO:46), operably linked 5' to the intron I-Zm.DnaK:l (SEQ ID NO:47), operably linked 5' to a GUS coding sequence, GOI-Ec.uidA+St.LSl:l:l (SEQ ID NO:42). The expression vectors used to assess the synthetic 3' UTRs comprised either T-Zm.GST7.nno:2 or T-Zm.GST59.nno:l operably linked 3' to the GUS coding sequence. One control vector comprised the 3' UTR TOs.LTP:! (SEQ ID NO:48) operably linked 3' to the GUS coding sequence. The other control vector lacked a 3 ' UTR.
[00185] A plasmid used in co-transformation of the protoplasts and normalization of the data was also constructed using methods known in the art. It comprised a transgene cassette comprised of, EXP-CaMV.35S (SEQ ID NO:46) operably linked 5' to a coding sequence encoding the NanoLuc® luciferase fluorescent protein (Promega, Madison, WI 53711), Nluc (SEQ ID NO:49), which was operably linked 5' to a 3' UTR, T-Os.LTP:l (SEQ ID NO:48).
[00186] Corn leaf protoplasts were transformed using a PEG-based transformation method, similar to those known in the art. Protoplast cells were transformed in a ninety six well format. Twelve micrograms of the test vector DNA or control vector DNA, and six micrograms of the NanoLuc® vector DNA were used to transform 3.2 X 105 protoplasts per well. After transformation, the protoplasts were incubated at 25°C in the dark for sixteen to twenty hours. Following incubation, the protoplasts were lysed and the lysate used for measuring luciferase and
GUS expression. To lyse the cells, the cells in the plate were pelleted through centrifugation, washed, resuspended in a smaller volume, and transferred to strip well tubes. The tubes were centrifuged again and supematant was aspirated leaving the protoplast cell pellet behind. The cell pellet was resuspended in QB buffer (100 mM KPO4, pH 7.8; 1 mM EDTA; 1% Triton X100; 10% Glycerol; 1 mM DTT). The cells were lysed by vigorously pipetting the cells several times, vortexing the tubes, and letting the tubes incubate on ice for five minutes. The lysate was then centrifuged to pellet the cell débris. The resulting lysate was then transferred to a clean plate.
[00187] Luciferase activity was assayed using the Nano-Glo® Luciferase Assay Substrate (Promega, Madison, WI 53711) in QB buffer. In short, a small volume of lysate, QB buffer, and the Nano-Glo® Luciferase Assay Substrate/QB solution were mixed together in white, ninety six well plates. Fluorescence was then measured using a PHERAstar® plate reader (BMG LABTECH Inc., Cary, NC 27513).
[00188] GUS activity was assayed using the fluorogenic substrate 4-methyleumbelliferyl-p-Dglucuronide (MUG) in a total reaction volume of 50 microliters. The reaction product, 4methlyumbelliferone (4-MU), is maximally fluorescent at high pH, where the hydroxyl group is ionized. Addition of a basic solution of sodium carbonate simultaneously stops the assay and adjusts the pH for quantifying the fluorescent product. An aliquot of lysate was mixed with an aliquot of MUG dissolved in QB buffer and incubated at 37°C. A small aliquot of the lysate/MUG reaction mixture was removed and added to a stop buffer at three different timepoints; (1) immediately after mixing the lysate/MUG reaction as “Time zéro minutes”; (2) twenty minutes; and (3) sixty minutes. Fluorescence was measured with excitation at 355 nm, émission at 460 nm using a using a PHERAstar® plate reader (BMG LABTECH Inc., Cary, NC 27513).
[00189] At least two plates were used in transformation with four to eight transformations per plate for each expression vector. For each plate, each construct is transformed in four to eight wells. An aliquot is taken out of each transformation for the MUG assay and “nM MUG hydrolyzed” is derived from the in-plate-standard curve. An aliquot is also taken out of each transformation for the NanoLuc® reading (NanoLuc® RLU). The mean nM MUG hydrolyzed/ NanoLuc® RLU for each expression vector is normalized with respect to the EXP-CaMV.35S/I60
Zm.DnaK:l/ T-Os.LTP:l expression vector which is set to 100%. Table 12 shows the average of the mean for ail the plates used in transformation for each expression vector comprising the synthetic 3' UTRs T-Zm.GST7.nno:2 and T-Zm.GST59.nno:l, and the Controls.
Table 12. Average of the mean nM MUG hydrolyzed/ NanoLuc® RLU for each expression vector.
| 3'UTR | Average of Mean | Stderr |
| T-Os.LTP:l | 100.00 | 8.09 |
| No 3'UTR | 51.95 | 4.71 |
| T-Zm.GST59.nno:l | 505.45 | 37.75 |
| T-Zm.GST7.nno:2 | 345.31 | 40.73 |
[00190] As can be seen in Table 12, the expression vector without a 3' UTR provided less expression than the T-Os.LTP:l control. Expression was enhanced by the synthetic 3' UTRs TZm.GST7.nno:2 and T-Zm.GST59.nno:l compared to the T-Os.LTP:l control. Analysis of the transcripts demonstrated proper termination imparted by the synthetic 3' UTRs TZm.GST7.nno:2 and T-Zm.GST59.nno:l. The synthetic 3' UTRs T-Zm.GST7.nno:2 and TZm.GST59.nno:l are able to modulate expression and properly terminate transcription in transformed corn leaf protoplast cells.
Example 15
Analysis of Regulatory Eléments Driving GUS in Cotton Leaf Protoplasts
[00191] Cotton leaf protoplasts were transformed with vectors, specifically expression vectors containing regulatory element groups driving expression of the β-glucuronidase (GUS) transgene. The resulting transformed cotton leaf protoplasts were analyzed for GUS protein expression to assess the effect of the selected regulatory element groups on expression.
[00192] Cotton protoplasts, derived from leaf tissue were transformed with expression vectors comprising synthetic expression éléments and compared to expression éléments known in the art. Separate experiments were conducted to assess the activity of the EXP’s, EXP-At.GSP571 (SEQ ID NO:4), EXP-At.GSP571.nno+At.GSI21.nno:10 (SEQ ID NO:8), EXPAt.GSP571.nno+At.GSI102.nno:l (SEQ ID NO:10), EXP-At.GSP564.nno+At.GSI17.nno:2 (SEQ ID NO: 16), and EXP-At.GSP579.nno+At.GSI102.nno:3 (SEQ ID NO:22). The expression éléments were cloned into expression vectors and operably linked to a GUS coding sequence, GOI-Ec.uidA+St.LSl:l:l (SEQ ID NO:42) that comprised a processable intron. The control expression vectors comprised different configurations of known expression éléments.
[00193] Two plasmids, for use in co-transformation and normalization of data, were also constructed using methods known in the art. Each plasmid contained a spécifie luciferase coding sequence that was driven by a constitutive EXP sequence. The plant vector pFLUC comprised a transgene cassette with a constitutive promoter operably linked 5' to an intron, (EXPCaMV.35S-enh+Zm.DnaK:l:l, SEQ ID NO: 53), operably linked 5' to a firefly (Photinus pyralis) luciferase coding sequence (LUCIFERASE: 1:3, SEQ ID NO: 54), operably linked 5' to a 3' UTR from the Agrobacterium tumefaciens nopaline synthase gene (T-AGRtu.nos-1:1:13, SEQ ID NO: 55). The plant vector pRLUC comprised a transgene cassette with a constitutive EXP sequence (EXP-CaMV.35S-enh-Lhcbl, SEQ ID NO: 56), operably linked 5' to a sea pansy (Renilla reniformis) luciferase coding sequence (CR-Ren.hRenilla Lucife-0:0:l, SEQ ID NO: 57), operably linked 5' to a 3' UTR from the Agrobacterium tumefaciens nopaline synthase gene (T-AGRtu.nos-1:1:13, SEQ IDNO: 55).
[00194] Cotton leaf protoplasts were transformed using a PEG-based transformation method, known in the art. Protoplast cells were transformed with the plasmids, pFLUC and pRLUC, and an equimolar quantity of the EXP expression vectors. Measurements of both GUS and luciferase were conducted by placing aliquots of a lysed préparation of cells transformed as above into two different small-well trays. One tray was used for GUS measurements, and a second tray was used to perform a dual luciferase assay using the dual luciferase reporter assay system (Promega Corp., Madison, WI; see for example, Promega Notes Magazine, No: 57, 1996, p.02). Sample measurements were based upon multiple transformations similar to that presented in Example 14. Mean GUS/FLUC values were calculated in a similar manner as in Example 14, but were not normalized relative to the control EXP vectors.
[00195] The EXPs, EXP-At.GSP571 (SEQ ID NO:4), EXP-At.GSP571.nno+At.GSI21.nno:10 (SEQ ID NO:8), and EXP-At.GSP571.nno+At.GSI102.nno:l (SEQ ID NO: 10) were cloned into plant expression vectors operably linked 5' to a GUS coding sequence (SEQ ID NO:42), operably linked 5' to the 3' UTR, T-Mt.Sali3-2-1:2:1 (SEQ ID NO:34). Two control plant expression vectors were constructed with the EXP, EXP-At.Bglu21+At.Cyco:2 (SEQ ID NO:50), known to express poorly in cotton leaf protoplasts and the EXP, EXP-CaMV.35Senh+PhDnaK:l:3 (SEQ ID NO:51), known to express well in cotton leaf protoplasts. The control EXPs were operably linked to the same GUS and 3' UTR sequence. In addition, a plant expression vector comprising a GUS transgene cassette comprising the EXP, EXP-At.GSP571 (SEQ ID NO:4), operably linked to GUS comprised the synthetic 3' UTR, T-Zm.GST7.nno:2 (SEQ ID NO:44) to assess the activity of the synthetic 3' UTR. The mean GUS/FLUC values for multiple transformations are presented in Table 13.
Table 13. Mean GUS/FLUC values from transformed cotton leaf protoplasts
| EXP | EXP SEQ IDNO: | 3'UTR | 3'UTR SEQID NO: | Mean GUS/FLUC |
| EXP-At.Bglu2 l+At.Cyco:2 | 50 | T-Mt.Sali3-2-l:2:l | 34 | 0.09 |
| EXP-CaMV.3 5S-enh+Ph.DnaK: 1:3 | 51 | T-Mt.Sali3-2-l:2:l | 34 | 1.70 |
| EXP-At.GSP571 | 4 | T-Mt.Sali3-2-l:2:l | 34 | 0.56 |
| EXP- At.GSP571 .nno+At.GSI21 .nno: 10 | 8 | T-Mt.Sali3-2-l:2:l | 34 | 1.02 |
| EXP- At.GSP571 .nno+At.GSI 102.nno: 1 | 10 | T-Mt.Sali3-2-l:2:l | 34 | 0.95 |
| EXP-At.GSP571 | 4 | T-Zm.GST7.nno:2 | 44 | 0.46 |
[00196] As can be seen in Table 13, the EXPs, EXP-At.GSP571 (SEQ ID NO:4), EXPAt.GSP571.nno+At.GSI21.nno:2 (SEQ ID NO:8), and EXP-At.GSP571.nno+At.GSI102.nno:l (SEQ ID NO: 10) demonstrated expression in cotton leaf protoplast cells. The synthetic 3' UTR, T-Zm.GST7.nno: 10 (SEQ ID NO:44) functioned in a similar manner as the endogenous 3' UTR, T-Mt.Sali3-2-l:2:l.
[00197] The EXP, EXP-At.GSP564.nno+At.GSI17.nno:2 (SEQ ID NO: 16) was cloned into a plant expression vectors operably linked 5' to a GUS coding sequence (SEQ ID NO:42), operably linked 5' to the endogenous 3' UTR, T-Mt.Oxr-l:2:l (SEQ ID NO:35). Two control plant expression vectors were constructed with the EXP, EXP-Gm.Sphasl:l:l (SEQ ID NO:52), known to express poorly in cotton leaf protoplasts and the EXP, EXP-CaMV.35S enh+Ph.DnaK:l:3 (SEQ ID N0:51), known to express well in cotton leaf protoplasts. The control EXPs were operably linked to the same GUS and 3' UTR sequence. The mean GUS/FLUC values for multiple transformations are presented in Table 14.
Table 14. Mean GUS/FLUC values from transformed cotton leaf protoplasts
| EXP | EXP SEQ ID NO: | 3 UTR | 3' UTR SEQ ID NO: | Mean GUS/FLUC |
| EXP-Gm.Sphasl:l:l | 52 | T-Mt.Oxr1:2:1 | 35 | 0.01 |
| EXP-CaMV.35S-enh+Ph.DnaK: 1:3 | 51 | T-Mt.Oxr1:2:1 | 35 | 2.30 |
| EXP- At.GSP564.nno+At.GSI17.nno:2 | 16 | T-Mt.Oxr1:2:1 | 35 | 0.34 |
[00198] As can be seen in Table 14, the synthetic EXP, EXP-At.GSP564.nno+At.GSI17.nno:l (SEQ ID NO: 16) demonstrated expression in cotton leaf cell protoplasts.
[00199] The EXP, EXP-At.GSP579.nno+At.GSI102.nno:3 (SEQ ID NO:22) was cloned into a plant expression vectors operably linked 5' to a GUS coding sequence (SEQ ID NO:42), operably linked 5' to the endogenous 3' UTR, T-Mt.RD22-1:2:1 (SEQ ID NO:37). Two control plant expression vectors were constructed with the EXP, EXP-Gm.Sphasl:l:l (SEQ ID NO:52), known to express poorly in cotton leaf protoplasts and the EXP, EXP-CaMV.35Senh+Ph.DnaK:l:3 (SEQ ID NO:51), known to express well in cotton leaf protoplasts. The control EXPs were operably linked to the same GUS and 3' UTR sequence. The mean
GUS/FLUC values for multiple transformations are presented in Table 15.
Table 15. Mean GUS/FLUC values from transformed cotton leaf protoplasts
| EXP | EXP SEQ ID NO: | 3'UTR | 3' UTR SEQ ID NO: | Mean GUS/FLUC |
| EXP-Gm.Sphasl:l:l | 52 | T-Mt.RD22- 1:2:1 | 37 | 0.01 |
| EXP-CaMV.35S-enh+Ph.DnaK: 1:3 | 51 | T-Mt.RD22- 1:2:1 | 37 | 2.88 |
| EXP-At.GSP579.nno+At.GSI102.nno:3 | 22 | T-Mt.RD22- 1:2:1 | 37 | 1.19 |
[00200] As can be seen in Table 15, the synthetic EXP, EXP-At.GSP579.nno+At.GSI102.nno:3 (SEQ ID NO:22), demonstrated expression in cotton leaf cell protoplasts.
[00201] Having illustrated and described the principles of the présent invention, it should be apparent to persons skilled in the art that the invention can be modified in arrangement and detail without departing from such principles. We claim ail modifications that are within the spirit and scope of the claims. Ail publications and published patent documents cited herein are hereby incorporated by reference to the same extent as if each individual publication or patent 10 application is specifically and individually indicated to be incorporated by reference.
Claims (18)
- WHAT IS CLAIMED IS:1. A recombinant DNA molécule comprising a DNA sequence selected from the group consisting of:a) a sequence with at least 85 percent sequence identity to any of SEQ ID NOs: 1-29 and 43-45;b) a sequence comprising any of SEQ ID NOs: 1-29 and 43-45; andc) a fragment of any of SEQ ID NOs: 1-29 and 43-45, wherein the fragment has generegulatory activity.
- 2. The recombinant DNA molécule of claim 1, wherein the DNA sequence is operably linked to a heterologous transcribable DNA molécule.
- 3. The recombinant DNA molécule of claim 1, wherein the DNA sequence has at least 90 percent sequence identity to the DNA sequence of any of SEQ ID NOs: 1-29 and 43-45.
- 4. The recombinant DNA molécule of claim 1, wherein the DNA sequence has at least 95 percent sequence identity to the DNA sequence of any of SEQ ID NOs:l-29 and 43-45.
- 5. The recombinant DNA molécule of claim 1, wherein the DNA sequence comprises generegulatory activity.
- 6. The recombinant DNA molécule of claim 2, wherein the heterologous transcribable DNA molécule comprises a gene of agronomie interest.
- 7. The recombinant DNA molécule of claim 6, wherein the gene of agronomie interest confers herbicide tolérance in plants.
- 8. The recombinant DNA molécule of claim 6, wherein the gene of agronomie interest confers pest résistance in plants.
- 9. A transgenic plant cell comprising the recombinant DNA molécule of claim 1.
- 10. The transgenic plant cell of claim 9, wherein the DNA sequence is operably linked to a heterologous transcribable DNA molécule.
- 11. The transgenic plant cell of claim 9, wherein said transgenic plant cell is a monocotyledonous plant cell.
- 12. The transgenic plant cell of claim 9, wherein said transgenic plant cell is a • dicotyledonous plant cell.
- 13. A transgenic plant, or part thereof, comprising the recombinant DNA molécule of claim 1.
- 14. A progeny plant of the transgenic plant of claim 13, or a part thereof, wherein the progeny plant or part thereof comprises the recombinant DNA molécule.
- 15. A transgenic seed, wherein the seed comprises the recombinant DNA molécule of claim 1.
- 16. A method of producing a commodity product comprising obtaining a transgenic plant or part thereof according to claim 13 and producing the commodity product therefrom.
- 17. The method of claim 16, wherein the commodity product is protein concentrate, protein isolate, grain, starch, seeds, meal, flour, biomass, or seed oïl.
- 18. A method of expressing a transcribable DNA molécule comprising obtaining a transgenic plant according to claim 13 and cultivating plant, wherein the transcribable DNA is expressed.
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| US62/448019 | 2017-01-19 |
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