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WO2008142146A1 - Amélioration du rendement dans des plantes par modulation de zmphdf - Google Patents

Amélioration du rendement dans des plantes par modulation de zmphdf Download PDF

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WO2008142146A1
WO2008142146A1 PCT/EP2008/056332 EP2008056332W WO2008142146A1 WO 2008142146 A1 WO2008142146 A1 WO 2008142146A1 EP 2008056332 W EP2008056332 W EP 2008056332W WO 2008142146 A1 WO2008142146 A1 WO 2008142146A1
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Prior art keywords
plant
zmphdf
polypeptide
seq
sequence
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Xiping Niu
Wesley B. Bruce
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CropDesign NV
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CropDesign NV
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • the present invention is drawn to the field of genetics and molecular biology. More particularly, the compositions and methods are directed to modulation of transcription and improving yield in plants.
  • the PHDF plant homeodomain-finger
  • the PHDF is a motif (-50 residue) found mainly in proteins involved in plant transcription regulation potentially controlling the expression of the homeotic genes through a mechanism thought to involve some aspect of chromatin structure.
  • the common conserved sequence characteristic of these proteins is a CysCysCysCys- HisCysCysCys-type zinc-binding motif.
  • a subset of the genes also include a second largely unknown domain of -170 amino acids referred to herein as the "LLIF" domain present near the C-terminal end.
  • the disclosed invention consists of a portion of the ZmPHDF gene that includes the LLIF domain (153 amino acid domain, SEQ ID NO: 5)
  • compositions and methods for modulating flower organ development, leaf formation, phototropism, apical dominance, fruit development, initiation of roots, and for increasing yield in a plant are provided.
  • the compositions include a ZmPHDF sequence.
  • Compositions of the invention comprise amino acid sequences and nucleotide sequences selected from SEQ ID NOS: 1-3 as well as variants and fragments thereof.
  • Nucleotide sequences encoding the ZmPHDF gene are provided in DNA constructs for expression in a plant of interest. Expression cassettes, plants, plant cells, plant parts, and seeds comprising the sequences of the invention are further provided. In specific embodiments, the polynucleotide is operably linked to a constitutive promoter.
  • Methods for modulating the level of a ZmPHDF sequence in a plant or a plant part comprise introducing into a plant or plant part a heterologous polynucleotide comprising a ZmPHDF sequence, a portion of this sequence that comprises the LLIF domain, or the whole sequence with a portion of the protein altered so that the C-terminal portion with the LLIF domain remains active.
  • the level of the ZmPHDF polypeptide can be increased or decreased.
  • Such method can be used to increase the yield in plants; in one embodiment, the method is used to increase grain yield in cereals.
  • Figure 1 provides an alignment of several ZmPHDF gene products from Zea mays, Arabidopsis thaliana, and Oryzae sativum.
  • the ZmPHDF consensus domain (SEQ ID NO: 15) is single-underlined and the LLIF consensus domain (SEQ ID NO: 16) is double underlined.
  • Figure 2 provides an amino acid alignment of several LLIF domain regions for Zea mays (SEQ ID NO: 5), Arabidopsis thaliana (SEQ ID NO: 13), Oryzae sativum (SEQ ID NO: 12), and Glycine max (SEQ ID NO: 14).
  • compositions are provided to promote floral organ development, root initiation, and yield, and for modulating leaf formation, phototropism, apical dominance, fruit development and the like, in plants.
  • the compositions and methods of the invention result in improved plant or crop yield by modulating in a plant the level of at least one ZmPHDF polypeptide or a polypeptide having a biologically active variant or fragment of a ZmPHDF polypeptide of the invention.
  • compositions of the invention include ZmPHDF polynucleotides and polypeptides and variants and fragments thereof that are involved in regulating transcription.
  • the ZmLLIF domain (SEQ ID NO: 5) is present in ZmPHDF (from amino acid residues 21 to 173 of SEQ ID NO: 3) corresponding to the nucleotide residues at positions 34 to 1329 in SEQ ID NO: 1.
  • the LLIF domain is highly conserved (See, Figure 2) among sequences found in Zea mays, Arabidopsis thaliana, Oryzae sativum, and Glycine max.
  • corresponding to is intended that the recited amino acid positions for each domain relate to the amino acid positions of the recited SEQ ID NO, and that polypeptides comprising these domains may be found by aligning the polypeptides with the recited SEQ ID NO: using standard alignment methods.
  • the family of PHD-finger genes has been suggested to regulate transcription by interaction with chromatin-related complexes (Aasland, R., TJ. Gibson, and A.F. Stewart, The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci, (1995) 20:56-9).
  • the ZmPHDF protein product of the invention acts as a negative regulator or dominant-negative effector interacting with other chromatin-related proteins possibly via the conserved LLIF domain but not binding to a target DNA.
  • the invention may also play a role in scaffolding key proteins into complexes but again unable to direct any DNA-binding itself and thus perturb the normal function of the complexes.
  • ZmPHDF is expressed throughout the plant at relatively low levels (approximately 0.5-1 % of maize polyubiquitin gene).
  • a "ZmPHDF” or “ZmPHDF” sequence comprises a polynucleotide encoding or a polypeptide having the PHD-finger and LLIF domain or a biologically active variant or fragment of the PHD-finger or LLIF domain. See, for example, Jurata and Gill (1997) MoI. Cell. Biol. 17:5688-98; and Franks, et al., (2002) Development 129:253-63.
  • the present invention provides isolated ZmPHDF polypeptides comprising amino acid sequences as shown in SEQ ID NOS: 2 and 3 and fragments and variants thereof. Further provided are polynucleotides comprising the nucleotide sequence set forth in SEQ ID NO: 1 and sequences comprising a polynucleotide encoding an LLIF domain (SEQ ID NO: 5) or a PHD-finger domain (SEQ ID NO: 4). In some embodiments, a polynucleotide of the invention will comprise sequences encoding both the LLIF and the PHD-finger domain.
  • the invention encompasses isolated or substantially purified polynucleotide or protein compositions.
  • An "isolated” or “purified” polynucleotide or protein, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or protein as found in its naturally occurring environment.
  • an isolated or purified polynucleotide or protein is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • an "isolated" polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5' and 3' ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived.
  • the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived.
  • a protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, 5% or 1% (by dry weight) of contaminating protein.
  • optimally culture medium represents less than about 30%, 20%, 10%, 5% or 1% (by dry weight) of chemical precursors or non-protein-of-interest chemicals.
  • Fragments and variants of the LLIF, PHD-finger domain or ZmPHDF polynucleotides and proteins encoded thereby are also encompassed by the methods and compositions of the present invention. By “fragment” is intended a portion of the polynucleotide or a portion of the amino acid sequence.
  • Fragments of a polynucleotide may encode protein fragments that retain the biological activity of the native protein and hence regulate transcription.
  • polypeptide fragments will comprise the PHD-finger domain (SEQ ID NO: 4), or the LLIF domain (SEQ ID NO: 5).
  • the polypeptide fragment will comprise both the PHD-finger domain and the LLIF domain.
  • fragments that are used for suppressing or silencing (i.e., decreasing the level of expression) of a ZmPHDF sequence need not encode a protein fragment, but will retain the ability to suppress expression of the target sequence.
  • fragments that are useful as hybridization probes generally do not encode fragment proteins retaining biological activity.
  • fragments of a nucleotide sequence may range from at least about 18 nucleotides, about 20 nucleotides, about 50 nucleotides, about 100 nucleotides and up to the full-length polynucleotide encoding the proteins of the invention.
  • a fragment of a polynucleotide encoding a ZmPHDF polypeptide, PHD-finger and the LLIF domains, or either the PHD-finger or LLIF domain will encode at least 15, 25, 30, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 675, 700, 725, 750, 775, 800, 825 contiguous amino acids, or up to the total number of amino acids present in a full-length ZmPHDF protein, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone.
  • Fragments of a ZmPHDF polynucleotide, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone that are useful as hybridization probes, PCR primers, or as suppression constructs generally need not encode a biologically active portion of a ZmPHDF protein or a ZmPHDF domain.
  • a biologically active portion of a polypeptide comprising a ZmPHDF protein and the LLIF domain, or LLIF domain alone can be prepared by isolating a portion of a ZmPHDF polynucleotide, expressing the encoded portion of the ZmPHDF protein (e.g., by recombinant expression in vitro), and assessing the activity of the encoded portion of the ZmPHDF protein.
  • Polynucleotides that are fragments of a ZmPHDF nucleotide sequence, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone comprise at least 16, 20, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 1 ,000, 1 ,100, 1 ,200, 1 ,300, 1 ,400, 1 ,500, 1 ,600, 1 ,700, 1 ,800, 1 ,900, 2,000, 2,050, 2,100, 2,150, 2,200, 2,250, 2,300, 2,350, 2,400, 2,450, 2,500 contiguous nucleotides, or up to the number of nucleotides present in a ZmPHDF polynucleotide (i.e., SEQ ID NOS: 1 , 1.526 nucleotides), and the LLIF domains together, or the LLIF domain alone.
  • a variant comprises a deletion and/or addition of one or more nucleotides at one or more internal sites within the native polynucleotide and/or a substitution of one or more nucleotides at one or more sites in the native polynucleotide.
  • a "native" polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively.
  • conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the ZmPHDF polypeptides, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone.
  • Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below.
  • Variant polynucleotides also include synthetically derived polynucleotide, such as those generated, for example, by using site-directed mutagenesis but which still encode a polypeptide comprising a ZmPHDF polypeptide, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone that is capable of regulating transcription or that is capable of reducing the level of expression (i.e., suppressing or silencing) of a ZmPHDF polynucleotide.
  • synthetically derived polynucleotide such as those generated, for example, by using site-directed mutagenesis but which still encode a polypeptide comprising a ZmPHDF polypeptide, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone that is capable of regulating transcription or that is capable of reducing the level of expression (i.e., suppressing or silencing) of a ZmPHDF polyn
  • variants of a particular polynucleotide of the invention will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters described elsewhere herein.
  • Variants of a particular polynucleotide of the invention can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide.
  • an isolated polynucleotide that encodes a polypeptide with a given percent sequence identity to the polypeptide of SEQ ID NO. 1 or SEQ ID NO: 2 are disclosed. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein.
  • the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
  • Variant protein is intended to mean a protein derived from the native protein by deletion or addition of one or more amino acids at one or more internal sites in the native protein and/or substitution of one or more amino acids at one or more sites in the native protein.
  • Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, that is, regulate transcription as described herein. Such variants may result from, for example, genetic polymorphism or from human manipulation.
  • Biologically active variants of a ZmPHDF protein of the invention, PHD- finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the ZmPHDF protein, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone as determined by sequence alignment programs and parameters described elsewhere herein.
  • a biologically active variant of a ZmPHDF protein of the invention, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
  • polynucleotides of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants and fragments of the ZmPHDF proteins, PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone can be prepared by mutations in the DNA. Methods for mutagenesis and polynucleotide alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel, et al., (1987) Methods in Enzymol.
  • the genes and polynucleotides of the invention include both the naturally occurring sequences as well as mutant forms.
  • the proteins of the invention encompass both naturally occurring proteins as well as variations and modified forms thereof.
  • Such variants will continue to possess the desired activity (i.e., the ability to regulate transcription or decrease the level of expression of a target ZmPHDF sequence).
  • the mutations that will be made in the DNA encoding the variant do not place the sequence out of reading frame and do not create complementary regions that could produce secondary mRNA structure. See, EP Patent Application Publication No. 75,444.
  • the deletions, insertions, and substitutions of the protein sequences encompassed herein are not expected to produce radical changes in the characteristics of the protein.
  • the activity of a ZmPHDF polypeptide can be evaluated by assaying for the ability of the polypeptide to regulate transcription.
  • Various methods can be used to assay for this activity, including, directly monitoring the level of expression of a target gene at the nucleotide or polypeptide level. Methods for such an analysis are known and include, for example, Northern blots, S1 protection assays, Western blots, enzymatic or colorimetric assays.
  • determining if a sequence has ZmPHDF activity can be assayed by monitoring for an increase or decrease in the level or activity of target genes.
  • a ZmPHDF sequence can modulate transcription of target genes as determined by changes in transcriptional profiles in vivo in the presence or absence of the ZmPHDF protein product (e.g., Zhao, S. and W. B. Bruce, Expression profiling using cDNA microarrays. Methods MoI Biol., (2003) 236:365-80).
  • methods to assay for a modulation of transcriptional activity can include monitoring for an alteration in the phenotype of the plant.
  • variant polynucleotides and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. With such a procedure, one or more different ZmPHDF coding sequences can be manipulated to create a new ZmPHDF sequence, PHD-finger and the LLIF sequences together, or either the PHD-finger or LLIF sequence alone possessing the desired properties.
  • libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo.
  • sequence motifs encoding a domain of interest may be shuffled between the ZmPHDF gene of the invention and other known ZmPHDF genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased K m in the case of an enzyme.
  • Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci.
  • the polynucleotides of the invention can be used to isolate corresponding sequences from other organisms, particularly other plants, more particularly other monocots.
  • sequences can be used to identify such sequences based on their sequence homology to the sequences set forth herein.
  • Sequences isolated based on their sequence identity to the entire ZmPHDF sequences, the PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone of the invention, set forth herein or to variants and fragments thereof are encompassed by the present invention.
  • Such sequences include sequences that are orthologs of the disclosed sequences. "Orthologs" is intended to mean genes derived from a common ancestral gene and which are found in different species as a result of speciation.
  • orthologs Genes found in different species are considered orthologs when their nucleotide sequences and/or their encoded protein sequences share at least 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater sequence identity. Functions of orthologs are often highly conserved among species.
  • isolated polynucleotides that can silence or suppress the expression of a ZmPHDF sequence or a polynucleotide that encodes for a ZmPHDF protein and which hybridize under stringent conditions to the ZmPHDF sequences disclosed herein, or to variants or fragments thereof, are encompassed by the present invention.
  • oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any plant of interest.
  • Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook, et al., (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, New York). See also, Innis, et ai, eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds.
  • PCR PCR Strategies
  • nested primers single specific primers
  • degenerate primers gene-specific primers
  • vector-specific primers partially- mismatched primers
  • hybridization techniques all or part of a known polynucleotide is used as a probe that selectively hybridizes to other corresponding polynucleotides present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen organism.
  • the hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32 P, or any other detectable marker.
  • probes for hybridization can be made by labeling synthetic oligonucleotides based on the ZmPHDF polynucleotide of the invention.
  • the entire ZmPHDF polynucleotide or a polynucleotide encoding the PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone disclosed herein, or one or more portions thereof, may be used as a probe capable of specifically hybridizing to corresponding ZmPHDF polynucleotide and messenger RNAs.
  • probes include sequences that are unique among ZmPHDF polynucleotide sequences and are optimally at least about 10 nucleotides in length, and most optimally at least about 20 nucleotides in length.
  • Such probes may be used to amplify corresponding ZmPHDF polynucleotide from a chosen plant by PCR. This technique may be used to isolate additional coding sequences from a desired plant or as a diagnostic assay to determine the presence of coding sequences in a plant.
  • Hybridization techniques include hybridization screening of plated DNA libraries (either plaques or colonies; see, for example, Sambrook, et al., (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, New York).
  • Hybridization of such sequences may be carried out under stringent conditions.
  • stringent conditions or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background).
  • Stringent conditions are sequence-dependent and will be different in different circumstances.
  • target sequences that are 100% complementary to the probe can be identified (homologous probing).
  • stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing).
  • a probe is less than about 1000 nucleotides in length, optimally less than 500 nucleotides in length.
  • stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30 0 C for short probes (e.g., 10 to 50 nucleotides) and at least about 60 0 C for long probes (e.g., greater than 50 nucleotides).
  • Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
  • Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCI, 1 % SDS at 37°C, and a wash in 0.5X to 1X SSC at 55 to 60 0 C.
  • Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCI, 1 % SDS at 37°C, and a wash in 0.1X SSC at 60 to 65°C.
  • wash buffers may comprise about 0.1 % to about 1 % SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.
  • T m 81.5 0 C + 16.6 (log M) + 0.41 (%GC) - 0.61 (% form) - 500/L; where M is the molarity of monovalent cations, %GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs.
  • the T m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. T m is reduced by about 1 °C for each 1% of mismatching; thus, T m , hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with >90% identity are sought, the T m can be decreased 10 0 C.
  • stringent conditions are selected to be about 5°C lower than the thermal melting point (T m ) for the specific sequence and its complement at a defined ionic strength and pH.
  • reference sequence is a defined sequence used as a basis for sequence comparison.
  • a reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
  • comparison window makes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two polynucleotides.
  • the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100 or longer.
  • Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, California); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys Inc., 9685 Scranton Road, San Diego, California, USA). Alignments using these programs can be performed using the default parameters.
  • the CLUSTAL program is well described by Higgins, et al., (1988) Gene 73:237-244 (1988); Higgins, et al., (1989) CABIOS 5:151-153; Corpet, et al., (1988) Nucleic Acids Res. 16:10881-90; Huang, et al., (1992) CABIOS 8:155-65; and Pearson, et al., (1994) Meth. MoI. Biol. 24:307-331.
  • the ALIGN program is based on the algorithm of Myers and Miller (1988) supra. A PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used with the ALIGN program when comparing amino acid sequences.
  • Gapped BLAST in BLAST 2.0
  • PSI-BLAST in BLAST 2.0
  • the default parameters of the respective programs e.g., BLASTN for nucleotide sequences, BLASTX for proteins
  • Alignment may also be performed manually by inspection.
  • sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof.
  • equivalent program is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
  • GAP uses the algorithm of Needleman and Wunsch (1970) J. MoI. Biol. 48:443-453, to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP must make a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty.
  • gap creation penalty values and gap extension penalty values in Version 10 of the GCG Wisconsin Genetics Software Package for protein sequences are 8 and 2, respectively.
  • the default gap creation penalty is 50 while the default gap extension penalty is 3.
  • the gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 200.
  • the gap creation and gap extension penalties can be 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65 or greater.
  • GAP presents one member of the family of best alignments. There may be many members of this family, but no other member has a better quality. GAP displays four figures of merit for alignments: Quality, Ratio, Identity, and Similarity.
  • the Quality is the metric maximized in order to align the sequences. Ratio is the quality divided by the number of bases in the shorter segment.
  • Percent Identity is the percent of the symbols that actually match.
  • Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored.
  • a similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold.
  • the scoring matrix used in Version 10 of the GCG Wisconsin Genetics Software Package is BLOSUM62 (see, Henikoff and Henikoff (1989) Proc. Natl. Acad. ScL USA 89:10915).
  • sequence identity or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
  • sequence identity or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
  • percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule.
  • sequences differ in conservative substitutions the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution.
  • Sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity”. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, California).
  • percentage of sequence identity means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide 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 nucleic acid base 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 window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
  • the invention provides plants, plant cells, and plant parts having altered levels (i.e., an increase or decrease) of a ZmPHDF sequence.
  • the plants and plant parts have stably incorporated into their genome at least one heterologous polynucleotide encoding a ZmPHDF polypeptide comprising the PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone or more optimally a biologically active variant or fragment thereof.
  • the polynucleotide encoding the ZmPHDF polypeptide is set forth in SEQ ID NO: 1 or a biologically active variant or fragment thereof.
  • plants and plant parts are provided in which the heterologous polynucleotide stably integrated into the genome of the plant or plant part comprises a polynucleotide which when expressed in a plant increases the level of a ZmPHDF polypeptide comprising the PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone or an active variant or fragment thereof.
  • Sequences that can be used to increase expression of a ZmPHDF polypeptide include, but are not limited to, the sequence set forth in SEQ ID NO: 1 or variants or fragments thereof.
  • such plants, plant cells, plant parts, and seeds can have an altered phenotype including, for example, altered flower organ development, leaf formation, phototropism, apical dominance, fruit development, root initiation, and improved yield.
  • the term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced or heterologous polynucleotides disclosed herein.
  • the present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots.
  • plant species of interest include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B.
  • juncea particularly those Brassica species useful as sources of seed oil, alfalfa ⁇ Medicago sativa), rice ⁇ Oryza sativa), rye ⁇ Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solarium tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot
  • Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo).
  • tomatoes Locopersicon esculentum
  • lettuce e.g., Lactuca sativa
  • green beans Phaseolus vulgaris
  • lima beans Phaseolus limensis
  • peas Lathyrus spp.
  • members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo).
  • Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum.
  • Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata); Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis).
  • pines such as loblolly pine (Pinus taeda), slash pine (P
  • plants of the present invention are crop plants (for example, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.).
  • corn and soybean plants are optimal, and in yet other embodiments corn plants are optimal.
  • plants of interest include grain plants that provide seeds of interest, oil-seed plants, and leguminous plants.
  • Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc.
  • Oil-seed plants include cotton, soybean, safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc.
  • Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
  • a “subject plant or plant cell” is one in which an alteration, such as transformation or introduction of a polypeptide, has occurred, or is a plant or plant cell which is descended from a plant or cell so altered and which comprises the alteration.
  • a “control” or “control plant” or “control plant cell” provides a reference point for measuring changes in phenotype of the subject plant or plant cell.
  • a control plant or plant cell may comprise, for example: (a) a wild-type plant or cell, i.e., of the same genotype as the starting material for the alteration which resulted in the subject plant or cell; (b) a plant or plant cell of the same genotype as the starting material but which has been transformed with a null construct (i.e., with a construct which has no known effect on the trait of interest, such as a construct comprising a marker gene); (c) a plant or plant cell which is a non- transformed segregant among progeny of a subject plant or plant cell; (d) a plant or plant cell genetically identical to the subject plant or plant cell but which is not exposed to conditions or stimuli that would induce expression of the gene of interest; or (e) the subject plant or plant cell itself, under conditions in which the gene of interest is not expressed.
  • a wild-type plant or cell i.e., of the same genotype as the starting material for the alteration which resulted in the subject plant or cell
  • polynucleotide is not intended to limit the present invention to polynucleotides comprising DNA.
  • polynucleotides can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides.
  • deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues.
  • the polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single-stranded forms, double- stranded forms, hairpins, stem-and-loop structures, and the like.
  • the various polynucleotides employed in the methods and compositions of the invention can be provided in expression cassettes for expression in the plant of interest.
  • the cassette will include 5' and 3' regulatory sequences operably linked to a polynucleotide of the invention.
  • "Operably linked" is intended to mean a functional linkage between two or more elements.
  • an operable linkage between a polynucleotide of interest and a regulatory sequence i.e., a promoter
  • Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame.
  • the cassette may additionally contain at least one additional gene to be cotransformed into the organism.
  • the additional gene(s) can be provided on multiple expression cassettes.
  • Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the ZmPHDF polynucleotide to be under the transcriptional regulation of the regulatory regions.
  • the expression cassette may additionally contain selectable marker genes.
  • the expression cassette can include in the 5'-3' direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a ZmPHDF polynucleotide, and a transcriptional and translational termination region (i.e., termination region) functional in plants.
  • the regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the ZmPHDF polynucleotide may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or the ZmPHDF polynucleotides may be heterologous to the host cell or to each other.
  • heterologous in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.
  • a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide.
  • a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.
  • the native promoter sequences may be used. Such constructs can change expression levels of a ZmPHDF transcript or protein in the plant or plant cell. Thus, the phenotype of the plant or plant cell can be altered.
  • the termination region may be native with the transcriptional initiation region, may be native with the operably linked ZmPHDF polynucleotide of interest, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous) to the promoter, the ZmPHDF polynucleotide of interest, the plant host, or any combination thereof. Convenient termination regions are available from the Ti-plasmid of A.
  • tumefaciens such as the octopine synthase and nopaline synthase termination regions. See also, Guerineau, et al., (1991 ) MoI. Gen. Genet. 262:141-144; Proudfoot (1991 ) Ce// 64:671-674; Sanfacon, et al., (1991 ) Genes Dev. 5:141-149; Mogen, et al., (1990) Plant Ce// 2:1261-1272; Munroe, et al., (1990) Gene 91 :151-158; Ballas, et al., (1989) Nucleic Acids Res. 17:7891-7903; and Joshi, et al., (1987) Nucleic Acids Res. 15:9627-9639.
  • the polynucleotides may be optimized for increased expression in the transformed plant. That is, the polynucleotides can be synthesized using plant-preferred codons for improved expression. See, for example, Campbell and Gowri (1990) Plant Physiol. 92:1-1 1 for a discussion of host-preferred codon usage. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Patent Numbers 5,380,831 , and 5,436,391 , and Murray, et al., (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.
  • Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon- intron splice site signals, transposon repeats, and other such well-characterized sequences that may be deleterious to gene expression.
  • the G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
  • the expression cassettes may additionally contain 5' leader sequences.
  • leader sequences can act to enhance translation.
  • Translation leaders are known in the art and include: picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5' noncoding region) (Elroy-Stein, et al., (1989) Proc. Natl. Acad. Sci.
  • TEV leader tobacco Etch Virus
  • MDMV leader Maize Dwarf Mosaic Virus ⁇ Virology 154:9-20
  • human immunoglobulin heavy-chain binding protein BiP
  • untranslated leader from the coat protein mRNA of alfalfa mosaic virus AMV RNA 4
  • tobacco mosaic virus leader TMV (GaIMe, et al., (1989) in Molecular Biology of RNA, ed.
  • Cech (Liss, New York), pp. 237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel, et al., (1991 ) Virology 81 :382-385). See also, Della-Cioppa, et al., (1987) Plant Physiol. 84:965-968.
  • MCMV chlorotic mottle virus leader
  • the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame.
  • adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like.
  • in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions may be involved.
  • promoters can be used in the practice of the invention, including the native promoter of the polynucleotide sequence of interest.
  • the promoters can be selected based on the desired outcome.
  • the nucleic acids can be combined with constitutive, tissue-preferred, or other promoters for expression in plants.
  • Such constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Patent Number 6,072,050; the core CaMV 35S promoter (Odell, et al., (1985) Nature 313:810-812); rice actin (McElroy, et al., (1990) Plant Cell 2:163-171 ); ubiquitin (Christensen, et al., (1989) Plant MoI. Biol. 12:619-632 and Christensen, et al., (1992) Plant MoI. Biol. 18:675-689); pEMU (Last, et al., (1991 ) Theor.
  • the expression cassette can also comprise a selectable marker gene for the selection of transformed cells.
  • Selectable marker genes are utilized for the selection of transformed cells or tissues.
  • Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase Il (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D).
  • Additional selectable markers include phenotypic markers such as ⁇ -galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su, et al., (2004) Biotechnol Bioeng 85:610-9 and Fetter, et al., (2004) Plant Cell 16:215-28), cyan florescent protein (CYP) (Bolte, et al., (2004) J. Cell Science 117:943-54 and Kato, et al., (2002) Plant Physiol 129:913-42), and yellow florescent protein (PhiYFPTM from Evrogen, see, Bolte, et al., (2004) J. Cell Science 117:943-54).
  • GFP green fluorescent protein
  • CYP cyan florescent protein
  • the polynucleotides of the present invention can be stacked with any combination of polynucleotide sequences of interest in order to create plants with a desired trait.
  • a trait refers to the phenotype derived from a particular sequence or groups of sequences.
  • the combinations generated can also include multiple copies of any one of the polynucleotides of interest.
  • the polynucleotides of the present invention can also be stacked with traits desirable for disease or herbicide resistance (e.g., fumonisin detoxification genes (U.S.
  • Patent Number 5,792,931 avirulence and disease resistance genes (Jones, et al., (1994) Science 266:789; Martin, et al., (1993) Science 262:1432; Mindrinos, et al., (1994) Cell 78:1089); acetolactate synthase (ALS) mutants that lead to herbicide resistance such as the S4 and/or Hra mutations; inhibitors of glutamine synthase such as phosphinothricin or basta (e.g., bar gene); and glyphosate resistance (EPSPS gene)); and traits desirable for processing or process products such as high oil (e.g., U.S.
  • ALS acetolactate synthase
  • Patent Number 6,232,529 modified oils (e.g., fatty acid desaturase genes (U.S. Patent Number 5,952,544; WO 94/1 1516)); modified starches (e.g., ADPG pyrophosphorylases (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDBE)); and polymers or bioplastics (e.g., U.S. Patent Number 5.602,321 ; beta-ketothiolase, polyhydroxybutyrate synthase, and acetoacetyl-CoA reductase (Schubert, et al., (1988) J. Bacteriol.
  • modified oils e.g., fatty acid desaturase genes (U.S. Patent Number 5,952,544; WO 94/1 1516)
  • modified starches e.g., ADPG pyrophosphorylases (AGPase), starch syntha
  • PHAs polyhydroxyalkanoates
  • agronomic traits such as male sterility (e.g., see U.S. Patent Number 5,583,210), stalk strength, flowering time, or transformation technology traits such as cell cycle regulation or gene targeting (e.g., WO 99/61619, WO 00/17364, and WO 99/25821 ); the disclosures of which are herein incorporated by reference.
  • stacked combinations can be created by any method including, but not limited to, cross- breeding plants by any conventional or TopCross methodology, or genetic transformation. If the sequences are stacked by genetically transforming the plants, the polynucleotide sequences of interest can be combined at any time and in any order. For example, a transgenic plant comprising one or more desired traits can be used as the target to introduce further traits by subsequent transformation. The traits can be introduced simultaneously in a co-transformation protocol with the polynucleotides of interest provided by any combination of transformation cassettes. For example, if two sequences will be introduced, the two sequences can be contained in separate transformation cassettes (trans) or contained on the same transformation cassette (cis).
  • sequences can be driven by the same promoter or by different promoters. In certain cases, it may be desirable to introduce a transformation cassette that will suppress the expression of the polynucleotide of interest. This may be combined with any combination of other suppression cassettes or overexpression cassettes to generate the desired combination of traits in the plant. It is further recognized that polynucleotide sequences can be stacked at a desired genomic location using a site-specific recombination system. See, for example, WO99/25821 , WO99/25854, WO99/25840, WO99/25855, and WO99/25853, all of which are herein incorporated by reference.
  • the methods of the invention involve introducing a polypeptide or polynucleotide into a plant.
  • "Introducing" is intended to mean presenting to the plant the polynucleotide or polypeptide in such a manner that the sequence gains access to the interior of a cell of the plant.
  • the methods of the invention do not depend on a particular method for introducing a sequence into a plant, only that the polynucleotide or polypeptides gains access to the interior of at least one cell of the plant.
  • Methods for introducing polynucleotide or polypeptides into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.
  • “Stable transformation” is intended to mean that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by the progeny thereof.
  • “Transient transformation” is intended to mean that a polynucleotide is introduced into the plant and does not integrate into the genome of the plant or a polypeptide is introduced into a plant.
  • Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing polypeptides and polynucleotides into plant cells include microinjection (Crossway, et ai, (1986) Biotechniques 4:320-334), electroporation (Riggs, et ai, (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-me ⁇ late ⁇ transformation (U.S. Patent Number 5,563,055 and U.S.
  • Patent Number 5,981 ,840 direct gene transfer (Paszkowski, et ai, (1984) EMBO J. 3:2717-2722), and ballistic particle acceleration (see, for example, U.S. Patent Number 4,945,050; U.S. Patent Number 5,879,918; U.S. Patent Numbers 5,886,244; and 5,932,782; Tomes, et ai, (1995) in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); McCabe, et ai, (1988) Biotechnology 6:923-926); and Led transformation (WO 00/28058).
  • the ZmPHDF sequences or variants and fragments thereof can be provided to a plant using a variety of transient transformation methods.
  • transient transformation methods include, but are not limited to, the introduction of the ZmPHDF protein or variants and fragments thereof directly into the plant or the introduction of the ZmPHDF transcript into the plant.
  • Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway, et al., (1986) MoI Gen. Genet. 202:179-185; Nomura, et al., (1986) Plant Sci. 44:53-58; Hepler, et al., (1994) Proc. Natl. Acad. Sci.
  • the ZmPHDF polynucleotide can be transiently transformed into the plant using techniques known in the art. Such techniques include viral vector system and the precipitation of the polynucleotide in a manner that precludes subsequent release of the DNA. Thus, the transcription from the particle-bound DNA can occur, but the frequency with which it is released to become integrated into the genome is greatly reduced. Such methods include the use particles coated with polyethylimine (PEI; Sigma #P3143).
  • the polynucleotide of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids.
  • such methods involve incorporating a nucleotide construct of the invention within a viral DNA or RNA molecule.
  • the a ZmPHDF sequence or a variant or fragment thereof may be initially synthesized as part of a viral polyprotein, which later may be processed by proteolysis in vivo or in vitro to produce the desired recombinant protein.
  • promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases.
  • Methods are known in the art for the targeted insertion of a polynucleotide at a specific location in the plant genome.
  • the insertion of the polynucleotide at a desired genomic location is achieved using a site-specific recombination system. See, for example,
  • the polynucleotide of the invention can be contained in transfer cassette flanked by two non-recombinogenic recombination sites.
  • the transfer cassette is introduced into a plant having stably incorporated into its genome a target site which is flanked by two non-recombinogenic recombination sites that correspond to the sites of the transfer cassette.
  • An appropriate recombinase is provided and the transfer cassette is integrated at the target site.
  • the polynucleotide of interest is thereby integrated at a specific chromosomal position in the plant genome.
  • the cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick, et al., (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting progeny having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as "transgenic seed") having a polynucleotide of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • a “modulated level” or “modulating level” of a polypeptide in the context of the methods of the present invention refers to any increase or decrease in the expression, concentration, or activity of a gene product, including any relative increment in expression, concentration or activity. Any method or composition that modulates expression of a target gene product, either at the level of transcription or translation, or modulates the activity of the target gene product can be used to achieve modulated expression, concentration, activity of the target gene product. In general, the level is increased or decreased by at least 1 %, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or greater relative to an appropriate control plant, plant part, or cell. Modulation in the present invention may occur during and/or subsequent to growth of the plant to the desired stage of development. In specific embodiments, the polypeptides of the present invention are modulated in monocots, particularly grain plants such as rice, wheat, maize, and the like.
  • the expression level of a polypeptide having the PHD-finger and the LLIF domains together, or either the PHD-finger or LLIF domain alone or a biologically active variant or fragment thereof may be measured directly, for example, by assaying for the level of the ZmPHDF polypeptide in the plant, or indirectly, for example, by measuring the level of the polynucleotide encoding the protein or by measuring the activity of the ZmPHDF polypeptide in the plant. Methods for determining the activity of the ZmPHDF polypeptide are described elsewhere herein.
  • the polypeptide or the polynucleotide of the invention is introduced into the plant cell.
  • a plant cell having the introduced sequence of the invention is selected using methods known to those of skill in the art such as, but not limited to, Southern blot analysis, DNA sequencing, PCR analysis, or phenotypic analysis.
  • a plant or plant part altered or modified by the foregoing embodiments is grown under plant forming conditions for a time sufficient to modulate the concentration and/or activity of polypeptides of the present invention in the plant. Plant forming conditions are well known in the art and discussed briefly elsewhere herein.
  • the level and/or activity of the polypeptide may be modulated by employing a polynucleotide that is not capable of directing, in a transformed plant, the expression of a protein or an RNA.
  • the polynucleotides of the invention may be used to design polynucleotide constructs that can be employed in methods for altering or mutating a genomic nucleotide sequence in an organism.
  • Such polynucleotide constructs include, but are not limited to, RNA:DNA vectors, RNA:DNA mutational vectors, RNA:DNA repair vectors, mixed-duplex oligonucleotides, self-complementary RNA:DNA oligonucleotides, and recombinogenic oligonucleobases.
  • Such nucleotide constructs and methods of use are known in the art. See, U.S. Patent Numbers 5,565,350; 5,731 ,181 ; 5,756,325; 5,760,012; 5,795,972; and 5,871 ,984; all of which are herein incorporated by reference.
  • methods of the present invention do not depend on the incorporation of the entire polynucleotide into the genome, only that the plant or cell thereof is altered as a result of the introduction of the polynucleotide into a cell.
  • the genome may be altered following the introduction of the polynucleotide into a cell.
  • the polynucleotide, or any part thereof may incorporate into the genome of the plant.
  • Alterations to the genome of the present invention include, but are not limited to, additions, deletions, and substitutions of nucleotides into the genome. While the methods of the present invention do not depend on additions, deletions, and substitutions of any particular number of nucleotides, it is recognized that such additions, deletions, or substitutions comprises at least one nucleotide.
  • the activity and/or level of a ZmPHDF polypeptide is increased.
  • An increase in the level and/or activity of the ZmPHDF polypeptide can be achieved by providing to the plant a ZmPHDF polypeptide or a biologically active variant or fragment thereof.
  • many methods are known in the art for providing a polypeptide to a plant including, but not limited to, direct introduction of the ZmPHDF polypeptide into the plant or introducing into the plant (transiently or stably) a polynucleotide construct encoding a polypeptide having ZmPHDF activity.
  • the methods of the invention may employ a polynucleotide that is not capable of directing in the transformed plant the expression of a protein or an RNA.
  • the level and/or activity of a ZmPHDF polypeptide may be increased by altering the gene encoding the ZmPHDF polypeptide or its promoter. See, e.g., Kmiec, U.S. Patent Number 5,565,350; Zarling, et al., PCT/US93/03868. Therefore, mutagenized plants that carry mutations in ZmPHDF genes, where the mutations increase expression of the ZmPHDF gene or increase the activity of the encoded ZmPHDF polypeptide, are provided.
  • the activity and/or level of the ZmPHDF polypeptide of the invention is reduced or eliminated by introducing into a plant a polynucleotide that inhibits the level or activity of a polypeptide.
  • the polynucleotide may inhibit the expression of ZmPHDF gene directly, by preventing translation of the ZmPHDF messenger RNA, or indirectly, by encoding a polypeptide that inhibits the transcription or translation of a ZmPHDF gene encoding a ZmPHDF protein.
  • Methods for inhibiting or eliminating the expression of a gene in a plant are well known in the art, and any such method may be used in the present invention to inhibit the expression of at least one ZmPHDF sequence in a plant.
  • the activity of a ZmPHDF polypeptide is reduced or eliminated by transforming a plant cell with a sequence encoding a polypeptide that inhibits the activity of the ZmPHDF polypeptide.
  • the activity of a ZmPHDF polypeptide may be reduced or eliminated by disrupting the gene encoding the ZmPHDF polypeptide.
  • the invention encompasses mutagenized plants that carry mutations in ZmPHDF genes, where the mutations reduce expression of the ZmPHDF gene or inhibit the ZmPHDF activity of the encoded ZmPHDF polypeptide.
  • Gene silencing Reduction of the activity of specific genes (also known as gene silencing or gene suppression) is desirable for several aspects of genetic engineering in plants.
  • Many techniques for gene silencing are well known to one of skill in the art, including, but not limited to, antisense technology (see, e.g., Sheehy, et al., (1988) Proc. Natl. Acad. Sci. USA 85:8805-8809; and U.S. Patent Numbers 5,107,065; 5,453,566; and 5,759,829); cosuppression (e.g., Taylor (1997) Plant Cell 9:1245; Jorgensen (1990) Trends Biotech. 8(12):340-344; Flavell (1994) Proc. Natl. Acad. Sci.
  • antisense constructions complementary to at least a portion of the messenger RNA (mRNA) for the ZmPHDF sequences can be constructed.
  • Antisense nucleotides are constructed to hybridize with the corresponding mRNA. Modifications of the antisense sequences may be made as long as the sequences hybridize to and interfere with expression of the corresponding mRNA. In this manner, antisense constructions having 70%, optimally 80%, more optimally 85% sequence identity to the corresponding antisensed sequences may be used.
  • portions of the antisense nucleotides may be used to disrupt the expression of the target gene. Generally, sequences of at least 50 nucleotides, 100 nucleotides, 200 nucleotides, 300, 400, 450, 500, 550 or greater may be used.
  • the polynucleotides of the present invention may also be used in the sense orientation to suppress the expression of endogenous genes in plants.
  • Methods for suppressing gene expression in plants using polynucleotides in the sense orientation are known in the art.
  • the methods generally involve transforming plants with a DNA construct comprising a promoter that drives expression in a plant operably linked to at least a portion of a polynucleotide that corresponds to the transcript of the endogenous gene.
  • a nucleotide sequence has substantial sequence identity to the sequence of the transcript of the endogenous gene, optimally greater than about 65% sequence identity, more optimally greater than about 85% sequence identity, most optimally greater than about 95% sequence identity. See, U.S. Patent Numbers 5,283,184 and 5,034,323; herein incorporated by reference.
  • a ZmPHDF polypeptide or a biologically active variant or fragment thereof may be used to reduce or eliminate the activity of at least one ZmPHDF polypeptide.
  • the level of a single ZmPHDF sequence can be modulated to produce the desired phenotype.
  • the expression of the heterologous polynucleotide which modulates the level of at least one ZmPHDF polypeptide can be regulated by a tissue- preferred promoter, particularly, a leaf-preferred promoter (i.e., mesophyll-preferred promoter or a bundle sheath preferred promoter) and/or a seed-preferred promoter (i.e., an endosperm- preferred promoter or an embryo-preferred promoter).
  • a tissue- preferred promoter particularly, a leaf-preferred promoter (i.e., mesophyll-preferred promoter or a bundle sheath preferred promoter) and/or a seed-preferred promoter (i.e., an endosperm- preferred promoter or an embryo-preferred promoter).
  • compositions of the invention can be used to increase grain yield in cereal plants.
  • the ZmPHDF coding sequence is expressed in a cereal plant of interest to increase expression of the ZmPHDF transcription factor.
  • the methods and compositions can be used to increase yield in a plant.
  • improved yield means any improvement in the yield of any measured plant product.
  • the improvement in yield can comprise a 0.1%, 0.5%, 1%, 3%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or greater increase in measured plant product.
  • the increased plant yield can comprise about a 0.5 fold, 1 fold, 2 fold, 4 fold, 8 fold, 16 fold or 32 fold increase in measured plant products.
  • an increase in the bu/acre yield of soybeans or corn derived from a crop having the present treatment as compared with the bu/acre yield from untreated soybeans or corn cultivated under the same conditions would be considered an improved yield.
  • increased yield is also intended at least one of an increase in total seed numbers, an increase in total seed weight, an increase in root biomass and an increase in harvest index.
  • Harvest index is defined as the ratio of yield biomass to the total cumulative biomass at harvest.
  • increasing yield of a plant or plant part comprises introducing into the plant or plant part a heterologous polynucleotide; and, expressing the heterologous polynucleotide in the plant or plant part.
  • the expression of the heterologous polynucleotide modulates the level of at least one ZmPHDF polypeptide in the plant or plant part, where the ZmPHDF polypeptide comprises the PHD-finger and LLIF domains together, or either the PHD-finger or LLIF domain alone having an amino acid sequence set forth in SEQ ID NO: 4 (PHD-finger domain) or SEQ ID NO: 5 (LLIF domain), or a variant or fragment of the domain.
  • modulation of the level of the ZmPHDF polypeptide comprises an increase in the level of at least one ZmPHDF polypeptide.
  • the heterologous polynucleotide introduced into the plant encodes a polypeptide having the PHD-finger and LLIF domains together, or either the PHD-finger or LLIF domain alone a biologically active variant or fragment thereof.
  • the heterologous polynucleotide comprises the sequence set forth in at least one SEQ ID NO: 1 and/or a biologically active variant or fragment thereof.
  • modulating the level of at least one ZmPHDF polypeptide comprises decreasing in the level of at least one ZmPHDF polypeptide.
  • the heterologous polynucleotide introduced into the plant need not encode a functional ZmPHDF polypeptide, but rather the expression of the polynucleotide results in the decreased expression of a ZmPHDF polypeptide comprising the PHD-finger and LLIF domains together, or either the PHD-finger or LLIF domain alone.
  • the ZmPHDF polypeptide having the decreased level is set forth in at least one of SEQ ID NO: 2 or a biologically active variant or fragment thereof.
  • Items 1 An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) the nucleotide sequence set forth in SEQ ID NO: 1 ; (b) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 2;
  • nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 1 wherein said nucleotide sequence encodes a polypeptide having ZmPHDF protein activity;
  • nucleotide sequence comprising at least 50 consecutive nucleotides of SEQ ID NO: 1 wherein said nucleotide sequence encodes a polypeptide having ZmPHDF protein activity;
  • nucleotide sequence encoding an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 2, wherein said nucleotide sequence encodes a polypeptide having ZmPHDF protein activity.
  • An expression cassette comprising the polynucleotide of item 1.
  • a method of increasing the level of a polypeptide in a plant comprising introducing into said plant the expression cassette of item 3 or item 4. 13. The method of item 12, wherein the yield of the plant is increased.
  • a method of increasing yield in a plant comprising increasing expression of a ZmPHDF polypeptide in said plant, wherein said ZmPHDF polypeptide has ZmPHDF protein activity and is selected from the group consisting of: (a) a polypeptide comprising an amino acid sequence having at least 80% sequence identity to the sequence set forth in SEQ ID NO: 2;
  • polypeptide comprising a ZmPHDF domain set forth in SEQ ID NO: 4 and an LLIFdomain set forth in SEQ ID NO: 5. 21. The method of item 20, wherein said polypeptide comprises an amino acid sequence having at least 95% sequence identity with the sequence set forth in SEQ ID NO: 2.
  • polypeptide comprises the amino acid sequence set forth in SEQ ID NO: 2.
  • nucleotide sequence encoding a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 2; and, (e) a nucleotide sequence encoding an amino acid sequence having at least 90% sequence identity to the sequence set forth in SEQ ID NO: 2.
  • step (b) regenerating a transformed plant from the transformed plant cell of step (a).
  • amino acid sequence comprising at least 50 consecutive amino acids of SEQ ID NO: 2, wherein said polypeptide retains the ability to modulate transcription.
  • the cDNA that encoded the ZmPHDF polypeptide from maize was identified by sequence homology from a collection of ESTs generated from a maize cDNA library using BLAST 2.0 (Altschul, et al., (1990) J. MoI. Biol. 215:403) against the NCBI DNA sequence database. From the EST plasmid, the maize ZmPHDF cDNA fragment was amplified by PCR using Hifi Taq DNA polymerase in standard conditions with maize ZmPHDF-specific primers that included the AttB site for GATEWAY® recombination cloning.
  • PCR fragment of the expected length was amplified and purified using standard methods as described by Sambrook, et al., (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, New York).
  • the first step of the GATEWAY® procedure the BP reaction, was then performed, during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce the "entry clone.”
  • Plasmid pDONR201 was purchased from Invitrogen, as part of the GATEWAY® technology (Invitrogen, Carlsbad, CA).
  • the entry clone was subsequently used in an LR reaction with a destination vector used for Oryza sativa transformation.
  • This vector contains as functional elements within the T-DNA borders, a plant selectable marker, a screenable marker, and a GATEWAY® cassette intended for LR in vivo recombination with the sequence of interest already cloned in the entry clone.
  • Upstream of this GATEWAY® cassette is the rice GOS2 promoter (Hensgens, et al., (1993) Plant MoI. Biol. 23:643-669) that confers moderate constitutive expression on the gene of interest.
  • the resulting expression vector pGOS2::ZmPHDF was transformed into Agrobacterium tumefaciens strain LBA4044 and subsequently into Oryza sativa var. Nipponbare plants (see, Chan, MT, et al., (1993) Plant MoI Biol., 22(3):491-506, and Chan, MT. et al, (1992) Plant Cell Physiol., 33(5):577-583). Transformed rice plants were grown and examined for various growth characteristics as described herein in Example 4.
  • High-velocity ballistic bombardment using metal particles coated with the nucleic acid constructs was used to transform wild-type rice (Klein, et al., (1987) Nature 327:70-73; U.S. Patent Number 4,945,050, incorporated by reference herein).
  • a Biolistic PDS-1000/He BioRAD Laboratories, Hercules, CA
  • the particle bombardment technique was used to transform wild-type rice with the pGOS2::ZmPHDF.
  • the bacterial hygromycin B phosphotransferase (Hpt II) gene from Streptomyces hygroscopicus (which confers resistance to the antibiotic) was used as the selectable marker for rice transformation.
  • the Hpt Il gene was engineered with the 35S promoter from Cauliflower Mosaic Virus and the termination and polyadenylation signals from the octopine synthase gene of Agrobacterium tumefaciens.
  • pML18 is described in WO 97/47731 , the disclosure of which is hereby incorporated by reference.
  • Embryogenic callus cultures derived from the scutellum of germinating rice seeds served as source material for transformation experiments. This material is generated by germinating sterile rice seeds on a callus initiation media (MS salts, Nitsch and Nitsch vitamins, 1.0 mg/l 2,4-D and 10 ⁇ M AgNO 3 ) in the dark at 27-28°C.
  • CM media N6 salts, Nitsch and Nitsch vitamins, 1 mg/l 2,4-D; Chu, et al., (1985) Sci. Sinica 18:659-668.
  • Callus cultures are maintained on CM by routine sub-culture at two week intervals and used for transformation within 10 weeks of initiation.
  • Callus is prepared for transformation by subculturing 0.5-1.0 mm pieces approximately 1 mm apart, arranged in a circular area of about 4 cm in diameter, in the center of a circle of Whatman #541 paper placed on CM media. The plates with callus are incubated in the dark at 27-28°C for 3-5 days.
  • the filters with callus Prior to bombardment, the filters with callus are transferred to CM supplemented with 0.25 M mannitol and 0.25 M sorbitol for 3 hr in the dark.
  • the petri dish lids are then left ajar for 20-45 minutes in a sterile hood to allow moisture on tissue to dissipate.
  • Each DNA fragment was co-precipitated with pML18 containing the selectable marker for rice transformation onto the surface of gold particles.
  • a total of 10 ⁇ g of DNA at a 2:1 ratio of trait:selectable marker DNAs were added to a 50 ⁇ l aliquot of gold particles that had been resuspended at a concentration of 60 mg ml "1 .
  • Calcium chloride (50 ⁇ l of a 2.5 M solution) and spermidine (20 ⁇ l of a 0.1 M solution) were then added to the gold-DNA suspension as the tube was vortexing for 3 min. The gold particles were centrifuged in a microfuge for 1 second and the supernatant removed.
  • the gold particles were then washed twice with 1 ml of absolute ethanol and resuspended in 50 ⁇ l of absolute ethanol and sonicated (bath sonicator) for one second to disperse the gold particles.
  • the gold suspension was incubated at -70 0 C for five minutes and sonicated (bath sonicator) to disperse the particles.
  • Six ⁇ l of the DNA-coated gold particles was then loaded onto mylar macrocarrier disks and the ethanol was allowed to evaporate.
  • a petri dish containing the tissue was placed in the chamber of the PDS-1000/He.
  • the air in the chamber was then evacuated to a vacuum of 28-29 inches Hg.
  • the macrocarrier was accelerated with a helium shock wave using a rupture membrane that bursts when the He pressure in the shock tube reaches 1080-1100 psi.
  • the tissue was placed approximately 8 cm from the stopping screen and the callus was bombarded two times. Two to four plates of tissue were bombarded in this way with the DNA-coated gold particles. Following bombardment, the callus tissue was transferred to CM media without supplemental sorbitol or mannitol.
  • SM media CM medium containing 50 mg/l hygromycin.
  • callus tissue was transferred from plates to sterile 50 ml conical tubes and weighed. Molten top-agar at 40 0 C was added using 2.5 ml of top agar/100 mg of callus. Callus clumps were broken into fragments of less than 2 mm diameter by repeated dispensing through a 10 ml pipette. Three ml aliquots of the callus suspension were plated onto fresh SM media and the plates were incubated in the dark for 4 weeks at 27-28°C. After 4 weeks, transgenic callus events were identified, transferred to fresh SM plates and grown for an additional 2 weeks in the dark at 27-28°C.
  • T1 evaluation Based on the results of the T1 evaluation (described herein), four events that showed improved growth and yield characteristics at the T1 level were chosen for further characterization in the T2 generation. To this extent, seed batches from the positive T1 plants (both hetero- and homozygotes), were screened by monitoring marker expression. For each chosen event, the heterozygote seed batches were then selected for T2 evaluation. An equal number of positive and negative plants within each seed batch were transplanted for evaluation in the greenhouse (i.e., for each event 40 plants, of which 20 were positives for the transgene and 20 were negative for the transgene). For the four events, a total of 160 plants were evaluated in the T2 generation. Both T1 and T2 plants were transferred to a greenhouse and evaluated for vegetative growth parameters, as described herein.
  • a two-factor ANOVA (analysis of variance) corrected for the unbalanced design was used as a statistical evaluation model for the numeric values of the observed plant phenotypic characteristics.
  • the numerical values were submitted to a t-test and an F-test.
  • the p-value was obtained by comparing the t-value to the t-distribution or, alternatively, by comparing the F-value to the F-distribution.
  • the p-value stands for the probability that the null hypothesis (i.e., no effect of the transgene) is correct.
  • a t-test was performed on all the values of all plants per event. Such a t-test was repeated for each event and for each growth characteristic. The t-test was carried out to check for an effect of the gene within one transformation event, also described herein as "line-specific effect.”
  • the threshold for a significant line-specific effect is set at 10% probability level. Therefore, data with a p-value of the t-test under 10% means that the phenotype observed in the transgenic plants of that line was caused by the presence of the transgene.
  • some events may be under or below this threshold. This difference may be due to the difference in the position of the transgene within the rice genome (i.e., a gene might only have an effect in certain positions of the genome). Therefore, the "line- specific effect" is sometimes referred to as the "position-dependent effect.”
  • the selected plants were grown in a greenhouse. Each plant received a unique barcode label to link the phenotyping data unambiguously to the corresponding plant.
  • Transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. From the stage of sowing until the stage of maturity (i.e., the stage were there is no more increase in biomass), the plants were passed weekly through a digital imaging cabinet. At each time point digital images (2048x1536 pixels, 16 million colors) were taken of each plant from at least 6 different angles. The parameters described herein were derived in an automated way from the digital images using image analysis software.
  • Plants were also passed through a root-imaging system that digitally photographs the root morphology and mass from the base of the clear-bottom pots. Plant above-ground area and root mass were determined by counting the total number of pixels from plant parts discriminated from the background. The above-ground value was averaged for the pictures taken on the same time point from the different angles and was converted to a physical surface value expressed in square mm by calibration. Experiments have shown that the above-ground plant area, which corresponds to the total maximum area, measured this way correlates with the biomass of plant parts above-ground. In addition to digital images during the growth of the plants, when the plants reached maturity and senescence the number of panicles per plant and the total number of florets per plant were counted by hand.
  • Dried florets were collected and those with filled seeds were mechanically separated from empty florets using an enclosed air-driven blower system. Dehusked seeds were then collected and counted using a seed counter and weighed using a standard balance. Harvest index was calculated using a ratio of the total weight of seeds produced per plant with the biomass calculated from digital images as described herein. Thousand kernel weight was calculated from the ratio of total seed weight per plant and the number of filled seeds per plant times 1000. The time to flower interval was recorded as the number of days between sowing and the emergence of the first panicle, extrapolated by the size of the panicles in the earliest imaging that a panicle was detected and the date of that imaging.
  • Immature maize embryos from greenhouse donor plants are bombarded with a plasmid containing a ZmPHDF sequence (such as ZmPHDF/SEQ ID NO: 1 ) under the control of the UBI promoter and the selectable marker gene PAT (Wohlleben, et ah, (1988) Gene 70:25-37), which confers resistance to the herbicide Bialaphos.
  • the selectable marker gene is provided on a separate plasmid. Transformation is performed as follows. Media recipes follow below.
  • the ears are husked and surface sterilized in 30% Clorox bleach plus 0.5% Micro detergent for 20 minutes, and rinsed two times with sterile water.
  • the immature embryos are excised and placed embryo axis side down (scutellum side up), 25 embryos per plate, on 560Y medium for 4 hours and then aligned within the 2.5cm target zone in preparation for bombardment.
  • a plasmid vector comprising the ZmPHDF sequence operably linked to a ubiquitin promoter is made.
  • This plasmid DNA plus plasmid DNA containing a PAT selectable marker is precipitated onto 1.1 ⁇ m (average diameter) tungsten pellets using a CaCI 2 precipitation procedure as follows: 100 ⁇ l prepared tungsten particles in water; 10 ⁇ l (1 ⁇ g) DNA in Tris EDTA buffer (1 ⁇ g total DNA); 100 ⁇ l 2.5 M CaCI 2 ; and, 10 ⁇ l 0.1 M spermidine.
  • Each reagent is added sequentially to the tungsten particle suspension, while maintained on the multitube vortexer.
  • the final mixture is sonicated briefly and allowed to incubate under constant vortexing for 10 minutes.
  • the tubes are centrifuged briefly, liquid removed, washed with 500 ml 100% ethanol, and centrifuged for 30 seconds. Again the liquid is removed, and 105 ⁇ l 100% ethanol is added to the final tungsten particle pellet.
  • the tungsten/DNA particles are briefly sonicated and 10 ⁇ l spotted onto the center of each macrocarrier and allowed to dry about 2 minutes before bombardment.
  • sample plates are bombarded at level #4 in particle gun (U.S. Patent Number 5,240,855). All samples receive a single shot at 650 PSI, with a total of ten aliquots taken from each tube of prepared particles/DNA.
  • the embryos are kept on 560Y medium for 2 days, then transferred to 560R selection medium containing 3 mg/liter Bialaphos, and subcultured every 2 weeks. After approximately 10 weeks of selection, selection-resistant callus clones are transferred to 288J medium to initiate plant regeneration. Following somatic embryo maturation (2-4 weeks), well- developed somatic embryos are transferred to medium for germination and transferred to the lighted culture room. Approximately 7-10 days later, developing plantlets are transferred to 272V hormone-free medium in tubes for 7-10 days until plantlets are well established.
  • Plants are then transferred to inserts in flats (equivalent to 2.5" pot) containing potting soil and grown for 1 week in a growth chamber, subsequently grown an additional 1-2 weeks in the greenhouse, then transferred to classic 600 pots (1.6 gallon) and grown to maturity. Plants are monitored and scored for an increase in nitrogen use efficiency, increase yield, or an increase in stress tolerance.
  • Bombardment medium comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix (1000X SIGMA-151 1 ), 0.5 mg/l thiamine HCI, 120.0 g/l sucrose, 1.0 mg/l 2,4-D, and 2.88 g/l L-proline (brought to volume with D-I H 2 O following adjustment to pH 5.8 with KOH); 2.0 g/l Gelrite (added after bringing to volume with D-I H 2 O); and 8.5 mg/l silver nitrate (added after sterilizing the medium and cooling to room temperature).
  • Selection medium comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix (1000X SIGMA-151 1 ), 0.5 mg/l thiamine HCI, 30.0 g/l sucrose, and 2.0 mg/l 2,4-D (brought to volume with D-I H 2 O following adjustment to pH 5.8 with KOH); 3.0 g/l Gelrite (added after bringing to volume with D-I H 2 O); and 0.85 mg/l silver nitrate and 3.0 mg/l bialaphos(both added after sterilizing the medium and cooling to room temperature).
  • Plant regeneration medium (288J) comprises 4.3 g/l MS salts (GIBCO 1 11 17-074), 5.0 ml/l MS vitamins stock solution (0.100 g nicotinic acid, 0.02 g/l thiamine HCL, 0.10 g/l pyridoxine HCL, and 0.40 g/l glycine brought to volume with polished D-I H 2 O) (Murashige and Skoog (1962) Physiol. Plant.
  • Hormone-free medium comprises 4.3 g/l MS salts (GIBCO 1 1 117-074), 5.0 ml/l MS vitamins stock solution (0.100 g/l nicotinic acid, 0.02 g/l thiamine HCL, 0.10 g/l pyridoxine HCL, and 0.40 g/l glycine brought to volume with polished D-I H 2 O), 0.1 g/l myo-inositol, and 40.0 g/l sucrose (brought to volume with polished D-I H 2 O after adjusting pH to 5.6); and 6 g/l bacto-agar (added after bringing to volume with polished D-I H 2 O), sterilized and cooled to 60 0 C.
  • step 1 the infection step.
  • the immature embryos are immersed in an Agrobacterium suspension for the initiation of inoculation.
  • the embryos are co-cultured for a time with the Agrobacterium (step 2: the co-cultivation step).
  • the immature embryos are cultured on solid medium following the infection step. Following this co-cultivation period an optional "resting" step is contemplated.
  • the embryos are incubated in the presence of at least one antibiotic known to inhibit the growth of Agrobacterium without the addition of a selective agent for plant transformants (step 3: resting step).
  • the immature embryos are cultured on solid medium with antibiotic, but without a selecting agent, for elimination of Agrobacterium and for a resting phase for the infected cells.
  • inoculated embryos are cultured on medium containing a selective agent and growing transformed callus is recovered (step 4: the selection step).
  • the immature embryos are cultured on solid medium with a selective agent resulting in the selective growth of transformed cells.
  • the callus is then regenerated into plants (step 5: the regeneration step), and calli grown on selective medium are cultured on solid medium to regenerate the plants.
  • Example 7 Soybean Embryo Transformation
  • Soybean embryogenic suspension cultures (cv. Jack) are maintained in 35 ml liquid medium SB196 (see recipes below) on rotary shaker, 150 rpm, 26°C with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of 60-85 ⁇ E/m2/s. Cultures are subcultured every 7 days to two weeks by inoculating approximately 35 mg of tissue into 35 ml of fresh liquid SB196 (the preferred subculture interval is every 7 days).
  • Soybean embryogenic suspension cultures are transformed with the plasmids and DNA fragments described in the following examples by the method of particle gun bombardment (Klein, et al., (1987) Nature, 327:70).
  • Soybean cultures are initiated twice each month with 5-7 days between each initiation.
  • soybeans with immature seeds from available soybean plants 45-55 days after planting are picked, removed from their shells and placed into a sterilized magenta box.
  • the soybean seeds are sterilized by shaking them for 15 minutes in a 5% Clorox solution with 1 drop of ivory soap (95 ml of autoclaved distilled water plus 5 ml Clorox and 1 drop of soap). Mix well.
  • Seeds are rinsed using 2 1 -liter bottles of sterile distilled water and those less than 4 mm are placed on individual microscope slides. The small ends of the seed are cut and the cotyledons pressed out of the seed coat. Cotyledons are transferred to plates containing SB1 medium (25-30 cotyledons per plate). Plates are wrapped with fiber tape and stored for 8 weeks. After this time secondary embryos are cut and placed into SB196 liquid media for 7 days.
  • Plasmid DNA for bombardment is routinely prepared and purified using the method described in the PromegaTM Protocols and Applications Guide, Second Edition (page 106). Fragments of the plasmids carrying a ZmPHDF polynucleotide are obtained by gel isolation of double digested plasmids. In each case, 100 ⁇ g of plasmid DNA is digested in 0.5 ml of the specific enzyme mix that is appropriate for the plasmid of interest.
  • DNA fragments are separated by gel electrophoresis on 1 % SeaPlaque GTG agarose (BioWhitaker Molecular Applications) and the DNA fragments containing the ZmPHDF polynucleotide are cut from the agarose gel.
  • DNA is purified from the agarose using the GELase digesting enzyme following the manufacturer's protocol.
  • a 50 ⁇ l aliquot of sterile distilled water containing 3 mg of gold particles (3 mg gold) is added to 5 ⁇ l of a 1 ⁇ g/ ⁇ l DNA solution (either intact plasmid or DNA fragment prepared as described above), 50 ⁇ l 2.5M CaC ⁇ and 20 ⁇ l of 0.1 M spermidine.
  • the mixture is shaken 3 min on level 3 of a vortex shaker and spun for 10 sec in a bench microfuge. After a wash with 400 ⁇ l 100% ethanol the pellet is suspended by sonication in 40 ⁇ l of 100% ethanol. Five ⁇ l of DNA suspension is dispensed to each flying disk of the Biolistic PDS1000/HE instrument disk. Each 5 ⁇ l aliquot contains approximately 0.375 mg gold per bombardment (i.e., per disk).
  • Tissue is bombarded 1 or 2 shots per plate with membrane rupture pressure set at 1 100 PSI and the chamber evacuated to a vacuum of 27-28 inches of mercury. Tissue is placed approximately 3.5 inches from the retaining/stopping screen.
  • Transformed embryos were selected either using hygromycin (when the hygromycin phosphotransferase, HPT, gene was used as the selectable marker) or chlorsulfuron (when the acetolactate synthase, ALS, gene was used as the selectable marker).
  • the tissue is placed into fresh SB196 media and cultured as described above.
  • the SB196 is exchanged with fresh SB196 containing a selection agent of 30 mg/L hygromycin.
  • the selection media is refreshed weekly.
  • green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates to generate new, clonally propagated, transformed embryogenic suspension cultures.
  • the tissue is divided between 2 flasks with fresh SB196 media and cultured as described above.
  • the SB196 is exchanged with fresh SB196 containing selection agent of 100 ng/ml Chlorsulfuron.
  • the selection media is refreshed weekly.
  • green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates containing SB196 to generate new, clonally propagated, transformed embryogenic suspension cultures.
  • Embryos are cultured for 4-6 weeks at 26°C in SB196 under cool white fluorescent (Phillips cool white Econowatt F40/CW/RS/EW) and Agro (Phillips F40 Agro) bulbs (40 watt) on a 16:8 hr photoperiod with light intensity of 90-120 uE/m2s. After this time embryo clusters are removed to a solid agar media, SB166, for 1-2 weeks. Clusters are then subcultured to medium SB103 for 3 weeks. During this period, individual embryos can be removed from the clusters and screened for levels of ZmPHDF expression and/or activity.
  • Matured individual embryos are desiccated by placing them into an empty, small petri dish (35 x 10 mm) for approximately 4-7 days. The plates are sealed with fiber tape (creating a small humidity chamber). Desiccated embryos are planted into SB71-4 medium where they were left to germinate under the same culture conditions described above. Germinated plantlets are removed from germination medium and rinsed thoroughly with water and then planted in Redi- Earth in 24-cell pack tray, covered with clear plastic dome. After 2 weeks the dome is removed and plants hardened off for a further week. If plantlets looked hardy they are transplanted to 10" pot of Redi-Earth with up to 3 plantlets per pot. After 10 to 16 weeks, mature seeds are harvested, chipped and analyzed for proteins.
  • SB1 solid medium (per liter) comprises: 1 pkg. MS salts (GIBCO/BRL - Cat# 1 11 17-066); 1 ml B5 vitamins 1000X stock; 31.5 g sucrose; 2 ml 2,4-D (20 mg/L final concentration); pH 5.7; and, 8 g TC agar.
  • SB 166 solid medium (per liter) comprises: 1 pkg. MS salts (GIBCO/BRL - Cat# 11 117-066); 1 ml B5 vitamins 1000X stock; 60 g maltose; 750 mg MgCI 2 hexahydrate; 5 g activated charcoal; pH 5.7; and, 2 g gelrite.
  • SB 103 solid medium (per liter) comprises: 1 pkg. MS salts (GIBCO/BRL - Cat# 1 1 117-066); 1 ml B5 vitamins 1000X stock; 60 g maltose; 750 mg MgCI2 hexahydrate; pH 5.7; and, 2 g gelrite.
  • SB 71-4 solid medium (per liter) comprises: 1 bottle Gamborg's B5 salts w/ sucrose (GIBCO/BRL - Cat# 21153-036); pH 5.7; and, 5 g TC agar.
  • 2,4-D stock is obtained premade from Phytotech cat# D 295 - concentration is 1 mg/ml.
  • B5 Vitamins Stock (per 100 ml) which is stored in aliquots at -20C comprises: 10 g myoinositol; 100 mg nicotinic acid; 100 mg pyridoxine HCI; and, 1 g thiamine. If the solution does not dissolve quickly enough, apply a low level of heat via the hot stir plate.
  • Chlorsulfuron Stock comprises: 1 mg / ml in 0.01 N Ammonium Hydroxide.
  • the ZmPHDF nucleotide sequences are used to generate variant nucleotide sequences having the nucleotide sequence of the open reading frame with about 70%, 75%, 80%, 85%, 90% and 95% nucleotide sequence identity when compared to the starting unaltered ORF nucleotide sequence of the corresponding SEQ ID NO. These functional variants are generated using a standard codon table. While the nucleotide sequence of the variants is altered, the amino acid sequence encoded by the open reading frames does not change.
  • Variant amino acid sequences of the ZmPHDF polypeptides are generated.
  • one amino acid is altered.
  • the open reading frames are reviewed to determine the appropriate amino acid alteration.
  • the selection of the amino acid to change is made by consulting the protein alignment (with the other orthologs and other gene family members from various species).
  • An amino acid is selected that is deemed not to be under high selection pressure (not highly conserved) and which is rather easily substituted by an amino acid with similar chemical characteristics (i.e., similar functional side-chain).
  • an appropriate amino acid can be changed. Once the targeted amino acid is identified, the procedure outlined in the following section C is followed.
  • the determination of which amino acid sequences are altered is made based on the conserved regions among ZmPHDF protein or among the other ZmPHDF polypeptides. Based on the sequence alignment, the various regions of the ZmPHDF polypeptide that can likely be altered are represented in lower case letters, while the conserved regions are represented by capital letters. It is recognized that conservative substitutions can be made in the conserved regions below without altering function. In addition, one of skill will understand that functional variants of the ZmPHDF sequence of the invention can have minor non- conserved amino acid alterations in the conserved domain.
  • H, C, and P are not changed in any circumstance.
  • the changes will occur with isoleucine first, sweeping N-terminal to C-terminal. Then leucine, and so on down the list until the desired target it reached. Interim number substitutions can be made so as not to cause reversal of changes.
  • the list is ordered 1-17, so start with as many isoleucine changes as needed before leucine, and so on down to methionine. Clearly many amino acids will in this manner not need to be changed.
  • L, I and V will involve a 50:50 substitution of the two alternate optimal substitutions.
  • variant amino acid sequences are written as output. Perl script is used to calculate the percent identities. Using this procedure, variants of the ZmPHDF polypeptides are generating having about 80%, 85%, 90% and 95% amino acid identity to the starting unaltered ORF nucleotide sequence of SEQ ID NO: 1.
  • Disrupted amino acid sequences of the ZmPHDF polypeptides are generated.
  • particular domains are disrupted or excluded from final polypeptide. If disrupting the N- terminal domain(s) or motif(s), the DNA codon for the starting ATG is altered by insertion, deletion or base substitution to prevent the translation of the first methionine. Generally the next available methionine will dominate the start of translation thus skipping the N-terminal portion of the polypeptide.
  • the DNA sequence corresponding to the first fourteen ATG's of the full-length rice PHDF-like can be altered by base substitution, deletion or insertion to effectively prevent translation starting at any of these ATG's and initiate downstream at amino acid residue #734 thus removing the first 733 amino acids of the rice PHDF-like polypeptide effectively disrupting the normal formation of the PHD-finger domain.
  • a stop codon at the desired site is created by insertion, deletion or base substitution or more commonly by PCR as described below. Premature stops may lead to translation of polypeptides missing the C-terminal domain(s).
  • An alternative method for selectively isolating a targeted domain(s) for expression is to design primers to PCR amplify the desired domain(s) with either a naturally occurring or engineered ATG sequence at the 5' end of the clone and a naturally occurring or engineered stop codon at the 3' end of the clone.
  • the resulting fragment will have the desired domain(s) to be cloned into expression vectors (see, Example 2).
  • a 5' primer was designed as complementary to the DNA sequence that included the corresponding internal and desired in-frame ATG codon, at amino acid residue #257, while the 3' primer was designed to the complementary DNA sequence to include the corresponding stop codon at amino acid residue # 1268 (final residue).
  • the 5' primer could be designed as complementary to any of the DNA sequence regions that include any one of the several in-frame ATG codons corresponding to the amino acid residues from #257 to #734.
  • Variants of the isolated polypeptide domain(s) or motif(s) generated as described in Examples 8A, B, or C having about 70%, 75%, 80%, 85%, 90% and 95% sequence identity are generated using these methods.

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Abstract

L'invention concerne des compositions et des procédés pour moduler le développement d'un organe de fleur, la formation de feuilles, le phototropisme, la dominance apicale, le développement de fruits, l'initiation des racines et pour augmenter le rendement dans une plante. Les compositions comprennent une séquence ZmPHDF. Les compositions de l'invention comprennent des séquences d'acides aminés et des séquences nucléotidiques choisies parmi SEQ ID NOS: 1-3, ainsi que des variants et des fragments de celles-ci. Des séquences nucléotidiques codant pour ZmPHDF sont fournies dans des produits de construction d'ADN pour une expression dans une plante d'intérêt, pour la modulation du taux d'une séquence ZmPHDF dans une plante ou une partie de plante. Les procédés comprennent l'introduction dans une plante ou partie de plante d'un polynucléotide hétérologue comprenant une séquence ZmPHDF de l'invention. Le taux du polypeptide ZmPHDF peut être augmenté ou diminué. Un tel procédé peut être utilisé pour augmenter le rendement dans des plantes ; dans un mode de réalisation, le procédé est utilisé pour augmenter le rendement de grains dans des céréales.
PCT/EP2008/056332 2007-05-22 2008-05-22 Amélioration du rendement dans des plantes par modulation de zmphdf Ceased WO2008142146A1 (fr)

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8722072B2 (en) 2010-01-22 2014-05-13 Bayer Intellectual Property Gmbh Acaricidal and/or insecticidal active ingredient combinations
US9265252B2 (en) 2011-08-10 2016-02-23 Bayer Intellectual Property Gmbh Active compound combinations comprising specific tetramic acid derivatives

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Publication number Priority date Publication date Assignee Title
WO2003025185A1 (fr) * 2001-09-14 2003-03-27 Cropdesign N.V. Procede destine a modifier le nombre de cellules, l'architecture et le rendement de plantes par surexpression du facteur de transcription de e2f
US20040034888A1 (en) * 1999-05-06 2004-02-19 Jingdong Liu Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement
WO2006056590A2 (fr) * 2004-11-25 2006-06-01 Cropdesign N.V. Plantes a rendement ameliore et procede d'elaboration

Patent Citations (3)

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US20040034888A1 (en) * 1999-05-06 2004-02-19 Jingdong Liu Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement
WO2003025185A1 (fr) * 2001-09-14 2003-03-27 Cropdesign N.V. Procede destine a modifier le nombre de cellules, l'architecture et le rendement de plantes par surexpression du facteur de transcription de e2f
WO2006056590A2 (fr) * 2004-11-25 2006-06-01 Cropdesign N.V. Plantes a rendement ameliore et procede d'elaboration

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DATABASE Geneseq [online] 21 April 2005 (2005-04-21), "Plant full length insert polynucleotide seqid 32074.", XP002497279, retrieved from EBI accession no. GSN:ADX61231 Database accession no. ADX61231 *
DATABASE Geneseq [online] 21 April 2005 (2005-04-21), "Plant full length insert polypeptide seqid 54616.", XP002497280, retrieved from EBI accession no. GSP:ADX91952 Database accession no. ADX91952 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8722072B2 (en) 2010-01-22 2014-05-13 Bayer Intellectual Property Gmbh Acaricidal and/or insecticidal active ingredient combinations
US9265252B2 (en) 2011-08-10 2016-02-23 Bayer Intellectual Property Gmbh Active compound combinations comprising specific tetramic acid derivatives

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