WO2014018849A1 - Preparation of biological devices and their use thereof for increasing the production of secondary metabolites from plants - Google Patents

Abstract

The preparation and use of biological devices for enhancing the physiological and biochemical properties of plants is described. The devices and methods, as described, increase the production of secondary metabolites such as, for example, phenolic compounds having industrial and economic value. Secondary metabolites produced by the devices and methods do not require ultra purification, which is common in conventional or commercial methods. The devices and methods also enhance the growth rate of plants as well as protect the plant against pathogens such as, for example, fungi.

Description

PREPARATION OF BIOLOGICAL DEVICES AND THEIR USE THEREOF FOR INCREASING THE PRODUCTION OF SECONDARY METABOLITES

FROM PLANTS

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority upon U.S. provisional application Serial No. 61/675,867, filed July 26, 2012. This application is hereby incorporated by reference in its entirety for all of its teachings.

CROSS REFERENCE TO SEQUENCE LISTING

The genetic components described herein are referred to by a sequence identifier number (SEQ ID NO). The SEQ ID NO corresponds numerically to the sequence identifiers <400>1, <400>2, etc. The Sequence Listing, in written computer readable format (CFR), is incorporated by reference in its entirety.

BACKGROUND

Tissue culturing is used in the propagation of new plant varieties, the production of doubled haploids, cryopreservation, conserving rare and endangered plants, difficult-to-propagate plants, and the production secondary metabolites and transgenic plants. Tissue culturing focuses on the production of high quality, disease- free plant materials for the growth of crop plants and fruit trees. However, major challenges are still associated with the production and distribution of high quality plant materials for plant breeding and the rapid production of improved plants.

Currently, tissue culturing is being used particularly for large-scale plant

multiplication and micro-propagation, which have wide applications in forestry and agriculture. Hundreds of commercial micro-propagation laboratories worldwide are currently multiplying large number of clones of desired varieties and local flora.

Different opinions among members of the general public have been established regarding plant transformation, particularly by those highly concerned about environmental issues. Among scientists, it is known that the plant that results from a specific targeted genetic alteration is indistinguishable from the plant that has been developed by a process of breeding and selection. The only difference is that the process of creating a target plant can be greatly accelerated because the genetic modifications can be directed rather than random. Directed modification by homologous recombination has been tested with homologous-recombination dependent gene targeting (hrdGT). The problem with this approach is that the rate of homologous recombination in plant cells is lower compared to the rate of random insertion by illegitimate recombination than it is in animal cells. Efforts to address this limitation by the expression of foreign genes in plant cells have been made.

These methods have had limited success in producing effective gene targeting.

Moreover, even when these modified cells are used to effect homologous

recombination, the resultant modified cell would still contain an exogenous gene used to select the homologous recombinants and be considered a genetically modified plant by regulators and environmentally-concerned entities.

Other methods in which homologous recombination is not involved and the utilization of specific recombination sites and recombinases derived from transposons have also been described in WO 01/85969 and WO 99/25821. The problem with this approach is the mixed structure of the oligonucleotide would likely prevent true recombination by genomic integration.

One of the most common techniques to genetically hybridize plants is the use of plasmid-carrying Agrobacterium tumefaciens. A part of the life cycle of the plasmid involves infection of plants. A. tumefaciens introduces the plasmid into the nucleus of plants in the form of a single strand. A recombinant A. tumefaciens plasmid can be used to introduce exogenous DNA into a plant cell.

Different bacteria plasmid gene treatments have been used. For example, a simple DNA recombinant plasmid or plasmid holding specific gene cassettes to ensure homologous recombination has been used. Plants hybridized by this method would be classified as genetically-modified organisms (GMOs). Thus it would still be a problem for the food and/or pharmaceutical industries.

Methods for increasing the transgenic plant size and yield as well as delaying flowering in the plant with nucleic acids that encode a plant transcription factor have been established. (US Patent No. 7,858,848) However, these methods also involve genetically transforming the plant. Moreover, the extraction of secondary metabolites usually requires higher amounts of initial plant biomass or material. In general, the extraction of plant metabolites is carried out from large amounts of fresh biomass material, which requires agronomic practices, the use of chemicals, and time consuming and expensive extraction methods. Secondary metabolites are generally low molecular weight compounds (e.g., 200-300). Moreover, they are produced in low concentrations, which makes the isolation of large quantities of the metabolites difficult.

SUMMARY

Described herein are the preparation and use of biological devices for enhancing the physiological and biochemical properties of plants. In one aspect, the devices and methods described herein increase the production of secondary metabolites such as, for example, phenolic compounds having industrial and economic value. Secondary metabolites produced by the devices and methods do not require ultra purification, which is common in conventional or commercial methods. The devices and methods described herein also enhance the growth rate of plants as well as protect the plant against pathogens such as, for example, fungi.

The advantages devices and methods described herein will be set forth in part in the description which follows, and in part will be obvious from the description, or may be learned by practice of the aspects described below. The advantages described below will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive.

BRIEF DESCRIPTION OF THE DRAWINGS The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several aspects described below.

Figure 1 shows a DNA construct described herein incorporated in a plasmid.

Figure 2 shows peanut (Arachis hypogaea) tissue culture without biological device. Metabolite (phenolic compounds) induction with chitosan, as compared to control culture without chitosan is shown.

Figure 3 shows peanuts {Arachis hypogaea) extracted from tissue culture assays. Induction of size increased in cultures treated with chitosan and the biological devices is shown. Size increased can be achieved with and/or without the biological device. The brownish agar media also indicates production of secondary metabolite (phenolic compounds).

Figure 4 shows the comparison of different phenolic compounds produced from peanut {Arachis hypogaea) callus treated and non-treated (control) with transformed bacteria {i.e., biological device) and/or chitosan addition as determined by HPLC.

DETAILED DESCRIPTION

Before the present compounds, compositions, articles, devices, and/or methods are disclosed and described, it is to be understood that the aspects described below are not limited to specific compounds, synthetic methods, or uses as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and is not intended to be limiting.

In this specification and in the claims that follow, reference will be made to a number of terms that shall be defined to have the following meanings:

It must be noted that, as used in the specification and the appended claims, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a bioactive agent" includes mixtures of two or more such agents, and the like. "Optional" or "optionally" means that the subsequently described event or circumstance can or cannot occur, and that the description includes instances where the event or circumstance occurs and instances where it does not. For example, the phrase "optional ingredient" means that the ingredient may or may not be present.

Ranges may be expressed herein as from "about" one particular value, and/or to "about" another particular value. When such a range is expressed, another aspect includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent "about," it will be understood that the particular value forms another aspect. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint.

Disclosed are materials and components that can be used for, can be used in conjunction with, can be used in preparation for, or are products of the disclosed compositions and methods. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combination and permutation of these compounds may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a bacterium is disclosed and discussed and a number of different compatible bacterial plasmids are discussed, each and every combination and permutation of bacterium and bacterial plasmid that is possible is specifically contemplated unless specifically indicated to the contrary. For example, if a class of molecules A, B, and C are disclosed as well as a class of molecules D, E, and F, and an example of a

combination molecule, A-D is disclosed, then even if each is not individually recited, each is individually and collectively contemplated. Thus, in this example, each of the combinations A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C-F are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. Likewise, any subset or combination of these is also specifically contemplated and disclosed. Thus, for example, the sub- group of A-E, B-F, and C-E is specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. This concept applies to all aspects of this disclosure including, but not limited to, steps in methods of making and using the disclosed compositions. Thus, If a variety of additional steps can be performed, it is understood that each of these additional steps can be performed with any specific embodiment or combination of embodiments of the disclosed methods, and that each such combination is specifically contemplated and should be considered disclosed.

References in the specification and concluding claims to parts by weight, of a particular element or component in a composition or article, denotes the weight relationship between the element or component and any other elements or components in the composition or article for which a part by weight is expressed. Thus, in a compound containing 2 parts by weight of component X and 5 parts by weight component Y, X and Y are present at a weight ratio of 2:5, and are present in such ratio regardless of whether additional components are contained in the compound.

A weight percent of a component, unless specifically stated to the contrary, is based on the total weight of the formulation or composition in which the component is included.

Described herein are devices and methods for enhancing the physiological and biochemical properties of a plant. The term "physiological and biochemical property" as defined herein includes any physical, chemical, or biological feature that is improved using the devices and methods described herein. In one aspect, the devices and methods can enhance the production of secondary metabolites produced by the plant. In other aspects, the devices and methods can enhance the growth rate of the plant. These are just some of the physiological properties that are enhanced using the devices and methods described herein.

As used herein, "plant" is used in a broad sense to include, for example, any species of woody, ornamental, crop, cereal, fruit, or vegetable plant, as well as photosynthetic green algae. "Plant" also refers to a plurality of plant cells that are differentiated into a structure that is present at any stage of a plant' s development. Such structures include, but are not limited to, fruits, shoots, stems, leaves, flower petals, roots, tubers, corms, bulbs, seeds, gametes, cotyledons, hypocotyls, radicles, embryos, gametophytes, tumors, and the like. "Plant cell," "plant cells," or "plant tissue" as used herein refers to differentiated and undifferentiated tissues of plants including those present in any of the tissues described above, as well as to cells in culture such as, for example, single cells, protoplasts, embryos, calluses, etc.

"Heterologous" genes and proteins are genes and proteins that have been experimentally inserted into a cell that are not normally expressed by that cell. A heterologous gene may be cloned or derived from a different cell type or species than the recipient cell or organism. Heterologous genes may be introduced into cells by transduction or transformation.

An "isolated" nucleic acid is one that has been separated from other nucleic acid molecules and/or cellular material (peptides, proteins, lipids, saccharides, and the like) normally present in the natural source of the nucleic acid. An "isolated" nucleic acid may optionally be free of the flanking sequences found on either side of the nucleic acid as it naturally occurs. An isolated nucleic acid can be naturally occurring, can be chemically synthesized, or can be a cDNA molecule (i.e., is synthesized from an mRNA template using reverse transcriptase and DNA polymerase enzymes).

"Transformation" or "transfection" as used herein refers to a process for introducing heterologous DNA into a host cell. Transformation can occur under natural conditions or may be induced using various methods known in the art. Many methods for transformation are known in the art and the skilled practitioner will know how to choose the best transformation method based on the type of cells being transformed. Methods for transformation include, for example, viral infection, electroporation, lipofection, chemical transformation, and particle bombardment. Cells may be stably transformed (i.e., the heterologous DNA is capable of replicating as an autonomous plasmid or as part of the host chromosome) or may be transiently transformed (i.e., the heterologous DNA is expressed only for a limited period of time).

"Competent cells" refers to microbial cells capable of taking up heterologous DNA. Competent cells can be purchased from a commercial source, or cells can be made competent using procedures known in the art. Exemplary procedures for producing competent cells are provided in the Examples.

I. DNA Constructs and Biological Devices

Biological devices described herein can be assembled and used to enhance the physiological and biochemical properties of the plant. In one aspect, the biological device can increase the production of a desired secondary metabolite produced by the plant. The term "secondary metabolite" as defined herein is any chemical compound produced by the plant, where it is desirable to produce increased quantities of the compound. Examples of secondary metabolites include compounds having nutritional, medicinal, or antimicrobial value as well as any other commercial value. The device is generally composed of host cells, where the host cells are transformed with a DNA construct described herein that promotes the expression of the secondary metabolite of interest in the plant cells.

It is understood that one way to define the variants and derivatives of the genetic components and DNA constructs described herein is through defining the variants and derivatives in terms of homology/identity to specific known sequences. Those of skill in the art readily understand how to determine the homology of two nucleic acids. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level. Another way of calculating homology can be performed by published algorithms (see Zuker, M. Science 244:48- 52, 1989, Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger et al. Methods Enzymol. 183:281-306, 1989, which are herein incorporated by reference for at least material related to nucleic acid alignment).

As used herein, "conservative" mutations are mutations that result in an amino acid change in the protein produced from a sequence of DNA. When a conservative mutation occurs, the new amino acid has similar properties as the wild type amino acid and generally does not drastically change the function or folding of the protein (e.g., switching isoleucine for valine is a conservative mutation since both are small, branched, hydrophobic amino acids). "Silent mutations," meanwhile, change the nucleic acid sequence of a gene encoding a protein but do not change the amino acid sequence of the protein.

It is understood that the description of conservative mutations and homology can be combined together in any combination, such as embodiments that have at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% homology to a particular sequence wherein the variants are conservative mutations. It is understood that any of the sequences described herein can be a variant or derivative having the homology values listed above.

In one aspect, a database such as, for example, GenBank, can be used to determine the sequences of genes and/or regulatory regions of interest, the species from which these elements originate, and related homologous sequences.

In one aspect, the DNA construct described herein can promote the expression of secondary metabolites such as phenolic compounds from plants. The term

"phenolic compound" is any aromatic compound having at least one hydroxyl group present on the aromatic ring. Examples of such phenolic compounds include, but are not limited to, gallic acid, p-hydroxybenzoic acid, caffeic acid, chatequin, and p- coumaric acid.

In one aspect, the DNA construct is an assemblage from 5 ' to 3' of the following genetic components in the following order (1) a PAL promoter, (2) a gene that expresses histidine/phenylalanine ammonia-lyase, (3) a ribosomal binding site, and (4) a terminator. In certain aspects, the DNA construct further comprises a ribosomal switch between the gene that expresses histidine/phenylalanine ammonia- lyase and the ribosomal binding site that can enhance translation and protein expression. Not wishing to be bound by theory, the genetic components listed above are specifically designed in short sequences and assembled in specific order for specific function (e.g., production of phenolic compounds). In one aspect, the construct and devices herein are designed and assembled for enhancing genes encoding for higher production of phenolic compounds in plants at earlier stage of development.

In one aspect, a regulatory sequence is already incorporated into a vector such as, for example, a plasmid, prior to genetic manipulation of the vector. In another aspect, the regulatory sequence can be incorporated into the vector through the use of restriction enzymes or any other technique known in the art.

In one aspect, the regulatory sequence is a promoter. The term "promoter" refers to a DNA sequence capable of controlling the expression of a coding sequence. In one aspect, the coding sequence to be controlled is located 3' to the promoter. In another aspect, the promoter is derived from a native gene. In an alternative aspect, the promoter is composed of multiple elements derived from different genes and/or promoters. A promoter can be assembled from elements found in nature, from artificial and/or synthetic elements, or from a combination thereof. It is understood by those skilled in the art that different promoters can direct the expression of genes in different tissues or cell types, at different stages of development, in response to different environmental or physiological conditions, and/or in different species. In one aspect, the promoter functions as a switch to activate the expression of a gene.

In one aspect, the promoter is "constitutive." A constitutive promoter is a promoter that causes a gene to be expressed in most cell types at most times. In another aspect, the promoter is "regulated." A regulated promoter is a promoter that becomes active in response to a specific stimulus. A promoter may be regulated chemically, such as, for example, in response to the presence or absence of a particular metabolite (e.g., lactose or tryptophan), a metal ion, a molecule secreted by a pathogen, or the like. A promoter may also be regulated physically, such as, for example, in response to heat, cold, water stress, salt stress, oxygen concentration, illumination, wounding, or the like.

Promoters that are useful to drive expression of the nucleotide sequences described herein are numerous and familiar to those skilled in the art. Suitable promoters include, but are not limited to, the following: PAL promoter, T3 promoter, T7 promoter, Fe promoter, and GALl promoter. Variants of these promoters are also contemplated. The skilled artisan will be able to use site-directed mutagenesis and/or other mutagenesis techniques to modify the promoters to promote more efficient function. The promoter may be positioned, for example, from 10-100 nucleotides away from a ribosomal binding site.

In one aspect, the PAL promoter in the DNA construct is SEQ ID NO. 1 or a derivative or variant thereof. In another aspect, the PAL promoter is SEQ ID NOS. 2, 3, or 4 or a derivative or variant thereof.

In another aspect, the gene that expresses histidine/phenylalanine ammonia- lyase in the DNA construct is SEQ ID NO. 5 or a derivative or variant thereof. In another aspect, the gene is SEQ ID NOS. 6 or 7 or a derivative or variant thereof.

The selection of the ribosomal binding site (and optional) ribosomal switch can vary depending upon the selection of the host cells. In one aspect, the ribosomal binding site in the DNA construct is SEQ ID NOS. 8 or 9, or a derivative or variant thereof (e.g., where n in SEQ ID NO. 8 can be A, T, G, or C).

In certain aspects, when the DNA construct further includes a ribosomal switch. The selection of the ribosomal binding switch can be selected in order to maximize the amount of protein (e.g., histidine/phenylalanine ammonia-lyase) ultimately expressed by the device. In certain aspects, the ribosomal switch can also be assembled as an aptamers that later in the process becomes the ribosomal switch. In these aspect, the use of the aptamers is desirable because due to its relatively short sequence. In one aspect, the ribosomal switch is SEQ ID NOS. 11 , 12, 13 or 14, or a derivative or variant thereof.

In another aspect, the regulatory sequence is a terminator or stop sequence. As used herein, a terminator is a sequence of DNA that marks the end of a gene or operon to be transcribed. In a further aspect, the terminator is an intrinsic terminator or a Rho-dependent transcription terminator. As used herein, an "intrinsic terminator" is a sequence wherein a hairpin structure can form in the nascent transcript and wherein the hairpin disrupts the mRNA/DNA/RNA polymerase complex. As used herein, a "Rho-dependent" transcription terminator requires a Rho factor protein complex to disrupt the mRNA/DNA/RNA polymerase complex. In another aspect, the terminator in the DNA construct is SEQ ID NO. 10 or a derivative or variant thereof.

In a further aspect, the regulatory sequence includes both a promoter and a terminator or stop sequence. In a still further aspect, the regulatory sequence can include multiple promoters or terminators. Other regulatory elements, such as enhancers, are also contemplated. Enhancers may be located from about 1 to about 2000 nucleotides in the 5' direction from the start codon of the DNA to be transcribed, or may be located 3' to the DNA to be transcribed. Enhancers may be "cis-acting," that is, located on the same molecule of DNA as the gene whose expression they affect.

In certain aspects, the DNA construct can include a gene that expresses a reporter protein. The reporter protein can be useful in ensuring that the biological device has been produced successfully and working properly. This is demonstrated in the Examples. The selection of the reporter protein can vary. For example, the reporter protein can be a yellow fluorescent protein, red fluorescent protein, a green fluorescent protein, and a cyan fluorescent protein. In one aspect, the gene that expresses the reporter protein has SEQ ID NO. 15. The amount of fluorescence that is produced by the biological device can be correlated to the amount of DNA incorporated into the plant cells. The fluorescence produced by the device can be detected and quantified using techniques known in the art. For example,

spectrophotometers are typically used to measure fluorescence. The Examples provide exemplary procedures for measuring the amount of fluorescence as a result of the expression of DNA.

The DNA construct described herein can be part of a vector. In one aspect, the vector is a plasmid, a phagemid, a cosmid, a yeast artificial chromosome, a bacterial artificial chromosome, a virus, a phage, or a transposon.

In general, plasmid vectors containing replicon and control sequences that are derived from species compatible with the host cell are used in connection with these hosts. Vectors capable of high levels of expression of recombinant genes and proteins are well known in the art. The vector ordinarily carries a replication origin as well as marking sequences that are capable of providing phenotypic selection in transformed cells. Plasmid vectors useful for the transformation of a variety of host cells are well known and are commercially available. Such vectors include, but are not limited to, pWLNEO, pSV2CAT, pOG44, PXT1, pSG (Stratagene), pSVK3, pBSK, pBR322, pYES, pYES2, pBSKII, and pUC vectors.

Plasmids are double-stranded, autonomously-replicating, genetic elements that are not integrated into host cell chromosomes. Further, these genetic elements are usually not part of the host cell's central metabolism. In bacteria, plasmids may range from 1 kilobase (kb) to over 200 kb. Plasmids can be engineered to encode a number of useful traits including the production of secondary metabolites, antibiotic resistance, the production of useful proteins, degradation of complex molecules and/or environmental toxins, and others. Plasmids have been the subject of much research in the field of genetic engineering, as plasmids are convenient expression vectors for foreign DNA in, for example, microorganisms. Plasmids generally contain regulatory elements such as promoters and terminators and also usually have independent replication origins. Ideally, plasmids will be present in multiple copies per host cell and will contain selectable markers (such as genes for antibiotic resistance) to allow the ordinarily skilled artisan to select host cells that have been successfully transfected with the plasmids (for example, by culturing the host cells in a medium containing the antibiotic).

In one aspect, the vector encodes a selection marker. In a further aspect, the selection marker is a gene that confers resistance to an antibiotic. In certain aspects, during fermentation of host cells transformed with the vector, the cells are contacted with the antibiotic. For example, the antibiotic may be included in the culture medium. Cells that have not been successfully transformed cannot survive in the presence of the antibiotic; only cells containing the vector that confers antibiotic resistance can survive. Optionally, only cells containing the vector to be expressed will be cultured, as this will result in the highest production efficiency of the desired gene products (e.g., peptides involved in the synthesis of desired secondary metabolites). Cells that do not contain the vector would otherwise compete with transformed cells for resources. In one aspect, the antibiotic is tetracycline, neomycin, kanamycin, ampicillin, hygromycin, chloramphenicol, amphotericin B, bacitracin, carbapenam, cephalosporin, ethambutol, fluoroquinolones, isonizid, methicillin, oxacillin, vancomycin, streptomycin, quinolines, rifampin, rifampicin, sulfonamides, cephalothin, erythromycin, streptomycin, gentamycin, penicillin, other commonly -used antibiotics, or a combination thereof.

In one aspect, when the vector is a plasmid, the plasmid can also contain a multiple cloning site or polylinker. In a further aspect, the polylinker contains recognition sites for multiple restriction enzymes. The polylinker can contain up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more than 20 recognition sites for restriction enzymes. Further, restriction sites may be added, disabled, or removed as required, using techniques known in the art. In one aspect, the plasmid contains restriction sites for any known restriction enzyme such as, for example, Hindlll, Kpnl, Sad, BamHI, BstXI, EcoRI, BsaBI, Notl, Xhol, Sphl, Sbal, Apal, Sail, Clal, EcoRV, Pstl, Smal, Xmal, Spel, Eagl, SacII, or any combination thereof. In a further aspect, the plasmid contains more than one recognition site for the same restriction enzyme.

In one aspect, the restriction enzyme can cleave DNA at a palindromic or an asymmetrical restriction site. In a further aspect, the restriction enzyme cleaves DNA to leave blunt ends; in an alternative aspect, the restriction enzyme cleaves DNA to leave "sticky" or overhanging ends. In another aspect, the enzyme can cleave DNA a distance of from 20 bases to over 1000 bases away from the restriction site. A variety of restriction enzymes are commercially available and their recognition sequences, as well as instructions for use (e.g. amount of DNA needed, precise volumes of reagents, purification techniques, as well as information about salt concentration, pH, optimum temperature, incubation time, and the like) are made available by commercial enzyme suppliers.

In one aspect, a plasmid with a polylinker containing one or more restriction sites can be digested with one restriction enzyme and a nucleotide sequence of interest can be ligated into the plasmid using a commercially-available DNA ligase enzyme. Several such enzymes are available, often as kits containing all reagents and instructions required for use. In another aspect, a plasmid with a polylinker containing two or more restriction sites can be simultaneously digested with two restriction enzymes and a nucleotide sequence of interest can be ligated into the plasmid using a DNA ligase enzyme. Using two restriction enzymes provides an asymmetric cut in the DNA, allowing for insertion of a nucleotide sequence of interest in a particular direction and/or on a particular strand of the double-stranded plasmid. Since RNA synthesis from a DNA template proceeds from 5' to 3', often starting just after a promoter, the order and direction of elements inserted into a plasmid is especially important. If a plasmid is to be simultaneously digested with multiple restriction enzymes, these enzymes must be compatible in terms of buffer, salt concentration, and other incubation parameters.

In some aspects, prior to ligation using a ligase enzyme, a plasmid that has been digested with a restriction enzyme is treated with an alkaline phosphatase enzyme to remove 5' terminal phosphate groups. This prevents self-ligation of the plasmid and thus facilitates ligation of heterologous nucleic acid fragments into the plasmid.

In one aspect, the nucleic acids (e.g., genes that express beta-carotene hydroxylase and lycopene epsilon-cyclase) used in the DNA constructs described herein can be amplified using the polymerase chain reaction (PCR) prior to being ligated into a plasmid or other vector. Typically, PCR-amplification techniques make use of primers or short, chemically-synthesized oligonucleotides that are

complementary to regions on each respective strand flanking the DNA or nucleotide sequence to be amplified. A person having ordinary skill in the art will be able to design or choose primers based on the desired experimental conditions. In general, primers should be designed to provide for efficient and faithful replication of the target nucleic acids. Two primers are required for the amplification of each gene, one for the sense strand (that is, the strand containing the gene of interest) and one for the antisense strand (that is, the strand complementary to the gene of interest). Pairs of primers should have similar melting temperatures that are close to the PCR reaction's annealing temperature. In order to facilitate the PCR reaction, the following features should be avoided in primers: mononucleotide repeats, complementarity with other primers in the mixture, self-complementarity, and internal hairpins and/or loops. Methods of primer design are known in the art; additionally, computer programs exist that can assist the ordinarily skilled practitioner with primer design. Primers can optionally incorporate restriction enzyme recognition sites at their 5' ends to assist in later ligation into plasmids or other vectors.

PCR can be carried out using purified DNA, unpurified DNA that has been integrated into a vector, or unpurified genomic DNA. The process for amplifying target DNA using PCR consists of introducing an excess of two primers having the characteristics described above to a mixture containing the sequence to be amplified, followed by a series of thermal cycles in the presence of a heat-tolerant or thermophilic DNA polymerase, such as, for example, any of Taq, Pfu, Pwo, Tfl, rTth, Tli, or Tma polymerases. A PCR "cycle" involves denaturation of the DNA through heating, followed by annealing of the primers to the target DNA, followed by extension of the primers using the thermophilic DNA polymerase and a supply of deoxynucleotide triphosphates (i.e., dCTP, dATP, dGTP, and TTP), along with buffers, salts, and other reagents as needed. In one aspect, the DNA segments created by primer extension during the PCR process can serve as templates for additional PCR cycles. Many PCR cycles can be performed to generate a large concentration of target DNA or gene. PCR can optionally be performed in a device or machine with programmable temperature cycles for denaturation, annealing, and extension steps. Further, PCR can be performed on multiple genes simultaneously in the same reaction vessel or microcentrifuge tube since the primers chosen will be specific to selected genes. PCR products can be purified by techniques known in the art such as, for example, gel electrophoresis followed by extraction from the gel using commercial kits and reagents.

In a further aspect, the vector can include an origin of replication, allowing it to use the host cell's replication machinery to create copies of itself. As used herein, "operably linked" refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one affects the function of another. For example, if sequences for multiple genes are inserted into a single plasmid, their expression may be operably linked. Alternatively, a promoter is said to be operably linked with a coding sequence when it is capable of affecting the expression of the coding sequence.

As used herein, "expression" refers to transcription and/or accumulation of an mRNA derived from a gene or DNA fragment. Expression may also be used to refer to translation of mRNA into a peptide, polypeptide, or protein.

Exemplary methods for producing the DNA constructs described herein are provided in the Examples. Restriction enzymes and purification techniques known in the art can be used to prepare the DNA constructs. After the vector incorporating the DNA construct has been produced, it can be incorporated into host cells using the methods described below.

In one aspect, a "biological device" is formed when a microbial cell is transfected with the DNA construct described herein. The biological devices are generally composed of microbial host cells, where the host cells are transformed with a DNA construct described herein.

In one aspect, the DNA construct is carried by the expression vector into the cell and is separate from the host cell's genome. In another aspect, the DNA construct is incorporated into the host cell's genome. In still another aspect, incorporation of the DNA construct into the host cell enables the host cell to produce lycopene.

The host cells as referred to herein include their progeny, which is any and all subsequent generations formed by cell division. It is understood that all progeny may not be identical due to deliberate or inadvertent mutations. A host cell may be "transfected" or "transformed," which refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell. A transformed cell includes the primary subject cell and its progeny. The selection of the host cells should be based on their ability to effectively hold a sufficient amount of the construct. Additionally, they should permit good expression of the specific functions of the construct as well withstand adverse environmental conditions.

The host cells can be naturally occurring cells or "recombinant" cells.

Recombinant cells are distinguishable from naturally occurring cells in that they do not contain heterologous nucleic acid sequences introduced using molecular biology techniques. In one aspect, the host cell is microbial. In another aspect, the host cell is a prokaryotic cell, such as, for example, Bacillus pumilus or E. coli. In other aspects, the host cell is yeast such as, for example, Saccharomyces cerevisiae. In one aspect, saprophytic bacteria (non-pathogenic) found commonly in soils where peanut plants grow can be used as host cells or microbial competent cells for assembling all genetic parts. Host cells transformed with DNA construct described herein are referred to as biological devices.

The DNA construct is first delivered into the host cell. This delivery may be accomplished in vitro, as in laboratory procedures for transforming cells lines using well developed procedures. Transformation of bacterial cell lines can be achieved using a variety of techniques. One method includes using calcium chloride. The exposure to the calcium ions renders the cells able to take up the DNA construct. Another method is electroporation. In this technique, a high- voltage electric field is applied briefly to cells, producing transient holes in the cell membrane through which the vector containing the DNA construct enters. Exemplary procedures for transforming yeast and bacteria with specific DNA are provided in the Examples. In certain aspects, two or more types of DNA can be incorporated into the host cells. Thus, different metabolites can be produced from the same plant at enhanced rates.

Once the DNA construct has been incorporated into the host cell, the cells are cultured such that the cells multiply. A satisfactory microbiological culture contains available sources of hydrogen donors and acceptors, carbon, nitrogen, sulfur, phosphorus, inorganic salts, and, in certain cases, vitamins or other growth promoting substances. The addition of peptone provides a readily available source of nitrogen and carbon. A variety of other carbon sources are contemplated, including, but not limited to: monosaccharides such as glucose and fructose, disaccharides such as lactose and sucrose, oligosaccharides, polysaccharides such as starch, and mixtures thereof. Unpurified mixtures extracted from feedstocks are also contemplated and can include molasses, barley malt, and related compounds and compositions. Other glycolytic and tricarboxylic acid cycle intermediates are also contemplated as carbon sources, as are one-carbon substrates such as carbon dioxide and/or methanol in the cases of compatible organisms. The carbon source utilized is limited only by the particular organism being cultured.

Furthermore, the use of different media results in different growth rates and different stationary phase densities. Secondary metabolite production is highest when cells are in stationary phase. A rich media results in a short doubling time and higher cell density at stationary phase. Minimal media results in slow growth and low final cell densities. Efficient agitation and aeration increase final cell densities. A skilled artisan will be able to determine which type of media is best suited to culture a particular species and/or strain of host cell.

Culturing or fermenting of host cells may be accomplished by any technique known in the art. In one aspect, batch fermentation can be conducted. In batch fermentation, the composition of the culture medium is set at the beginning of culturing and the system is closed to future artificial alterations. In some aspects, a limited form of batch fermentation can be carried out, wherein factors such as oxygen concentration and pH are manipulated, but additional carbon is not added.

Continuous fermentation methods are also contemplated. In continuous fermentation, equal amounts of a defined medium are continuously added to and removed from a bioreactor. In other aspects, microbial host cells are immobilized on a substrate. Fermentation can be carried out on any scale and may include methods in which literal "fermentation" is carried out as well as other culture methods that are non- fermentative.

II. Methods for Enhancing the Physiological and Biochemical Properties of Plants

The selection of the plant used in the methods described herein can vary depending upon the application. For example, a specific plant can be selected that produces certain desirable secondary metabolites (e.g., plants that produce phenolic compounds). In one aspect, the plant can be a plant that produces phenolic compounds at different rates and concentrations. In one aspect, the plant can include but is not limited to peanuts (Arachis hypogaea), tomatoes (Solanum lycopersicum), and soybeans (Glycine max). In another aspect, the plant is not Theobroma cacao or a variant thereof.

In one aspect, plant cells when contacted with the biological devices described above can enhance the production of phenolic compounds. Recipient cell targets include, but are not limited to, meristem cells, Type I, Type II, and Type III callus, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant may be regenerated is useful as a recipient cell. Type I, Type II, and Type III callus may be initiated from tissue sources including, but not limited to, immature embryos, immature

inflorescenses, seedling apical meristems, microspores and the like. Those cells that are capable of proliferating as callus also are also useful herein. Methods for growing plant cells are known in the art (see U.S. Patent No. 7,919,679). Exemplary procedures for growing plant calluses are provided in the Examples. In one aspect, plant calluses grown from 2 to 4 weeks can be used herein. The plant cells can also be derived from plants varying in age. For example, plants that are 80 days to 120 days old after pollination can be used to produce calluses useful herein.

The plant cells can be contacted with the biological device in a number of different ways. In one aspect, the device can be added to a media containing the plant cells. In another aspect, the device can be injected into the plant cells via syringe. The amount of device and the duration of exposure to the device can vary as well. In one aspect, the concentration of the device is about 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, or 10⁹ cells/mL of water. In one aspect, when the host cell is bacteria the concentration of the device is 10⁶. In another aspect, when the host cell is yeast, the concentration of the device is 10⁹. Different volumes of the biological device can be used as well, ranging from 25 μΐ to 500 μΐ. Once the plants cells have been in contact with the biological device for a sufficient time to produce phenolic compounds, the phenolic compounds are isolated. In one aspect, the phenolic compounds are extracted from the media containing the biological device and the plant cells. The selection of the extraction solvent can vary depending upon the solubility of the metabolite. Exemplary procedures for extracting metabolites produced by the biological devices described herein are provided in the Examples.

With current techniques, the extraction of secondary metabolites produced from plants usually requires higher amounts of initial plant biomass or material. For example, these plants require growth periods more than three months, typically in harsh, unpredictable environmental conditions. However, the use of the biological devices described herein produces significantly higher amounts of metabolites such as phenolic compounds, which means smaller amounts of biomass are required in order to produce and isolate the metabolites when compared to existing techniques. For example, the biological devices described herein can produce increased amounts of phenolic compounds from embryonic plants (i.e., plants that are 1-2 weeks old) under predictable conditions.

The extraction of plant metabolites using current techniques also requires fresh biomass, which entails agronomic practices, the use of chemicals, and time consuming extraction methods. Therefore, the use of the biological devices described herein is more cost-effective and safer to the environment.

In other aspects, the devices and methods described herein can increase the growth rate of a plant. In particular, the devices and methods described herein are effective in accelerating plant development in the early stages of tissue culturing. By accelerating plant development in the early stages, it is possible to harvest more metabolites from the plant. Additionally, the devices and methods described herein protect plant tissue cultures against microbial contamination, which is a problem associated with tissue culturing. Indeed, microbial contamination of the plants grown in the fields can result in increased cost of metabolite production as well as produce unpredictable yields of the metabolite. Finally, conventional methods for tissue culture involve the use of synthetic growth factors such as 2-4-D, which can pose environmental concerns as well as human health concerns. The devices and methods described herein avoid the need of such compounds.

In certain aspects, any of the biological devices described above can be used in combination with a polysaccharide to enhance one or more physiological and biological properties of the plant. For example, as demonstrated in the Examples, the polysaccharide can enhance the production of a secondary metabolite. In one aspect, the plant cells are first contacted with the polysaccharide then subsequently contacted with the biological device. In another aspect, the plant cells are first contacted with the polysaccharide then subsequently contacted with the biological device. In a further aspect, the plant cells are first contacted with the biological device then subsequently contacted with the polysaccharide. In another aspect, the plant cells are only contacted with a polysaccharide and not contacted with the biological device.

In one aspect, the polysaccharide includes chitosan, glucosamine (GlcN), N- acetylglucosamine (NAG), or any combination thereof. Chitosan is generally composed of glucosamine units and N-acetylglucosamine units and can be chemically or enzymatically extracted from chitin, which is a component of arthropod exoskeletons and fungal and microbial cell walls. In certain aspects, the chitosan can be acetylated to a specific degree of acetylation in order to enhance tissue growth during culturing as well as metabolite production. In one aspect, the chitosan is from 60% to about 100%, 70% to 90%, 75% to 85%, or about 80% acetylated. Exemplary procedures for producing and isolating the chitosan are provided in the Examples. In one aspect, chitosan isolated from the shells of crab, shrimp, lobster, and/or krill is useful herein.

The molecular weight of the chitosan can vary, as well. For example, the chitosan comprises about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 glucosamine units and/or N-acetylglucosamine units. In another aspect, the chitosan includes 5 to 7 glucosamine units and/or N-acetylglucosamine units. In one aspect, the chitosan is in a solution of water and acetic acid at less than 1 % by weight, less than 0.75% by weight, less than 0.50% by weight, less than 0.25% by weight, or less than 0.10 % by weight. In another aspect, amount of chitosan that is applied to the plant cells is from 0.10% to 0.01% by weight, from 0.075% to 0.025% by weight, or is about 0.05% by weight. The polysaccharides used herein are generally natural polymers and thus present no environmental concerns. Additionally, the

polysaccharide can be used in acceptably low concentrations. In certain aspects, the polysaccharide can be used in combination with one or more growth regulators.

In one aspect, the plant growth regulator is an auxin, a cytokinin, a gibberellin, abscisic acid, or a polyamine. In a further aspect, the auxin is a natural or synthetic auxin. In a still further aspect, the auxin is indole-3-acetic acid (IAA), 4- chloroindole- 3 -acetic acid (4-Cl-IAA), 2-phenylacetic acid (PAA), indole-3 -butyric acid (IBA), 2,4-dichlorophenoxyacetic acid (2,4-D), oc-naphthalene acetic acid (oc- NAA), 2-methoxy-3,6-dichlorobenzoic acid (dicamba), 4-amino-3,5,6- trichloropicolinic acid (torden or picloram), 2,4,5-trichloropicolinic acid (2,4,5-T), or a combination thereof. In another aspect, the cytokinin is zeatin, kinetin, 6- benzylaminopurine, diphenylurea, thidizuron (TDZ), 6-(γ,γ- dimethylallylamino)purine, or a combination thereof. In another aspect, the gibberellin is gibberellin Al (GA1), gibberellic acid (GA3), eni-gibberellane, ent- kaurene, or a combination thereof. In yet another aspect, the polyamine is putrescine, spermidine, or a combination thereof.

In one aspect, the plant cell or callus is first contacted with a polysaccharide and subsequently contacted with a plant growth regulator. In another aspect, the plant cell or callus is first contacted with a plant growth regulator and subsequently contacted with a polysaccharide. In an alternative aspect, the plant cell or callus is simultaneously contacted with a polysaccharide and a plant growth regulator. In a further aspect, the plant cell or callus is only contacted with a polysaccharide and is not contacted with a plant growth regulator.

The plant cells can be contacted with the polysaccharide using a number of techniques. In one aspect, the plant cells or reproductive organs (e.g., a plant embryo) can be cultured in agar and medium with a solution of the polysaccharide. In other aspects, the polysaccharide can be applied to a plant callus by techniques such as, for example, coating the callus or injecting the polysaccharide into the callus. In this aspect, the age of the callus can vary depending upon the type of plant. The amount of polysaccharide can vary depending upon, among other things, the selection and number of plant cells. The use of the polysaccharide in the methods described herein permits rapid tissue culturing at room temperature. Due to the ability of the polysaccharide to prevent microbial contamination, the tissue cultures can grow for extended periods of time ranging from days to several weeks. Moreover, tissue culturing with the polysaccharide can occur in the dark and/or light. As discussed above, the plant cells can optionally be contacted with any of the biological devices described above. Thus, the use of the polysaccharides and biological devices described herein is a versatile way to culture and grow plant cells - and, ultimately, plants of interest - with enhanced physiological properties.

In other aspects, the plant cells can be cultured in a liquid medium on a larger scale in a bioreactor. For example, plant cells can be cultured in agar and medium, then subsequently contacted with (e.g., injected) with a biological device described herein. After a sufficient culturing time (e.g., two to four weeks), the plant cells are introduced into a container with the same medium used above and, additionally, the polysaccharide. In certain aspects, the polysaccharide can be introduced with anionic polysaccharides including, but not limited to, alginates (e.g., sodium, calcium, potassium, etc.). After the introduction of the polysaccharide, the solution is mixed for a sufficient time to produce a desired result (e.g., production of a desired metabolite).

In one aspect, the plant callus is immersed in a solution of polysaccharide (e.g. chitosan), then inoculated with device. In one aspect, the plant callus is that of peanut (Arachis hypogaea), tomato (Solanum lycopersicum), or soybean (Glycine max). The plant callus can be from 2 days up to 20 days old prior to inoculation with the device. The plant callus is then allowed to grow for a sufficient time so that the callus is of the desired weight and size. In one aspect, the plant callus is allowed to grow (i.e.

culture) for 1 to 10 weeks after inoculation. After a growing period, metabolites can be extracted from the callus by any technique known in the art. In another aspect, a plant callus as described above can be allowed to grow and mature into a plant bearing stems, leaves, seeds, and/or fruit. In one aspect, metabolites can be extracted from a plant that has been grown from a plant callus inoculated with a device described herein and optionally contacted with a polysaccharide (e.g. chitosan). In one aspect, metabolites can be removed from stems, fruits, seeds, or leaves of a plant grown with the devices described herein.

In one aspect, the amounts of metabolites produced by the plant cells, plant callus, and/or plants that have been contacted with the biological device as described herein are from 1.1 to 10-fold greater than the amounts of metabolites produced by otherwise identical plant cells, plant callus, and/or plants that have not been contacted with the biological devices as described herein.

The devices and methods described herein also enhance the growth rate of plants. For example, plants grown using the devices and methods described herein can be grown in 2 to 4 weeks versus 32 months typically required for conventional field growth. Moreover, the devices and methods described herein do not require the use of synthetic chemicals and can be used in a closed environment and not in the field. Thus, the devices and methods described herein provide a versatile and cost- effective way to grow plants and produce desirable metabolites in significant quantities.

In another embodiment, the metabolite produced by the devices and methods described herein can be used to prevent the plant from contracting one or more diseases as well as enhance the physical properties of the plant. For example, the metabolites can be used as an antifungal agent. EXAMPLES

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, and methods described and claimed herein are made and evaluated, and are intended to be purely exemplary and are not intended to limit the scope of what the inventors regard as their invention. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.) but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in °C or is at ambient temperature, and pressure is at or near atmospheric. There are numerous variations and combinations of reaction conditions, e.g., component concentrations, desired solvents, solvent mixtures, temperatures, pressures and other reaction ranges and conditions that can be used to optimize the product purity and yield obtained from the described process. Only reasonable and routine experimentation will be required to optimize such process conditions

Plant Callus Treatment and Development

Peanuts (Arachis hypogaea) were tested to determine the effectiveness of the methods described herein. For each plant, somatic embryos from mature and immature sexual embryos were developed. The embryogenic potential varied with the organ and its maturity, however mature seeds gave better results for peanut.

Different sources of explants were used including complete or segmented organs, roots, and hypocotyls. In the case where seeds were used as the explant, seeds having different ages were used, including seeds that were harvested from plants that were 10, 20, 50, 80, or 120 days old. Older seeds such as those of 80 and 120 days were preferred.

Disinfection treatments varied depending upon the type of explant. For peanut seeds, mature seeds were immersed for 24 hours in a solution of carbendazim (2mL/L). Next, under complete aseptic conditions in a laminar flow chamber, the seeds were disinfected with sodium hypochlorite 2% for 15 minutes and rinsed three times with sterile distilled water. In order to isolate the embryos, explants were planted in Petri dishes in culture medium composed of mineral salts and microelements of Murashige and Skoog (MS), with gel-rite agar (2.4 g/L) as a gelling agent. Different times for exposure were tested, ranging from 4 to 24 hours, with a 16-hour photoperiod, with radiation of 40 μιηο1ιη-28-1) as the preferred time.

Next, the embryos from explants and segments of epicotyls and leaves from plantlets were isolated and subcultured on nutrient MS medium with the same composition but with the addition of 2.4-D (2mg/L) or chitosan (0.01 %, 0.05% and 0.1 %) and incubated in complete darkness. Complete root and plant germination was observed after 10 and 15 days of incubation. In order maintain callus growth, fresh medium was added every four weeks.

Construction of DNA Construct

The DNA construct was composed of genetic components described herein and assembled in higher copy plasmid vectors (e.g., pYES and pBSK). Sequences of genes and/or proteins with desired properties were identified in GenBank. These sequences were synthesized by CloneTex Systems, Inc. (Austin, TX). Other genetic parts were also obtained for inclusion in the DNA constructs including, for example, promoter genes (e.g., Fe promoter, PAL promoter), reporter genes (e.g. yellow fluorescent reporter protein, cyan fluorescent reporter protein), terminator sequences, and regulatory proteins (e.g., ribosomal binding site, ribosomal switch). These genetic parts included restriction sites for ease of insertion into plasmid vectors.

The cloning of the DNA construct into the biological devices was performed as follows. Sequences of individual genes were amplified by polymerase chain reaction using primers that incorporated restriction sites at their 5' ends to facilitate construction of the full sequence to be inserted into the plasmid. Genes were then ligated using standard protocols to form an insert. A plasmid was then digested with Hindlll restriction enzyme according to directions and using reagents provided by the enzyme' s supplier (Promega). The complete insert, containing Hindlll recognition sites on each end, was then ligated into the plasmid. Successful construction of the insert and ligation of the insert into the plasmid were confirmed using gel electrophoresis.

PCR was used to enhance DNA concentration using a standard 5332

Eppendorf Thermocycler (Eppendorf North America. 102 Motor Parkway,

Hauppauge, NY, 11788) with specific sequence primers and the standard method for amplification (Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: A Laboratory Manual, 2nd ed., vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY). Digestion and ligation were used to ensure assembly of DNA synthesized parts using Promega restriction enzymes and reagents (Promega PCR master mix, restriction enzymes: Xhol, Kpnl, Xbal EcoRI, BamHI and Hindlll, Alkaline Phosphatase and quick ligation kit among others ). DNA was quantified using a nano view spectrophotometer GE nanospectrophotometer (GE Healthcare Biosciences P.O. Box 643065 Pittsburgh, PA 15264-3065), and also regular standard UV/visual spectrophotometer within a 260/280 wave length (GE Healthcare

Biosciences P.O. Box 643065 Pittsburgh, PA 15264-3065). In order to verify final ligations, DNA was visualized and purified with electrophoresis using standard Thermo EC (EC- 150) electrophoresis equipment.

The DNA construct was made with different gene parts of different sequence sizes ranging from 30 bp to 1000 bps, including gene parts fundamental for expression such as, for example, ribosomal biding site, native and constitutive promoters, reporter genes, and transcriptional terminators or stops. Backbone plasmids at different ratios ranging from 1:1, 1:2, 1:3, 1:4, and up to 1:5 were evaluated, with 1:4 as the preferred ratio. Different gene parts and the position of the parts were assembled in different order or sequence of alignment from each other in the host cell. Thus, this approach obtains different types of transformed host cells or induction devices.

The DNA construct for phenolic compound induction was constructed by assembling a plasmid (PBSKII) having the genetic components in the following order: (1) PAL promoter (SEQ ID NO. 1), (2) gene that expresses histidine/phenylalanine ammonia-lyase (SEQ ID NO. 5), (3) ribosomal switch RpoS (SEQ ID NO. 11), (4) ribosomal binding site (SEQ ID NO. 8), and (5) terminator (SEQ ID NO. 10). In certain embodiments, the reporter protein (SEQ ID NO. 15) that produces fluorescence can be added in between the ribosomal binding site and the terminator. The amount of fluorescence correlates to metabolite production in the tissues and media. This DNA construct was transformed into cells as described below to produce the phenolic devices. A plasmid containing the DNA construct is shown in Figure 1.

Host Cell Purification and Transformation

Yeast (Saccharomyces cerevisiae ATCC 200892) or bacteria cells such as

Escherichia coli (Invitrogen TOP10 Chemically Competent Cells, DH10B) or Bacillus pumilus ATCC 8471) were transformed with the DNA construct. Host cells were in some cases isolated as entophytes from fruits and plant tissues. Fruits and plant tissues were disinfected under full aseptic conditions in a laminar flow and placed in a solution of ethanol (70%) for two minutes, then in sodium hypochlorite (5%) for two minutes, then rinsed three times with sterile distilled water. Dilution of disinfected samples and slices of samples were placed in different selective and nonselective media for bacteria and yeast and place under anaerobic and aerobic conditions. After incubation, different bacteria and yeast were isolated. After pathogenesis assays, the cells that were less pathogenic were selected as ideal host cells for plant tissue induction. Cells selected were identified by ribosomal RNA gene sequencing in Accugenix, Newark, DE 19702. Identified bacteria were purchased after identification in ATCC.

Transformation proceeded according to manufacturing protocols. In case of E.coli, it was transformed chemically. The yeast devices were transformed by the methods disclosed in Gietz, R.D. and R.H. Schiestl {Nature Protocols "Quick and easy yeast transformation using the LiAc/SS carrier DNA/PEG method," 2007, Vol 2, 35-37). Bacillus pumilus was made by electroporation of competent cells using 1.25 V/mm for 3.9 seconds and recovering the cells with 1 ml of thioglycolate broth enriched with sucrose 250 mM, 1 mM of MgCl₂, and 5mM of MgS0₄ for an hour at 30 °C and plated on Muller Hilton agar with ampicillin. Cells were made competent by a new chemical treatment preparation with an electroporation buffer containing 0.5 M HEPES, 0.5 M sucrose, glycerol at 80%, and 25 mM of MgCl₂. The buffer was added to pelleted cells after overnight growth in aseptic conditions at a temperature of 4 °C. The pellet was centrifuged and washed three times with the buffer, aliquotted, and used immediately or stored at -80 °C.

DNA expression and effectiveness of transformation was determined by fluorescence of the transformed cells expressed in Florescence units (FSUs) using a Promega 20/20 Luminometer, according to instructions provided by the manufacturer. The Luminometer' s blue fluorescence module (450/600 wavelength) was used.

Plasmid DNA extraction, purification, PCR, and gel electrophoresis were also used to confirm transformation.

Different transformed devices were obtained. Different types of fluorescent reporter proteins were used (yellow fluorescent protein, red fluorescent protein, green fluorescent protein, and cyan fluorescent protein) for all transformed cells or devices. However, the cyan fluorescent protein was preferred. When no fluorescent reporter protein was assembled, no fluorescence was observed.

Chitosan

Chitosan is a natural linear polysaccharide compound composed of randomly- distributed, -(l,4)-linked D-glucosamine and N-acetyl-D-glucosamine. The chitosan was extracted from the exoskeletons of crustaceans to produce acetylated chitosan (the degree of acetylation was approximately 80%). Here, the chitosan was dissolved in glacial acetic acid and used as a concentrate of 1%. In Vitro Assays

Callus derived from somatic embryogenesis was sown on MS medium. The MS medium was prepared as follows: to 200 ml of distilled water were added 4.3 g MS salt mixture, 2 ml of growth regulator 2,4-D, 5 ml of myo-inositol (100 mg/L), and 30 g of sucrose to produce a first medium. In a separate container, 2.4 g of agar was added to 800 ml of distilled water in order to completely dilute the agar. This was added to the contents of the first medium, and mixed while boiling and autoclaved at 121 °C for 20 minutes at 15 psi.

To this medium was added a stock solution of chitosan to achieve a chitosan concentration of 0.01%, 0.05%, 0.1%, or 0.5%. The pH was adjusted with a solution of 1 M NaOH. The media was served in disposable sterile plastic petri dishes and calluses were subcultured.

The phenolic DNA construct transformed in different host cells were replicated overnight in LB broth (Luria Brethani) and YPD broth (Yeast extract-

Peptone-D-glucose) with ampicillin to produce the biological device. Serial dilutions of these cultures were made until reaching dilution 10⁹ in sterile water to a final volume of 5 ml. Dilutions 10³, 10⁶, and 10⁹ were used for all devices; however the use of smaller dilutions was preferable. The number of cells of each dilution was calculated with a standard growth curve of absorbance vs. Colony Forming Units

(CFU), to ensure the concentration of cells used in each of the dilutions. Absorbance was measured with a regular standard UV/visual spectrophotometer using a 520 to 600 nm wavelength range (GE Healthcare Biosciences P.O. Box 643065 Pittsburgh, PA, 15264-3065).

For the inoculation process, different volumes of the biological device were tested to standardize the amount necessary to induce metabolite production and avoid plant damage including 0.1, 0.25, 0.3, 0.5, 0.7, 0.9, 1.0 and 1.25 ml of device. The 0.25 ml volume was preferred and showed better induction results; therefore, 0.25 ml of the device was prepared at a concentration of 1 x 10³ from solutions initially containing 10⁹ and 10¹⁰ cells. The device was added to the callus a number of ways including via a micro-pipette or, in the alternative, injecting the device into the callus with a thin syringe.

Sample treatment depended on the type of plant tissue culture, the number and type of DNA constructs and host cells, and the metabolite or other type of induction expected. Control treatment was plant tissue culture alone without any device inoculation or chitosan. Plant tissue culture alone without any device inoculation but with chitosan added to the media was also evaluated. Device treatments with and without chitosan were compared. 3 different dilutions of each device were evaluated giving a total of 8 treatments per assay. When more than one device was evaluated, the number of treatments increased. For each treatment, 3 replicates with 3 and 4 calluses per replicate were used giving a total of 12 calluses per treatment. Samples were incubated at 25 °C with stirring at 50 rpm in the dark.

A daily record was made taking into account the following variables: callus size, germination structures, callus color, and media color. Gene expression including RNA concentration, DNA concentration, and fluorescence (in case of devices containing protein reporter gene) were also regularly monitored.

From the fourth day on, differences in morphology, size, callus coloration and media color were observed. In the case of inoculations with devices that induced these types of visible changes, secondary metabolites were released into the media.

For samples in which no phenotypic difference was observed, chemical extraction and analysis of produced compounds were performed. For phenolic content analysis, the Folin-Ciocalteu method and HPLC were used to determine metabolite presence and concentration.

Production of Phenolic Compounds from Peanuts

Figures 2-4 and Tables 1-3 below summarize the results of using the methods described herein for producing phenolic compounds from peanuts. The phenolic device I used in these experiments is E. coli transformed with DNA construct. Figure 2 shows peanut (Arachis hypogaea) tissue culture with and without chitosan, as compared to control culture without chitosan. Figure 3 shows the size increased significantly in peanut tissue cultures treated with chitosan and phenolic device I.

Table 3 shows biomass production of peanut callus treated and non-treated

(control) with phenolic device I and/or chitosan addition. Induction of size increase in cultures treated with the phenolic device I and/or chitosan was significantly higher compared to the control.

Figure 4 shows the comparison of different phenolic compounds produced from peanut (Arachis hypogaea) callus treated and non-treated (control) with transformed bacteria (i.e., biological device) and/or chitosan addition as determined by HPLC. As shown in Table 1, the tissue culture with chitosan produced about 10- fold increase in gallic acid compared to control tissue culture. In the case when the tissue was cultured with the phenolic device I and chitosan, there was about a 60-fold increase in gallic acid compared to the control tissue culture. Table 2 shows the concentrations of different phenolic acids and flavonoid compounds extracted from peanut callus treated with the phenolic device I and/or chitosan. As can be seen in Table 2, the use of the phenolic device I and chitosan significantly increased the production of certain phenolic compounds.

Table 1. Concentration of total phenolic compounds extracted from peanut (Arachis hypogaea) callus treated and non-treated (control) with phenolic device I and/or chitosan as determined by Folin-Ciocalteu. The difference in concentrations shows the induction of phenolic compound production by chitosan and phenolic device I.

EGA: equivalents in gallic acid.

Table 2. Concentration of different phenolic acids and flavonoids compounds extracted from peanut (Arachis hypogaea) callus treated and non-treated (control) with phenolic device I and/or chitosan as determined by HPLC. The difference in concentrations shows the induction of phenolic compound production by chitosan and 5 phenolic device I.

Table 3. Biomass production of peanut (Arachis hypogaea) callus treated and non- treated (control) with phenolic device I and/or chitosan addition. Induction of size increase in cultures treated with phenolic device I and chitosan is shown.

Throughout this application, various publications are referenced. The 5 disclosures of these publications in their entireties are hereby incorporated by

reference into this application in order to more fully describe the compounds, compositions and methods described herein.

Various modifications and variations can be made to the compounds, compositions and methods described herein. Other aspects of the compounds, compositions and methods described herein will be apparent from consideration of the specification and practice of the compounds, compositions and methods disclosed herein. It is intended that the specification and examples be considered as exemplary.

Claims

What is claimed:

1. A DNA construct comprising from 5' to 3' the following genetic components in the following order: (1) a PAL promoter, 2) a gene that expresses histidine/phenylalanine ammonia-lyase, (3) a ribosomal binding site, and (4) a terminator.

2. The construct of claim 1, wherein the construct further comprises a ribosomal switch between the gene that expresses histidine/phenylalanine ammonia-lyase and the ribosomal binding site.

3. The construct of claim 1, wherein the PAL promoter is SEQ ID NOS. 1, 2, 3, or 4 or a derivative or variant thereof.

4. The construct of claim 1, wherein the gene that expresses

histidine/phenylalanine ammonia-lyase is SEQ ID NOS. 5, 6, 7 or a derivative or variant thereof.

5. The construct of claim 1, wherein the PAL promoter is SEQ ID NO. 1 ; the gene that expresses histidine/phenylalanine ammonia-lyase is SEQ ID NO. 5; the ribosomal switch RpoS is SEQ ID NO. 11; the ribosomal binding site is SEQ ID NO. 8; and the terminator is SEQ ID NO. 10.

6. A vector comprising the construct of claim 1.

7. The vector of claim 6, wherein the vector is a plasmid.

8. The vector of claim 6, wherein the vector is pWLNEO, pSV2CAT, pOG44, PXT1, pSG (Stratagene) pSVK3, pBSK, pBR322, pYES, PBSKII, or pUC.

9. A biological device comprising host cells transformed with the vector of claims 6-8.

10. The device of claim 9, wherein the host cells comprise yeast or bacteria.

11. The device of claim 10, wherein the bacteria comprises non-pathogenic

saprophytic bacteria, Bacillus pumilus, or E. coli.

12. A method for producing one or more phenolic compounds from plant cells, the method comprising contacting the plant cells with a biological device of claim 9, wherein the plant cells are not plant cells from Theobroma cacao or a variant thereof.

13. The method of claim 12, wherein the plant cells comprise meristem cells, callus cells, immature embryos, gametic cells, or any combination thereof.

14. The method of claim 12, wherein the plant cells comprise callus cells.

15. The method of claim 12, wherein the plant cells are derived from peanuts (Arachis hypogaea), tomatoes (Solanum lycopersicum), and soybeans (Glycine max)

16. The method of claim 12, wherein the plant cells are further contacted with a polysaccharide.

17. The method of claim 16, wherein the polysaccharide comprises chitosan, glucosamine, N-acetylglucosamine, or any combination thereof.

18. The method of claim 16, wherein the polysaccharide comprises chitosan, wherein the chitosan is from 60% to 100% acetylated.

19. The method of claim 18, wherein the chitosan comprises from 3 to 20

glucosamine units and/or N-acetylglucosamine units.

20. The method of claim 12, wherein the plant cells are derived from culturing plant gamete cells or a plant reproductive organ in the presence of a polysaccharide.

21. A plant grown by the process comprising contacting plant gamete cells or a plant reproductive organ with the device of claims 9-11, wherein the plant is not Theobroma cocao or a variant thereof.

22. A method for preventing a plant from contracting one or more diseases, the method comprising growing a plant from plant cells that have been contacted with the device of claim 9, wherein the plant cells are plant cells from

Theobroma cocao or a variant thereof.

23. The method of claim 22, wherein the disease is a fungal disease.

24. A method for delivering the DNA construct of claims 1-5 to plant cells, the method comprising contacting the plant cells with the biological device of claim 9, wherein the plant cells are not plant cells from Theobroma cocao or a variant thereof.