# Patent

## Title
Cytokinin synthase enzymes, constructs, and related methods

## Abstract

The present disclosure relates to a new class of cytokinin biosynthetic enzymes, cytokinin synthases, which have two domains: an isopentenyl transfer (IPT)-like domain and a cytokinin nucleotide phosphoribohydrolase (PRH)-like domain. The invention provides compositions and methods for the recombinant production of cytokinin synthase, host cells and transformants that include the cytokinin synthases, as well as compositions and formulations that include the disclosed cytokinin synthase.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
The present application claims priority to U.S. Provisional Application No. 62/001,849, filed May 22, 2014, which is incorporated herein by reference in its entirety.


REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
The substitute sequence listing filed electronically via EFS-Web on Nov. 30, 2015 as the ASCII formatted file named “75913_ST25v3.txt” was created Nov. 30, 2015, has a size of 189 kilobytes, is part of the specification, and is herein incorporated by reference in its entirety.
FIELD OF THE INVENTION
The invention relates generally to the fields of molecular biology and biochemistry. More specifically the invention relates to a class of cytokinin synthase enzymes that produce cytokinin. The invention provides recombinant polynucleotides that encode these enzymes and methods for the production of cytokinins in vitro, in host cells, and in plants. The invention further provides plants and compositions that include recombinant polynucleotides of the invention, the cytokinin synthases of the invention, and/or cytokinins produced by the cytokinin synthases of the invention.
BACKGROUND
Cytokinins are small molecules produced by plants that regulate growth and development processes under normal growing conditions as well as under stress conditions. It is well established that cytokinins stimulate growth and differentiation of cultured plant cells. Cytokinin signaling has been shown to correlate with production of tissues during bud outgrowth and root nodule formation. Faiss et al., Plant J., 12(2): 401-15 (1997); Ferguson et al., Plant Physiol., 149(4): 1929-1944 (2009), Tirichine et al., Science, 315(5808):104-107 (2007) and Held et al., Plant Cell, 26(2): 678-694 (2014). Cytokinin inactivation during abiotic stress, e.g., due to drought, cold, or excess salt leads to decreased plant productivity, reduced seed size, increased tip kernel abortion and decreased seed set. (Jones and Setter, in CSSA Special Publication No. 29, pp. 25-42. American Society of Agronomy, Madison, Wis. (1999)). Transgenic expression of cytokinin biosynthesis enzymes has been reported to increase plant productivity, including under abiotic stress. Rivero et al., Proc. Natl. Acad. Sciences USA, 104(49) 19631-36 (2007); Merewitz et al., J. Exp. Bot., 63(3): 1315-1328 (2012). Additionally, formulations of cytokinin derived from algae and other formulations of cytokinin (benzyl adenine) have been registered and approved for uses that include application to field crops, vegetable crops, small fruits, vines, tree fruit, young trees, ornamentals, and golf courses to increase fruit size, yield, blossoms, branching, healthy appearance, and other desirable growth effects. U.S. Environmental Protection Agency Registration Eligibility Decision (RD), EPA-738-R-95-025, December 1995 and N-6 benzyladenine Registration Review Case 2040 (PC Code 116901) March 2011. In plant leaves, foliar applications of exogenous cytokinin (benzyl adenine) have been used to reverse the effects of drying roots, which can be sustained by repeated applications and leads to development of lateral shoots. Stoll et al. J. Exp. Bot., 51(350): 1627-1634 (2000).
The biosynthesis of cytokinins in plants is complex and involves a primary and secondary pathway. Motkya et al., Plant Physiol. 112: 1035-1043 (1996). In the primary pathway, cytokinins are synthesized de novo in a multiple step reaction that begins with the activity of adenosine phosphate-isopentenyltransferases (IPTs), which preferably catalyzes the condensation of adenosine diphosphate (ADP) or adenosine triphosphate (ATP) with prenyl donors to form iP riboside 5′-diphosphate (iPRDP) or iP riboside 5′-triphosphate (iPRTP), respectively. These precursors are either hydrolyzed by cytokinin nucleotide phosphoribohydrolases to form the cytokinin N6-(Δ2-isopentenyl)adenine (iP) or, alternatively, they are converted to corresponding trans-zeatin nucleotides (tZN), which are then hydrolyzed to form the cytokinin trans-zeatin (tZ). In the secondary pathway, cytokinins are generated by degradation of transfer RNA (tRNA). The first step of the pathway involves tRNA-isopentenyltransferase (tRNA-IPT) enzyme that post-transcriptionally modifies tRNA to make prenylated tRNA. This precursor is further modified and condensed with adenine to generate cis-zeatin riboside (cZR) which is hydrolyzed to generate primarily cis-zeatin. Generally, the cytokinin pool produced by the primary pathway is understood to be biologically more active.
The infectious crown gall forming bacterium Agrobacterium tumefaciens has two genes which encode IPTs that preferentially catalyzes the condensation of adenosine monophosphate (AMP) with hydroxymethylbutenyl diphosphate (HMBDP) or dimethylallyl diphosphate (DMAPP) to form trans-zeatin ribosyl monophosphate (tZRMP) which is subsequently hydrolyzed by cytokinin nucleotide phosphoribohydrolases to form trans-zeatin (tZ). Thus, the mechanism of cytokinin biosynthesis in Agrobacterium involves at least two enzymes and produces predominantly tZ cytokinin.
There is a desire for new compositions and methods that can be used to produce or regulate the production of cytokinin in vitro or in vivo. For example, there is a desire for compositions and methods that use a single polypeptide to produce cytokinin directly from precursor. These can be less dependent on the presence of additional upstream or downstream effectors for the production of cytokinins. Such compositions and methods can be used to produce cytokinin formulations for applications to plants. Additionally such can be used to modulate cytokinin production in plants and thereby regulate plant growth and development.
BRIEF SUMMARY
The disclosed invention is based, in part, on the discovery of a class of genes in certain plant-associated fungi that encode a cytokinin biosynthetic enzyme (“cytokinin synthase”) having two domains: an isopentenyl transfer (IPT)-like domain and a cytokinin nucleotide phosphoribohydrolase (PRH)-like domain. Multiple members of this class of cytokinin synthases are identified and characterized herein including, for example, Epichloe festucae (EfCKS), Balansia obtecta (BoCKS), Ilyonectria radicola (IrCKS), Aciculosporium take (AtCKS), Atkinsonella hypoxylon (AhCKS), Fusarium fujikuroi (FfCKS), and others disclosed herein. The cytokinin synthase of the invention can be used to catalyze the conversion of cytokinin precursors (e.g., adenosine monophosphate (AMP) or a prenyl donor such as dimethylallyl diphosphate (DMAPP)) directly to a cytokinin (isopentenyl adenine).
Thus the invention provides a method that includes contacting a cytokinin precursor (e.g., AMP or DMAPP) with a two-domain cytokinin synthase of the invention, wherein the cytokinin synthase converts the precursor to cytokinin such as isopentenyl adenine. The invention improves upon prior isopentenyl transferase (IPT) enzymes that, because they only catalyze an initial step, may require one or more additional enzymes (a transhydroxylase (CYP735) or phosphoribohydrolase (CKA)), to effectively complete the conversion of AMP or DMAPP to a cytokinin such as trans-zeatin (tz) or isopentenyl adenine (iP). See FIG. 2.
The disclosure provides cytokinin synthases that vary in amino acid sequence while retaining enzymatic function. Thus, the invention discloses a cytokinin synthase having at least 57%, at least 60%, at least 65%, at least 70%, at least 80%, at least 90%, or at least 95% amino acid sequence identity to a disclosed cytokinin synthase. The invention further provides a recombinant polynucleotide that comprises (a) a coding sequence for any of the two-domain cytokinin synthase disclosed herein and (b) a heterologous nucleotide sequence such as, e.g., a heterologous promoter sequence, vector sequence, or a host-genome targeting sequence. In certain embodiments, the two-domain cytokinin synthase coding sequence is optimized for expression in a host cell, e.g., a bacteria, yeast, or plant host cell. In some embodiments, the cytokinin synthase coding sequence is covalently linked to a heterologous amino acid sequence, such as a protein fusion tag.
The disclosed invention identifies and provides functionally important domains, motifs, and individual residues. For example, the disclosure provides methods for identifying and/or making isopentenyl transfer (IPT)-like domain and cytokinin nucleotide phosphoribohydrolase (PRH)-like domains. Thus, the invention provides a two-domain cytokinin synthase that includes these motifs. Referring to the sequence alignment of FIG. 6, a first motif was identified at consensus positions 13-20: GPTXaa1Xaa2GKT (SEQ ID NO:30), wherein Xaa1 is G or A and Xaa2 is V, S, or A; a second motif was identified at consensus positions 96-104: PXaa3Xaa4Xaa5GGSXaa6S (SEQ ID NO:31), wherein Xaa3 is I or V, Xaa4 is L or V, Xaa5 is V or C, and Xaa6 is T or I; a third motif was identified at consensus positions 333-338: XaaXaaYGGG Xaa7Xaa8YGGG (SEQ ID NO:32), wherein Xaa7 is L or I, and Xaa8 is V or I; and a fourth motif was identified at consensus/alignment positions 426-438 Xaa9GGYGT Xaa10EEL (SEQ ID NO:33), where Xaa9 is S or P and Xaa10 is L or M. The foregoing motifs, as exemplified in fungal cytokinin synthases, are set forth more fully in Example 8 herein.
The motifs identified in the IPT-like domains of the fungal two-domain cytokinin synthases were also compared to non-fungal isopentenyl transferases to identify residues that could be varied within cytokinin synthases of the invention. Thus, in a different aspect, the invention provides two-domain cytokinin synthases wherein one or more of the disclosed motifs within the IPT-like domain (SEQ ID NO:30, SEQ ID NO:31, or SEQ ID NO:32) is varied to include the corresponding motifs identified in non-fungal IPT domains as more fully described in Example 9.
Additionally, the invention discloses for the first time individual amino acid residues which are functionally important for cytokinin synthase activity as revealed by the results of alanine scanning mutagenesis. Individual residues are indicated in FIG. 6 and their effect on activity is shown in FIG. 7, and discussed in more detail herein.
In further embodiments, the recombinant polynucleotide encoding the two-domain cytokinin synthase is transformed into a host cell. In some embodiments, the host cell is a transgenic plant cell and the encoded cytokinin synthase modulates cytokinin activity in the plant cell. In certain embodiments, the plant cell is regenerated to create transgenic plant tissue or a transgenic plant that includes the recombinant polynucleotide of the invention. In particular embodiments, the recombinant polynucleotide expresses the encoded cytokinin synthase and thereby modulates cytokinin levels in the transgenic plant. In additional embodiments, the host cell is an expression host cell (e.g., a bacteria or yeast) that can be used to produce the encoded cytokinin synthase. The cytokinin synthase can be isolated or purified from the host cell material. Thus, the invention also provides an isolated or purified cytokinin synthase polypeptide that has an IPT-like domain and a PRH-like domain. In certain embodiments, the invention provides an isolated or purified cytokinin synthase fused to a heterologous amino acid sequence such as a protein fusion tag.
The invention provides methods of using the recombinant polynucleotides of the invention to produce cytokinins in host cells, plants, and in vitro. In one aspect, the invention provides a method of using the recombinant polynucleotide to express a two domain cytokinin synthase that is capable of converting cytokinin precursor (e.g., adenosine monophosphate (AMP) or dimethylallyl diphosphate (DMAPP)) directly to cytokinin in a host cell, a plant, or in vitro. By contrast, prior art polynucleotides encoding a prior art isopentenyl transferase (IPT) also required expression of one or more additional enzymes to complete the conversion of AMP or DMAPP to a cytokinin such as tZ or iP. See FIG. 2.
In yet another aspect, the cytokinin synthase of the invention can be used to produce cytokinins in a host cell or in vitro, which can be isolated or purified for use as an active ingredient. The cytokinins produced according to the invention can be mixed with inert ingredients to create formulations which are useful for application to field crops, vegetable crops, small fruits, vines, tree fruit, young trees, ornamentals, and grasses in industrial applications.
The compositions and methods of the invention are disclosed in more detail herein.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a schematic diagram of the domain architecture of a cytokinin synthase of the invention, including IPT-like domain and PRH-like domain.
FIG. 2 provides models of cytokinin biosynthesis in plants and Agrobacterium and a model of fungal cytokinin biosynthesis based on the cytokinin synthases disclosed herein.
FIG. 3 provides an image of a Coomassie-stained SDS-PAGE gel showing overexpressed recombinant Epichloe festucae cytokinin synthase (EfCKS.1) and a truncated version EfCKS.1 (1-255), and FIG. 3 also provides a bar graph showing results of culture broth assays for secreted cytokinin from the host cells expressing EfCKS.1 and EfCKS.1 (1-255). Above these, FIG. 3 further provides a schematic diagram of EfCKS.1 and EfCKS.1 (1-255).
FIG. 4 is a pair of graphs showing the results of in vitro assays for activity of purified EfCKS.1 and purified isopentenyl transferase from Agrobacterium tumefaciens (AtuIPT).
FIG. 5 is a bar graph showing results of broth assays for secreted product of recombinant cytokinin synthases according to the invention.
FIG. 6 is a sequence alignment of cytokinin synthases of the invention that shows conserved residues (boxed areas) and the effect of mutations on indicated conserved residues: severe effect on activity indicated by wedge (▴) or small effect on activity indicated by open diamond (⋄).
FIG. 7 is a bar graph showing results of broth assays for secreted product of the recombinant cytokinin synthase enzyme and mutants thereof, including sixty-six distinct alanine scanning substitution mutants.
FIG. 8 provides cDNA sequence of polynucleotide (SEQ ID NO:1) encoding cytokinin synthase polypeptide EfCKS.1.
FIG. 9 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:2) and the encoded cytokinin synthase polypeptide EfCKS.1 (SEQ ID NO:3).
FIG. 10 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:4) and the encoded cytokinin synthase polypeptide EfCKS.1 (SEQ ID NO:5) which includes an N-terminal fused protein (polyhistidine) tag.
FIG. 11 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:6) and the encoded IPT-like domain of EfCKS.1 (SEQ ID NO:7), which is truncated at the amino acid corresponding to position 255 of full-length EfCKS.1 and which includes an N-terminal fused polyhistidine tag.
FIG. 12 provides the sequence of polynucleotide (SEQ ID NO:8) encoding cytokinin synthase polypeptide AtCKS.1 (SEQ ID NO:9).
FIG. 13 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:10) and the encoded cytokinin synthase polypeptide AtCKS.1 (SEQ ID NO:11) which includes an N-terminal fused protein (polyhistidine) tag.
FIG. 14 provides the sequence of polynucleotide (SEQ ID NO:12) encoding cytokinin synthase polypeptide BoCKS.1 (SEQ ID NO:13).
FIG. 15 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:14) and the encoded cytokinin synthase polypeptide BoCKS.1 (SEQ ID NO:15) which includes an N-terminal fused protein (polyhistidine) tag.
FIG. 16 provides the sequence of polynucleotide (SEQ ID NO:16) encoding cytokinin synthase polypeptide IrCKS.1 (SEQ ID NO:17).
FIG. 17 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:18) and the encoded cytokinin synthase polypeptide IrCKS.1 (SEQ ID NO:19) which includes an N-terminal fused protein (polyhistidine) tag.
FIG. 18 provides the sequence of polynucleotide (SEQ ID NO:20) encoding cytokinin synthase polypeptide AhCKS.1 (SEQ ID NO:21).
FIG. 19 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:24) and the encoded cytokinin synthase polypeptide AhCKS.1 (SEQ ID NO:23) which includes an N-terminal fused protein (polyhistidine) tag.
FIG. 20 provides the sequence of polynucleotide (SEQ ID NO:24) encoding cytokinin synthase polypeptide FfCKS.1 (SEQ ID NO:25).
FIG. 21 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:26) and the encoded cytokinin synthase polypeptide FfCKS.1 (SEQ ID NO:27) which includes an N-terminal fused protein (polyhistidine) tag.
FIG. 22 provides an E. coli codon optimized coding sequence polynucleotide (SEQ ID NO:16) and the encoded IPT with N-terminal fused polyhistidine tag (SEQ ID NO:17) of AtuCKS.1.
FIG. 23 provides a phylogenetic tree showing evolutionary distances between cytokinin synthases of the invention.
FIG. 24 provides the following cytokinin synthases of the invention: SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, and SEQ ID NO:37.
FIG. 25 provides the following cytokinin synthases of the invention: SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, and SEQ ID NO:41.
FIG. 26 provides the following cytokinin synthases of the invention: SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, and SEQ ID NO:45,
FIG. 27 provides the following cytokinin synthases of the invention: SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, and SEQ ID NO:49.
FIG. 28 provides the following cytokinin synthases of the invention: SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, and SEQ ID NO:53,
FIG. 29 provides the following cytokinin synthases of the invention: SEQ ID NO:54
FIG. 30 is a set of schematic diagrams showing four functional motifs and their locations within the domain architecture of cytokinin synthases disclosed herein.



TERMS
In describing and claiming the invention, the following terminology will be used in accordance with the definitions set forth below.
The term “about” as used herein means greater or lesser than the value or range of values stated by 10 percent, but is not intended to designate any value or range of values to only this broader definition. Each value or range of values preceded by the term “about” is also intended to encompass the embodiment of the stated absolute value or range of values. The term “about 100%” means less than 100%.
As used herein, the term “plant” includes a whole plant and any descendant, cell, tissue, or plant part. The term “plant parts” include any part(s) of a plant, including, for example and without limitation: seed (including mature seed and immature seed); a plant cutting; a plant cell; a plant cell culture; a plant organ (e.g., pollen, embryos, flowers, fruits, shoots, leaves, roots, stems, and explants). A plant tissue or plant organ may be a seed, callus, or any other group of plant cells that is organized into a structural or functional unit. A plant cell or tissue culture may be capable of regenerating a plant having the physiological and morphological characteristics of the plant from which the cell or tissue was obtained, and of regenerating a plant having substantially the same genotype as the plant. In contrast, some plant cells are not capable of being regenerated to produce plants. Regenerable cells in a plant cell or tissue culture may be embryos, protoplasts, meristematic cells, callus, pollen, leaves, anthers, roots, root tips, silk, flowers, kernels, ears, cobs, husks, or stalks.
A plant cell is the structural and physiological unit of the plant. Plant cells, as used herein, includes protoplasts and protoplasts with a cell wall. A plant cell may be in the form of an isolated single cell, or an aggregate of cells (e.g., a friable callus and a cultured cell), and may be part of a higher organized unit (e.g., a plant tissue, plant organ, and plant). Thus, a plant cell may be a protoplast, a gamete producing cell, or a cell or collection of cells that can regenerate into a whole plant. As such, a seed, which comprises multiple plant cells and is capable of regenerating into a whole plant, is considered a “plant part” in embodiments herein.
The term “dicot” or “dicotyledonous” refers to plants having two cotyledons. Examples include crop plants such as soybean, sunflower, cotton, canola, rape, and mustard.
The term “monocot” or “monocotyledonous” refers to plants having a single cotyledon. Examples include crop plants such as maize, rice, wheat, oat, and barley.
The term “heterologous” is used herein to describe a nucleotide sequence that is not found in ant naturally occurring polynucleotide that encodes a cytokinin kinase.
The term “recombinant” means with regard to a polynucleotide or a host cell that the polynucleotide or host cell has been altered by recombinant methods. For example, the term recombinant polynucleotide refers to a polynucleotide that includes a first nucleic acid sequence (e.g. a sequence encoding cytokinin synthase of the invention) that has been covalently linked to a heterologous molecule (e.g., a heterologous nucleic acid) by ligation, cloning, amplification recombination, or chemical modification. The term recombinant also refers to a polynucleotide that has been artificially synthesized in a laboratory or industrial setting.
The term “recombinant” with regard to a polypeptide means that the polypeptide has been produced by recombinant methods, e.g., by expressing a recombinant polynucleotide that encodes the recombinant polypeptide. The term recombinant also refers to a polypeptide that has been artificially synthesized in a laboratory or industrial setting.
The term “transgenic” refers to a cell or organism comprising a transgene, for example a “transgenic plant” refers to a plant comprising a transgene, i.e., a nucleic acid molecule artificially incorporated into the organism's genome as a result of human intervention.
The term “transgenic event” in reference to a plant refers to a recombinant plant produced by transformation and regeneration of a single plant cell with heterologous DNA, for example, an expression cassette that includes a transgene of interest. The term event refers to the original transformant and/or progeny of the transformant that includes the heterologous DNA. The term event also refers to progeny produced by a sexual outcross between the transformant and another plant. Even after repeated backcrossing to a recurrent parent, the inserted DNA and the flanking DNA from the transformed parent is present in the progeny of the cross at the same chromosomal location. Normally, transformation of plant tissue produces multiple events, each of which represent insertion of a DNA construct into a different location in the genome of a plant cell. Based on the expression of the transgene or other desirable characteristics, a particular event is selected. In embodiments of the subject disclosure the particular event comprises a gene expression cassette polynucleotide inserted within a genomic locus.
As used herein the terms “native” or “natural” define a condition found in nature. A “native DNA sequence” is a DNA sequence present in nature that was produced by natural means or traditional breeding techniques but not generated by genetic engineering (e.g., using molecular biology/transformation techniques).
As used herein, the term “codon-optimized” or “codon optimization” refers to a process of modifying an existing coding sequence (or designing a coding sequence) to improve transcription of a coding sequence and/or to improve translation of a transcript RNA molecule transcribed from the coding sequence, for example, in a host cell. Codon optimization includes, but is not limited to, processes that include selecting codons for the coding sequence to suit the codon preference of an expression host organism. Polynucleotide can be prepared or altered synthetically to take advantage of the known codon preferences of the host where the polynucleotide is intended to be expressed. For example, although polynucleotides may be expressed in some embodiments in both monocotyledonous and dicotyledonous plant species, a polynucleotide sequence may be modified (e.g., optimized) to account for the specific codon preferences and GC content preferences of monocots or dicots. See, e.g., Murray et al. (1989) Nucl. Acids Res. 17:477-98 (Maize codon usage for 28 genes from maize plants).
The term “isolated” as used herein means that a polynucleotide or a polypeptide has been removed from its natural environment. An “isolated polynucleotide” or “isolated polypeptide” also encompasses a polynucleotide or polypeptide, respectively, which has been synthesized or amplified under laboratory or industrial conditions.
The term “purified,” as used herein relates to the isolation of a molecule or compound in a form that is substantially free of contaminants normally associated with the molecule or compound in a native or natural environment. The term describes a molecule or compound that has been increased in purity as a result of being separated from other components of the original composition.
The terms “polypeptide,” “peptide,” and “protein” are used interchangeably to refer to a polymer of amino acid residues. The term also applies to amino acid polymers in which one or more amino acids are chemical analogues or modified derivatives of a corresponding naturally-occurring amino acids.
The term “heterologous sequence” as used herein is any nucleic acid sequence that is (i) covalently bound to and flanking another nucleic acid sequence, and (i) not found in nature flanking the other nucleic acid. Thus, when a nucleic acid of interest is removed from its native location and inserted into a new location that alters the sequences flanking the nucleic acid of interest, the flanking sequences in the new location are “heterologous sequence.” For example, an exogenous DNA sequence may comprise a sequence from another species, vector, and/or gene cassette.
A “fusion” molecule is a molecule in which two or more subunit molecules are linked, for example, covalently. The subunit molecules can be the same chemical type of molecule, or can be different chemical types of molecules.
For the purposes of the present disclosure, a “gene,” includes a DNA region encoding a gene product, as well as all DNA regions which regulate the production of the gene product, whether or not such regulatory sequences are adjacent to coding and/or transcribed sequences. Accordingly, a gene may include, but is not necessarily limited to, promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites and locus control regions.
“Gene expression” refers to the conversion of the information, contained in a gene, into a gene product. A gene product can be the direct transcriptional product of a gene (e.g., mRNA, tRNA, rRNA, antisense RNA, interfering RNA, ribozyme, structural RNA or any other type of RNA) or a protein produced by translation of an mRNA. Gene products also include RNAs which are modified, by processes such as capping, polyadenylation, methylation, and editing, and proteins modified by, for example, methylation, acetylation, phosphorylation, ubiquitination, ADP-ribosylation, myristilation, and glycosylation.
As used herein, the term isopentenyl transfer (IPT)-like domain refers to a sequence of amino acids identified by the National Center for Biotechnology (NCBI) CCD conserved domain database as a domain in the ATP-binding cassette transporter nucleotide-binding (ABC_ATPase) domain superfamily (e.g., accession: c121455) that is characteristic of an isopentenylpyrophosphate domain. Such domains include, for example, MiaA and miaA tRNA dimethyltransferase tRNA delta(2)-isopentenylpyrophosphate transferases (accessions: COG0324 and PRK00091, respectively), tRNA dimethylallyltransferases (accessions: TIGR00174, PLN02840, or PLN02748); adenylate isopentenyltransferase (accession: PLN02165); and IPP transferase, EC:2.5.1.8; tRNA delta(2)-isopentenylpyrophosphate transferase, (accession: pfam01715). For information regarding the CCD conserved domain database see Marchler-Bauer A et al. (2015), Nucl. Acids Res., 43:D222-226 and Marchler-Bauer A et al. (2011), Nucl. Acids Res., 39:D225-229, which are incorporated herein by reference in their entirety.
As used herein, the term phosphoribohydrolase (PRH)-like domain refers to a sequence of amino acids identified by NCBI's CCD conserved domain database as a domain in the bacterial Toll-like receptors (TIR) domain superfamily (e.g., accession c122440) that is characteristic of TIGR00730 family protein and potential lysine decarboxylases. Such domains include, for example, LOG_family_protein_YJL055W (accession TIGR00730); lysine decarboxylase (accession pfam03641); and predicted Rossman fold nucleotide-binding protein (accession COG1611). For information regarding the CCD conserved domain database see Marchler-Bauer A et al. (2015), Nucl. Acids Res., 43:D222-226 and Marchler-Bauer A et al. (2011), Nucl. Acids Res., 39:D225-229, which are incorporated herein by reference in their entirety. To the extent they have been annotated in genomic databases, the PRH-like domain of the cytokinin synthases disclosed herein were mistakenly annotated as being lysine decarboxylases. This annotation was also mistakenly applied to other proteins containing the same domain as verified by Kurakawa et al. (2007), Nature 445(8): 652-655.
The term “sequence identity” or “identity,” as used herein in the context of two nucleic acid sequences or two polypeptide sequences, refers to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
As used herein, references to “percentage of sequence identity” or “percent (%) sequence identity” refers to the value determined by comparing two optimally aligned sequences (e.g., nucleic acid sequences, and amino acid sequences) over a comparison window, wherein the portion of the sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleotide or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the comparison window, and multiplying the result by 100 to yield the percentage of sequence identity. Methods for aligning sequences for comparison are well-known in the art. Various programs and alignment algorithms are described in, for example: Smith and Waterman (1981) Adv. Appl. Math. 2:482; Needleman and Wunsch (1970) J. Mol. Biol. 48:443; Pearson and Lipman (1988) Proc. Natl. Acad. Sci. U.S.A. 85:2444; Higgins and Sharp (1988) Gene 73:237-44; Higgins and Sharp (1989) CABIOS 5:151-3; Corpet et al. (1988) Nucl. Acids Res. 16:10881-90; Huang et al. (1992) Comp. Appl. Biosci. 8:155-65; Pearson et al. (1994) Methods Mol. Biol. 24:307-31; Tatiana et al. (1999) FEMS Microbiol. Lett. 174:247-50. A detailed consideration of sequence alignment methods and homology calculations can be found in, e.g., Altschul et al. (1990) J. Mol. Biol. 215:403-10. The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLASTTM; Altschul et al. (1990)) is available from several sources, including the National Center for Biotechnology Information (Bethesda, Md.), and on the internet, for use in connection with several sequence analysis programs. A description of how to determine sequence identity using this program is available on the internet under the “help” section for BLASTTM. For comparisons of nucleic acid sequences, the “Blast 2 sequences” function of the BLASTTM (BLASTN) program may be employed using the default parameters. Nucleic acid sequences with progressively greater similarity to the reference sequences will show increasing percentage identity when assessed by this method. For comparison of amino acid sequences, the BLASTTM (BLASTP or blastp suite) program may be used with the default parameters, which employs the BLOSUM62 matrix as a default to create an alignment of amino acid sequences and determine whether aligned amino acids are “positives” (identical or conservative substitutions) at each position in the alignment. See Altschul et al. (1997), Nucl. Acids Res. 25(17):3389-3402.
As used herein, the terms “specifically hybridizable” and “specifically complementary” are terms that indicate a sufficient degree of complementarity, such that stable and specific binding occurs between the nucleic acid molecule and a target nucleic acid molecule under non-stringent conditions.
Hybridization conditions resulting in particular degrees of stringency will vary depending upon the nature of the hybridization method of choice and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (especially the Na+ and/or Mg++ concentration) of the hybridization buffer will determine the stringency of hybridization, though wash times also influence stringency. Calculations regarding hybridization conditions required for attaining particular degrees of stringency are known to those of ordinary skill in the art, and are discussed, for example, in Sambrook et al. (ed.) Molecular Cloning: A Laboratory Manual, 3rd ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001, chapters 9, 10 and 11; and Hames and Higgins (eds.) Nucleic Acid Hybridization, IRL Press, Oxford, 1985. Further detailed instruction and guidance with regard to the hybridization of nucleic acids may be found, for example, in Tijssen, “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” in Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes, Part I, Chapter 2, Elsevier, N.Y., 1993; and Ausubel et al., Eds., Current Protocols in Molecular Biology, Chapter 2, Greene Publishing and Wiley-Interscience, NY, 1995.
As used herein, “moderate stringency” conditions are those under which molecules with more than 20% sequence mismatch will not hybridize; conditions of “high stringency” are those under which sequences with more than 10% mismatch will not hybridize; and conditions of “very high stringency” are those under which sequences with more than 5% mismatch will not hybridize. The following are representative, non-limiting hybridization conditions.
High Stringency condition (detects sequences that share at least 90% sequence identity): Hybridization in 5×SSC and 0.1% SDS buffer at 65° C. for 16 hours; wash twice in 2×SSC and 0.1% SDS buffer at room temperature for 15 minutes each; and wash twice in 0.5×SSC and 0.1% SDS buffer at 65° C. for 20 minutes each.
Moderate Stringency condition (detects sequences that share at least 80% sequence identity): Hybridization in 5×-6×SSC and 0.1% SDS buffer at 65-70° C. for 16-20 hours; wash twice in 2×SSC and 0.1% SDS buffer at room temperature for 5-20 minutes each; and wash twice in 1×SSC and 0.1% SDS buffer at 55-70° C. for 30 minutes each.
Non-stringent control condition (sequences that share at least 50% sequence identity will hybridize): Hybridization in 6×SSC and 0.1% SDS buffer at room temperature to 55° C. for 16-20 hours; wash at least twice in 2×-3×SSC and 0.1% SDS buffer at room temperature to 55° C. for 20-30 minutes each.
As used herein, the term “substantially homologous” or “substantial homology,” with regard to a contiguous nucleic acid sequence, refers to contiguous nucleotide sequences that hybridize under stringent conditions to the reference nucleic acid sequence. For example, nucleic acid sequences that are substantially homologous to a reference nucleic acid sequence are those nucleic acid sequences that hybridize under moderate stringent conditions to the reference nucleic acid sequence. Substantially homologous sequences have at least 80% sequence identity. For example, substantially homologous sequences may have from about 80% to 100% sequence identity, such as about 81%; about 82%; about 83%; about 84%; about 85%; about 86%; about 87%; about 88%; about 89%; about 90%; about 91%; about 92%; about 93%; about 94% about 95%; about 96%; about 97%; about 98%; about 98.5%; about 99%; about 99.5%; about 99.9%, and about 100%. The property of substantial homology is closely related to specific hybridization. For example, a nucleic acid molecule is specifically hybridizable when there is a sufficient degree of complementarity to avoid non-specific binding of the nucleic acid to non-target sequences under conditions where specific binding is desired.
As used herein, two nucleic acid sequence molecules are said to be “complementary” or exhibit “complementarity” when every nucleotide of a sequence read in the 5′ to 3′ direction is complementary to every nucleotide of the other sequence when read in the 3′ to 5′ direction. A nucleotide sequence that is complementary to a reference nucleotide sequence will exhibit a sequence identical to the reverse complement sequence of the reference nucleotide sequence. These terms and descriptions are well defined in the art, and are easily understood by those of ordinary skill in the art.
When determining the percentage of sequence identity between amino acid sequences, it is well-known by those of skill in the art that the identity of the amino acid in a given position provided by an alignment may differ without affecting desired properties of the polypeptides comprising the aligned sequences. In these instances, the percent sequence identity may be adjusted to account for similarity between conservatively substituted amino acids. These adjustments are well-known and commonly used by those of skill in the art. See, e.g., Myers and Miller (1988) Computer Applications in Biosciences 4:11-7. Statistical methods are known in the art and can be used in analysis of the identified 5,286 optimal genomic loci.
As used herein, the term “operably linked” refers to a linkage between two moieties that establishes a functional relationship between the two moieties. For example two amino acid sequences can be operably linked, or two nucleotide sequence can be operably linked, to form a contiguous sequence wherein the first sequence imparts functionality to the second. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. When recombinantly produced, operably linked nucleotide sequences are generally contiguous and, where necessary to join two protein-coding regions, in the same reading frame. However, nucleotide sequences need not be contiguous to be operably linked.
The term, “operably linked,” when used in reference to a regulatory sequence and a coding sequence, means that the regulatory sequence affects the expression of the linked coding sequence. “Regulatory sequences,” “regulatory elements,” or “control elements,” refer to nucleotide sequences that influence the timing and level/amount of transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters; translation leader sequences; introns; enhancers; stem-loop structures; repressor binding sequences; termination sequences; polyadenylation recognition sequences; etc. Particular regulatory sequences may be located upstream and/or downstream of a coding sequence operably linked thereto. Also, particular regulatory sequences operably linked to a coding sequence may be located on the associated complementary strand of a double-stranded nucleic acid molecule. In a further example, a right and left T-DNA border when operably linked to a T-DNA sequence will allow the transfer of the T-DNA from a plasmid to another location.
When used in reference to two or more amino acid sequences, the term “operably linked” means that the first amino acid sequence is in a functional relationship with at least one of the additional amino acid sequences.
As used herein, the term “transformation” or “transforming” refers to the transfer and integration of a nucleic acid or fragment thereof into a host organism, resulting in genetically stable inheritance. Host organisms containing a transforming nucleic acid are referred to as “transgenic,” “recombinant,” or “transformed” organisms. Known methods of transformation include, for example: Agrobacterium-mediated transformation (e.g., using a Agrobacterium tumefaciens, Agrobacterium rhizogenes, or another Agrobacterium bacterial strain to transform the plant material); calcium phosphate transformation; polybrene transformation; electroporation; ultrasonic methods (e.g., sonoporation); liposome transformation; microinjection; transformation with naked DNA; transformation with plasmid vectors; transformation with viral vectors; biolistic transformation (e.g., microparticle bombardment); silicon carbide WHISKERSTM-mediated transformation; aerosol beaming; and PEG-mediated transformation.
The terms “plasmid” and “vector,” as used herein are interchangeable and refer to a recombinant element that can autonomously replicate or integrate into a chromosome in a host cell and which carries one or more gene(s) that are heterologous to the host cell. Plasmids and vectors typically are circular double-stranded DNA molecules. However, plasmids and vectors may be linear or circular nucleic acids, of a single- or double-stranded DNA or RNA, and may be derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction that is capable of introducing a promoter fragment and a coding polynucleotide sequence along with any appropriate 3′ untranslated sequence into a cell. In examples, plasmids and vectors may comprise autonomously replicating sequences, genome integrating sequences, and/or phage or nucleotide sequences.
The term “gene expression cassette” refers to a nucleic acid construct comprising a heterologous nucleic acid which encodes a polypeptide under the control of a promoter, and terminated by a 3′-UTR.
The term “selectable marker” refers to a gene or polynucleotide whose expression allows identification of cells that have been transformed with a DNA construct or vector containing the gene or polynucleotide. Non-limiting examples of selectable markers include herbicide tolerance, antibiotic resistance, and visual reporter markers.
The term “synthesis” or “synthesize,” refers to formation of a particular chemical compound from its constituent parts using an enzymatic synthesis or chemical processes.
The term “derivative,” as used herein, refers to a modification of a sequence set forth in the present disclosure. Illustrative of such modifications would be the substitution, insertion, and/or deletion of one or more bases relating to a nucleic acid sequence of a coding sequence or an operon within a plasmid/vector disclosed herein that preserve, slightly alter, or increase the function of a coding sequence disclosed herein in bacterial species. Such derivatives can be readily determined by one skilled in the art, for example, using computer modeling techniques for predicting and optimizing sequence structure. The term “derivative” thus also includes nucleic acid sequences having substantial sequence identity with the disclosed coding sequences herein such that they are able to have the disclosed functionalities for use in producing embodiments of the present disclosure.
DETAILED DESCRIPTION
The disclosed invention provides a new class of polypeptides each referred to herein as a cytokinin synthase. The disclosed invention also provides polynucleotides that encode the cytokinin synthase. The cytokinin synthase of the invention has two domains: an isopentenyl transfer (IPT)-like domain and a phosphoribohydrolase (PRH)-like domain. In particular embodiments, the IPT-like domain and the PRH-like domain can be covalently linked together, as shown in FIG. 1.
Unlike conventional adenosine phosphate isopentenyltransferases (IPTs) in plants and Agrobacterium, the disclosed cytokinin synthase is covalently linked to a PRH-like domain. Furthermore, the IPT-like domain of the disclosed cytokinin synthase does not closely resemble the amino acid sequences of known IPTs in plants or Agrobacteria, nor does it closely resemble known tRNA-IPT enzymes. For example, the Epichloe festucae cytokinin synthase (EfCKS) disclosed herein comprises an IPT-like domain with less than 30% sequence identity to yeast tRNA-IPT and even lower sequence identity to plant (Arabidopsis) adenylate isopentenyltransferase (plant IPT1) and less than 10% sequence identity to the canonical Agrobacterium IPT. Surprisingly, the disclosed cytokinin synthase exhibits activity in multiple assays for de novo biosynthesis of cytokinin (iP) from adenosine 5′monophosphate (AMP).
The surprising nature of the activity disclosed herein is underscored by the fact that there is very little characterization of enzymes containing PRH domains. Moreover, genes that encode PRH-like domains are found in many organisms that do not make cytokinins. Therefore, the disclosed cytokinin synthase activity was not predictable before the invention disclosed herein linked cytokinin synthases to cytokinin production.
Isolated Polynucleotides and Codon-Optimized Polynucleotides
In one aspect, the invention provides an isolated polynucleotide that includes a sequence encoding the two-domain cytokinin synthase disclosed herein. As used herein the term isolated means that the polynucleotide has been removed from its natural environment or that the polynucleotide has been non-naturally synthesized or amplified, e.g., in a laboratory or industrial setting. Thus, in one embodiment the invention provides an isolated polynucleotide that encodes the cytokinin synthase of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS). The invention also provides an isolated polynucleotide that encodes the cytokinin synthase of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54. In certain embodiments, the isolated polynucleotide is a purified polynucleotide, e.g., one that is substantially free of other molecules normally associated with such a polynucleotide or a similar one in its native or natural environment. Accordingly, for example, the isolated polynucleotide encoding the cytokinin synthase of SEQ ID NO:3, SEQ ID NO:9, SEQ ID NO:13, SEQ ID NO:17, SEQ ID NO:21, or SEQ ID NO:25 can be purified so that the isolated polynucleotide is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of non-polynucleotide, cellular material by dry weight. Also, for example, the isolated polynucleotide encoding the cytokinin synthase of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54 can be purified so that the isolated polynucleotide is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of non-polynucleotide, cellular material by dry weight. Methods of achieving and confirming the purity of polynucleotides are known in the art. See e.g., Tan et al., J. Biomedicine and Biotech., Article ID 574398 (2009); Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001); and Adila et al. Mal. J. Microbiol., 3(1): 7-13 (2007).
In particular embodiments, the isolated polynucleotide encoding the foregoing cytokinin synthase is SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:20 (AhCKS), or SEQ ID NO:24 (FfCKS), respectively; and in certain examples of these embodiments, the isolated polynucleotide is purified so that the isolated polynucleotide is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of non-polynucleotide, cellular material by dry weight.
In other embodiments, the invention provides an isolated polynucleotide encoding a cytokinin synthase that is homologous to each of the foregoing cytokinin synthases, wherein the encoded homolog has cytokinin synthase activity. The isolated polynucleotide includes a polynucleotide encoding a cytokinin synthase that is substantially homologous to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), SEQ ID NO:25 (FfCKS), SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54. As shown by the amino acid sequence identity analysis in Example 4, the invention provides polynucleotides and encoded cytokinin synthases that have at least 57% or 58% amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS) and have cytokinin synthase activity. The invention also provides polynucleotides and encoded cytokinin synthases that have at least 60%, at least 62%, at least 63%, at least 64% at least 65%, at least 66%, at least 67%, at least 70%, or at least 75% amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS) and have cytokinin synthase activity. In another embodiment, the invention provides polynucleotides and encoded cytokinin synthases that have from about 80% to about 100% amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS). In certain examples, the isolated polynucleotide encodes a cytokinin synthase that has about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS). In additional examples, the invention provides an isolated polynucleotide that encodes a cytokinin synthase that has about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54. Optionally, the isolated polynucleotide encoding a cytokinin synthase is purified so that the isolated polynucleotide is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of non-polynucleotide, cellular material by dry weight. Amino acids that may be varied and those that should be largely conserved in homologous cytokinin synthases are discussed in more detail below. The cytokinin synthase activity homologous cytokinin synthases can be determined by any method, e.g., the methods disclosed herein or known in the art.
In still another embodiment, the invention provides additional isolated polynucleotide that encodes a cytokinin synthase, wherein the polynucleotide is substantially homologous to one of SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:20 (AhCKS), or SEQ ID NO:24 (FfCKS). The substantially homologous isolated polynucleotide can have, for example, from about 80% to about 100% nucleotide sequence identity to one of SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:20 (AhCKS), or SEQ ID NO:24 (FfCKS). For example, the polynucleotide can have about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more nucleotide sequence identity to one of SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:20 (AhCKS), or SEQ ID NO:24 (FfCKS). Optionally, this isolated polynucleotide encoding a cytokinin synthase is purified so that the isolated polynucleotide is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of non-polynucleotide, cellular material by dry weight.
In another aspect, the invention also provides an isolated polynucleotide encoding any of the cytokinin synthases disclosed herein, wherein the coding sequence is codon-optimized for expression in a host cell. Specific host cells and methods for codon-optimizing the coding sequence are known in the art and described herein. Thus in one embodiment of this aspect, the invention provides an isolated polynucleotide that includes a coding sequence that (i) encodes the cytokinin synthase of one of SEQ ID NO:3, SEQ ID NO:9, SEQ ID NO:13, SEQ ID NO:17, SEQ ID NO:21, or SEQ ID NO:25 and (ii) is codon-optimized for expression in a host cell such as, for example, bacteria, yeast, plant, dicot plant, monocot plant, maize, soybean, canola, cotton, wheat, Arabidopsis thaliana, rice, sunflower, grass, creeping bentgrass, tall fescue, tobacco, or poplar hybrid cell. In another embodiment, the invention provides an isolated polynucleotide that includes a coding sequence that (i) encodes the cytokinin synthase of one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54 and (ii) is codon-optimized for expression in a host cell such as, for example, bacteria, yeast, plant, dicot plant, monocot plant, maize, soybean, canola, cotton, wheat, Arabidopsis thaliana, rice, sunflower, grass, creeping bentgrass, tall fescue, tobacco, or poplar hybrid cell.
In a further embodiment, the invention provides an isolated polynucleotide that includes a coding sequence that (i) encodes a cytokinin synthase having at least about 57%, at least about 58%, at least 60%, at least 62%, at least 63%, at least 64% at least 65%, at least 66%, at least 67%, at least 70%, or at least 75% amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS) and (ii) is codon-optimized for expression in a host cell such as, for example, bacteria, yeast, plant, dicot plant, monocot plant, maize, soybean, canola, cotton, wheat, Arabidopsis thaliana, rice, sunflower, grass, creeping bentgrass, tall fescue, tobacco, or poplar hybrid cell. In certain embodiments, the invention provides an isolated polynucleotide that includes a coding sequence that (i) encodes a cytokinin synthase having from about 80% to about 100% amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS) and (ii) is codon-optimized for expression in a host cell such as, for example, bacteria, yeast, plant, dicot plant, monocot plant, maize, soybean, canola, cotton, wheat, Arabidopsis thaliana, rice, sunflower, grass, creeping bentgrass, tall fescue, tobacco, or poplar hybrid cell. For example, the codon-optimized isolated polynucleotide can encode a cytokinin synthase having about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS). In another example, the invention provides an isolated polynucleotide that includes a coding sequence that (i) encodes a cytokinin synthase having about 80% or more; 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54 and (ii) is codon-optimized for expression in a host cell such as, for example, bacteria, yeast, plant, dicot plant, monocot plant, maize, soybean, canola, cotton, wheat, Arabidopsis thaliana, rice, sunflower, grass, creeping bentgrass, tall fescue, tobacco, or poplar hybrid cell. Amino acids that may be varied and those that should be largely conserved in homologous cytokinin synthases are discussed in more detail below. Optionally, the isolated codon-optimized polynucleotide encoding a cytokinin synthase is purified so that the isolated polynucleotide is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of non-polynucleotide, cellular material by dry weight.
The codon-optimized polynucleotides of the invention can be codon optimized for expression in bacteria, yeast, plant, dicot plant, monocot plant, maize (Zea mays), soybean (Glycine max), canola (Brassica napus or Brassica rapa), cotton (Gossypium hirsutum or Gossypium barbadense, wheat (e.g., Triticum aestivum or Triticum durum), or Arabidopsis thaliana, rice (e.g., Oryza sativa). In other embodiments the codon-optimized polynucleotides of the invention can be codon optimized for expression in sunflower (Helianthus annuus), grass, creeping bentgrass (e.g., Agrostis stolonifera), tall fescue (Festuca arundinacea), tobacco (Nicotiana tabacum), and poplar (e.g., members of genus Populus) hybrid or Liriodendron tulipifera. Methods of optimizing codon based on the codon usage frequency and patterns observed in particular species are well known and can be done, for example, using publicly available codon usage databases and software packages. See, e.g., Nakamura et al., Nucl. Acids Res., 28(1): 292 (2000); Bode et al., Nucl. Acids Res., 37 (Web Server issue):W214-221 (2009); Liu et al., Mol. Biol. Rep., 37(2)6777-684 (2010); Y. Batard et al., Arch. Biochem. Biophys., 379: 161-169 (2000); Gustafsson et al., Trends in Biotech, 22(7): 346-3536 (2004).
Any of the isolated polynucleotides of the invention can be synthesized de novo using methods for artificial gene synthesis that do not require pre-existing nucleic acid template. In some embodiments, such methods involve solid-phase DNA synthesis of gene fragments that are subsequently assembled, e.g., by annealing, ligation, and/or polymerase reactions to generate a completely synthetic isolated polynucleotides of the invention. See, e.g., Schwartz et al., Nat. Methods, 9(9): 913-915 (2012) and Tian et al., Mol. BioSyst., 5:714-722 (2009). In other embodiments, the isolated polynucleotides of the invention can be generated by more conventional recombinant techniques such as cloning, amplification by polymerase chain reaction (PCR), and/or mutagenesis (if needed). For example, cDNA encoding a cytokinin synthase may be generated from a plant associated fungus such as Epichloe festucae, Epichloe gansuensis, Balansia obtecta, Ilyonectria radicola, Aciculosporium take, Atkinsonella hypoxylon, or Fusarium fujikuroi to make a non-natural polynucleotide encoding a two-domain cytokinin synthase of the invention such as EfCKS, BoCKS, IrCKS, AtCKS, AhCKS, or FfCKS, respectively. Such cDNA may be modified by PCR, mutagenesis, site directed mutagenesis to make a variant, e.g., a codon-optimized, isolated polynucleotide of the invention.
Recombinant Polynucleotides, Host Cells and Related Methods
In a further aspect, the invention provides a recombinant polynucleotide that includes any of the cytokinin synthase-encoding polynucleotides disclosed herein covalently linked to a heterologous polynucleotide sequence. The heterologous sequence can be any sequence not found in nature covalently linked to the cytokinin synthase coding sequence. Examples of such a heterologous sequence include a heterologous promoter sequence, vector sequence, a gene cassette sequence, a promoter sequence, a termination sequence, or a sequence encoding a protein fusion tag.
Thus, in one embodiment, the invention provides a recombinant polynucleotide that includes a heterologous sequence covalently linked to one of the following sequences encoding a polypeptide with cytokinin synthase activity, wherein the linked coding sequence:
(i) encodes the cytokinin synthase SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS);
(ii) encodes a cytokinin synthase that is substantially homologous to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS);
(iii) encodes a cytokinin synthase that has about 57% or more, about 58% or more, about 60% or more, about 62% or more, about 63% or more, about 64% or more, about 65% or more, about 66% or more, about 67% or more, about 70% or more, about 75% or more, about 80% or more, about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS);
(iv) includes SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:20 (AhCKS), or SEQ ID NO:24 (FfCKS);
(v) includes a sequence that is substantially homologous to one of SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:20 (AhCKS), or SEQ ID NO:24 (FfCKS);
(vi) includes a sequence that has about 57% or more, about 58% or more, about 60% or more, about 62% or more, about 63% or more, about 64% or more, about 65% or more, about 66% or more, about 67% or more, about 70% or more, about 75% or more, about 80% or more, 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more nucleotide sequence identity to one of SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:20 (AhCKS), or SEQ ID NO:24 (FfCKS);
(vii) includes codon-optimized sequence encoding the cytokinin synthase of one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS),
(viii) includes codon-optimized sequence encoding a cytokinin synthase having has about 57% or more, about 58% or more, about 60% or more, about 62% or more, about 63% or more, about 64% or more, about 65% or more, about 66% or more, about 67% or more, about 70% or more, about 75% or more, about 80% or more, 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS);
(ix) includes codon-optimized sequence encoding cytokinin synthase variant having about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS),
(x) encodes the cytokinin synthase of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54;
(xi) encodes a cytokinin synthase that is substantially homologous to one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54;
(xii) encodes a cytokinin synthase that has about 57% or more, about 58% or more, about 60% or more, about 62% or more, about 63% or more, about 64% or more, about 65% or more, about 66% or more, about 67% or more, about 70% or more, about 75% or more, about 80% or more, about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54,
(xiii) includes a codon optimized sequence that encodes the cytokinin synthase of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54,
(xiv) includes a codon optimized sequence that encodes a cytokinin synthase that has about 57% or more, about 58% or more, about 60% or more, about 62% or more, about 63% or more, about 64% or more, about 65% or more, about 66% or more, about 67% or more, about 70% or more, about 75% or more, about 80% or more, about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54 or
(xv) the two-domain cytokinin synthase coding sequences of any one of foregoing (i)-(xiv), wherein the coding sequence, when aligned with the consensus sequence (of SEQ ID NO:3, SEQ ID NO:9, SEQ ID NO:13, SEQ ID NO:17, SEQ ID NO:21, and SEQ ID NO:25) in FIG. 6, also includes (i) a first motif: GPTXaa1Xaa2GKT (SEQ ID NO:30), wherein Xaa1 is G or A and Xaa2 is V, S, A, or T, at consensus sequence amino acid positions 13-20; (ii) a second motif: PXaa3Xaa4Xaa5GGSXaa6S (SEQ ID NO:31), wherein Xaa3 is I or V, Xaa4 is L or V, Xaa5 is V or C, and Xaa6 is T or I, at consensus sequence amino acid positions 96-104; (iii) a third motif: Xaa7Xaa8YGGG (SEQ ID NO:32), wherein Xaa7 is L or I, and Xaa8 is V or I, at consensus sequence amino acid positions 333-338, and (iv) a fourth motif: Xaa9GGYGT Xaa10EEL (SEQ ID NO:33), where Xaa9 is S or P and Xaa10 is L or M, at consensus sequence amino acid positions 426-438. The term “when aligned with the consensus sequence” in FIG. 6, means that the cytokinin synthase coding sequence of (xv) is aligned with SEQ ID NO:3, SEQ ID NO:9, SEQ ID NO:13, SEQ ID NO:17, SEQ ID NO:21, and SEQ ID NO:25, as described in Example 6 herein. The schematic in FIG. 30 shows the relative positions of the four motifs within a two-domain cytokinin synthase coding sequence of (xv).
In certain embodiments of the invention, the recombinant polynucleotide includes any of the foregoing two-domain cytokinin synthase coding sequences (i)-(xv) covalently linked to a vector sequence, expression cassette, heterologous promoter (e.g., a plant promoter, bacterial promoter, a heterologous fungal promoter, or a yeast promoter), or heterologous terminator sequence (e.g., for use in plants, bacteria, or yeast). The recombinant polynucleotide can be used for recombinant expression of the encoded cytokinin synthase in a host cell such as a bacteria, yeast or plant. Thus, the recombinant polynucleotide can include the coding sequence of (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for expression in bacteria and which is covalently linked to bacterial vector, expression cassette, and/or promoter. The recombinant polynucleotide can include the coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is coding optimized for expression in yeast and which is covalently linked to yeast vector, expression cassette, and/or promoter. The recombinant polynucleotide can include the coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is coding optimized for expression in a plant and which is covalently linked to plant vector, expression cassette, and/or promoter. In particular examples, recombinant polynucleotide includes the coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for expression in a dicot plant or a monocot plant and which is covalently linked to a vector, expression cassette, and/or promoter for a dicot plant or monocot plant, respectively. In other particular examples, recombinant polynucleotide includes the coding sequence (vii), (viii), or (ix), (xiii), (xiv), or (xv) which is optimized for expression in a maize, soybean, canola, cotton, wheat, or Arabidopsis thaliana and which is covalently linked to a vector, expression cassette, and/or promoter for maize, soybean, canola, cotton, wheat, or Arabidopsis thaliana, respectively. In still other particular examples, recombinant polynucleotide includes the coding sequence of (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for expression in rice, sunflower, grass, creeping bentgrass, tall fescue, tobacco, or poplar hybrid and which is covalently linked to a vector, expression cassette, and/or promoter for rice, sunflower, grass, creeping bentgrass, tall fescue, tobacco, or poplar hybrid, respectively. Vectors, expression cassettes, and promoters are discussed in more detail below.
In additional examples, the recombinant polynucleotide can include the coding sequence of (vii), (viii), (ix), (xiii), (xiv), or (xv) which is coding optimized for expression in a plant and which is covalently linked to plant vector or expression cassette. The recombinant polynucleotide can include the coding sequence of (vii), (viii), (ix), (xiii), (xiv), or (xv) which is coding optimized for expression in yeast or bacteria host cell and which is covalently linked to yeast promoter or bacterial promoter, respectively.
In other embodiments of the invention, the recombinant polynucleotide includes any of the foregoing two-domain cytokinin synthase coding sequences (i)-(ix) covalently linked to a sequence encoding a protein fusion tag. The encoded protein fusion tag can be a poly-histidine, poly-arginine, haloalkane dehalogenase, streptavidin-binding, glutathione s-transferase (GST), maltose-binding protein (MBP), thioredoxin, small ubiquitin-like modifier (SUMO), N-utilization substance A (NusA), protein disulfide isomerase I (DsbA), Mistic, Ketosteroid isomerase (KSI), or TrpE, c-myc, hemaglutinin antigen (HA), FLAG, 1D4, calmodulin-binding peptide, chitin-binding domain, cellulose-binding domain, S-tag, or Softag3 protein fusion tag. These can be used in methods of producing, isolating, or purifying any cytokinin synthase of the invention.
Host Cells, Plants, and Methods of Making Recombinant Cytokinin Synthase of the Invention
In another aspect the invention also provides a host cell that includes any embodiment or example of the isolated or recombinant polynucleotide disclosed herein that encodes a cytokinin synthase. In another aspect the invention provides a method of making such a host cell that includes, transforming or transfecting the isolated or recombinant polynucleotide of the invention into a host cell. Accordingly, the invention provides a bacteria, yeast or plant host cell which harbors the recombinant polynucleotide disclosed above that includes one (or more) of the foregoing two-domain cytokinin synthase coding sequences (i)-(ix). In certain embodiments, the two domain recombinant polynucleotide includes the codon-optimized two-domain cytokinin synthase coding sequences (vii), (viii), or (ix) in the appropriate host cell for which the polynucleotide is codon-optimized. For example, the invention provides a bacteria cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), or (ix), which is optimized for bacteria. In another example, the invention provides a yeast cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), or (ix), which is optimized for yeast. Methods for the transformation or transfection of bacterial and yeast host cells are known in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001) and Ausubel et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience (1987).
In still other examples, the invention provides: a transgenic dicot plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for dicots; a transgenic monocot plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for monocots; a transgenic maize plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), or (ix), which is codon-optimized for maize; a transgenic soybean plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for soybean; a transgenic canola plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for canola; a transgenic cotton plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (viii) or (ix) which is optimized for cotton; a transgenic wheat plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for wheat; and a transgenic Arabidopsis thaliana plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for Arabidopsis thaliana. In yet other examples the invention provides: a transgenic rice plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), which is codon-optimized for rice; a transgenic sunflower plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for sunflower; a transgenic creeping bentgrass plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for creeping bentgrass; a transgenic tall fescue plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for tall fescue; a transgenic tobacco plant cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for tobacco; and a transgenic poplar cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for poplar.
In another aspect, the invention provides a transgenic plant that is regenerated from any of the foregoing plant host cells. In this regard the recombinant polynucleotide can include the codon-optimized coding sequence of (vii), (viii), (ix), (xiii), (xiv), or (xv) described above, which is covalently linked to a vector or expression cassette for the plant transformant. For example, the invention provides a transgenic dicot plant that includes codon-optimized coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for dicots and which is for example in an appropriate vector or expression cassette; a transgenic monocot plant that includes codon-optimized coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for monocots; a transgenic maize plant that includes codon-optimized coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for maize; a transgenic soybean plant that includes codon-optimized coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for soybean; a transgenic canola plant that includes codon-optimized coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for canola; a transgenic cotton plant that includes codon-optimized coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for cotton; a transgenic wheat plant that includes codon-optimized coding sequence (viii) (ix), (xiii), (xiv), or (xv) which is optimized for wheat; a transgenic Arabidopsis thaliana plant that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for Arabidopsis thaliana, and a transgenic rice plant that includes codon-optimized coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for rice. In yet other examples the invention provides: a transgenic sunflower plant that includes the codon-optimized coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for sunflower; a transgenic creeping bentgrass plant that includes codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for creeping bentgrass; a transgenic tall fescue plant that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for tall fescue; a transgenic tobacco plant that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for tobacco; and a transgenic poplar that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is codon-optimized for poplar.
Methods of transforming plants to make transgenic plants are known in the art and discussed in more detail below.
The invention also provides methods of making a recombinant cytokinin synthase disclosed herein. In one aspect the method includes expressing cytokinin synthase in any of the foregoing host cells which includes any of the two-domain cytokinin synthase coding sequences (i)-(xv). In certain embodiments, the host cell has includes a recombinant polynucleotide in which the cytokinin synthase coding sequence of any one of (i)-(xv) disclosed above is covalently linked to a sequence encoding a protein fusion tag to facilitate detecting, isolating, and or purifying the cytokinin synthase encoded by anyone of (i)-(xv). In particular embodiments, the host cell includes a recombinant polynucleotide that includes the codon-optimized two-domain cytokinin synthase coding sequences (vii), (viii), (ix), (xiii), (xiv), or (xv) in the appropriate host cell for which the polynucleotide is codon-optimized. For example, the method of making a recombinant cytokinin synthase of the invention can include expressing cytokinin synthase in a bacteria cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for bacteria and which, optionally, is covalently linked to a protein fusion tag. In another example, the method can include expressing cytokinin synthase in a yeast cell that includes the codon-optimized two-domain cytokinin synthase coding sequence (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for yeast and which, optionally, is covalently linked to a protein fusion tag.
In further embodiments the method can include isolating the expressed cytokinin synthase from the host cell and, optionally, purifying the encoded cytokinin synthase so that it is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of host cellular material, e.g., by dry weight.
Isolated or Recombinant Cytokinin Synthase of the Invention
In another aspect, the invention provides an isolated or recombinant cytokinin synthase having two domains: an isopentenyl transfer (IPT)-like domain and a cytokinin nucleotide phosphoribohydrolase (PRH)-like domain. In one embodiment, the invention provides the isolated or recombinant cytokinin synthase of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS). In another embodiment, the invention provides the isolated or recombinant cytokinin synthase of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54. In certain embodiments, the isolated cytokinin synthase is purified and is substantially free of other molecules normally associated with such a polynucleotide or a similar one in its native or natural environment. Accordingly, for example, the isolated or recombinant cytokinin synthase of SEQ ID NO:3, SEQ ID NO:9, SEQ ID NO:13, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:25, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54 can be purified so that the cytokinin synthase is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of cellular and other (non-cytokinin synthase) material by dry weight. The extent that purified cytokinin synthase is free of other material can be readily determined by art-known methods, including for example, analysis by SDS-PAGE and with protein staining. See e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001).
In another embodiment, the invention provides an isolated or recombinant cytokinin synthase that is homologous to each of the foregoing cytokinin synthases and has cytokinin synthase activity. The isolated or recombinant cytokinin synthase can be substantially homologous to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), SEQ ID NO:25 (FfCKS), SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54. For example, the isolated or recombinant can have about 57% or more, about 58% or more, about 60% or more, about 62% or more, about 63% or more, about 64% or more, about 65% or more, about 66% or more, about 67% or more, about 70% or more, about 75% or more, or from about 80% to about 100% amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS). In certain examples, the isolated or recombinant cytokinin synthase has about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS). In further examples, the isolated or recombinant cytokinin synthase has about 80 or more; 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54. Optionally, the isolated or recombinant cytokinin synthase variant is purified so that the isolated polynucleotide is more than 50%, more than 60%, more than 70%, more than 80, more than 90%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% free of cellular or other material by dry weight.
Amino acids may be varied by substitutions, deletions, or additions to the particular cytokinin synthase of the invention using the guidance provided by the sequence alignment shown at FIG. 6. The cytokinin synthase derivatives thus generated can be readily tested to confirm cytokinin synthase activity using any known method, e.g., the methods disclosed herein or methods known in the art. See, e.g., Barry et al., Proc. Nat'l. Acad. Sci. USA, 81: 4776-4780 (1984) and Kakimoto, Plant Cell Physiol., 42 (7): 677-685 (2001). In this regard, the sequence of SEQ ID NO:25 (FfCKS) is only about 60% identical to the sequence of either SEQ ID NO:9 (AtCKS) or SEQ ID NO:21 (AhCKS), yet all three exhibit cytokinin synthase activity shown in FIG. 6. The sequences of SEQ ID NO:17 (IrCKS) is less than 70% identical to SEQ ID NO:3 (EfCKS) or SEQ ID NO:13 (BoCKS), yet all three of these also exhibit the cytokinin synthase activity shown in FIG. 6. Therefore, a person of ordinary skill in the art would understand that functional cytokinin synthase derivatives of the foregoing sequences can readily be made by multiple substitutions, deletions, or additions. In particular embodiments, functional cytokinin synthase derivatives can include multiple substitutions, deletions, or additions when most or all of the conserved amino acid residues identified in FIG. 6 are not varied.
Conserved amino acid residues within the cytokinin synthases in FIG. 6 are indicated by boxes. In particular embodiments of the invention, a cytokinin synthase derivative is made based on one of the sequences in FIG. 6, without varying any of the indicated conserved amino acids residues (except for the starting methionine at first position of the depicted sequences which can be readily varied, for example, when adding a protein fusion tag). In other embodiments, a small number (e.g., 1, 2, 3, 4, 5, or 6) of such conserved residues may be varied by conservative substitutions.
Additionally, cytokinin synthases can be varied at conserved amino acid positions identified as having a small effect of cytokinin synthase activity. FIG. 6 shows conserved amino acids that, when altered, have a small effect on activity by open diamond (indicated by open diamond ⋄). Polynucleotides encoding cytokinin synthases that include mutations having a small effect on cytokinin synthase activity can be used when, for example, lower than wild type activity is desirable. Accordingly, the invention provides cytokinin synthases having activities that range from wild type activity to activities reduced by a small amount (e.g., mutants identified in FIG. 6 and Table 9 below as having a small effect). FIG. 6 also shows mutations to amino acids identified as having a severe effect on activity (indicated by wedge (▴) in FIG. 6. See Example 5 and Tables 8 and 9 below for more details on the effects of mutating various conserved amino acids in the cytokinin synthases specifically disclosed herein.
Additionally, considering the significant variation in sections of non-conserved amino acid residues (residues that are not boxed) among the cytokinin synthase sequences in FIG. 6 and the cytokinin synthase activity assay results disclosed in the Examples herein, it is readily apparent that each of the sequences of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), SEQ ID NO:25 (FfCKS) SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, and SEQ ID NO:54 can be varied to include up to 5, up to 10, up to 15, up to 20, up to 25, up to 30, up to 35, or up to 40 amino acid additions, deletions, or substitutions while still retaining cytokinin synthase activity. In this regard, a high probability of retaining activity will also occur if the variations are conservative substitutions. Amino acids may be placed in the following classes: non-polar, uncharged polar, basic, and acidic. Conservative substitutions whereby an amino acid of one class is replaced with another amino acid of the same type are least likely to materially alter the biological activity of the variant. Table 1 provides a listing of examples of amino acids belonging to each class.








TABLE 1





Class of Amino Acid
Examples of Amino Acids







Nonpolar Side Chains
Ala, Val, Leu, Ile, Pro, Met, Phe, Trp


Uncharged Polar Side Chains
Gly, Ser, Thr, Cys, Tyr, Asn, Gln


Acidic Side Chains
Asp, Glu


Basic Side Chains
Lys, Arg, His


Beta-branched Side Chains
Thr, Val, Ile


Aromatic Side Chains
Tyr, Phe, Trp, His









In some instances, non-conservative substitutions can also be made. The critical factor is that these substitutions must not significantly detract from the cytokinin synthase activity of the variant. Cytokinin synthase variants can also be designed that differ at the sequence level but that retain the same or similar overall essential three-dimensional structure, surface charge distribution, and the like. See, e.g., U.S. Pat. No. 7,058,515; Larson et al., Protein Sci., 11: 2804-2813 (2002); Stemmer, Nature, 370: 389-391 (1994); Stemmer, Bio/Technology, 13: 549-553 (1995) and Crameri et al. Nat. Med., 2: 100-103. (1996), Crameri et al., Nat. Biotech. 14: 315-319 (1996), Crameri et al., Nat. Biotech., 15: 436-438 (1997), and U.S. Pat. No. 8,513,492. For example, conservative substitutions of alanine for methionine or leucine (shown at positions 343 or 367, respectively, of the consensus alignment in FIG. 6) did not substantially affect the activity of the cytokinin synthase mutant.
In particular examples of the foregoing, the isolated or recombinant cytokinin synthases is covalently linked to a protein fusion tag. Thus, the invention provides an isolated cytokinin synthase that includes a protein fusion tag linked to
(a) the cytokinin synthase of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS);
(b) a cytokinin synthase that is substantially homologous to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS);
(c) a cytokinin synthase that has about 57% or more, about 58% or more, about 60% or more, about 62% or more, about 63% or more, about 64% or more, about 65% or more, about 66% or more, about 67% or more, about 70% or more, about 75% or more amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS);
(d) a cytokinin synthase that has about 80% to about 100% amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS);
(e) a cytokinin synthase that has about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS),
(f) a cytokinin synthase that includes the sequence of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), and SEQ ID NO:25 (FfCKS) with up to 5, up to 10, up to 15, up to 20, up to 25, up to 30, up to 35, or up to 40 amino acid additions, deletions, or substitutions,
(g) the cytokinin synthase of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54,
(h) a cytokinin synthase that has about 80% or more; about 81% or more; about 82% or more; about 83% or more; about 84% or more; about 85% or more; about 86% or more; about 87% or more; about 88% or more; about 89% or more; about 90% or more; about 91% or more; about 92% or more; about 93% or more; about 94% or more; about 95% or more; about 96% or more; about 97% or more; about 98% or more; about 98.5% or more; about 99% or more; about 99.5% or more; or about 99.9% or more amino acid sequence identity to one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54,
(i) a cytokinin synthase that includes the sequence of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54 with up to 5, up to 10, up to 15, up to 20, up to 25, up to 30, up to 35, or up to 40 amino acid additions, deletions, or substitutions, or
(j) the cytokinin synthase of any one of foregoing (a), (b), (c), (d), (e), (f), (g), (h), or (i), wherein the sequence, in alignment with coding sequences in FIG. 6, includes the motifs corresponding to FIG. 6 alignment consensus positions 13-20 (SEQ ID NO:30), at consensus positions 96-104 (SEQ ID NO:31), at consensus positions 333-338 (SEQ ID NO:32), and at consensus/alignment positions 426-438 (SEQ ID NO:33)
In particular examples, the cytokinin synthase of (a), (b), (c), (d), (e), (f), (g), (h), (i) or (j) is linked to a protein fusion tag that is a poly-histidine, poly-arginine, haloalkane dehalogenase, streptavidin-binding, glutathione s-transferase (GST), maltose-binding protein (MBP), thioredoxin, small ubiquitin-like modifier (SUMO), N-utilization substance A (NusA), protein disulfide isomerase I (DsbA), Mistic, Ketosteroid isomerase (KSI), or TrpE, c-myc, hemaglutinin antigen (HA), FLAG, 1D4, calmodulin-binding peptide, chitin-binding domain, cellulose-binding domain, S-tag, or Softag3 protein fusion tag.
Formulations of Cytokinins and Methods of Use
The isolated or recombinant cytokinins of the invention, e.g., the cytokinin synthase of (a), (b), (c), (d), (e), (f), (g), (h), (i) or (j) above, can be mixed with inert ingredients to create formulations which are useful for application to food crops, feed crops, vegetable crops, greenhouse food crops, greenhouse, non-food crops, outdoor residential plants forestry planting, and/or indoor residential plants.
Thus, the invention provides cytokinin synthase formulations that include a cytokinin (produced by a cytokinin synthase of the invention described herein) in mixture with one or more suitable inert ingredients suitable for application to one or more of the following plant classes:
Food crops: anise, asparagus, banana, broccoli, brussels sprouts, cabbage, carrot (including tops), catjang (jerusalem/marble pea), cauliflower, celery, cucumber, eggplant, fennel, garbanzos (including chick peas), garlic, leek, lettuce, melons, cantaloupe, honeydew, muskmelons, watermelons, okra, onion, parsley, peach, pepper, pepper (chili type), plantain, pumpkin, radish, shallot, spinach, squash (all or unspecified), strawberry, sweet potato, wheat, yam
Food+Feed crops: apple; beans; beans, dried-type; beans, mung; beans, succulent (lima); beans, succulent (snap); beets; citrus fruits; corn; corn, field; corn (pop; or sweet); cotton; cowpea/blackeyed pea; grapes; leafy vegetables; orange; peanuts; peas, field; peas, pigeon; peas, southern; potato, white/irish; rice; sorghum; sorghum; soybeans sugar beet; tomato; triticale; wheat
Feed crops: alfalfa, capes, lupine
Greenhouse Food crops: asparagus; banana; beans; broccoli; broccoli, Chinese; Brussels sprouts; cabbage; carrot (including tops); cauliflower; celery; corn, pop; corn, sweet; cucumber; cucurbit vegetables; eggplant; lettuce; melons; nectarine; onion; parsley; parsley, turnip-rooted; peach; pepper; pepper (chili type); plantain; potato, white/irish; pumpkin; radish; shallot; spinach; squash (all or unspecified); squash (winter); squash (zucchini); strawberry; sweet potato; tomato
Non-Food Crop: commercial/industrial lawns, fruits (unspecified), golf course turf, jujube, ornamental lawns and turf, ornamental sod farm (turf), recreation area lawns, small fruits
Outdoor Residential and Greenhouse non-food: ornamental and/or shade trees, ornamental herbaceous plants, ornamental lawns and turf, ornamental nonflowering plants, ornamental woody shrubs and vines,
Forestry: forest plantings (reforestation programs), pine (forest/shelter belt)
Outdoor Residential: ornamental lawns and turf
Indoor Residential: ornamental trees, ornamental herbaceous plants, ornamental nonflowering plants
The invention also provides a method of applying a cytokinin as a plant regulator. The method includes applying a formulation that includes the cytokinin (produced by a cytokinin synthase of the invention described herein) in a mixture with one or more suitable inert ingredients to a plant belonging to one of the foregoing plant classes, i.e., a food crop, a food+feed crop, a feed crop, a greenhouse house food crop, a non-food crop, an outdoor residential or greenhouse non-food plant, forestry plant, an outdoor residential plant, or an indoor residential plant. In some applications the cytokinin formulation is applied at an appropriate pre-harvest interval, depending on the crop or plant class.
The cytokinin formulation provided by the invention for application to the plant classes described herein includes the cytokinin (produced by a cytokinin synthase of the invention described herein) mixed with one or more inert ingredients selected from a solvent or adjuvant. The resulting mixture can form a liquid formulation, water-soluble concentrate, emulsifiable concentrate, flowable suspension, an aqueous suspension, sprayable formulation, dry formulation, granule, pellet, wettable powder, soluble powder, water dispersible granule, or dry flowable formulation that includes the cytokinin produced by a cytokinin synthase of the invention described herein.
The invention also provides a method of manufacturing cytokinin for use in one or more of the foregoing cytokinin formulations. Generally, the method includes synthesizing or expressing a cytokinin synthase disclosed herein. The cytokinin synthase can be synthesized in vitro or expressed in a host cell. For example, host cells expressing cytokinin synthase can be cultured in fermentation containers. In some embodiments, the synthesized or expressed cytokinin synthase can be purified or isolated. In other embodiments, the synthesized or expressed cytokinin is used directly, without substantial purification or isolation or without any purification or isolation. The cytokinin synthase is provided with starting material substrate (e.g., adenosine monophosphate (AMP) or dimethylallyl diphosphate (DMAPP)), which the cytokinin synthase can then convert to a cytokinin (isopentenyl adenine). The cytokinin can be isolated or purified and then mixed with inert ingredients to make a cytokinin formulation.
Codon Optimization.
The invention provides polynucleotides encoding a cytokinin synthase, wherein the coding sequence has been modified for expression in a host cell (e.g., a plant cell).
The genetic code is redundant with 64 possible codons, but most organism preferentially use a subset of these codons. The codons that used most often in a species are called “optimal codons,” and those used less often are classified as “rare” or “low-usage codons.” Zhang et al. (1991) Gene 105:61-72. Codons may be substituted to reflect the preferred codon usage of a particular host in a process sometimes referred to as “codon optimization.” Optimized coding sequences containing codons preferred by a particular host may be prepared, for example, to increase the rate of translation, or to produce recombinant RNA transcripts having desirable properties (e.g., a longer half-life, as compared with transcripts produced from a non-optimized sequence).
In some embodiments, the invention provides codon-optimized nucleic acid that designed or derived from a desired polypeptide or gene product (for example, a particular cytokinin synthase polypeptide) to be expressed from the nucleic acid. In particular embodiments, the desired polypeptide to be expressed may be designed or derived from a reference amino acid sequence of interest; for example, a reference protein (e.g., SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), SEQ ID NO:25 (FfCKS), SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54) or reference protein domain (e.g., IPT-like domain or PRH-like domain).
In some embodiments, only the cytokinin synthase encoding region of a nucleic acid molecule is codon-optimized to design a synthetic cytokinin synthase gene of the invention. In particular embodiments, the nucleotide sequence of a synthetic nucleic acid molecule is optimized, such that the primary structure of an encoded polypeptide (e.g., a cytokinin synthase protein) is unchanged. The structure of an encoded polypeptide is determined, to the greatest extent, by the amino acid sequence of the polypeptide. Thus, a desired structure for an encoded polypeptide places limitations on its nucleotide coding sequence that are determined by the degeneracy of the genetic code and standard codon usage.
A synthetic nucleic acid sequence of the invention may be designed and produced for a variety of reasons known to those of skill in the art; e.g., to increase expression, to adapt the nucleic acid sequence to be expressed in a new host cell or organism, and to introduce functional and/or non-functional mutations into an encoded polypeptide. Typically in embodiments where a reference amino acid sequence is a naturally-occurring gene product (e.g., native cytokinin synthase), or portion of a naturally-occurring gene product (e.g., an isolated IPT-like or PRH-like domain), a naturally-occurring nucleic acid sequence encoding the reference amino acid sequence may be obtained, for example, by searching genome databases or cloning from a source genome. In many cases, homologues or orthologs of such nucleic acid sequences may also be found in the genomes of other organisms.
A variety of methods are available to those skilled in the art for optimizing the coding sequence of a nucleic acid molecule according to predetermined parameters. For example, the skilled artisan may optimize a coding sequence by inspection, e.g., to better conform to the codon usage bias of an expression host organism. More commonly, a computer-implemented software program may be used to optimize a coding sequence. Such software programs may comprise one or more algorithms that optimize factors selected from the group comprising: factors that may affect the expression of an encoded polypeptide of interest, factors that may affect the rate of translation initiation of a transcript, and factors that may affect the rate of translational elongation of the encoded polypeptide or its precursor. Particular examples of such software programs include, without limitation, OptGeneTM (Ocimum Biosolutions), Accelrys GCGTM (Accelrys Software, Inc.), OPTIMIZERTM (available for public use on the world-wide web at genomes.urv.es/OPTIMIZER), and OptimumGeneTM (GenScript). In some embodiments, polynucleotides encoding cytokinin synthase have been optimized for expression in both a monocot and dicot host cell, using a hemicodon table (US Patent Publication No. 2003/0182685 A1).
Codon optimization also includes, for example, the process sometimes referred to as “codon harmonization,” wherein codons of a codon sequence that are recognized as low-usage codons in the source organism are altered to codons that are recognized as low-usage in the new expression host. This process may help expressed polypeptides to fold normally by introducing natural and appropriate pauses during translation/extension. Birkholtz et al. (2008) Malaria J. 7:197-217.
Factors that may affect the expression of a polypeptide of interest that is encoded by a nucleic acid sequence may be influenced by the particular codons chosen to encode the amino acids of the polypeptide. Factors affecting the rate of production of mRNA from the template nucleic acid sequence may include: the RNA polymerase type used for transcription; the RNA polymerase level present in the expression system; and the transcription promoter sequence used. The mRNA levels may also be affected by the mRNA degradation rate, which in turn may be influenced by mRNA destabilizing motifs; RNAse recognition sequences; mRNA secondary structure; and polyA addition signals. The mRNA levels may also be affected by mRNA structures at the translational initiation site, at the ribosome binding site, at the start codon, and/or around the initial 10-50 codons of the coding sequence (or elsewhere within, or following, the open reading frame); transcriptional termination motifs present before or within the open reading frame; and signals within the transcribed sequence such as those that direct, alter, or modify mRNA splicing and/or nuclear export. A particular example of a factor affecting the rate of mRNA production from a template sequence is nucleotide repeat-induced polymerase slippage. Nucleotide repeat-induced polymerase slippage involves nucleotide sequence repeats that have been shown to cause slippage or stuttering of DNA polymerase which can result in frameshift mutations. Such nucleotide repeats can also cause slippage of RNA polymerase. For example, in an organism with a high G+C content bias, there can be a higher degree of G or C nucleotide repeats. Therefore, one method of reducing the possibility of inducing RNA polymerase slippage includes altering extended repeats of G or C nucleotides.
Factors that may affect the rate of translational initiation for a particular transcript include: the sequence of the ribosome binding site; sequences upstream of the ribosome binding site; sequences around the start codon (e.g., Kozak consensus sequences); the presence, relative location, and sequence of internal ribosome entry sites; the sequence and distance between the ribosome entry site (or the ribosome binding site or the 5′ end of the mRNA) and the start codon; the mRNA structures at the translational initiation site; the mRNA structures at the ribosome binding site; the mRNA structures at the start codon; the mRNA structures around the initial 10-50 codons of the coding sequence; the sequence of the initial 10-20 codons; the GC bias of the initial 10-20 codons; the codon used at the codon adjacent to the start codon; the sequence of the start codon (AUG, UUG, or GUG); the ribosome concentration; the growth conditions before induction of expression; the growth conditions during expression; the temperature prior to induction of expression; and the temperature during expression.
Specific examples of factors that may affect the rate of translational initiation for a particular transcript include alternate translational initiation and interfering mRNA secondary structures. Alternate translational initiation may occur in a synthetic polynucleotide sequence that inadvertently contains one or more motifs capable of functioning as a ribosome binding site (RBS). These sites can result in initiating translation of a truncated protein from a gene-internal site. One method of reducing the possibility of producing a truncated protein, which can be difficult to remove during purification, includes modifying putative internal RBS sequences from an optimized polynucleotide sequence. Interfering secondary structures may sequester the RBS sequence or initiation codon, and have been correlated to a reduction in protein expression. Stem-loop structures can also be involved in transcriptional pausing and attenuation. An optimized polynucleotide sequence may thus contain minimal secondary structures in the RBS and gene coding regions of the nucleotide sequence to allow for improved transcription and translation.
Factors that may affect the rate of translational elongation include the level of charged tRNAs (Elf et al. (2003) Science 300:1718-22), which depends upon tRNA concentrations, tRNA charging rates, and amino acid availability. For example, a translational pause induced by a rare (or non-preferred) codon according to the host organism's codon usage bias may reduce the rate of heterologous protein expression. A rare codon-induced translational pause includes the presence of codons in the polynucleotide of interest that are rarely used in the host organism and may have a negative effect on protein translation due to their scarcity in the available tRNA pool. These factors also include the rate of ribosomal tRNA selection (decoding rate), which depends upon: the strength of the codon-anticodon interaction; the preceding codon (P-site codon); the wobble base of the preceding codon; and the wobble base of the codon being read. Factors that may affect ribosomal fidelity include those that influence ribosomal frameshifts, such as homopolymer stretches, G/C islands, A/T islands, and homopolymer stretches near pause sites. Furthermore, some polypeptides may be hindered in the ribosomal exit channel, which depends in part upon the sequence of the initial 10-20 amino acids of the polypeptide. In view of the foregoing, one method of improving optimal translation in a host organism includes performing codon optimization which can result in rare host codons being modified in a synthetic nucleic acid sequence.
Another class of nucleic acid sequence element that may affect (albeit indirectly) heterologous protein expression includes restriction sites. Thus, optimization of a nucleic acid sequence may include modification of restriction sites that could, for example, interfere with subsequent sub-cloning of transcription units into host expression vectors.
In some embodiments of the invention, a nucleic acid encoding a cytokinin synthase may be codon-optimized by first deducing (e.g., by in silico translation) the amino acid sequence encoded by a reference cytokinin synthase nucleic acid (e.g., SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:20 (AhCKS), or SEQ ID NO:24 (FfCKS) or the coding sequence for SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41 SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54). In further embodiments, the amino acid sequence of a cytokinin synthase may be used directly to obtain a codon-optimized nucleic acid sequence. For example, the amino acid sequence of a cytokinin synthase (whether deduced from a nucleic acid sequence or provided directly) may be used to deduce a codon-optimized nucleic acid sequence encoding the cytokinin synthase (e.g., in silico reverse-translation), for example, by using a computer-implemented software program that is capable of optimizing a coding sequence according to predetermined parameters. In specific examples, a codon-optimized nucleic acid may be deduced using the standard genetic code and an appropriate codon usage bias table for an expression host organism. It may be desirable in some embodiments to deduce multiple codon-optimized nucleic acid sequences encoding a cytokinin synthase protein.
All or a portion of a nucleic acid sequence may be optimized. In some examples, a desired modulation of expression may be achieved by optimizing essentially an entire reference cytokinin synthase encoding nucleic acid. In other examples, a desired modulation may be achieved by optimizing part, but not all, of a reference cytokinin synthase encoding nucleic acid.
Synthetic cytokinin synthase encoding, codon-optimized polynucleotides of the invention may be designed for use in a variety of applications, for example, to produce a recombinant polypeptide; to develop a new expression system; to compare expression properties to those of other nucleic acid sequences; and for diagnostic applications, as well as for introducing or increasing drought stress tolerance in a host organism. Additional guidance regarding the production of synthetic genes can be found in, for example, PCT International Patent Publication No. WO 97/13402, and U.S. Pat. Nos. 6,166,302 and 5,380,831.
Heterologous Sequences for Use in Recombinant Polynucleotides of the Invention
Plant Promoters.
A number of promoters that direct expression of a gene in a plant can be operably linked to a cytokinin synthase sequence disclosed herein, e.g., to create a gene expression cassette. Such promoters can be selected from constitutive, chemically-regulated, inducible, tissue-specific, and seed-preferred promoters. The promoter used to direct expression of a nucleic acid depends on the particular application. For example, a strong constitutive promoter suited to the host cell is typically used for expression and purification of expressed proteins.
Examples of plant promoters that can be used as heterologous sequence in the recombinant polynucleotides of the invention include promoter sequences derived from ZmSEE1 (Li et al. Plant Cell Reports, 22: 816-821 (2004) and Robson et al., Plant Biotechnol. J. 2: 101-112 (2004)) SAG12 (Gan et al., Science, 270: 1986-1988 (1995); Sýkorová et al., J. Experimental Botany, 59: 377-387 (2008); Zhang et al., Journal of Integrative Plant Biology, 52: 653-669 (2010); Zhang et al., J. American Society for Horticultural Science, 135: 108-115 (2010)), SAUR (Li et al., Developmental biology, 153: 386-395 (1992)), maize hsp70 (Medford et al., The Plant Cell Online, 1: 403-413 (1989)); ZmUBI1 (Hu et al., Plant Cell Reports, 23: 705-709 (2005)), chalcone synthase (chs) promoter (PCHS) from Antirrhinum majus (Wang et al., Functional Plant Biology, 24: 661-672 (1997)), proteinase inhibitor II (PI-IIK) (Smigocki et al., Plant Molecular Biology, 23: 325-335 (1993)); and SARK (Rivero et al., Proc. Nat'l. Acad. Sci., 104: 19631-19636 (2007)).
Additional non-limiting examples of plant promoters that can be used in the recombinant polynucleotide of the invention include promoter sequences derived from A. thaliana ubiquitin-10 (ubi-10) (Callis, et al., J. Biol. Chem., 265:12486-12493 (1990); A. tumefaciens mannopine synthase (Δmas) (Petolino et al., U.S. Pat. No. 6,730,824); and/or Cassava Vein Mosaic Virus (CsVMV) (Verdaguer et al., Plant Molecular Biology, 31:1129-1139 (1996). Other constitutive promoters include, for example, the core Cauliflower Mosaic Virus 35S promoter (Odell et al. Nature 313:810-812 (1985)); Rice Actin promoter (McElroy et al., Plant Cell 2:163-171 (1990)); Maize Ubiquitin promoter (U.S. Pat. No. 5,510,474; Christensen et al., Plant Mol. Biol. 12:619-632 (1989) and Christensen et al., Plant Mol. Biol. 18:675-689 (1992)); pEMU promoter (Last et al., Theor. Appl. Genet., 81:581-588 (1991)); ALS promoter (U.S. Pat. No. 5,659,026); Maize Histone promoter (Chabouté et al. Plant Molecular Biology, 8:179-191 (1987)); and the like.
Other useful plant promoters include tissue specific and inducible promoters. An inducible promoter is one that is capable of directly or indirectly activating transcription of one or more DNA sequences or genes in response to an inducer. The inducer can be a chemical agent such as a protein, metabolite, growth regulator, herbicide or phenolic compound or the inducer can be a physiological stress imposed by heat, cold, salt, or toxic elements. Other inducers act indirectly through the action of a pathogen or disease agent such as a virus. A plant cell containing an inducible regulatory element may be exposed to an inducer by externally applying the inducer to the cell or plant such as by spraying, watering, heating or similar methods.
Any inducible promoter can be used in the embodiments of the instant disclosure. See Ward et al., Plant Mol. Biol. 22: 361-366 (1993). Exemplary inducible promoters include ecdysone receptor promoters (U.S. Pat. No. 6,504,082); promoters from the ACE1 system which respond to copper (Mett et al., Proc. Natl. Acad. Sci. USA 90: 4567-4571 (1993)); In2-1 and In2-2 gene from maize which respond to benzenesulfonamide herbicide safeners (U.S. Pat. No. 5,364,780; Hershey et al., Mol. Gen. Genetics 227: 229-237 (1991) and Gatz et al., Mol. Gen. Genetics 243: 32-38 (1994)); Tet repressor from Tn10 (Gatz et al., Mol. Gen. Genet. 227: 229-237 (1991); or promoters from a steroid hormone gene, the transcriptional activity of which is induced by a glucocorticosteroid hormone, Schena et al., Proc. Natl. Acad. Sci. USA 88: 10421 (1991) and McNellis et al., (1998) Plant J. 14(2):247-257; the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides (see U.S. Pat. No. 5,965,387 and International Patent Application, Publication No. WO 93/001294); and the tobacco PR-1a promoter, which is activated by salicylic acid (see Ono S, Kusama M, Ogura R, Hiratsuka K., “Evaluation of the Use of the Tobacco PR-1a Promoter to Monitor Defense Gene Expression by the Luciferase Bioluminescence Reporter System,” Biosci Biotechnol Biochem. 2011 Sep. 23; 75(9):1796-800). Other chemical-regulated promoters of interest include tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al., (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156).
Other regulatable promoters of interest include a cold responsive regulatory element or a heat shock regulatory element, the transcription of which can be effected in response to exposure to cold or heat, respectively (Takahashi et al., Plant Physiol. 99:383-390, 1992)); the promoter of the alcohol dehydrogenase gene (Gerlach et al., Proc. Natl. Acad. Sci. USA 79:2981-2985 (1982); Walker et al., Proc. Natl. Acad. Sci. USA 84(19):6624-6628 (1987)), inducible by anaerobic conditions; and the light-inducible promoter derived from the pea rbcS gene or pea psaDb gene (Yamamoto et al., Plant J. 12(2):255-265 (1997)); a light-inducible regulatory element (Feinbaum et al., Mol. Gen. Genet. 226:449 (1991); Lam and Chua, Science 248:471 (1990); Matsuoka et al. Proc. Natl. Acad. Sci. USA 90(20):9586-9590 (1993); Orozco et al. (1993) Plant Mol. Bio. 23(6):1129-1138), a plant hormone inducible regulatory element (Yamaguchi-Shinozaki et al., Plant Mol. Biol. 15:905 (1990); Kares et al., Plant Mol. Biol. 15:225 (1990)), and the like. An inducible regulatory element also can be the promoter of the maize In2-1 or In2-2 gene, which responds to benzenesulfonamide herbicide safeners (Hershey et al., Mol. Gen. Gene. 227:229-237 (1991); Gatz et al., Mol. Gen. Genet. 243:32-38 (1994)), and the Tet repressor of transposon Tn10 (Gatz et al., Mol. Gen. Genet. 227:229-237 (1991)). Stress inducible promoters include salt/water stress-inducible promoters such as PSCS (Zang et al., (1997) Plant Sciences 129:81-89); cold-inducible promoters, such as, cor15a (Hajela et al., Plant Physiol. 93:1246-1252 (1990)), cor15b (Wilhelm et al., Plant Mol. Biol. 23:1073-1077 (1993)), wsc1 (Ouellet et al., (1998) FEBS Lett. 423-324-328), ci7 (Kirch et al., Plant Mol Biol. 33:897-909 (1997)), ci21A (Schneider et al., Plant Physiol. 113:335-45 (1997)); drought-inducible promoters, such as Trg-31 (Chaudhary et al., Plant Mol. Biol., 30:1247-57 (1996)), rd29 (Kasuga et al., Nature Biotechnology 18:287-291 (1999)); osmotic inducible promoters, such as Rab17 (Vilardell et al., Plant Mol. Biol. 17:985-93 (1991)) and osmotin (Raghothama et al., Plant Mol. Biol. 23:1117-28 (1993)); and heat inducible promoters, such as heat shock proteins (Barros et al., Plant Mol. 19:665-75 (1992); Marrs et al., Dev. Genet. 14:27-41 (1993)), smHSP (Waters et al., J Experimental Botany 47:325-338 (1996), and the heat-shock inducible element from the parsley ubiquitin promoter (WO 03/102198). Other stress-inducible promoters include rip2 (U.S. Pat. No. 5,332,808 and U.S. Publication No. 2003/0217393) and rd29a (Yamaguchi-Shinozaki et al., Mol. Gen. Genetics 236:331-340 (1993)). Certain promoters are inducible by wounding, including the Agrobacterium pMAS promoter (Guevara-Garcia et al., Plant J. 4(3):495-505 (1993)) and the Agrobacterium ORF13 promoter (Hansen et al., Mol. Gen. Genet. 254(3):337-343 (1997)).
Tissue-preferred promoters can be utilized to target enhanced transcription and/or expression within a particular plant tissue. When referring to preferential expression, what is meant is expression at a higher level in the particular plant tissue than in other plant tissue. Examples of these types of promoters include seed preferred expression such as that provided by the phaseolin promoter (Bustos et al., The Plant Cell Vol. 1, 839-853 (1989)), and the maize globulin-1 gene (Belanger, et al. Genetics 129:863-972 (1991)). For dicots, seed-preferred promoters include, but are not limited to, bean β-phaseolin, napin, β-conglycinin, soybean lectin, cruciferin, and the like. For monocots, seed-preferred promoters include, but are not limited to, maize 15 kDa zein, 22 kDa zein, 27 kDa zein, γ-zein, waxy, shrunken 1, shrunken 2, globulin 1, ZmGS2, ZmSTP13, ZmGSTU6, etc. Seed-preferred promoters also include those promoters that direct gene expression predominantly to specific tissues within the seed such as, for example, the endosperm-preferred promoter of γ-zein, the cryptic promoter from tobacco (Fobert et al., Plant J. 4: 567-577 (1994)), the P-gene promoter from maize (Chopra et al., Plant Cell 7:1149-1158 (1996), Erratum in Plant Cell. 1:109 (1997), the globulin-1 promoter from maize (Belenger and Kriz, Genetics 129: 863-972 (1991)), and promoters that direct expression to the seed coat or hull of maize kernels, for example the pericarp-specific glutamine synthetase promoter (Muhitch et al., Plant Science 163:865-872 (2002)).
In addition to the promoter, the gene expression cassette (which can be in, e.g., a vector) typically contains a transcription unit or expression cassette that contains all the additional elements required for the expression of the nucleic acid in host cells, either prokaryotic or eukaryotic. A typical expression cassette thus contains a promoter operably linked to a nucleic acid sequence encoding a gene product (e.g., a protein). The gene expression cassette may also include additional elements which are operably linked according to methods known art: signals required for efficient polyadenylation of the transcript, transcriptional termination, ribosome binding sites, or translation termination. Additionally, the expression cassette may include enhancers and/or heterologous splicing signals.
Components of Gene Expression Cassette.
Other components of the gene expression cassette are provided as embodiments. Examples include selectable markers, targeting or regulatory sequences, transit peptide sequences such as the optimized transit peptide sequence (see U.S. Pat. No. 5,510,471) stabilizing sequences such as RB7 MAR (see Thompson and Myatt, Plant Mol. Biol., 34: 687-692 (1997) and International Patent Publication No. WO9727207) or leader sequences, introns etc. General descriptions and examples of plant expression vectors and reporter genes can be found in Gruber, et al., “Vectors for Plant Transformation” in Methods in Plant Molecular Biology and Biotechnology, Glick et al., eds; CRC Press pp. 89-119 (1993). The selection of an appropriate expression vector will depend upon the host and the method of introducing the expression vector into the host. The gene expression cassette will also include at the 3′ terminus of the heterologous nucleotide sequence of interest, a transcriptional and translational termination region functional in plants. The termination region can be native with the promoter nucleotide sequence of embodiments of the present disclosure, can be native with the DNA sequence of interest, or can be derived from another source. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase (nos) termination regions (Depicker et al., Mol. and Appl. Genet. 1:561-573 (1982) and Shaw et al. Nucl. Acids Research vol. 12, No. 20 pp 7831-7846(nos) (1984)); see also Guerineau et al. Mol. Gen. Genet. 262:141-144 (1991); Proudfoot, Cell 64:671-674 (1991); Sanfacon et al. Genes Dev. 5:141-149 (1991); Mogen et al. Plant Cell 2:1261-1272 (1990); Munroe et al. Gene 91:151-158 (1990); Ballas et al., Nucl. Acids Res. 17:7891-7903 (1989); Joshi et al. Nucl. Acids Res. 15:9627-9639 (1987).
The gene expression cassettes can additionally contain 5′ leader sequences. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include by way of example, picornavirus leaders, EMCV leader (Encephalomyocarditis 5′ noncoding region), Elroy-Stein et al., Proc. Nat. Acad. Sci. USA 86:6126-6130 (1989); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) Carrington and Freed, J. Virology, 64:1590-1597 (1990), MDMV leader (Maize Dwarf Mosaic Virus), Allison et al., Virology 154:9-20 (1986); human immunoglobulin heavy-chain binding protein (BiP), Macejak et al., Nature 353:90-94 (1991); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4), Jobling et al., Nature 325:622-625 (1987); Tobacco mosaic virus leader (TMV), Gallie et al., (1989) Molecular Biology of RNA, pages 237-256; and maize chlorotic mottle virus leader (MCMV) Lommel et al., Virology 81:382-385 (1991). See also Della-Cioppa et al., Plant Physiology 84:965-968 (1987).
The gene expression cassette construct can also contain sequences that enhance translation and/or mRNA stability such as introns. An example of one such intron is the first intron of gene II of the histone H3.III variant of Arabidopsis thaliana. Chaubet et al., J Mol. Biology, 225:569-574 (1992).
In those instances where it is desirable for the expression cassette to express a gene product that is directed to a particular organelle, particularly the plastid, amyloplast, or to the endoplasmic reticulum, or secreted at the cell's surface or extracellularly, the expression cassette can further comprise a coding sequence for a transit peptide. Such transit peptides are well known in the art and include, but are not limited to, the transit peptide for the acyl carrier protein, the small subunit of RUBISCO, plant EPSP synthase and Helianthus annuus (U.S. Pat. No. 5,510,417), Zea mays Brittle-1 chloroplast transit peptide (Nelson et al., Plant Physiol. 117(4):1235-1252 (1998); Sullivan et al., Plant Cell 3(12):1337-48 (1991); Sullivan et al., Planta 196(3):477-84 (1995); Sullivan et al., J. Biol. Chem. 267(26):18999-9004 (1992)) and the like. In addition, chimeric chloroplast transit peptides are known in the art, such as the Optimized Transit Peptide (U.S. Pat. No. 5,510,471). Additional chloroplast transit peptides have been described previously in U.S. Pat. No. 5,717,084 and U.S. Pat. No. 5,728,925. One skilled in the art will readily appreciate the many options available in expressing a product to a particular organelle. For example, the barley alpha amylase sequence is often used to direct expression to the endoplasmic reticulum (Rogers, J. Biol. Chem. 260:3731-3738 (1985)).
It will be appreciated by one skilled in the art that use of recombinant DNA technologies can improve control of expression of transformed nucleic acid molecules by manipulating, for example, the number of copies of the nucleic acid molecules within the host cell, the efficiency with which those nucleic acid molecules are transcribed, the efficiency with which the resultant transcripts are translated, and the efficiency of post-translational modifications. Additionally, the promoter sequence might be genetically engineered to improve the level of expression as compared to the native promoter. Recombinant techniques useful for controlling the expression of nucleic acid molecules include, but are not limited to, stable integration of the nucleic acid molecules into one or more host cell chromosomes, addition of vector stability sequences to plasmids, substitutions or modifications of transcription control signals (e.g., promoters, operators, enhancers), substitutions or modifications of translational control signals (e.g., ribosome binding sites, Shine-Dalgarno or Kozak sequences), modification of nucleic acid molecules to correspond to the codon usage of the host cell, and deletion of sequences that destabilize transcripts.
Reporter or marker genes for selection of transformed cells or tissues or plant parts or plants can be included in the transformation vectors. Examples of selectable markers include those that confer resistance to anti-metabolites such as herbicides or antibiotics, for example, dihydrofolate reductase, which confers resistance to methotrexate (Reiss, Plant Physiol. (Life Sci. Adv.) 13:143-149 (1994); see also Herrera Estrella et al., Nature 303:209-213, (1983); Meijer et al., Plant Mol. Biol. 16:807-820, (1991)); neomycin phosphotransferase, which confers resistance to the aminoglycosides neomycin, kanamycin and paromycin (Herrera-Estrella, EMBO J. 2:987-995 (1983) and Fraley et al., Proc. Natl. Acad. Sci USA 80:4803 (1983)) and hygromycin phosphotransferase, which confers resistance to hygromycin (Marsh, Gene 32:481-485, (1984); see also Waldron et al., Plant Mol. Biol. 5:103-108, (1985); Zhijian et al., Plant Science 108:219-227, (1995)); trpB, which allows cells to utilize indole in place of tryptophan; hisD, which allows cells to utilize histinol in place of histidine (Hartman, Proc. Natl. Acad. Sci. USA 85:8047, (1988)); mannose-6-phosphate isomerase which allows cells to utilize mannose (International Patent Application No. WO 94/20627); ornithine decarboxylase, which confers resistance to the ornithine decarboxylase inhibitor, 2-(difluoromethyl)-DL-ornithine (DFMO; McConlogue, 1987, In: Current Communications in Molecular Biology, Cold Spring Harbor Laboratory ed.); and deaminase from Aspergillus terreus, which confers resistance to Blasticidin S (Tamura, Biosci. Biotechnol. Biochem. 59:2336-2338, (1995)).
Additional selectable markers include, for example, a mutant acetolactate synthase, which confers imidazolinone or sulfonylurea resistance (Lee et al., EMBO J. 7:1241-1248, (1988)), a mutant psbA, which confers resistance to atrazine (Smeda et al., Plant Physiol. 103:911-917, (1993)), or a mutant protoporphyrinogen oxidase (see U.S. Pat. No. 5,767,373), or other markers conferring resistance to an herbicide such as glufosinate. Examples of suitable selectable marker genes include, but are not limited to, genes encoding resistance to chloramphenicol (Herrera Estrella et al., EMBO J. 2:987-992, (1983)); streptomycin (Jones et al., Mol. Gen. Genet. 210:86-91, (1987)); spectinomycin (Bretagne-Sagnard et al., Transgenic Res. 5:131-137, (1996)); bleomycin (Hille et al., Plant Mol. Biol. 7:171-176, (1990)); sulfonamide (Guerineau et al., Plant Mol. Biol. 15:127-136, (1990)); bromoxynil (Stalker et al., Science 242:419-423, (1988)); glyphosate (Shaw et al., Science 233:478-481, (1986)); phosphinothricin (DeBlock et al., EMBO J. 6:2513-2518, (1987)), and the like.
One option for use of a selective gene is a glufosinate-resistance encoding DNA and in one embodiment can be the phosphinothricin acetyl transferase (pat), maize optimized pat gene or bar gene under the control of the Cassava Vein Mosaic Virus promoter. These genes confer resistance to bialaphos. See, (see, Wohlleben et al., (1988) Gene 70: 25-37); Gordon-Kamm et al., Plant Cell 2:603; 1990; Uchimiya et al., BioTechnology 11:835, 1993; White et al., Nucl. Acids Res. 18:1062, 1990; Spencer et al., Theor. Appl. Genet. 79:625-631, 1990; and Anzai et al., Mol. Gen. Gen. 219:492, 1989). A version of the pat gene is the maize optimized pat gene, described in U.S. Pat. No. 6,096,947.
In addition, markers that facilitate identification of a plant cell containing the polynucleotide encoding the marker may be employed. Scorable or screenable markers are useful, where presence of the sequence produces a measurable product and can produce the product without destruction of the plant cell. Examples include a β-glucuronidase, or uidA gene (GUS), which encodes an enzyme for which various chromogenic substrates are known (for example, U.S. Pat. Nos. 5,268,463 and 5,599,670); chloramphenicol acetyl transferase (Jefferson et al., EMBO J 6(13): 3901-3907 (1987)); and alkaline phosphatase. In a preferred embodiment, the marker used is beta-carotene or provitamin A (Ye et al., Science 287:303-305-(2000)). The gene has been used to enhance the nutrition of rice, but in this instance it is employed instead as a screenable marker, and the presence of the gene linked to a gene of interest is detected by the golden color provided. Unlike the situation where the gene is used for its nutritional contribution to the plant, a smaller amount of the protein suffices for marking purposes. Other screenable markers include the anthocyanin/flavonoid genes in general (See discussion at Taylor and Briggs, The Plant Cell 2:115-127 (1990)) including, for example, a R-locus gene, which encodes a product that regulates the production of anthocyanin pigments (red color) in plant tissues (Dellaporta et al., in Chromosome Structure and Function, Kluwer Academic Publishers, Appels and Gustafson eds., pp. 263-282 (1988)); the genes which control biosynthesis of flavonoid pigments, such as the maize C1 gene (Kao et al., Plant Cell (1996) 8: 1171-1179; Scheffler et al., Mol. Gen. Genet. 242:40-48 (1994)) and maize C2 (Wienand et al., Mol. Gen. Genet. 203:202-207 (1986)); the B gene (Chandler et al., Plant Cell 1:1175-1183 (1989)), the p1 gene (Grotewold et al., Proc. Natl. Acad. Sci USA 88:4587-4591 (1991); Grotewold et al., Cell 76:543-553 (1994); Sidorenko et al., Plant Mol. Biol. (1999)39:11-19); the bronze locus genes (Ralston et al., Genetics (1988) 119:185-197; Nash et al., Plant Cell (1990) 2(11): 1039-1049), among others.
Further examples of suitable markers include the cyan fluorescent protein (CYP) gene (Bolte et al., J. Cell Science 117: 943-54 (2004) and Kato et al., Plant Physiol 129: 913-42 (2002)), the yellow fluorescent protein gene (PHIYFPTM from Evrogen; see Bolte et al., J. Cell Science 117: 943-54 (2004)); a lux gene, which encodes a luciferase, the presence of which may be detected using, for example, X-ray film, scintillation counting, fluorescent spectrophotometry, low-light video cameras, photon counting cameras or multi-well luminometry (Teeri et al. EMBO J. 8:343 (1989)); a green fluorescent protein (GFP) gene (Sheen et al., Plant J. 8(5):777-84 (1995)); and DsRed2 where plant cells transformed with the marker gene are red in color, and thus visually selectable (Dietrich et al., Biotechniques 2(2):286-293 (2002)). Additional examples include a β-lactamase gene (Sutcliffe, Proc. Nat'l. Acad. Sci. U.S.A. (1978) 75:3737), which encodes an enzyme for which various chromogenic substrates are known (e.g., PADAC, a chromogenic cephalosporin); a xylE gene (Zukowsky et al., Proc. Nat'l. Acad. Sci. USA 80:1101 (1983)), which encodes a catechol dioxygenase that can convert chromogenic catechols; an α-amylase gene (Ikuta et al., Biotech. 8:241 (1990)); and a tyrosinase gene (Katz et al., J. Gen. Microbiol. 129:2703 (1983)), which encodes an enzyme capable of oxidizing tyrosine to DOPA and dopaquinone, which in turn condenses to form the easily detectable compound melanin. Clearly, many such markers are available and known to one skilled in the art.
In certain embodiments, the nucleotide sequence of the transgene encoding a gene product in an expression cassette can be optionally combined with another nucleotide sequence of interest in the cassette and/or the plant. For example, in certain embodiments the transgene can be combined or “stacked” with another nucleotide sequence of interest that provides additional resistance or tolerance to glyphosate or another herbicide, and/or provides resistance to select insects or diseases and/or nutritional enhancements, and/or improved agronomic characteristics, and/or proteins or other products useful in feed, food, industrial, pharmaceutical or other uses. The “stacking” of two or more nucleic acid sequences of interest within a plant genome can be accomplished, for example, via conventional plant breeding using two or more events, transformation of a plant with a construct which contains the sequences of interest, re-transformation of a transgenic plant, or addition of new traits through integration via homologous recombination.
Such nucleotide sequences of interest include, but are not limited to, those examples of genes or coding sequences that confer (1) resistance to pests or disease, (2) resistance to herbicides, and (3) value added traits provided below:
1. Genes or Coding Sequences (e.g. iRNA) that Confer Resistance to Pests or Disease
(A) Plant Disease Resistance Genes. Plant defenses are often activated by specific interaction between the product of a disease resistance gene (R) in the plant and the product of a corresponding avirulence (Avr) gene in the pathogen. A plant variety can be transformed with cloned resistance gene to engineer plants that are resistant to specific pathogen strains. Examples of such genes include, the tomato Cf-9 gene for resistance to Cladosporium flavum (Jones et al., 1994 Science 266:789), tomato Pto gene, which encodes a protein kinase, for resistance to Pseudomonas syringae pv. tomato (Martin et al., Science 262:1432 (1993)), and Arabidopsis RSSP2 gene for resistance to Pseudomonas syringae (Mindrinos et al., Cell 78:1089 (1994)).
(B) A Bacillus thuringiensis protein, a derivative thereof or a synthetic polypeptide modeled thereon, such as, a nucleotide sequence of a Bt δ-endotoxin gene (Geiser et al., 1986 Gene 48:109), and a vegetative insecticidal (VIP) gene (see, e.g., Estruch et al., Proc. Natl. Acad. Sci. USA 93:5389-94 (1996)). Moreover, DNA molecules encoding δ-endotoxin genes can be purchased from American Type Culture Collection (Rockville, Md.), under ATCC accession numbers 40098, 67136, 31995 and 31998.
(C) A lectin, such as, nucleotide sequences of several Clivia miniata mannose-binding lectin genes (Van Damme et al., Plant Molec. Biol. 24:825 (1994)).
(D) A vitamin binding protein, such as avidin and avidin homologs which are useful as larvicides against insect pests. See U.S. Pat. No. 5,659,026.
(E) An enzyme inhibitor, e.g., a protease inhibitor or an amylase inhibitor.
Examples of such genes include a rice cysteine proteinase inhibitor (Abe et al., J. Biol. Chem. 262:16793 (1987), a tobacco proteinase inhibitor I (Huub et al., Plant Molec. Biol. 21:985 (1993)), and an α-amylase inhibitor (Sumitani et al., Biosci. Biotech. Biochem. 57:1243 (1993)).
(F) An insect-specific hormone or pheromone such as an ecdysteroid and juvenile hormone a variant thereof, a mimetic based thereon, or an antagonist or agonist thereof, such as baculovirus expression of cloned juvenile hormone esterase, an inactivator of juvenile hormone (Hammock et al., Nature 344:458 (1990).
(G) An insect-specific peptide or neuropeptide which, upon expression, disrupts the physiology of the affected pest. Examples of such genes include an insect diuretic hormone receptor (Regan, J. Biol. Chem. 269(1):9-12 (1994)), an allatostatin identified in Diploptera punctata (Pratt, Biochem Biophys Res Commun. 163(3):1243-7 (1989)), and insect-specific, paralytic neurotoxins (U.S. Pat. No. 5,266,361).
(H) An insect-specific venom produced in nature by a snake, a wasp, etc., such as a scorpion insectotoxic peptide (Pang, Gene 116:165 (1992)).
(I) An enzyme responsible for a hyperaccumulation of monoterpene, a sesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivative or another non-protein molecule with insecticidal activity.
(J) An enzyme involved in the modification, including the post-translational modification, of a biologically active molecule; for example, glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme, a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, a phosphatase, a kinase, a phosphorylase, a polymerase, an elastase, a chitinase and a glucanase, whether natural or synthetic. Examples of such genes include, a callas gene (PCT published application WO93/02197), chitinase-encoding sequences (which can be obtained, for example, from the ATCC under accession numbers 3999637 and 67152), tobacco hookworm chitinase (Kramer et al., Insect Molec. Biol. 23:691 (1993)), and parsley ubi4-2 polyubiquitin gene (Kawalleck et al., Plant Molec. Biol. 21:673 (1993)).
(K) A molecule that stimulates signal transduction. Examples of such molecules include nucleotide sequences for mung bean calmodulin cDNA clones (Botella et al., Plant Molec. Biol. 24:757 (1994)) and a nucleotide sequence of a maize calmodulin cDNA clone (Griess et al., Plant Physiol. 104:1467 (1994)).
(L) A hydrophobic moment peptide. See U.S. Pat. Nos. 5,659,026 and 5,607,914; the latter teaches synthetic antimicrobial peptides that confer disease resistance.
(M) A membrane permease, a channel former or a channel blocker, such as a cecropin-β lytic peptide analog (Jaynes et al., Plant Sci. 89:43 (1993)) which renders transgenic tobacco plants resistant to Pseudomonas solanacearum. 
(N) A viral-invasive protein or a complex toxin derived therefrom. For example, the accumulation of viral coat proteins in transformed plant cells imparts resistance to viral infection and/or disease development effected by the virus from which the coat protein gene is derived, as well as by related viruses. Coat protein-mediated resistance has been conferred upon transformed plants against alfalfa mosaic virus, cucumber mosaic virus, tobacco streak virus, potato virus X, potato virus Y, tobacco etch virus, tobacco rattle virus and tobacco mosaic virus. See, for example, Beachy et al. Ann. Rev. Phytopathol. 28:451 (1990).
(O) An insect-specific antibody or an immunotoxin derived therefrom. Thus, an antibody targeted to a critical metabolic function in the insect gut would inactivate an affected enzyme, killing the insect. For example, Taylor et al., Abstract #497, Seventh Int'l. Symposium on Molecular Plant-Microbe Interactions shows enzymatic inactivation in transgenic tobacco via production of single-chain antibody fragments (1994).
(P) A virus-specific antibody. See, for example, Tavladoraki et al., Nature 266:469 (1993), which shows that transgenic plants expressing recombinant antibody genes are protected from virus attack.
(Q) A developmental-arrestive protein produced in nature by a pathogen or a parasite. Thus, fungal endo α-1,4-D polygalacturonases facilitate fungal colonization and plant nutrient release by solubilizing plant cell wall homo-α-1,4-D-galacturonase (Lamb et al., Bio/Technology 10:1436 (1992)). The cloning and characterization of a gene which encodes a bean endopolygalacturonase-inhibiting protein is described by (Toubart et al., Plant J. 2:367 (1992)).
(R) A developmental-arrestive protein produced in nature by a plant, such as the barley ribosome-inactivating gene that provides an increased resistance to fungal disease (Longemann et al., Bio/Technology 10:3305 (1992)).
(S) RNA interference, in which a DNA polynucleotide encoding an RNA molecule is used to inhibit expression of a target gene. An RNA molecule in one example is partially or fully double stranded, which triggers a silencing response, resulting in cleavage of dsRNA into small interfering RNAs, which are then incorporated into a targeting complex that destroys homologous mRNAs. See, e.g., Fire et al., U.S. Pat. No. 6,506,559; Graham et al., U.S. Pat. No. 6,573,099.
2. Genes or Coding Sequences that Confer Resistance to a Herbicide
(A) Genes encoding resistance or tolerance to a herbicide that inhibits the growing point or meristem, such as an imidazalinone, sulfonanilide or sulfonylurea herbicide. Exemplary genes in this category code for a mutant ALS enzyme (Lee et al., EMBO J. 7:1241 (1988)), which is also known as AHAS enzyme (Miki et al., Theor. Appl. Genet. 80:449 (1990)).
(B) One or more additional genes encoding resistance or tolerance to glyphosate imparted by mutant EPSP synthase and aroA genes, or through metabolic inactivation by genes such as GAT (glyphosate acetyltransferase) or GOX (glyphosate oxidase) and other phosphono compounds such as glufosinate (pat and bar genes; DSM-2), and aryloxyphenoxypropionic acids and cyclohexanediones (ACCase inhibitor encoding genes). See, for example, U.S. Pat. No. 4,940,835, which discloses the nucleotide sequence of a form of EPSP which can confer glyphosate resistance. A DNA molecule encoding a mutant aroA gene can be obtained under ATCC Accession Number 39256, and the nucleotide sequence of the mutant gene is disclosed in U.S. Pat. No. 4,769,061. European Patent application No. 0 333 033 and U.S. Pat. No. 4,975,374 disclose nucleotide sequences of glutamine synthetase genes which confer resistance to herbicides such as L-phosphinothricin. The nucleotide sequence of a phosphinothricin acetyltransferase gene is provided in European Patent application No. 0 242 246. De Greef et al., Bio/Technology 7:61 (1989) describes the production of transgenic plants that express chimeric bar genes coding for phosphinothricin acetyl transferase activity. Exemplary of genes conferring resistance to aryloxyphenoxypropionic acids and cyclohexanediones, such as sethoxydim and haloxyfop, are the Acc1-S1, Acc1-S2 and Acc1-S3 genes described by Marshall et al., Theor. Appl. Genet. 83:435 (1992).
(C) Genes encoding resistance or tolerance to a herbicide that inhibits photosynthesis, such as a triazine (psbA and gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al., Plant Cell 3:169 (1991) describe the use of plasmids encoding mutant psbA genes to transform Chlamydomonas. Nucleotide sequences for nitrilase genes in U.S. Pat. No. 4,810,648, and DNA molecules containing these genes are available under ATCC accession numbers 53435, 67441 and 67442. Cloning and expression of DNA coding for a glutathione S-transferase is described by Hayes et al., Biochem. J. 285:173 (1992).
(D) Genes encoding resistance or tolerance to a herbicide that bind to hydroxyphenylpyruvate dioxygenases (HPPD), enzymes which catalyze the reaction in which para-hydroxyphenylpyruvate (HPP) is transformed into homogentisate. This includes herbicides such as isoxazoles (European Patent No. 418175, European Patent No. 470856, European Patent No. 487352, European Patent No. 527036, European Patent No. 560482, European Patent No. 682659, U.S. Pat. No. 5,424,276), in particular isoxaflutole, which is a selective herbicide for maize, diketonitriles (European Patent No. 496630, and European Patent No. 496631), in particular 2-cyano-3-cyclopropyl-1-(2-SO2CH3-4-CF3 phenyl) propane-1,3-dione and 2-cyano-3-cyclopropyl-1-(2-SO2CH3-4-2,3Cl2phenyl) propane-1,3-dione, triketones (European Patent No. 625505, European Patent No. 625508, U.S. Pat. No. 5,506,195), in particular sulcotrione, and pyrazolinates. A gene that produces an overabundance of HPPD in plants can provide tolerance or resistance to such herbicides, including, for example, genes described in U.S. Pat. Nos. 6,268,549 and 6,245,968 and U.S. Patent Publication No. 20030066102.
(E) Genes encoding resistance or tolerance to phenoxy auxin herbicides, such as 2,4-dichlorophenoxyacetic acid (2,4-D) and which may also confer resistance or tolerance to aryloxyphenoxypropionate (AOPP) herbicides. Examples of such genes include the α-ketoglutarate-dependent dioxygenase enzyme (aad-1) gene, described in U.S. Pat. No. 7,838,733.
(F) Genes encoding resistance or tolerance to phenoxy auxin herbicides, such as 2,4-dichlorophenoxyacetic acid (2,4-D) and which may also confer resistance or tolerance to pyridyloxy auxin herbicides, such as fluroxypyr or triclopyr. Examples of such genes include the α-ketoglutarate-dependent dioxygenase enzyme gene (aad-12), described in WO 2007/053482 A2.
(G) Genes encoding resistance or tolerance to dicamba (see, e.g., U.S. Patent Publication No. 20030135879).
(H) Genes providing resistance or tolerance to herbicides that inhibit protoporphyrinogen oxidase (PPO) (see U.S. Pat. No. 5,767,373).
(I) Genes providing resistance or tolerance to triazine herbicides (such as atrazine) and urea derivatives (such as diuron) herbicides which bind to core proteins of photosystem II reaction centers (PS II) (See Brussian et al., EMBO J. 8(4): 1237-1245 (1989).
3. Genes that Confer or Contribute to a Value-Added Trait
(A) Modified fatty acid metabolism, for example, by transforming maize or Brassica with an antisense gene or stearoyl-ACP desaturase to increase stearic acid content of the plant (Knultzon et al., Proc. Nat. Acad. Sci. USA 89:2624 (1992).
(B) Decreased phytate content.
(1) Introduction of a phytase-encoding gene, such as the Aspergillus niger phytase gene (Van Hartingsveldt et al., Gene 127:87 (1993)), enhances breakdown of phytate, adding more free phosphate to the transformed plant.
(2) A gene could be introduced that reduces phytate content. In maize, this, for example, could be accomplished by cloning and then reintroducing DNA associated with the single allele which is responsible for maize mutants characterized by low levels of phytic acid (Raboy et al., Maydica 35:383 (1990)).
(C) Modified carbohydrate composition effected, for example, by transforming plants with a gene coding for an enzyme that alters the branching pattern of starch. Examples of such enzymes include, Streptococcus mucus fructosyltransferase gene (Shiroza et al., J. Bacteriol. 170:810 (1988)), Bacillus subtilis levansucrase gene (Steinmetz et al., Mol. Gen. Genel. 200:220 (1985)), Bacillus licheniformis α-amylase (Pen et al., Bio/Technology 10:292 (1992)), tomato invertase genes (Elliot et al., (1993)), barley amylase gene (Sogaard et al., J. Biol. Chem. 268:22480 (1993)), and maize endosperm starch branching enzyme II (Fisher et al., Plant Physiol. 102:10450 (1993)).
Transgenic Plant Cells and Plants
The recombinant polynucleotide of the invention can be introduced (transformed) into a plant cell. A wide variety of plants and plant cell systems may be engineered to include the cytokinin synthase gene expression constructs of the present disclosure using one or more of the various transformation methods disclosed above. In embodiments, target plants and plant cells for engineering include, but are not limited to, those monocotyledonous and dicotyledonous plants, such as crops including grain crops (e.g., wheat, maize, rice, millet, barley), fruit crops (e.g., tomato, apple, pear, strawberry, orange), forage crops (e.g., alfalfa), root vegetable crops (e.g., carrot, potato, sugar beets, yam), leafy vegetable crops (e.g., lettuce, spinach); flowering plants (e.g., petunia, rose, chrysanthemum), conifers and pine trees (e.g., pine fir, spruce); plants used in phytoremediation (e.g., heavy metal accumulating plants); oil crops (e.g., sunflower, rape seed) and plants used for experimental purposes (e.g., Arabidopsis). Thus, the disclosed methods and compositions can be used to generate transgenic plants and transgenic plants cells, including, but not limited to, species from the genera Asparagus, Avena, Brassica, Citrus, Citrullus, Capsicum, Cucurbita, Daucus, Erigeron, Glycine, Gossypium, Hordeum, Lactuca, Lolium, Lycopersicon, Malus, Manihot, Nicotiana, Orychophragmus, Oryza, Persea, Phaseolus, Pisum, Pyrus, Prunus, Raphanus, Secale, Solanum, Sorghum, Triticum, Vitis, Vigna, and Zea mays, transformed with a recombinant polynucleotide of the invention that includes the two-domain cytokinin synthase coding sequences (i), (ii), (iii), (iv), (v), (vi), (vii), (viii), (ix), (x), (xi), (xii), (xiii), (xiv), or (xv) described above. In particular the invention provides one of the foregoing transgenic plants or plant cells comprising a transgenic construct that includes the coding sequence of recombinant polynucleotide (vii), (viii), (ix), (xiii), (xiv), or (xv) which is optimized for expression in the plant or plant cell.
Plant transformation methods that can be used with the recombinant polynucleotide of the invention include, but are not limited to, site-specific microparticle bombardment, Agrobacterium transformation method, calcium phosphate transformation method, polybrene transformation method, electroporation transformation method, ultrasonic transformation method, liposome transformation method, microinjection transformation method, naked DNA transformation method, plasmid vector transformation method, viral vector transformation method, silicon carbide mediated transformation method, aerosol beaming transformation method, or PEG transformation method. Generally any plant transformation method can be used to insert DNA or any other polynucleotide sequence into the genome of a host cell. Thus, any method that provides for efficient transformation/transfection may be employed.
Numerous methods for plant transformation have been developed, including biological and physical transformation protocols for dicotyledonous plants as well as monocotyledonous plants (e.g., Goto-Fumiyuki et al., Nature Biotech, 17:282-286 (1999); Miki et al., Methods in Plant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J. E. Eds., CRC Press, Inc., Boca Raton, pp. 67-88 (1993)). In addition, vectors comprising gene expression cassettes and in vitro culture methods for plant cell or tissue transformation and regeneration of plants are available, for example, in Gruber et al., Methods in Plant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J. E. Eds., CRC Press, Inc., Boca Raton, pp. 8 (1993)). A large number of techniques are available for inserting DNA comprising a gene expression cassette into a plant host cell. Those techniques include transformation with disarmed T-DNA using Agrobacterium tumefaciens or Agrobacterium rhizogenes as the transformation agent, calcium phosphate transfection, polybrene transformation, protoplast fusion, electroporation, ultrasonic methods (e.g., sonoporation), liposome transformation, microinjection, naked DNA, plasmid vectors, viral vectors, biolistics (microparticle bombardment), silicon carbide WHISKERSTM mediated transformation, aerosol beaming, or Poly Ethylene Glycol mediated transformation as well as other possible methods 9-119 (1993).
For example, a gene expression cassette encoding a cytokinin synthase according to the invention may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts. Such plant transformation methods include, for example, protoplast transformation through calcium chloride precipitation, poly ethylene glycol (PEG) or electroporation-mediated uptake of DNA (see Paszkowski et al. EMBO J 3:2717-2722 (1984), Potrykus et al. Molec. Gen. Genet. 199:169-177 (1985); Fromm et al. Proc. Nat. Acad. Sci. USA 82:5824-5828 (1985); and Shimamoto Nature 338:274-276 (1989)) and electroporation of plant tissues (D'Halluin et al. Plant Cell 4:1495-1505 (1992)).
Expression vectors encoding a cytokinin synthase can be introduced directly to plant tissue using biolistic methods, such as DNA particle bombardment (see, e.g., Klein et al. Nature 327:70-73 (1987)). Biolistic methods include microprojectile-mediated transformation wherein DNA is carried on the surface of microprojectiles. In this method, the expression vector is introduced into plant tissues with a biolistic device that accelerates the microprojectiles to speeds sufficient to penetrate plant cell walls and membranes. Sanford et al., Part. Sci. Technol. 5:27 (1987), Sanford, J. C., Trends Biotech. 6:299 (1988), Sanford, J. C., Physiol. Plant 79:206 (1990), Klein et al., Biotechnology 10:268 (1992).
Additional methods for plant cell transformation include microinjection via silicon carbide WHISKERSTM mediated DNA uptake (Kaeppler et al. Plant Cell Reporter 9:415-418 (1990)). Alternatively, the DNA construct can be introduced into the plant cell via nanoparticle transformation (see, e.g., U.S. patent application Ser. No. 12/245,685, which is incorporated herein by reference in its entirety).
A widely utilized method for introducing a vector comprising a gene expression cassette into plants is based on the natural transformation system of Agrobacterium. Horsch et al., Science 227:1229 (1985). A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteria known to be useful to genetically transform plant cells. The Ti and Ri plasmids of A. tumefaciens and A. rhizogenes, respectively, carry genes responsible for genetic transformation of the plant. Kado, C. I., Crit. Rev. Plant. Sci. 10:1 (1991). Descriptions of Agrobacterium vector systems and methods for Agrobacterium-mediated gene transfer are also available, for example, Gruber et al., supra, Miki et al., supra, Moloney et al., Plant Cell Reports 8:238 (1989), and U.S. Pat. Nos. 4,940,838 and 5,464,763.
When Agrobacterium is used for plant transformation, DNA encoding a cytokinin synthase can be cloned into a special plasmid referred to as an intermediate vector or into a binary vector. Intermediate vectors cannot replicate in Agrobacterium in the absence of a helper plasmid (conjugation). The Japan Tobacco Superbinary system is an example of such a system (see review by Komari et al., (2006) In: Methods in Molecular Biology No. 343: Agrobacterium Protocols (2nd Edition, Vol. 1) (K. Wang, ed.) Humana Press Inc., Totowa, N.J., pp. 15-41; and Komori et al., Plant Physiol. 145:1155-1160 (2007)).
Binary vectors can replicate in both E. coli and in Agrobacterium. They comprise a selection marker gene and a linker or polylinker which are framed by the right and left T-DNA border regions. Binary vectors can be transformed directly into Agrobacterium (Holsters, 1978). The Agrobacterium can be used as a host cell comprising a plasmid, e.g., the Ti or RI plasmid carrying a vir region which, typically, is necessary for the transfer of the T-DNA into the plant cell.
The virulence of an Agrobacterium tumefaciens host can be used to direct the insertion of a T-strand containing DNA encoding a cytokinin synthase disclosed herein into the haploid tissue or cell that is infected by Agrobacterium binary T DNA vector technology (Bevan, Nucl. Acids Res. 12:8711-8721 (1984)) or the co-cultivation procedure (Horsch et al. Science 227:1229-1231 (1985)). Generally, the Agrobacterium transformation system is used to engineer dicotyledonous plants (Bevan et al. Ann. Rev. Genet 16:357-384 (1982); Rogers et al. Methods Enzymol. 118:627-641 (1986)). The Agrobacterium transformation system may also be used to transform, as well as transfer, DNA to monocotyledonous plants and plant cells. See U.S. Pat. No. 5,591,616; Hernalsteen et al. EMBO J3:3039-3041 (1984); Hooykass-Van Slogteren et al. Nature 311:763-764 (1984); Grimsley et al. Nature 325:1677-179 (1987); Boulton et al. Plant Mol. Biol. 12:31-40 (1989); and Gould et al. Plant Physiol. 95:426-434 (1991).
Following introduction of the genetic construct comprising a gene expression cassette by plant transformation, plant cells can be grown and upon emergence of differentiating tissue such as shoots and roots, mature plants can be generated. In some embodiments, a plurality of plants can be generated. Methods for regenerating plants are known to those of ordinary skill in the art and can be found, for example, in Plant Cell and Tissue Culture, 1994, Vasil and Thorpe Eds. Kluwer Academic Publishers and in Plant Cell Culture Protocols (Methods in Molecular Biology 111, 1999 Hall Eds Humana Press). The genetically modified plant described herein can be cultured in a fermentation medium or grown in a suitable medium such as soil. In some embodiments, a suitable growth medium for higher plants can include any growth medium for plants, including, but not limited to, soil, sand, any other particulate media that support root growth (e.g., vermiculite, perlite, etc.) or hydroponic culture, as well as suitable light, water and nutritional supplements which optimize the growth of the higher plant.
Transformed plant cells which produced by foregoing plant transformation techniques can be cultured to regenerate a whole plant that includes a polynucleotide encoding a cytokinin synthase according to the invention. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker which has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans, et al., “Protoplasts Isolation and Culture” in Handbook of Plant Cell Culture, pp. 124-176, Macmillian Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, pollens, embryos or parts thereof. Such regeneration techniques are described generally in Klee et al. Ann. Rev. of Plant Phys. 38:467-486 (1987).
A transformed plant cell, callus, tissue or plant may be identified and isolated by selecting or screening the engineered plant material for traits encoded by the marker genes (heterologous sequences) present on the transforming DNA. Such selection and screening methods are well known to those skilled in the art. For instance, selection can be performed by growing the engineered plant material on media containing an inhibitory amount of the antibiotic or herbicide to which the transforming gene construct confers resistance. Further, transformed plants and plant cells can also be identified by screening for the activities of any visible marker genes (e.g., the β-glucuronidase, luciferase, or gfp genes) that may be present on the recombinant nucleic acid constructs. Additionally, molecular confirmation methods can be used to identify transgenic plants. Such method include use of molecular beacons, hydrolysis probe assay, otherwise known as TAQMAN® (Life Technologies, Foster City, Calif.), and KASPar® assays.
In other embodiments, the gene expression cassette may be introduced in the context of inserting a nucleic acid into the genome of a cell, including transformation into the cell, as well as crossing a plant having the sequence with another plant, so that the second plant contains the heterologous sequence, as in conventional plant breeding techniques. Such breeding techniques are well known to one skilled in the art. For a discussion of plant breeding techniques, see Poehlman Breeding Field Crops, AVI Publication Co., Westport Conn., 4th Edit. (1995). Backcrossing methods may be used to introduce a gene into the plants. This technique has been used for decades to introduce traits into a plant. An example of a description of this and other plant breeding methodologies that are well known can be found in references such as Poehlman, supra, and Plant Breeding Methodology, edit. Neal Jensen, John Wiley & Sons, Inc. (1988). In a typical backcross protocol, the original variety of interest (recurrent parent) is crossed to a second variety (nonrecurrent parent) that carries the single gene of interest to be transferred. The resulting progeny from this cross are then crossed again to the recurrent parent and the process is repeated until a plant is obtained wherein essentially all of the desired morphological and physiological characteristics of the recurrent parent are recovered in the converted plant, in addition to the single transferred gene from the nonrecurrent parent.
It should be understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and the scope of the appended claims. These examples should not be construed as limiting.
EXAMPLE 1
Preparation of Plasmid Vectors and Host Cells Containing Polynucleotides Encoding Fungal Cytokinin Synthases According to the Invention
The E. coli expression vector pET28a(+) was digested with NcoI restriction enzyme and treated with Antarctic Phosphatase (“AP”). Both enzymes were obtained from New England Biolabs (NEB), Ipswich, Mass., USA. NcoI cut and AP-treated vector was purified using a QIAQUICK PCR purification kit according to instructions from the manufacturer (Qiagen, Germantown, Md., USA). Approximately 50 nanograms of the vector was mixed with three synthetic double stranded DNA fragments, which were codon-optimized for E. coli and which encode the following fungal cytokinin synthases: SEQ ID NO:3 (EfCKS.1), SEQ ID NO:7 (truncated EfCKS.1 (a.a. 1-255)), SEQ ID NO:15 (N-polyhistidine-BoCKS.1), SEQ ID NO:19 (N-polyhistidine-IrCKS.1), SEQ ID NO:11 (N-polyhistidine-AtCKS. 1), SEQ ID NO:23 (N-polyhistidine-AhCKS.1), and SEQ ID NO:27 (N-polyhistidine-FfCKS.1). For comparison, a construct was created that includes the same vector sequence and sequence which was codon-optimized for E. coli and encodes Agrobacterium IPT SEQ ID NO:29 (N-polyhistidine-AtuIPT). The vector and synthetic gene fragments coding each fungal cytokinin synthase were assembled into a final vector using the Gibson Assembly method and 2× Gibson Assembly Mastermix® from NEB, according to the manufacturer's instructions. Gibson Assembly reaction products were diluted and transformed into OneShot® TOP10 competent E. coli cells from Life Technologies Corp. (Carlsbad, Calif., USA) according to the manufacturer's instructions. Cells were plated onto LB agar containing 50 micrograms/milliliter kanamycin sulfate for selection and clones for each fungal cytokinin synthase were sequenced to identify host cells containing vectors with complete coding sequences for cytokinin synthases according to the invention.
EXAMPLE 2
Methods of Screening and Quantification of Cytokinin Synthase Activity Provided by the Invention
Polynucleotide vectors encoding SEQ ID NO:3 (EfCKS.1), SEQ ID NO:7 (truncated EfCKS.1 (a.a. 1-255) were isolated from host cells produced according to Example 1 and vectors were transformed into OneShot® BL21 (DE3) E. coli protein expression strains from Life Technologies Corp. A single colony from each transformation was inoculated into 3 milliliters of LB broth containing 50 micrograms/milliliter kanamycin sulfate in a 15 milliliter culture tube and grown at 37° C. in an orbital shaker at 250 RPM for 4-6 hours. The cells were then diluted into a fresh 3 milliliters of LB broth to a final OD600 of 0.1. The cells were grown for 1 hour at 37° C. in a shaker at 250 RPM and then transferred to ice. 500 microliters of LB containing isopropylthiogalactoside (IPTG) inducer was added to make 100 micromolar final IPTG concentration. These cultures were then grown at 18° C. in a shaker at 250 RPM overnight and samples were taken for analyses of total proteins and cytokinin synthase activity.
Total protein was analyzed by taking 500 microliters of culture, centrifuging at 14,000 RPM for 2 minutes and resuspending the cell pellet in 200 μL of LDS buffer. Samples were heated at 99° C. and loaded onto a SDS-PAGE, 4-12% Bis-Tris gradient gel in MES buffer. The gel was stained with coomassie blue reagent and the presence of overexpressed gene products for EfCKS.1 (about 49 kDa) and truncated EfCKS.1 (about 30 kDa) were confirmed by comparison to molecular weight standard as shown in FIG. 3.
Cytokinin synthase activity was assayed by culture broth assay. Two milliliters samples of the overnight culture were centrifuged at 15,000 RPM for 3 minutes, and the culture broth supernatant was directly analyzed by separating cytokinins and cytokinin precursors on a SunFire C18 5 μM HPLC column from Waters Corp (Milford, Mass., USA) and analyzing the separated compounds using an Agilent 1200 Series high performance liquid chromatography system linked to a G1969A time-of-flight mass spectrometer detector (HPLC-TOF) from Agilent Technologies Inc. (Santa Clara, Calif., USA). The mobile phases used were HPLC grade water with 0.1% v/v formic acid and HPLC grade methanol with 0.1% v/v formic acid. The gradient used was 0% methanol for 1 minute, from 1 to 5 minutes a linear gradient to 60% methanol, from 5 to 7 minutes a linear gradient from 60 to 80% methanol and from 7 to 10 minutes 0% methanol. Using these conditions, trans-zeatin elutes from the column at about 3.1 minutes, isopentenyl adenine elutes from the column at about 4.4 minutes, isopentenyl adenine riboside elutes at 5.6 minutes, and isopentenyladenosine-5′-monophosphate elutes between about 7.2-7.6 minutes.
For these culture broth assays, with the TOF detector in positive ion mode, ions corresponding to the mass to charge ratio (m/z) of isopentenyl adenine (iP, 204.124), isopentenyl adenosine riboside (iPR, 336.166), isopentenyladenosine-5′-monophosphate (iPRMP, 416.133), and trans or cis-zeatin (tZ or cZ, 220.119) were extracted from the chromatogram and used to quantify the amount of each species in the culture broth.
Results of the culture broth assays are shown in the bar graph of FIG. 3 (error bars represent standard deviation three biological replicates). These results demonstrate that the disclosed recombinant polynucleotide can be used to express a two domain cytokinin synthase according to the invention in a host cell and that the recombinant cytokinin synthase is active and produces cytokinin (isopentenyl adenine).
EXAMPLE 3
Purification of Cytokinin Synthases of Invention and Agrobacterium Control, Confirmation and Quantification of the Cytokinin Synthase Activity Provided by the Purified Cytokinin Synthases
OneShot® BL21 (DE3) E. coli host cell transformed with vectors containing Epichloe festucae cytokinin synthase (EfCKS) gene with coding sequence for an N-terminal 6× histidine tag (N-polyhistidine EfCKS) (SEQ ID NO:4) and the TAKARA pGro7 chaperone expression plasmid according to instructions from the manufacturer Takara Bio Inc. (Mountain View, Calif., USA). A single colony from each transformation was inoculated into 75 milliliters of LB broth containing 50 micrograms/milliliter kanamycin sulfate and chloramphenicol in a 250 milliliter Erlenmeyer flask and grown at 30° C. in a shaker at 250 RPM overnight. Fifteen milliliters of the overnight culture was inoculated into each of three 2.8-liter fernbach flasks containing 1-liter of LB broth. Each inoculated liter of LB broth contained 50 micrograms per milliliter kanamycin sulfate and chloramphenicol and was grown at 37° C. and 250 RPM for 1.5 hours. Each culture was then placed on ice and supplemented with L-arabinose (0.75 milligrams/milliliters final concentration) and IPTG (100 micromolar final concentration). Cultures were shaken at 18° C. and 250 RPM for 8 hours. The cultures were then centrifuged at 8000 RPM for 15 minutes. The cell pellet was resuspended in approximately 125 milliliters of buffer A containing 25 mM HEPES pH 7.4, 150 mM sodium chloride, 2 mM magnesium chloride, and 2 mM dithiothreitol. Cells were lysed using a microfluidizer. Lysed cells were centrifuged at 20,000 RPM for 20 minutes. Clarified lysate was loaded into a superloop and injected onto a 5 milliliter HisPrep FastFlow® column (GE Healthcare Bioscences, Uppsala, Sweden)) at 5 mL per minute. After loading the column with the clarified lysate, the column was washed with 10 column volumes of buffer A. The column was then washed with buffer A supplemented with 20 millimolar imidazole for 6 column volumes. EfCKS was eluted from the column with buffer A supplemented with 200 millimolar imidazole. Within 5 minutes of elution from the column the eluted protein was assayed for cytokinin synthase activity.
For comparison, Agrobacterium tumefaciens isopentenyl transferase (AtuIPT) fused to N-terminal 6× histidine tag was expressed from a plasmid vector in BL21 (DE3) E. coli host cells as described above, with the following differences: L-arabinose supplementation was omitted and, following induction with IPTG and centrifugation, the cell pellet was resuspended in approximately 40 milliliters of buffer A. Cells were lysed, sonicated, centrifuged, and the resulting clarified lysate was loaded into a superloop and injected onto a 5 milliliter HisTrap HP® column (GE Healthcare) at 5 mL per minute. After loading the column with the clarified lysate, the column was washed with 8 column volumes of buffer A. The column was then washed with supplemented buffer and AtuIPT was eluted as described above for EfCKS.
Cytokinin synthase activity was assayed by diluting the eluted protein fraction two-fold in buffer A supplemented with 100 micromolar adenosine-5′-monophosphate (AMP) and 0.1 mg/mL dimethylallyl pyrophosphate. The assay was quenched by mixing an equal volume of the reaction mix with a solution of 2% v/v formic acid. The quenched assay was directly analyzed using the HPLC-TOF method described in Example 2. For in vitro enzyme activity assays, the chromatograms were blank corrected with an injection that contained buffer and enzyme, but no reactants, and the absorbance of eluted products at 268 nanometers was used to quantify cytokinins and cytokinin precursors.
The results shown in FIG. 4, first panel, demonstrate that the purified, recombinant cytokinin synthase (EfCKS) according to the invention provides cytokinin biosynthetic activity in vitro. The only detectable major product of EfCKS was cytokinin (isopentenyl adenine or iP). By contrast, as shown in FIG. 4, second panel, the only detectable product of Agrobacterium tumefaciens (AtuIPT) was isopentenyladenosine-5′-monophosphate (iPRMP) along with residual, apparently unconverted AMP reactant. These results also show that, as compared with AtuIPT, the cytokinin synthase of the invention has new and different product specificity.
EXAMPLE 4
Identification of Additional Fungal Two-Domain Cytokinin Synthase Enzymes and Amino Acid Sequence Identity Analysis Percentage
Cytokinin synthase sequences were identified in the following plant-associated fungi: Epichloe festucae (EfCKS), Balansia obtecta (BoCKS), Ilyonectria radicola cytokinin synthase (IrCKS), Aciculosporium take (AtCKS), Atkinsonella hypoxylon (AhCKS), and Fusarium fujikuroi (FfCKS). Sequences were manually inspected for the presence of sequence errors and mis-predicted exons.
The cytokinin synthase sequences were analyzed for amino acid sequence identity using the BLASTTM (BLASTP or blastp suite) program and BLOSUM62 matrix. The program generated a single sequence alignment for each pair of cytokinin synthases and determined the number of identical amino acids (amino acid percent identity), “Positives” (amino acids that are identical or classified as positive substitutions by the BLOSUM62 matrix), and gaps at each position in the alignment. See Altschul et al. (1997), Nucl. Acids Res 25(17):3389-3402. The following tables provide the percentage of amino acid identity, positives, gaps for each pairwise BLASTp alignment of EfCKS, AtCKS, BoCKS, IrCKS, AhCKS, and FfCKS. The number of amino acids that are identical, “Positives,” or gaps at each position in each alignment are indicated in parenthesis over the number of positions (length) of the relevant alignment.







TABLE 2







Amino Acid Identity, Positives, and Gaps from


EfCKS Alignments









CYTOKININ SYNTHASE PAIRS













EfCKS-
EfCKS-
EfCKS-
EfCKS-
EfCKS-



AtCKS
BoCKS
IrCKS
AhCKS
FfCKs
















Amino Acid
67%
67%
66%
70%
57%


Identity
(343/509)
(332/495)
(323/491)
(346/495)
(284/495)


Positives
80%
80%
80%
83%
70%



(412/509)
(400/495)
(394/491)
(412/495)
(350/497)


Gaps
 3%
 0%
 0%
%0
 2%



 (19/509)
 (4/495)
 (4/491)
 (4/495)
 (12/495)
















TABLE 3







Amino Acid Identity, Positives, and Gaps from


AtCKS Alignments









CYTOKININ SYNTHASE PAIRS













AtCKS-
AtCKS-
AtCKS-
AtCKS-
AtCKS-



BoCKS
IrCKS
AhCKS
FfCKs
EfCKS
















Amino Acid
63%
63%
64%
57%
67%


Identity
(322/510)
(308/486)
(328/510)
(282/497)
(343/509)


Positives
76%
76%
77%
70%
80%



(391/510)
(371/486)
(393/510)
(346/492)
(412/509)


Gaps
 3%
 3%
 3%
 5%
 3%



 (17/510)
 (17/486)
 (17/510)
 (28/492)
 (19/509)
















TABLE 4







Amino Acid Identity, Positives, and Gaps from


BoCKS Alignments









CYTOKININ SYNTHASE PAIRS













BoCKS-
BoCKS-
BoCKS-
BoCKS-
BoCKS-



IrCKS
AhCKS
FfCKs
EfCKS
AtCKS
















Amino Acid
64%
84%
58%
67%
63%


Identity
(317/495)
(415/495)
(291/498)
(332/495)
(322/510)


Positives
78%
91%
71%
80%
76%



(387/495)
(454/495)
(354/498)
(400/495)
(391/510)


Gaps
 1%
 0%
 2%
 0%
 3%



 (8/495)
 (0/495)
 (14/498)
 (4/495)
 (17/510)
















TABLE 5







Amino Acid Identity, Positives, and Gaps from


IrCKS Alignments









CYTOKININ SYNTHASE PAIRS













IrCKS-
IrCKS-
IrCKS-
IrCKS-
IrCKS-


Alignment
AhCKS
FfCKs
EfCKS
AtCKS
BoCKS





Amino Acid
64%
63%
66%
63%
64%


Identity
(319/495)
(311/491)
(323/491)
(308/486)
(317/495)


Positives
78%
75%
80%
76%
78%



(387/495)
(372/491)
(394/491)
(371/486)
(387/495)


Gaps
 1%
 1%
 0%
 3%
 1%



 (8/495)
 (8/491)
 (4/491)
 (17/486)
 (8/495)
















TABLE 6







Amino Acid Identity, Positives, and Gaps from


AhCKS Alignments









CYTOKININ SYNTHASE PAIRS













AhCKS-
AhCKS-
AhCKS-
AhCKS-
AhCKS-



FfCKS
EfCKS
AtCKS
BoCKS
IrCKS
















Amino Acid
58%
70%
64%
84%
64%


Identity
(292/500)
(346/495)
(328/510)
(415/495)
(319/495)


Positives
71%
83%
77%
91%
78%



(357/500)
(412/495)
(393/510)
(454/495)
(387/495)


Gaps
 3%
 %0
 3%
 0%
 1%



 (18/500)
 (4/495)
 (17/510)
 (0/495)
 (8/495)
















TABLE 7







Amino Acid Identity, Positives, and Gaps from


FfCKS Alignments









CYTOKININ SYNTHASE PAIRS













FfCKs-
FfCKs-
FfCKs-
FfCKs-
FfCKs-



EfCKS
AtCKS
BoCKS
IrCKS
AhCKS
















Amino Acid
57%
57%
58%
63%
58%


Identity
(284/495)
(282/497)
(291/498)
(311/491)
(292/500)


Positives
70%
70%
71%
75%
71%



(350/497)
(346/492)
(354/498)
(372/491)
(357/500)


Gaps
 2%
 5%
 2%
 1%
 3%



 (12/495)
 (28/492)
 (14/498)
 (8/491)
 (18/500)









Combined with experiments confirming cytokinin synthase activity described in Example 5, below, the foregoing demonstrates that the invention provides cytokinin synthases with varied amino acid sequences that have, for example, at least 57%-58% amino-acid sequence identity to a disclosed sequence (see, e.g., EfCKS-FfCKs, AtCKS-FfCKs, BoCKS-FfCKs, and AhCKS-FfCKS, which have at least 70%-71% “Positives”) that retain functional cytokinin synthase activity. The invention provides cytokinin synthases having at least 63%-64% amino acid sequence identity to a disclosed sequence (see, e.g., AtCKS-BoCKS, AtCKS-IrCKS, IrCKS-FfCKs, AtCKS-AhCKS, BoCKS-IrCKS, IrCKS-AhCKS, AhCKS-FfCKS, which have at least 75%-78% “Positives”) that retain functional cytokinin synthase activity. The invention provides cytokinin synthases having at least 65%-68% amino acid sequence identity to a disclosed sequence (see, e.g., EfCKS-AtCKS, EfCKS-BoCKS, and EfCKS-IrCKS, which have at least 80% “Positives”) that retain functional cytokinin synthase activity. In further embodiments, the invention provides cytokinin synthases having at least 70% amino acid sequence identity to a disclosed sequence (see, e.g., EfCKS-AhCKS, which have at least 83% “Positives”) that retain functional cytokinin synthase activity.
EXAMPLE 5
Methods of Screening and Quantification of Cytokinin Synthase Activity Provided by the Invention
Polynucleotide vectors encoding the following cytokinin synthases linked at the N-terminus to a poly-histidine protein fusion tag SEQ ID NO:5 (N-polyhistidine-EfCKS.1), SEQ ID NO:7 (N-polyhistidine-truncated EfCKS.1 (a.a. 1-255); SEQ ID NO:11 (N-polyhistidine-AtCKS.1), SEQ ID NO:15 (N-polyhistidine-BoCKS.1), SEQ ID NO:19 (N-polyhistidine-IrCKS. 1), (v) SEQ ID NO:22 (N-polyhistidine-AhCKS.1), and SEQ ID NO:27 (N-polyhistidine-FfCKS.1) were isolated from host cells produced according to Example 1, transformed into OneShot® BL21 (DE3) E. coli protein expression strains, and directly analyzed for cytokinin synthase activity according to the culture broth assay described in Example 2.
The results of the culture broth assays shown in FIG. 5 indicate that all of the foregoing two-domain cytokinin synthases produce a greater than 10-fold increase in host cell secretion of cytokinin (isopentenyl adenine), relative to host cell expressing negative control truncated EfCKS.1 (a.a. 1-255) (SEQ ID NO:7). For SEQ ID NOs: 15 and 22 an increase in host cell secretion of trans-zeatin (tZ) was also detected. These results demonstrate that the disclosed recombinant polynucleotides can be used to express two domain cytokinin synthases according to the invention in a host cell and that the recombinant cytokinin synthases actively produce cytokinin.
EXAMPLE 6
Identification of Conserved Residues Among Cytokinin Synthases and Testing to Identify Conserved Residues that Impact Cytokinin Synthase Function
EfCKS, AtCKS, BoCKS, IrCKS, AhCKS, and FfCKS sequences were aligned using the T-COFFEE multiple sequence alignment algorithm (default settings) and visualized with Jalview software package as described in T-Coffee: A novel method for multiple sequence alignments. Notredame et al., J. Mol. Biol. 302(205-217) 2000, incorporated by reference herein in its entirety. The alignment was then used to identify amino acid residues that are conserved in more than 80% of the cytokinin synthase sequences. The multiple sequence alignment, including conserved residues indicated by boxes, is shown in FIG. 6.
Individual amino acid residues were selected for targeted mutations to determine their effect on cytokinin synthase function based on degree of sequence conservation and proximity to other nearby conserved residues. Selected residues are indicated by wedges below the relevant alignment of FIG. 6. The plasmid containing EfCKS.1.Ec.his (SEQ ID NO:4) was altered by site-directed mutagenesis to create sixty-six different targeted mutants.
Targeted mutations were generated using the following protocol for single primer site-directed mutagenesis. 400 nanograms of pET28a(+) plasmid containing EfCKS.1.Ec.his (see Example 3, above) was mixed with 100 nanomolar of mutagenic primer containing the desired mutation, 200 micromolar dNTPs, 1 microliter of Pfu DNA polymerase, and 1×Pfu reaction buffer in a total volume of 50 microliters. The plasmid was amplified by the polymerase chain reaction with the following conditions: initial denaturation at 95° C. for 3 minutes, followed by 18 cycles of the following; 95° C. for 30 seconds, 53° C. for 1 minute, 68° C. for 15 minutes, and a final extension round at 68° C. for 30 minutes. The mutagenic PCR reaction mix (4 microliters) was added to 0.5 microliters of Dpn1 restriction enzyme, and 1×CutSmart buffer (NEB, Ipswich, Mass., USA) in a total reaction volume of 20 microliters. The restriction digest was incubated at 37° C. for 2.5-3 hours. After the restriction digest was complete, 6 microliters of the restriction digest was used to transform OneShot® Top10 E. coli cells according to the manufacturer's instructions. The cells were plated onto LB+kanamycin sulfate plates and grown overnight. Single colonies were selected and used to isolate sequence-verified clones of the plasmid with the targeted mutation. Each sequence-verified plasmid containing the targeted mutation was then used to transform OneShot® BL21 DE3 E. coli according to the manufacturer's instructions. Isolated single colonies were used to generate glycerol stocks containing BL21 DE3 E. coli containing each targeted mutant of EfCKS.1.Ec.his. in pET28a vectors.
The glycerol stocks were used to inoculate deep well 96-well plates containing 600 microliters of LB broth+kanamycin sulfate and grown at 33° C. and 250 RPM for about 15 hours. The cultures were used to inoculate three deep well 24-well plates containing 2 mL of LB broth+kanamycin sulfate. Cultures were then grown at 36° C. for 2.5 hours and induced with 50 micromolar IPTG. The OD600 of the cells at induction was 0.65-0.70. Induced cultures were grown at 18° C. and 250 RPM. Samples were collected at 4 hours, 8 hours, and 16 hours by removing 300 microliters of culture broth from the deep well plates. Culture samples were centrifuged at 4,000 RPM for 10 minutes and the supernatant was filtered over 0.2 micron filters and transferred to a 96-well plate for quantification of cytokinins. Quantification involved injecting 20 microliters of filter-sterilized into HPLC-MS time of flight (HPLC-TOF) system as described in Example 2 above, with a modification to the gradient to decrease the run time. The gradient used was 2% methanol to 70% methanol in 3.5 minutes, 1.5 minutes at 70% methanol, then to 2% methanol in 0.9 minutes. To normalize cytokinin production across mutants, the extracted ion chromatogram peak area for isopentenyl adenine (204.124 m/z) was divided by the extracted ion chromatogram peak area at 220.119 m/z, a byproduct of normal E. coli metabolism that is excreted into the broth during growth. Residues were determined to be functional if they substantially decreased cytokinin accumulation in the LB broth relative to the wild-type EfCKS.1.Ec.his at each of the time points tested.
The bar graph in FIG. 7 shows the effect of each mutation on cytokinin synthase activity at 16 hours post-induction relative to the histidine tagged EfCKS (“Wild Type”) and to negative control histidine tagged truncated EfCKS.1 SEQ ID NO:7). The activity of each mutant is indicated along the x-axis by reference to the amino acid position of the alanine substitution in histidine-tagged EfCKS (SEQ ID NO:5). Table 8 shows cytokinin synthase activity at 16 hours, 8 hours, and 4 hours post-induction of wild-type EfCKS (SEQ ID NO:5), truncated EfCKS (a.a. 1-255) negative control (SEQ ID NO:7). Table 9 shows cytokinin synthase activity at 16 hours, 8 hours, and 4 hours post-induction of alanine-scanning substitution mutants. The first column of Table 9 (rows G23 to W500) refer to amino acid positions substituted with alanine in histidine-tagged EfCKS (SEQ ID NO:5) and the second column (rows G13 to W490) refers to corresponding amino acid positions in wild type EfCKS (SEQ ID NO:3).












TABLE 8







EFFECT







ON CKS

8


His-EFCKs
EfCKS
ACTIVITY
16 HOURS
HOURS
4 HOURS



















WT

100
100
100


Frameshift (a.a. 1-255)
SEVERE
1
4
10





















TABLE 9







EFFECT







ON CKS

8


His-EFCKs
EfCKS
ACTIVITY
16 HOURS
HOURS
4 HOURS




















G23
G13
SEVERE
1
4
10


P24
P14
SEVERE
2
5
19


T25
T15
SEVERE
1
2
10


G28
G18
SEVERE
2
2
10


T30
T20
SEVERE
1
4
10


D48
D38
SEVERE
1
2
10


Y53
Y43
SEVERE
1
2
10


T60
T50
SEVERE
3
5
10


E67
E57
SEVERE
6
7
19


H74
H64
SEVERE
1
2
14


L75
L65
SEVERE
4
6
14


Y78
Y68
SEVERE
1
2
14


E83
E73
SEVERE
19
19
29


E84
E74
SEVERE
2
4
10


P106
P96
SEVERE
7
11
19


G110
G100
SEVERE
1
2
10


G111
G101
SEVERE
1
4
14


S112
S102
SEVERE
1
2
5


S114
S104
SEVERE
2
5
10


S140
S130
SMALL
66
67
71


M153
M143
SEVERE
2
4
19


G157
G147
SEVERE
1
4
10


E161
E151
SEVERE
4
5
10


G182
G172
SEVERE
2
4
14


W184
W174
SEVERE
1
2
14


G188
G178
SEVERE
4
9
14


Y189
Y179
SEVERE
1
2
10


E191
E181
SEVERE
3
6
10


Y227
Y217
SEVERE
1
2
10


W234
W224
SEVERE
1
2
10


L239
L229
SEVERE
2
4
10


L253
L243
SEVERE
1
2
10


W261
W251
SMALL
94
77
67


F299
F289
SEVERE
11
16
33


G301
G291
SEVERE
52
57
52


S302
S292
SMALL
61
67
62


S303
S293
SMALL
66
72
71


E312
E302
SMALL
68
78
76


L328
L318
SEVERE
11
12
24


V329
V319
SEVERE
8
10
19


G331
G321
SEVERE
34
33
38


G332
G322
SMALL
94
73
71


G333
G323
SMALL
94
83
10


M338
M328
SMALL
69
62
57


V354
V344
SEVERE
12
14
24


G356
G346
SMALL
65
77
67


P359
P349
SEVERE
35
32
33


L362
L352
SMALL
64
78
67


E366
E356
SEVERE
46
41
33


H392
H382
SMALL
94
74
62


R394
R384
SMALL
119
93
81


K395
K385
SEVERE
49
48
48


G416
G406
SEVERE
8
12
14


G417
G407
SEVERE
31
32
33


G419
G409
SEVERE
49
54
57


T420
T410
SEVERE
27
19
33


E422
E412
SEVERE
49
47
52


E423
E413
SMALL
101
75
67


T429
T419
SMALL
85
67
62


Q432
Q422
SMALL
75
84
62


G434
G424
SEVERE
40
40
33


H436
H426
SEVERE
49
58
48


G447
G437
SEVERE
9
16
29


L453
L443
SEVERE
8
10
24


F464
F454
SEVERE
11
12
33


W500
W490
SEVERE
55
43
43









For each mutant in Table 9, the corresponding amino acid position in wild-type EfCKS (SEQ ID NO:3) is determined by subtracting 10 amino acids due to the histidine tag added to the N-terminus of SEQ ID NO:5. Furthermore, each corresponding amino acid position can be determined in EfCKS, AtCKS, BoCKS, IrCKS, AhCKS.1, and FfCKS by reference to FIG. 6, which indicates in each cytokinin synthase sequence the conserved amino acids that, when altered, has a (i) severe effect on activity (indicated by wedge ▴), or (ii) small effect on activity (indicated by open diamond ⋄).
The foregoing results provide guidance on which amino acid residues should be conserved in cytokinin synthases of the invention to preserve a wild-type level of cytokinin synthase activity. Thus, the invention provides functional cytokinin synthases having, for example, at least 57%-58% amino acid sequence identity to a disclosed sequence (see, e.g., EfCKS-FfCKs, AtCKS-FfCKs, BoCKS-FfCKs, and AhCKS-FfCKS); at least 63%-64% amino acid sequence identity to a disclosed sequence (see, e.g., AtCKS-BoCKS, AtCKS-IrCKS, IrCKS-FfCKs, AtCKS-AhCKS, BoCKS-IrCKS, IrCKS-AhCKS, AhCKS-FfCKS); at least 65%-68% amino acid sequence identity to a disclosed sequence (see, e.g., EfCKS-AtCKS, EfCKS-BoCKS, and EfCKS-IrCKS); or at least 70% amino acid sequence identity to a disclosed sequence (see, e.g., EfCKS-AhCKS) which—when aligned with the disclosed amino acids (as in FIG. 6)—include the residues identified in Table 9 and FIG. 7 as having severe or small effects on activity.
The foregoing results also demonstrate that, in other embodiments, the invention provides cytokinin synthases having cytokinin synthase activity that is reduced by a small amount. In some embodiments, the invention provides functional cytokinin synthases having, for example, at least 57%-58% amino acid sequence identity to a disclosed sequence; at least 63%-64% amino acid sequence identity to a disclosed sequence; at least 65%-68% amino acid sequence identity to a disclosed sequence; or at least 70% amino acid sequence identity to a disclosed sequence, which—when aligned with the disclosed amino acids (as in FIG. 6)—include the residues identified in Table 9 and FIG. 7 as having a small effect on activity.
EXAMPLE 7
Further Identification of Additional Fungal Two-Domain Cytokinin Synthase Enzymes and Amino Acid Sequence Identity Analysis Percentage
Further cytokinin synthase sequences were identified by searching genomic databases for fungal genes encoding an isopentenyl transfer (IPT)-like domain and a phosphoribohydrolase (PRH)-like domain in accordance with the invention. Additional cytokinin synthases are manually inspected for the presence of sequence errors and mis-predicted exons and are assayed to confirm cytokinin synthase activity. The amino acid sequences of the additional cytokinin synthases of the invention are provided as SEQ ID NOs:34 to 54 and are shown in FIGS. 24-29. Table 10 indicates the fungal source for each amino acid sequence (as well as corresponding Gene Id (gi/jgi) or abbreviation for the cytokinin synthase used in the phylogenetic tree in FIG. 23).








TABLE 10





Fungal Source (CKS gene identifier or abbreviation)
SEQ ID NO







Botryosphaeria dothidea (jgi|Botdo1_1|289339)
SEQ ID NO: 34


Claviceps purpurea (gi|399168795 20.1)
SEQ ID NO: 35


Fusarium oxysporum vasinfectum 25433 (gi|591501391)
SEQ ID NO: 36


Fusarium oxysporum f. sp. raphani 54005 (gi|590069068)
SEQ ID NO: 37


Fusarium oxysporum Fo5176 (gi|342882308)
SEQ ID NO: 38


Fusarium oxysporum f. sp. pisi HDV247 (gi|587753796)
SEQ ID NO: 39


Fusarium oxysporum FOSC 3-a (gi|587670126)
SEQ ID NO: 40


Fusarium oxysporum f. sp. melonis 26406 (gi|590047683)
SEQ ID NO: 41


Fusarium oxysporum f. sp. vasinfectum 25433 (gi|591490727)
SEQ ID NO: 42


Fusarium oxysporum f. sp. conglutinans race 2 54008 (gi|591441911)
SEQ ID NO: 43


Fusarium oxysporum f. sp. raphani 54005 (gi|590053069)
SEQ ID NO: 44


Fusarium oxysporum f. sp. cubense tropical race 4 54006 (gi|591467821)
SEQ ID NO: 45


Fusarium oxysporum f. sp. pisi HDV247 (gi|587748549)
SEQ ID NO: 46


Fusarium fujikuroi IMI 58289 (gi|517314372)
SEQ ID NO: 47


Fusarium pseudograminearum CS3096 (gi|685861465)
SEQ ID NO: 48


Fusarium verticillioides 7600 (gi|584135303)
SEQ ID NO: 49


Epichloe gansuensis EgCKS
SEQ ID NO: 50


Atkinsonella texensis AteCKS
SEQ ID NO: 51


Claviceps fusiformis CfCKS
SEQ ID NO: 52


Epichloe baconii (EbCKS
SEQ ID NO: 53


Claviceps paspali (CpaCKS)
SEQ ID NO: 54









EXAMPLE 8
Identification of Functional Motifs in Cytokinin Synthases of the Invention and Testing to Identify Conserved Residues that Impact Cytokinin Synthase Function
The alignment shown in FIG. 6 and the site-directed mutagenesis results described in Example 6 and Table 8 were analyzed in further view of additional cytokinin synthases identified in Example 7 to identify functionally significant motifs in each fungal cytokinin synthase. Referring to the consensus amino acid sequence positions in the alignment of FIG. 6, the following four motifs were identified: (1) GPTXaa1Xaa2GKT (SEQ ID NO:30), wherein Xaa1 is G or A and Xaa2 is V, S, A, or T, at consensus sequence amino acid positions 13-20, (2) PXaa3Xaa4Xaa5GGSXaa6S (SEQ ID NO:31), wherein Xaa3 is I or V, Xaa4 is L or V, Xaa5 is V or C, and Xaa6 is T or I, at consensus sequence amino acid positions 96-104, (3) Xaa7Xaa8YGGG (SEQ ID NO:32), wherein Xaa7 is L or I, and Xaa8 is V or I, at consensus sequence amino acid positions 333-338, and (4) Xaa9GGYGT Xaa10EEL (SEQ ID NO:33), where Xaa9 is S or P and Xaa10 is L or M, at consensus sequence amino acid positions 426-438. Table 11 below shows the precise sequence corresponding the foregoing motifs as exemplified in each of the fungal cytokinin synthases disclosed herein.











TABLE 11






MOTIF 1
MOTIF 2

MOTIF 4



GPTXaa1Xaa2G
PXaa3Xaa4Xaa5
MOTIF 3
Xaa9GGYGT



KTK
GGSXaa6S
Xaa7Xaa8YGGG
Xaa10EEL


SPECIES (SEQ ID NO)
(SEQ ID NO: 30)
(SEQ ID NO: 31)
(SEQ ID NO: 32)
(SEQ ID NO: 33)







AhCKS.1 (SEQ ID NO: 21)
GPTGVGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 59)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


AtCKS.1 (SEQ ID NO: 9)
GPTASGKTK
PVLVGGSTS
LVYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 64)
(SEQ ID NO: 68)
(SEQ ID NO: 72)


 


AteCKS.1 (SEQ ID NO: 51)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


BoCKS.1 (SEQ ID NO: 13)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


CfCKS.1 (SEQ ID NO: 52)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 72)


 


CpaCKS.1 Claviceps paspali
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTMEEL


(SEQ ID NO: 54)
(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 72)


 


EbCKS.1 Epichlo baconii
GPTASGKTK
PVLVGGSTS
LVYGGG
SGGYGTMEEL


(SEQ ID NO: 53)
(SEQ ID NO: 60)
(SEQ ID NO: 64)
(SEQ ID NO: 68)
(SEQ ID NO: 72)


 


EfCKS.1 (SEQ ID NO: 3)
GPTASGKTK
PVLVGGSTS
LVYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 64)
(SEQ ID NO: 68)
(SEQ ID NO: 72)


 


EgCKS.1 (SEQ ID NO: 50)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 72)


 


FfCKS.1 (SEQ ID NO: 25)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


gi|342882308 (SEQ ID NO: 38)
GPTASGKTK
PVLVGGSTS
LIYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 64)
(SEQ ID NO: 69)
(SEQ ID NO: 72)


 


gi|399168795 (SEQ ID NO: 35)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


gi|517314372 (SEQ ID NO: 47)
GPTASGKTK
PVVVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 65)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


gi|584135303 (SEQ ID NO: 49)
GPTGAGKTK
PVVVGGSTS
IVYGGG
SGGYGTLEEL



(SEQ ID NO: 61)
(SEQ ID NO: 65)
(SEQ ID NO: 70)
(SEQ ID NO: 71)


 


gi|587670126 (SEQ ID NO: 40)
GPTGVGKTK
PVLVGGSTS
LIYGGG
SGGYGTMEEL



(SEQ ID NO: 59)
(SEQ ID NO: 64)
(SEQ ID NO: 69)
(SEQ ID NO: 72)


 


gi|587748549 (SEQ ID NO: 46)
GPTGTGKTK
PILVGGSIS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 62)
(SEQ ID NO: 66)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


gi|587753796 (SEQ ID NO: 39)
GPTASGKTK
PVLVGGSTS
LIYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 64)
(SEQ ID NO: 69)
(SEQ ID NO: 72)


 


gi|590047683 (SEQ ID NO: 41)
GPTASGKTK
PVLVGGSTS
LIYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 64)
(SEQ ID NO: 69)
(SEQ ID NO: 72)


 


gi|590053069 (SEQ ID NO: 44)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


gi|590069068 (SEQ ID NO: 37)
GPTASGKTK
PVLVGGSTS
LIYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 64)
(SEQ ID NO: 69)
(SEQ ID NO: 72)


 


gi|591441911 (SEQ ID NO: 43)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


gi|591467821 (SEQ ID NO: 45)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


gi|591490727 (SEQ ID NO: 42)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


gi|591501391 (SEQ ID NO: 36)
GPTASGKTK
PVLVGGSTS
LIYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 64)
(SEQ ID NO: 69)
(SEQ ID NO: 72)


 


gi|685861465 (SEQ ID NO: 48)
GPTASGKTK
PVVVGGSTS
LVYGGG
SGGYGTLEEL



(SEQ ID NO: 60)
(SEQ ID NO: 65)
(SEQ ID NO: 68)
(SEQ ID NO: 71)


 


IrCKS.1 (SEQ ID NO: 17)
GPTASGKTK
PILVGGSTS
LVYGGG
SGGYGTMEEL



(SEQ ID NO: 60)
(SEQ ID NO: 63)
(SEQ ID NO: 68)
(SEQ ID NO: 72)


 


jgi|Botdo1_1|289339 1
GPTASGKTK
PILCGGSTS
LVYGGG
PGGYGTMEEL


(SEQ ID NO: 34)
(SEQ ID NO: 60)
(SEQ ID NO: 67)
(SEQ ID NO: 68)
(SEQ ID NO: 73)









The foregoing demonstrates embodiments of the invention that relate to a two domain cytokinin synthase that includes (i) an isopentenyl transfer (IPT)-like domain, (ii) a phosphoribohydrolase (PRH)-like domain and (iii) each of the foregoing four motifs.
EXAMPLE 9
Confirmation of the Functional Motifs in Non Fungal Proteins Having an IPT-Like Domain or PRH-Like Domains and their Use for Making Modified Cytokinin Synthases
Proteins containing IPT-like domain were interrogated for the presence of the first and second motif identified in foregoing Example 8. Table 12 provides a representative set of such motifs that were identified in bacterial homologues of the Agrobacterium tumefaciens isopentenyl transferase (each homologue is identified by Gene ID (gi)).











TABLE 12






MOTIF 1
MOTIF 2





GlyXaa11Xaa12Xaa13
Xaa16Xaa17Xaa18Xaa19GlyGly





Xaa14GlyLysXaa15
Xaa20Xaa21Xaa22
MOTIF 3
MOTIF 4


Gene ID
(SEQ ID NO: 55)
(SEQ ID NO: 56)
(SEQ ID NO: 57)
(SEQ ID NO: 58)







gi|787755613
GPTCSGKT
VILEGGSIS
N/A
N/A



(SEQ ID NO: 74)
(SEQ ID NO: 84)




 


gi|763386594
GATTTGKT
FILEGGSVS
N/A
N/A



(SEQ ID NO: 75)
(SEQ ID NO: 85)




 


gi|757628273
GVTSMGKT
IIIEGGSVS
N/A
N/A



(SEQ ID NO: 76)
(SEQ ID NO: 86)




 


gi|748744591
GPTSTGKT
VIIEGGSVS
N/A
N/A



(SEQ ID NO: 77)
(SEQ ID NO: 87)




 


gi|738063466
GPTTTGKT
IILEGGSMS
N/A
N/A



(SEQ ID NO: 78)
(SEQ ID NO: 88)




 


gi|695262623
GPTCTGKT
LILEGGSIS
N/A
N/A



(SEQ ID NO: 79)
(SEQ ID NO: 89)




 


gi|671637394
GATCTGKT
VILEGGSIS
N/A
N/A



(SEQ ID NO: 80)
(SEQ ID NO: 84)




 


gi|658535282
GPTSTGKT
VILEGGSVS
N/A
N/A



(SEQ ID NO: 77)
(SEQ ID NO: 90)




 


gi|653760120
GPTSTGKT
LILEGGSIS
N/A
N/A



(SEQ ID NO: 77)
(SEQ ID NO: 89)




 


gi|652910097
GPTTAGKT
LILEGGSVS
N/A
N/A



(SEQ ID NO: 81)
(SEQ ID NO: 91)




 


gi|652343402
GPTSTGKT
IILEGGSVS
N/A
N/A



(SEQ ID NO: 77)
(SEQ ID NO: 92)




 


gi|504873554
GATCTGKT
VILEGGSIS
N/A
N/A



(SEQ ID NO: 80)
(SEQ ID NO: 84)




 


gi|501825808
GPTSTGKT
VILEGGSIS
N/A
N/A



(SEQ ID NO: 77)
(SEQ ID NO: 84)




 


gi|499303622
GPTSVGKT
LILEGGSIS
N/A
N/A



(SEQ ID NO: 82)
(SEQ ID NO: 89)




 


gi|499194825
GPTCTGKT
LILEGGSTS
N/A
N/A



(SEQ ID NO: 79)
(SEQ ID NO: 93)




 


gi|499193920
GPTCTGKT
LILEGGSIS
N/A
N/A



(SEQ ID NO: 79)
(SEQ ID NO: 89)




 


gi|489573415
GPTCSGKT
VILEGGSIS
N/A
N/A



(SEQ ID NO: 74)
(SEQ ID NO: 84)




 


gi|489370511
GATTTGKT
LILEGGSVS
N/A
N/A



(SEQ ID NO: 75)
(SEQ ID NO: 91)




 


gi|4586310
GPTCTGKT
LILEGGSIS
N/A
N/A



(SEQ ID NO: 79)
(SEQ ID NO: 89)




 


gi|441422009
GATCTGKT
VILEGGSIS
N/A
N/A



(SEQ ID NO: 80)
(SEQ ID NO: 84)




 


gi|344175716
GATTTGKT
LILEGGSVS
N/A
N/A



(SEQ ID NO: 75)
(SEQ ID NO: 91)




 


gi|297155133
GPTGVGKS
VIVEGGSIS
N/A
N/A



(SEQ ID NO: 83)
(SEQ ID NO: 94)









Table 13 provides a representative set of such motifs that were identified in bacterial homologues of Escherichia coli tRNA isopentenyl transferase (each homologue is identified by Gene ID (gi)).












TABLE 13






MOTIF 1
MOTIF 2





GlyXaa11Xaa12Xaa13
Xaa16Xaa17Xaa18Xaa19GlyGly





Xaa14GlyLysXaa15
Xaa20Xaa21Xaa22
MOTIF 3
MOTIF 4


Gene ID
(SEQ ID NO: 55)
(SEQ ID NO: 56)
(SEQ ID NO: 57)
(SEQ ID NO: 58)







gi|164423202
GSTGTGKS
PIVVGGTSY
N/A
N/A



(SEQ ID NO: 95)
(SEQ ID NO: 100)




 


gi|398366035
GTTGVGKS
PIVVGGTHY
N/A
N/A



(SEQ ID NO: 96)
(SEQ ID NO: 101)




 


gi|22326902
GPTGAGKS
PIVTGGTGL
N/A
N/A



(SEQ ID NO: 97)
(SEQ ID NO: 102)




 


gi|25144712
GCTGTGKS
PVIVGGTTY
N/A
N/A



(SEQ ID NO: 98)
(SEQ ID NO: 103)




 


gi|127087
GPTASGKT
PLLVGGTML
N/A
N/A



(SEQ ID NO: 99)
(SEQ ID NO: 104)









Table 14 provides a representative set of such motifs that were identified in bacterial homologues of plant adenylate isopentenyl transferases (each homologue is identified by Gene ID (gi)).












TABLE 14






MOTIF 1
MOTIF 2





GlyXaa11Xaa12Xaa13Xaa14Gly
Xaa16Xaa17Xaa18Xaa19





LysXaa15
GlyGlyXaa20Xaa21Xaa22
MOTIF 3
MOTIF 4


Gene ID
(SEQ ID NO: 55)
(SEQ ID NO: 56)
(SEQ ID NO: 57)
(SEQ ID NO: 58)







gi|15221410
GATGAGKS
PIIAGGSNS
N/A
N/A



(SEQ ID NO: 105)
(SEQ ID NO: 111)




 


gi|15222583
GTTGTGKS
PIVVGGSNS
N/A
N/A



(SEQ ID NO: 106)
(SEQ ID NO: 112)




 


gi|15230294
GATGSGKS
PIIAGGSNS
N/A
N/A



(SEQ ID NO: 107)
(SEQ ID NO: 111)




 


gi|15233904
GATGSGKS
PILAGGSNS
N/A
N/A



(SEQ ID NO: 107)
(SEQ ID NO: 113)




 


gi|15239638
GATGTGKS
PIIAGGSNS
N/A
N/A



(SEQ ID NO: 108)
(SEQ ID NO: 111)




 


gi|18403831
GATGSGKS
PIVAGGSNS
N/A
N/A



(SEQ ID NO: 107)
(SEQ ID NO: 114)




 


gi|18412615
GATGTGKS
PIIVGGSNS
N/A
N/A



(SEQ ID NO: 108)
(SEQ ID NO: 115)




 


gi|357114975
GATGTGKS
PVLAGGSNS
N/A
N/A



(SEQ ID NO: 108)
(SEQ ID NO: 116)




 


gi|357119123
GATGTGKT
PVVAGGSNS
N/A
N/A



(SEQ ID NO: 109)
(SEQ ID NO: 117)




 


gi|357119795
GATATGKS
PVVAGGSNT
N/A
N/A



(SEQ ID NO: 110)
(SEQ ID NO: 118)




 


gi|357128230
GATATGKS
PIVAGGSNR
N/A
N/A



(SEQ ID NO: 110)
(SEQ ID NO: 119)




 


gi|357128580
GATGTGKT
PVVAGGSNS
N/A
N/A



(SEQ ID NO: 109)
(SEQ ID NO: 117)




 


gi|721643516
GATGTGKT
PVVAGGSNS
N/A
N/A



(SEQ ID NO: 109)
(SEQ ID NO: 117)









Proteins containing PRH-like domain were interrogated for the presence of the third and fourth motif identified in foregoing Example 8. Table 15 provides a representative set of such motifs that were identified in plant cytokinin riboside 5′-monophosphate phosphoribohydrolase (each homologue is identified by Gene ID (gi)).











TABLE 15









MOTIF 4





MOTIF 3
ProGlyGlyTyrGlyThr



MOTIF 1
MOTIF 2
LVYGGG
Xaa23Xaa24GluLeu


Gene ID
(SEQ ID NO: 55)
(SEQ ID NO: 56)
(SEQ ID NO: 57)
(SEQ ID NO: 58)







gi|79567911
N/A
N/A
LVYGGG
PGGYGTFEEL





(SEQ ID NO: 57)
(SEQ ID NO: 120)


 


gi|79507209
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|721692766
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|721635070
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|357154491
N/A
N/A
LVYGGG
PGGYGTLDEL





(SEQ ID NO: 57)
(SEQ ID NO: 122)


 


gi|357150282
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|357146658
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|357136124
N/A
N/A
LVYGGG
PGGYGTMEEL





(SEQ ID NO: 57)
(SEQ ID NO: 123)


 


gi|357135368
N/A
N/A
LVYGGG
PGGYGTLDEL





(SEQ ID NO: 57)
(SEQ ID NO: 122)


 


gi|357118466
N/A
N/A
LVYGGG
PGGYGTIEEL





(SEQ ID NO: 57)
(SEQ ID NO: 124)


 


gi|357114642
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|30687072
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|30683873
N/A
N/A
LVYGGG
PGGYGTMEEL





(SEQ ID NO: 57)
(SEQ ID NO: 123)


 


gi|18418592
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|18401696
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)


 


gi|15231816
N/A
N/A
LVYGGG
PGGYGTLEEL





(SEQ ID NO: 57)
(SEQ ID NO: 121)









The foregoing evidence supports that the four motifs disclosed by the invention are functional in non-fugal proteins that have either an IPT-like domains or a PRH-like domain. The foregoing also provides guidance for modifying the cytokinin synthases disclosed herein to include a motif 1, a motif 2, or both a motif 1 and a motif 2 disclosed in Tables 12, 13 or 14 and/or to include a motif 3, a motif 4, or both a motif 3 and a motif 4 in Table 15. Thus, when aligned with a consensus sequence of SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS) as shown in FIG. 6, any cytokinin synthase disclosed herein can be modified as follows:

    
    
        (a) motif 1 (SEQ ID NO:30) at consensus sequence amino acid positions 13-20 is substituted with the amino acids of a motif 1 in Tables 12, 13 or 14,
        (b) motif 2 (SEQ ID NO:31) at consensus sequence amino acid positions 96-104 is substituted with the amino acids of motif 2 in Tables 12, 13 or 14,
        (c) motif 3 (SEQ ID NO:32) at consensus sequence amino acid positions 333-338 is substituted with the amino acids of motif 3 in Table 15,
        (d) motif 4 (SEQ ID NO:33) at consensus sequence amino acid positions 333-338 is substituted with the amino acids of motif 4 from Table 15, or
        (e) a combination of two or more of the motif substitutions of (a), (b), (c), and (d).

## Claims

1. A recombinant polynucleotide comprising a cytokinin synthase coding sequence, and a heterologous sequence, wherein the cytokinin synthase comprises an isopentenyl transfer (IPT)-like domain and a phosphoribohydrolase (PRH)-like domain and the encoded cytokinin synthase comprises a sequence having at least 90% amino acid sequence identity to SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS).

2. The polynucleotide of claim 1, wherein the cytokinin synthase coding sequence comprises a sequence having at least 70% nucleotide sequence identity to SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:24 (FfCKS).

3. The polynucleotide of claim 1, wherein the cytokinin synthase coding sequence comprises a sequence having at least 90% nucleotide sequence identity to SEQ ID NO:1 (EfCKS), SEQ ID NO:8 (AtCKS), SEQ ID NO:12 (BoCKS), SEQ ID NO:16 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:24 (FfCKS).

4. The polynucleotide of claim 1, wherein the encoded cytokinin synthase comprises a sequence having at least 95% amino acid sequence identity to SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS).

5. The polynucleotide of claim 1, encoded cytokinin synthase comprises SEQ ID NO:3 (EfCKS), SEQ ID NO:9 (AtCKS), SEQ ID NO:13 (BoCKS), SEQ ID NO:17 (IrCKS), SEQ ID NO:21 (AhCKS), or SEQ ID NO:25 (FfCKS).

6. The polynucleotide of claim 1, wherein the cytokinin synthase coding sequence is optimized for expression in a host cell.

7. The polynucleotide of claim 1, wherein the cytokinin synthase coding sequence is optimized for expression in a host cell selected from the group consisting of a bacteria, yeast, plant, dicot plant, monocot plant, maize, soybean, canola, cotton, wheat, Arabidopsis thaliana, rice (Oryza sativa), sunflower, grass, creeping bentgrass (Agrostis stolonifera), tall fescue (Festuca arundinacea), tobacco (Nicotiana tabacum), and poplar hybrid.

8. The polynucleotide of claim 1, wherein the heterologous sequence is a heterologous promoter and the promoter is operably linked to the cytokinin synthase coding sequence.

9. The polynucleotide of claim 8, wherein the promoter is a bacteria promoter, heterologous fungal promoter, yeast promoter, or plant promoter.

10. The polynucleotide of claim 8, wherein the promoter is a dicot promoter or a monocot promoter.

11. The polynucleotide of claim 8, wherein the promoter is a maize promoter.

12. The polynucleotide of claim 8, wherein the promoter is a 35S CaMV, 34S FMV, Napin, 7S alpha, 7S alpha′, Glob, Lec, ZmGS2, ZmSTP13, or ZmGSTU6 promoter.

13. The polynucleotide of claim 1, wherein the cytokinin synthase coding sequence is flanked by a first upstream heterologous sequence and a second downstream heterologous sequence, and the first and second heterologous sequences are (i) more than 80% identical genomic sequence from a heterologous host and (ii) suitable for catalyzing integration by homologous recombination into the host.

14. A gene expression cassette comprising the polynucleotide of claim 1.

15. A recombinant vector comprising
a. the gene expression cassette of claim 14; and
b. a selectable marker.

16. The recombinant vector of claim 15, wherein
a. the gene expression cassette comprises the polynucleotide of claim 10; and
b. the vector comprises an origin of replication that is functional in bacteria or yeast.

17. The polynucleotide of claim 1, wherein the heterologous sequence encodes a protein fusion tag.

18. The polynucleotide of claim 17, wherein the encoded protein fusion tag is a poly-histidine, poly-arginine, haloalkane dehalogenase, streptavidin-binding, glutathione s-transferase (GST), maltose-binding protein (MBP), thioredoxin, small ubiquitin-like modifier (SUMO), N-utilization substance A (NusA), protein disulfide isomerase I (DsbA), Mistic, Ketosteroid isomerase (KSI), TrpE, c-myc, hemaglutinin antigen (HA), FLAG, 1D4, calmodulin-binding peptide, chitin-binding domain, cellulose-binding domain, S-tag, or Softag3 protein fusion tag.

19. A host cell comprising the polynucleotide of claim 1.

20. The host cell of claim 19, wherein the host cell is a transformed bacteria cell, a trans-formed fungus cell, a transformed yeast cell, or a transgenic plant cell.

21. The host cell of claim 20, wherein the host cell is a transgenic monocot plant cell or a transgenic dicot plant cell.

22. The host cell of claim 21, wherein the host cell is a soybean host cell or a maize host cell.

23. A transgenic plant comprising the host cell of claim 21.

24. A method for producing recombinant cytokinin synthase, wherein the method comprises,
a. expressing the recombinant cytokinin synthase in the host cell of claim 19; and
b. isolating the cytokinin synthase from host cell materials.

25. A transgenic plant comprising the host cell of claim 22.

26. The transgenic plant of claim 25, wherein the transgenic plant is a soybean plant.

27. The transgenic plant of claim 25, wherein the plant is a maize plant.