WO2018162330A1 - Variants de la hppd et procédé d'utilisation - Google Patents

Variants de la hppd et procédé d'utilisation Download PDF

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WO2018162330A1
WO2018162330A1 PCT/EP2018/055102 EP2018055102W WO2018162330A1 WO 2018162330 A1 WO2018162330 A1 WO 2018162330A1 EP 2018055102 W EP2018055102 W EP 2018055102W WO 2018162330 A1 WO2018162330 A1 WO 2018162330A1
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Prior art keywords
amino acid
acid position
seq
position corresponding
hppd
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PCT/EP2018/055102
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English (en)
Inventor
Marc LINKA
Fabien Poree
Bernd Laber
Gudrun Lange
Ernst Weber
Michael Strerath
Sandra Geske
Heike BALVEN-ROSS
Nina Wobst
Wayne Coco
Nikolaus Pawlowski
Jan Tebbe
Christina THIES
Manuel Dubald
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Bayer Cropscience Aktiengesellschaft
Bayer Cropscience Lp
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Priority to BR112019018059-1A priority Critical patent/BR112019018059A2/pt
Priority to US16/489,996 priority patent/US11371056B2/en
Priority to CA3055396A priority patent/CA3055396A1/fr
Publication of WO2018162330A1 publication Critical patent/WO2018162330A1/fr

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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
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8274—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for herbicide resistance
    • 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
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0069—Oxidoreductases (1.) acting on single donors with incorporation of molecular oxygen, i.e. oxygenases (1.13)

Definitions

  • This invention relates to plant molecular biology, particularly novel HPPD polypeptides that confer improved tolerance to HPPD inhibitor herbicides.
  • HPPDs The 4-hydroxyphenylpyruvate dioxygenases
  • HPP para-hydroxyphenylpyruvate
  • HGA homogentisate
  • Tocopherol acts as a membrane-associated antioxidant.
  • Plastoquinone firstly acts as an electron carrier between PSII and the cytochrome b6/f complex and secondly, is a redox cofactor for phytoene desaturase, which is involved in the biosynthesis of carotenoids.
  • Rhodococcus (WO2011/076892), of protists such as Blepharisma (WO2011/076882), of euryarchaeota such as Picrophilus (WO2011/076885), of algae such as Chlamydomonas reinhardtii (ES2275365; WO2011/145015), Scenedesmus (WO2015/022634), of plants such as Arabidopsis (W096/38567, GENBANK® AF047834), carrot (WO 96/38567, GENBANK® 87257), Avena sativa
  • HPPD inhibitor herbicides Some molecules which inhibit HPPD (hereinafter named HPPD inhibitor herbicides), and which inhibit transformation of the HPP into HGA while binding specifically to the enzyme, have proven to be very effective herbicides.
  • HPPD inhibitor herbicides belong to one of these chemical families, as listed below:
  • benzobicyclon i.e. 3-[2-chloro-4-(methylsulfonyl)benzoyl]-4- (phenylsulfanyl)bicyclo[3.2.1]oct-3-en-2-one]
  • sulcotrione i.e. 2-[2-chloro-4-(methylsulfonyl)benzoyl]- 1,3-cyclohexanedione]
  • mesotrione i.e. 2-[4-(methylsulfonyl)-2-nitrobenzoyl]-l,3-cyclohexanedione] (abbreviated herein as MST); tembotrione [i.e.
  • bicyclopyrone [i. e. 4-hydroxy-3 - [[2- [(2-methoxyethoxy)methyl] -6-(trifluoromethyl)-3 - pyridinyl]carbonyl]bicyclo[3.2.1]oct-3-en-2-one]; en3 ⁇ 4 , i/moincwe [i.e. 2-[[8-chloro-3,4-dihydro-4-(4- methoxyphenyl)-3-oxo-2-quinoxalinyl]carbonyl]-l,3-cyclohexanedione], and as described in
  • isoxazoles e.g. isoxaflutole [i.e. (5-cyclopropyl-4-isoxazolyl)[2-(methylsulfonyl)-4- (trifluoromethyl)phenyl]methanone].
  • isoxaflutole (abbreviated herein as IFT) is rapidly metabolized to DK , a diketonitrile compound which exhibits the HPPD inhibitor property;
  • hydroxypyrazoles e.g. pyrazoxyfen [i.e. 2-[[4-(2,4-dichlorobenzoyl)-l,3-dimethyl-lH-pyrazol-5- yl] oxy] - 1 -phenylethanone] ; benzofenap [i.e. 2- [[4-(2,4-dichloro-3 -methylbenzoyl)- 1 ,3 -dimethyl- 1 H- pyrazol-5-yl]oxy]-l-(4-methylphenyl)ethanone]; pyrazolynate [i.e.
  • WO2014/192936 WO2015/052152, WO2015/052178 and the N-(l ,3,4-oxadiazol-2-yl)benzamides as described in WO2012/126932, and EP2562174, WO2013/064459, WO2013/087577, WO2013/124238, WO2013/124228, WO2013/124245, WO2013/164333, WO2013/037342, WO2014/1053473,
  • WO2014/086737 WO2015/007662, WO2015/007632, WO2015/007633; e.g. 2-methyl-N-(5-methyl- l,3,4-oxadiazol-2-yl)-3-(methylsulfonyl)-4-(trifluoromethyl)benzamide; 2-chloro-N-(5-methyl-l,3,4- oxadiazol-2-yl)-3-(methylsulfonyl)-4-(trifluoromethyl)benzamide; 2-chloro-3-(ethylsulfonyl)-N-(5- methyl-l,3,4-oxadiazol-2-yl)-4-(trifluoromethyl)benzamide;
  • HPPD inhibitor herbicides can be used against grass and/or broad leaf weeds in field of crop plants that display metabolic tolerance, such as maize (Zea mays), rice (Oryza sativa) and wheat (Triticum aestivum) in which they are rapidly degraded (Schulz et al. (1993), FEBS letters, 318, 162- 166; Mitchell et al. (2001), Pest Management Science, Vol 57, 120-128; Garcia et al. (2000), Biochem., 39, 7501-7507; Pallett et al. (2001), Pest Management Science, Vol 57, 133-142).
  • a tolerance level acceptable under agronomic field conditions such as maize (Zea mays), rice (Oryza sativa) and wheat (Triticum aestivum) in which they are rapidly degraded (Schulz et al. (1993), FEBS letters, 318, 162- 166; Mitchell et al. (2001), Pest Management Science,
  • a third strategy was to mutate the HPPD polypeptide in order to obtain a target enzyme which, while retaining its properties of catalyzing the transformation of HPP into HGA, is less sensitive to HPPD inhibitors than is the native HPPD polypeptide before mutation.
  • Pro215Leu, Gly336Glu, Gly336Ile, and more particularly Gly336Trp positions of the mutated amino acid are indicated with reference to the wild-type Pseudomonas fluorescens HPPD polypeptide corresponding to SEQ ID NO: 1 of present invention) were identified as mutations which are responsible for an increased tolerance to treatment with these diketonitrile herbicides.
  • nucleic acid sequences encoding an hydroxyphenylpyruvate dioxygenase (HPPD) with specific mutations at position 336 of the Pseudomonas fluorescens HPPD protein and their use for obtaining plants which are tolerant to HPPD inhibitor herbicides was disclosed.
  • a method to generate plants tolerant to HPPD inhibitor herbicides by overexpressing not only a gene coding for a tolerant HPPD, as for example from Avena sativa (US2011/0173718) or Arabidopsis (WO2013/064964, WO2014/177999), but also in combination with several plant genes coding for an HST (homogentisate solanesyltransferase) protein is disclosed.
  • HST homogentisate solanesyltransferase
  • transgenic plants expressing the identified genes did not display any improvement in tolerance to the tested HPPD inhibitor herbicides.
  • US 2012/0042413 describes mutant maize HPPD polypeptides having HPPD activity but also showing a certain insensitivity to at least one HPPD inhibitor herbicide and further suggests a certain set of mutations at different positions of HPPD polypeptides and finally discloses biochemical data as well as tolerance levels of plants containing few of such mutated HPPD polypeptides.
  • EP 2453012 several mutants of HPPD polypeptides have been described; however, the improved tolerance of the described mutants was not demonstrated in planta against several HPPD inhibitor herbicides.
  • nucleic acid molecules encoding the Pseudomonas spp. HPPD polypeptides consisting of an amino acid sequence comprising a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO:l; or a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO:l and a tryptophan at the amino acid position corresponding to amino acid position 336 of SEQ ID NO: 1 ; or a serine at the amino acid position corresponding to amino acid position 335 of SEQ ID NO:l, a serine at the amino acid position corresponding to amino acid position 336 of SEQ ID NO:l, a threonine at the amino acid position corresponding to amino acid position 339 of SEQ ID NO:l, and a glutamine at the amino acid position corresponding to amino acid position 340 of SEQ ID NO: 1 ; or a tryptophan at the amino acid position corresponding to amino acid position 188 of
  • HPPD inhibitor herbicides act as slow- binding or slow, tight-binding inhibitors (see Morrison (1982) Trends Biochem. Sci. 7, 102-105). These inhibitors bind slowly (i.e. they have slow rates of association, kon) but not covalently to the HPPD polypeptide (i.e. they produce time-dependent inhibition), and are released very slowly (i.e. they have exceptionally slow rates of dissociation, koff) due to their exceedingly tight interaction with the enzyme. These inhibitors bind so tightly that stoichiometric titrations with the enzyme are possible.
  • slow-binding or slow, tight-binding inhibitors are not only extraordinary potent HPPD-inhibitor, but, in addition, have features that make them attractive agrochemicals for weed control.
  • the slow rate of dissociation enhances inhibitor effectiveness to such an extent that ideally only one inhibitor molecule per HPPD polypeptide active site is sufficient to fully inhibit the activity and to maintain this level of inhibition for a long time period even in the absence of free inhibitor molecules in the plant cell. This translates into low application rates of these inhibitors to control undesired weeds in crop growing areas.
  • HPPD inhibitor herbicides belong to structurally diverse chemical classes, such as the triketones, the diketonitriles, the isoxazoles, the hydroxypyrazoles, the N-(l ,2,5-oxadiazol-3- yl)benzamides, the N-(l ,3,4-oxadiazol-2-yl)benzamides, the N-(tetrazol-5-yl)- or N-(triazol-5- yl)arylcarboxamides, the pyridazinone derivatives, the oxoprazine derivatives, the N-(triazol-2-yl), the triazinones, and the pyrazolones.
  • the currently described state of the art HPPD polypeptides demonstrate a rather narrow range of tolerance to structurally diverse HPPD inhibitor herbicides.
  • HPPD polypeptides and plants containing them showing a full tolerance against one or more HPPD inhibitor herbicides belonging to various chemical classes. It turned out that in order to generate such HPPD polypeptides with maximized and broad tolerance against several classes of HPPD inhibitor herbicides, it is important to reduce the affinity to the HPPD polypeptide (ki) concerning the respective HPPD inhibitor herbicide(s) and simultaneously to ensure an improved rate of dissociation (koff) of a slow-binding or slow, tight-binding inhibitor as known from the wild-type and several mutant HPPD polypeptides to achieve high level of inhibitor tolerance.
  • ki affinity to the HPPD polypeptide
  • koff rate of dissociation
  • this goal was achieved by developing a set of HPPD polypeptides, which have either no or only a significantly reduced affinity to HPPD inhibitor herbicides and, at the same time, the rate of dissociation of the HPPD inhibitor herbicides of the enzyme is increased to such an extent that the HPPD inhibitor herbicides no longer act as slow-binding or slow, tight-binding inhibitors but, instead of this, have become fully reversible inhibitors.
  • compositions and methods for obtaining a new set of HPPD polypeptides having the before mentioned characteristics i.e. no or only a significantly reduced affinity to HPPD inhibitor herbicides, increased rate of dissociation of the HPPD inhibitor herbicides of the enzyme; HPPD inhibitor herbicides no longer act as slow-binding or slow, tight-binding inhibitors but have become fully reversible inhibitors
  • compositions include HPPD polypeptides and isolated, recombinant or chimeric nucleic acid molecules encoding such HPPD polypeptides, vectors and host cells comprising those nucleic acid molecules.
  • Compositions also include the antibodies to those polypeptides.
  • the nucleotide sequences can be used in DNA constructs or expression cassettes for transformation and expression in organisms, including microorganisms and plants.
  • the nucleotide sequences may be synthetic sequences that have been designed for expression in an organism including, but not limited to, a microorganism or a plant.
  • compositions include nucleic acid molecules encoding herbicide tolerant HPPD
  • polypeptides including nucleic acid molecules encoding an HPPD polypeptide having (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: 1 , (b) a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO:l, (c) a histidine or an aspartic acid at the position corresponding to amino acid position 336 of SEQ ID NO:l, and (d) a serine at the position corresponding to amino acid position 337 of SEQ ID NO: 1 , and wherein said HPPD polypeptide is tolerant to one or more HPPD inhibitor herbicide(s) and, optionally, one or more further amino acid substitutions at the positions corresponding to amino acid positions 213, 215, 264, 268, 270, 340, 344, 345 of SEQ ID NO: 1, including the HPPD polypeptides set forth in any of SEQ ID NO:2 to NO:69 as well as fragments thereof.
  • Compositions also comprise transformed plants, plant cells, tissues, and seeds that are tolerant to the HPPD inhibitor herbicides by the introduction of the nucleic acid sequence of the invention into the genome of the plants, plant cells, tissues, and seeds.
  • the introduction of the sequence allows for HPPD inhibitor herbicides to be applied to plants to selectively kill HPPD inhibitor sensitive weeds or other untransformed plants, but not the transformed organism.
  • the sequences can additionally be used as a marker for selection of plant cells growing in the presence of one or more HPPD inhibitor herbicides.
  • compositions and methods of the invention are useful for the production of organisms with enhanced tolerance to HPPD inhibitor herbicides. These organisms and compositions comprising the organisms are desirable for agricultural purposes. Plants or seeds comprising the nucleic acid sequence encoding an HPPD polypeptide according to the invention can be grown in a field and harvested to obtain a plant product. The compositions of the invention are also useful for detecting the presence of HPPD inhibitor herbicide tolerant polypeptides or nucleic acids in products or organisms.
  • Figure 1 shows a simplistic scheme of the coupled HPPD activity assay used in this invention to determine the enzymatic activity of the exemplary HPPD polypeptides.
  • Figure 2 shows exemplary kinetic changes in absorbance at 320 nm (Abs320) in raw extracts samples of wild-type and knock-out HPPD polypetide observed with 200 ⁇ HPP and 0, 4 or 13 ⁇ Cmpd. 1 (2- chloro-3 -(methylsulfanyl)-N-( 1 -methyl- 1 H-tetrazol-5 -yl)-4-(trifluoromethyl)benzamide) according to Example 3 in the coupled HPPD activity assay.
  • the knock-out HPPD polypeptide was obtained by exchanging a histidine to an alanine at the amino acid position corresponding to amino acid position 162 of SEQ ID NO : 1. This position is well known for its importance due to its involvement in the coordinated binding of the iron atom in the active site of the HPPD polypeptide (Serre et al. (1999), Structure, 7, 977-988).
  • HPPD inhibitor herbicides described above it is still necessary to develop and/or improve the tolerance of plants to newer or to several different HPPD inhibitor herbicides belonging to various chemical classes, particularly HPPD inhibitor herbicides belonging to the classes of triketones (e.g.
  • benzobicyclon sulcotrione mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (e.g. isoxaflutole), hydroxypyrazoles (e.g. pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3-yl)benzamides, N-(l ,3,4- oxadiazol-2-yl)benzamides (e.g.
  • HPPD inhibitor herbicides like those of the class of triketones (e.g.
  • benzobicyclon sulcotrione mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (e.g. isoxaflutole), hydroxypyrazoles (e.g. pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3-yl)benzamides, N-(l ,3,4- oxadiazol-2-yl)benzamides (e.g.
  • herbicide is understood as being a herbicidally active substance on its own or such a substance which is combined with an additive which alters its efficacy, such as, for example, an agent which increases its activity (a synergistic agent) or which limits its activity (a safener).
  • the herbicide may further comprise solid or liquid adjuvants or carriers that are ordinarily employed in formulation technology (e.g. natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, emulsifiers, growth promoting agents, and the like), as well as one or more additional herbicides and/or one or more pesticides (e.g. insecticides, virucides, microbicides, amoebicides, pesticides, fungicides, bactericides, nematicides, molluscicides, and the like).
  • pesticides e.g. insecticides, virucides, microbicides, amoebicides, pesticides, fungicides,
  • the methods involve transforming organisms with nucleotide sequences encoding an HPPD inhibitor herbicide tolerance gene of the invention or otherwise introducing such HPPD inhibitor herbicide tolerance genes in organisms not containing them (e.g. by mating, cell fusion, or by crossing organisms containing an introduced HPPD inhibitor herbicide tolerance gene of the invention with organisms not containing it and obtaining progeny containing such gene).
  • nucleotide sequences of the invention are useful for preparing plants that show increased tolerance to HPPD inhibitor herbicides, particularly increased tolerance to HPPD inhibitor herbicides of the class of triketones (preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, or fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole), hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, or tolpyralate), N-(l,2,5-oxadiazol-3- yl)benzamides, N-(l,3,4-oxadiazol-2-yl)benzamides (preferably 2-methyl-N-(5-methyl-l,3,4-oxadiazol- 2-yl)-3-(methylsulfonyl)-4-(trifluoromethyl
  • HPPD inhibitor herbicide tolerance gene of the invention may also result in tolerance towards the "coumarone-derivative herbicides" (described in WO2009/090401 ,
  • a "coumarone-derivative herbicide” or "HST inhibitor herbicide” encompasses compounds which fall under the IUPAC nomenclature of 5H-thiopyrano[4,3- b]pyridin-8-ol, 5H-thiopyrano[3,4-b]pyrazin-8-ol, oxathiino[5,6-b]pyridin-4-ol, and oxathiino[5, 6- b]pyrazin-4-ol.
  • HPPD inhibitor herbicide tolerance gene of the invention is intended a gene encoding a polypeptide that confers upon a cell or organism the ability to tolerate a higher concentration of an HPPD inhibitor herbicide than such cell or organism that does not express the protein, or to tolerate a certain concentration of an HPPD inhibitor herbicide for a longer time than such cell or organism that does not express the protein, or that confers upon a cell or organism the ability to perform
  • HPPD inhibitor herbicide tolerance polypeptide comprises a polypeptide that confers upon a cell or organism the ability to tolerate a higher concentration of HPPD inhibitor herbicides than such cell or organism that does not express the protein, or to tolerate a certain concentration of HPPD inhibitor herbicides for a longer period of time than such cell or organism that does not express the polypeptide, or that confers upon a cell or organism the ability to perform photosynthesis, grow, and/or reproduce with less damage or growth inhibition observed than such cell or organism not expressing such polypeptide.
  • polypeptide comprises proteins such as enzymes, antibodies and medium-length polypeptides and short peptides down to an amino acid sequence length below ten.
  • enzyme means in the present invention any polypeptide catalyzing the reaction in which para-hydroxyphenylpyruvate is transformed into homogentisate. It includes naturally- occurring enzymes, as well as enzyme variants and derivatives thereof. It also comprises any fragment of such an enzyme, and variants engineered by insertion, deletion, recombination and/or any other method, that leads to enzymes that differ in their amino acid sequence from the naturally- occurring enzyme or the enzyme variants. It also comprises protein molecules with posttranslational and/or chemical modifications, e.g. glycosylation, gamma carboxylation and acetylation, any molecular complex or fusion protein comprising one of the aforementioned proteins.
  • polypeptide variant or “mutant polypeptide” means any polypeptide molecule obtained by mutagenesis, preferably by site-directed or random mutagenesis with an altered amino acid sequence compared to the respective wild-type sequence.
  • tolerate By “tolerate”, “tolerance” or “resistant” is intended either to survive a particular HPPD inhibitor herbicide application, or the ability to carry out essential cellular functions such as photosynthesis, protein synthesis or respiration and reproduction in a manner that is not readily discernable from untreated cells or organisms, or the ability to have no significant difference in yield or even improved yield for plants treated with HPPD inhibitor herbicide compared to such plants not treated with such herbicide (but where weeds have been removed or prevented by a mechanism other than application of the HPPD inhibitor herbicide, such as the methods described in WO2011/100302, which is herein incorporated by reference in its entirety).
  • the HPPD nucleic acid sequences of the invention encode polypeptides having HPPD activity, i.e. catalyzing the reaction in which para-hydroxyphenylpyravate (HPP) is transformed into homogentisate.
  • HPPD activity i.e. catalyzing the reaction in which para-hydroxyphenylpyravate (HPP) is transformed into homogentisate.
  • HPP para-hydroxyphenylpyravate
  • the catalytic activity of an HPPD polypeptide may be defined by various methods well-known in the art. WO2009/144079 and WO2014/043435 describe various suitable screening methods.
  • the enzymatic activity of HPPD polypeptides can be measured by any method that makes it possible either to measure the decrease in the amount of the HPP or O2 substrates, or to measure the accumulation of any of the products derived from the enzymatic reaction, i.e. homogentisate or CO2.
  • the HPPD activity can be measured by means of the method described in WO2009/144079; Garcia et al. (1997), Biochem. J. 325, 761-769; Garcia et al. (1999), Plant Physiol. 119, 1507-1516; or in WO2012/021785, which are incorporated herein by reference.
  • a “reference” HPPD polypeptide is any HPPD polypeptide or nucleic acid against which the HPPD polypeptide or HPPD nucleic acid of the invention is being compared.
  • the terms “protein” and “polypeptide” are used interchangeably.
  • This reference HPPD polypeptide can be a native plant, bacterial, or animal HPPD, or can be a mutated HPPD polypeptide that is known in the art such as the PfP215L and PfG336F mutants described in
  • HPPD polypeptide can be used to determine whether the HPPD polypeptide or nucleic acid of the invention has a particular property of interest (e.g., improved, comparable or decreased HPPD inhibitor herbicide tolerance or HPPD polypeptide enzymatic activity; improved, comparable or decreased expression in a host cell; improved, comparable or decreased protein stability, and the like).
  • a particular property of interest e.g., improved, comparable or decreased HPPD inhibitor herbicide tolerance or HPPD polypeptide enzymatic activity; improved, comparable or decreased expression in a host cell; improved, comparable or decreased protein stability, and the like).
  • the HPPD inhibitor herbicide tolerant polypeptide encoded by a nucleic acid including isolated, recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleic acid, HPPD polypeptides and compositions thereof encoded by the nucleic acid, as well as methods of using the polypeptide encoded by the nucleic acid for increasing tolerance of a plant to HPPD inhibitor herbicides, particularly increased tolerance to HPPD inhibitor herbicides of the class of triketones (preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole), hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-
  • (trifluoromethyl)benzamide (hereinafter also named "Cmpd. 1"), 2-(methoxymethyl)-3-(methylsulfinyl)- N-(l-methyl-lH-tetrazol-5-yl)-4-(trifluoromethyl)benzamide), pyridazinone derivatives, oxoprazine derivatives, N-(triazol-2-yl)arylcarboxamides, triazinones, and pyrazolones) has (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l, (b) a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO: l, (c) a histidine or an aspartic acid at the position corresponding to amino acid position 336 of SEQ ID NO: l, and (d) a serine at the position corresponding to amino acid position 337 of SEQ ID NO: 1 , and
  • corresponding to is intended the nucleotide or amino acid position relative to that position in SEQ ID NO:l when two (or more) sequences are aligned using standard alignment algorithms.
  • position in a polynucleotide or polypeptide refers to specific single bases or amino acids in the sequence of the polynucleotide or polypeptide, respectively.
  • site in a polynucleotide or polypeptide refers to a certain position or region in the sequence of the polynucleotide or polypeptide, respectively.
  • polynucleotide corresponds to any genetic material of any length and any sequence, comprising single-stranded and double-stranded DNA and RNA molecules, including regulatory elements, structural genes, groups of genes, plasmids, whole genomes, and fragments thereof.
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) consists of an amino acid sequence comprising
  • HPPD polypeptide is tolerant to one or more HPPD inhibitor herbicide(s).
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: 1 , (b) a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO: 1 , (c) a histidine or an aspartic acid at the position corresponding to amino acid position 336 of SEQ ID NO: l, and (d) a serine at the position corresponding to amino acid position 337 of SEQ ID NO: l, and further comprising i. a lysine or leucine at the amino acid position corresponding to amino acid position 213 of
  • viii a lysine, arginine, methionine, alanine, or valine at the amino acid position corresponding to amino acid position 345 of SEQ ID NO:l .
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l, (b) a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO: 1 , (c) a histidine or an aspartic acid at the position corresponding to amino acid position 336 of SEQ ID NO: 1 , and (d) a serine at the position corresponding to amino acid position 337 of SEQ ID NO: 1 , and further comprising
  • viii a lysine, valine, or methionine at the amino acid position corresponding to amino acid position 345 of SEQ ID NO: l .
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l, (b) a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO: 1 , (c) a histidine or an aspartic acid at the position corresponding to amino acid position 336 of SEQ ID NO: 1 , and (d) a serine at the position corresponding to amino acid position 337 of SEQ ID NO: 1 , and further comprising
  • viii a lysine, valine, or methionine at the amino acid position corresponding to amino acid position 345 of SEQ ID NO: l .
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: 1 , (b) a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO: 1 , (c) a histidine or an aspartic acid at the position corresponding to amino acid position 336 of SEQ ID NO: l, and (d) a serine at the position corresponding to amino acid position 337 of SEQ ID NO: l, and further comprising
  • viii a lysine, valine, or methionine at the amino acid position corresponding to amino acid position 345 of SEQ ID NO: 1.
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising
  • vii. a valine, lysine, or methionine at the amino acid position corresponding to amino acid position 345 of SEQ ID NO: 1.
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l,
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l,
  • v. a valine, lysine, or methionine at the amino acid position corresponding to amino acid position 345 of SEQ ID NO: 1.
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO:l,
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l,
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l,
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l,
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO: l,
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising
  • the HPPD polypeptide of the present invention (including the nucleotide sequence encoding it and recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleotide sequence encoding the HPPD polypeptide of the invention) being tolerant to one or more HPPD inhibitor herbicides consists of an amino acid sequence comprising
  • Table 1 summarizes the respective amino acid positions in comparison to the reference wild-type Pseudomonas fluorescens HPPD polypeptide (SEQ ID NO: l) where the HPPD polypeptide variants according to the invention comprising three or more amino acid substitutions. If not otherwise explicitly stated the exchanges at the relevant amino acid positions are always referred to the reference wild-type Pseudomonas fluorescens HPPD polypeptide corresponding to SEQ ID NO: l .
  • Table 1 Overview of exemplary amino acid exchanges relative to the HPPD polypeptide corresponding to SEQ ID NO: 1
  • Amino acids are referred to herein using the name of the amino acid, the three letter abbreviation or the single letter abbreviation.
  • the table below provides a list of the standard amino acids together with their abbreviations.
  • the genetic code is degenerate, that is more than one codon triplet can code for the same amino acid. Therefore, the amino acid sequences provided herein, can be generated by alternate sequences that use different codons to encode the same amino acid sequence.
  • HPPD polypeptides according to the invention have at least 53%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the amino acid sequence set forth herein as SEQ ID NO:l .
  • the HPPD polypeptide of the invention may also comprise further modifications, for example, wherein some amino acids (e.g. 1 to 17 amino acids) have been replaced, added or deleted for cloning purposes, to make a transit peptide fusion, and the like, which retains HPPD activity, i.e.
  • HPPD polypeptides according to present invention and being tolerant to one or more HPPD inhibitor herbicides are equivalent to SEQ ID NO:l (Pseudomonas fluorescens) beside the amino acids being replaced according to present invention, ie.
  • HPPD polypeptide is identical to SEQ ID NO:l but having
  • HPPD polypeptides according to present invention being tolerant to one or more HPPD inhibitor herbicides are equivalent to SEQ ID NO:l (Pseudomonas fluorescens) beside the amino acids being replaced according to present invention, ie., the respective HPPD polypeptide is identical to SEQ ID NO:l but having one or more amino acid exchanges at the respective amino acid position according to Table 1 , above, with the proviso that an glutamine or a lysine exist at position 315 of SEQ ID NO:l, a proline exists at position 335 of SEQ ID NO:l, a histidine or an aspartic acid exists at position 336 of SEQ ID NO:l and a serine exists at position 337 of SEQ ID NO:l.
  • SEQ ID NO:l Pseudomonas fluorescens
  • HPPD polypeptides according to present invention being tolerant to one or more HPPD inhibitor herbicides are equivalent to SEQ ID NO:l (Pseudomonas fluorescens) beside the amino acids being replaced according to present invention, i.e., the respective HPPD polypeptide is identical to SEQ ID NO:l but having amino acid exchanges at respective amino acid position(s) as defined in Table 2 (below).
  • the nucleotide sequence of the invention (including isolated, recombinant and chimeric genes thereof, vectors, host cells, plants, plant parts, and seeds comprising the nucleic acid sequence, amino acid sequences and compositions thereof encoded by the nucleic acid sequence, as well as methods of using the nucleic acid sequence for increasing tolerance of a plant to HPPD inhibitor herbicides, particularly increased tolerance to HPPD inhibitor herbicides of the class of triketones (preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole) hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3- yl)benz
  • Any suitable method for measuring tolerance to HPPD inhibitor herbicides can be used to evaluate the HPPD polypeptides of the invention.
  • Tolerance can be measured by monitoring the ability of a cell or organism to survive a particular HPPD inhibitor herbicide application, or the ability to carry out essential cellular functions such as photosynthesis, protein synthesis or respiration and reproduction in a manner that is not readily discernable from untreated cells or organisms, or the ability to have no significant difference in yield or even improved yield for plants treated with HPPD inhibitor herbicide compared to such plants not treated with such herbicide (but where weeds have been removed or prevented by a mechanism other than application of the HPPD inhibitor herbicide).
  • tolerance can be measured according to a visible indicator phenotype of the cell or organism transformed with a nucleic acid comprising the gene coding for the respective HPPD polypeptide, or in an in vitro assay of the HPPD polypeptide, in the presence of different concentrations of the various HPPD inhibitor herbicides.
  • Dose responses and relative shifts in dose responses associated with these indicator phenotypes are conveniently expressed in terms, for example, of GR50 (concentration for 50% reduction of growth) or MIC (minimum inhibitory concentration) values where increases in values correspond to increases in inherent tolerance of the expressed HPPD polypeptide, in the normal manner based upon plant damage, meristematic bleaching symptoms etc. at a range of different concentrations of herbicides.
  • GR50 values derived from dose/response curves having "dose” plotted on the x-axis and “percentage kill", “herbicidal effect”, “numbers of emerging green plants” etc. plotted on the y-axis where increased GR50 values correspond to increased levels of inherent tolerance of the expressed HPPD polypeptide.
  • Herbicides can suitably be applied pre-emergence or post emergence.
  • tolerance level of the nucleic acid or gene encoding an HPPD polypeptide according to the invention, or the HPPD polypeptide of the invention can be screened via transgenesis, regeneration, breeding and spray testing of a test plant such as tobacco, or a crop plant such as soybean, corn, or cotton.
  • a test plant such as tobacco, or a crop plant such as soybean, corn, or cotton.
  • such plants are more tolerant, desirably tolerant to at least 2 times the normal dose recommended for field applications, even more preferably tolerant up to 4 times the normal dose recommended for field applications, to HPPD inhibitor herbicides (e.g.
  • HPPD inhibitor herbicides of the class of triketones preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole), hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3-yl)benzamides, N-(l ,3,4- oxadiazol-2-yl)benzamides (preferably 2-methyl-N-(5-methyl-l,3,4-oxadiazol-2-yl)-3-(methylsulfonyl)- 4-(trifluoromethyl)benzamide, N-(tetrazol-5-yl)- or N-(triazol-5-yl)arylcar
  • the term “capable of increasing the tolerance of a plant to at least one herbicide acting on HPPD” denotes a tolerance by the plant expressing the HPPD of the invention to at least lx, 2x, or 3x, or 4x, or greater, the normal field dose of the HPPD inhibitor herbicide as compared to a plant only expressing its endogenous HPPD or a plant expressing a reference HPPD polypeptide.
  • the term “herbicide acting on HPPD” is not limited to substances which are known and/or used as herbicides but to any substances which inhibit the catalytic activity of HPPD polypeptides.
  • herbicide tolerance means also the ability of an enzyme to perform its respective catalytic reaction in the presence of an inhibitor / herbicide or after an exposition to an inhibitor/herbicide.
  • the herbicide tolerance of enzymes i.e. their ability to resist the inhibitory effect of the herbicide, can be expressed qualitatively and quantitatively. Qualitatively, enzymes that tolerate different entities or even different classes of inhibitors have a high tolerance and vice versa.
  • the tolerance of an enzyme compared to one herbicide can be expressed as the respective "residual activity” or “residual turnover” observed in one sample of this enzyme calculated as ratio of activities (ka PP , kinetic measure) or total substrate turnover (change in signal, endpoint measurement) in the absence and presence of one inhibitor (Bergmeyer, H.U.:
  • the apparent kinetic constant (ka PP ) of the determined substrate conversion can be measured as kinetic changes in absorbance at 320 nm in a coupled assay, in that homogentisate (HGA) formed by HPPD from HPP is directly converted into the well absorbing molecule maleylacetoacetate (MAA) by a second enzyme homogentisate dioxygenase (HGD), applied in excess uniformly in all assays.
  • HGA homogentisate
  • MAA molecule maleylacetoacetate
  • HSD homogentisate dioxygenase
  • a competitive inhibitor exhibits an apparent increase in kM and thereby a reciprocal decrease in k app at non-saturating substrate concentrations.
  • both k app measurements in the presence and absence of inhibitor are performed by use of the identical enzyme sample, raw or purified, and thereby at the same enzyme concentration, the enzyme
  • HPPD polypeptide sequences of the invention is a colorimetric assay (as described, for example, see US 6,768,044).
  • HPPDx means any gene coding for a putative HPPD polypeptide; basic vector "pSE420” was obtained from Invitrogen Düsseldorf, Germany) or a modified version of pSE420 (pSE420(RI)NX)-HPPDx are producing soluble melaninlike pigments from the tyrosine catabolism when the overexpressed HPPD polypeptide is active.
  • These melanin- like pigments are assayed in a liquid culture or by applying E. coli culture on LB-broth type solid agar . After 16 hours to 8 days at 20-30°C, the culture medium or agar wells which have been inoculated with an E. coli culture containing the empty vector pSE420 do not alter the color of the medium, or those which have been seeded with an E. coli culture containing a vector pSE420-HPPDx containing a gene coding for an inactive HPPD also do not alter the color of the medium, while the wells inoculated with an E. coli culture containing the vector pSE420-HPPDx coding for an active HPPD are brownish.
  • the replacement can be effected in the nucleic acid sequence which encodes the reference HPPD polypeptide as defined above by any means which is appropriate for replacing, in the said sequence, the codon which encodes the amino acid to be replaced with the codon which corresponds to the amino acid which is to replace it, with the said codons being widely described in the literature and well known to the skilled person.
  • a useful method for preparing a mutated nucleic acid sequence according to the invention and the corresponding protein comprises carrying out site-directed mutagenesis on codons encoding one or more amino acids which are selected in advance.
  • the methods for obtaining these site-directed mutations are well known to the skilled person and widely described in the literature (in particular: Directed Mutagenesis: A Practical Approach, 1991, Edited by M.J. McPHERSON, IRL PRESS), or are methods for which it is possible to employ commercial kits (for example the QUIKCHANGETM lightening mutagenesis kit from Qiagen or Stratagene).
  • the site-directed mutagenesis it is useful to select the cells which contain a mutated HPPD which is less sensitive to an HPPD inhibitor by using an appropriate screening aid. Appropriate screening methods to achieve this have been described above.
  • a DNA sequence encoding the reference HPPD polypeptide can be modified in silico to encode an HPPD polypeptide having one or more of the substitutions recited herein, and then synthesized de novo. This method is also well known in the art, described in the literature.
  • the nucleotide sequence encoding the mutated HPPD polypeptide can be introduced into a host cell as described elsewhere herein.
  • the present invention comprises isolated or recombinant
  • polynucleotide corresponds to any genetic material of any length and any sequence, comprising single-stranded and double-stranded DNA and RNA molecules, including regulatory elements, structural genes, groups of genes, plasmids, whole genomes, and fragments thereof.
  • a "recombinant" polynucleotide or polypeptide/protein, or biologically active portion thereof, as defined herein is no longer present in its original, native organism, such as when contained in a heterologous host cell or in a transgenic plant cell, seed or plant.
  • a recombinant polynucleotide is free of sequences (for example, protein encoding or regulatory sequences) that naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the polynucleotide is derived.
  • the term "recombinant” encompasses polynucleotides or polypeptides that have been manipulated with respect to the native polynucleotide or polypeptide, such that the polynucleotide or polypeptide differs (e.g., in chemical composition or structure) from what is occurring in nature.
  • a "recombinant" polynucleotide is free of internal sequences (i.e. introns) that naturally occur in the genomic DNA of the organism from which the polynucleotide is derived.
  • a typical example of such polynucleotide is a so- called Complementary DNA (cDNA).
  • the isolated HPPD inhibitor herbicide tolerance-encoding 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 flanks the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived.
  • Nucleic acid molecules of the invention include those that encode the HPPD of the invention.
  • the nucleic acid molecule of the invention is operably linked to a promoter capable of directing expression of the nucleic acid molecule in a host cell (e.g., a plant host cell or a bacterial host cell).
  • the present invention further contemplates exemplary variants and fragments of any nucleic acid sequence encoding the amino acid sequences set forth in any of SEQ ID NO:2 to NO:69.
  • a "fragment" of a polynucleotide may encode a biologically active portion of a polypeptide, or it may be a fragment that can be used as a hybridization probe or PCR primer using methods disclosed elsewhere herein.
  • Polynucleotides that are fragments of a polynucleotide comprise at least about 15, 20, 50, 75,
  • contiguous nucleotides are intended nucleotide residues that are immediately adjacent to one another.
  • Fragments of the polynucleotides of the present invention generally will encode polypeptide fragments that retain the biological activity of the full-length HPPD inhibitor herbicide tolerance protein; i.e., herbicide-tolerance activity.
  • herbicide-tolerance activity By "retains herbicide tolerance activity” is intended that the fragment will have at least about 30%, at least about 50%, at least about 70%, at least about 80%, 85%, 90%, 95%, 100%, 110%, 125%, 150%, 175%, 200%, 250%, at least about 300% or greater of the herbicide tolerance activity of the full-length HPPD inhibitor herbicide tolerance protein disclosed herein as SEQ ID NO:2 to NO:69. Methods for measuring herbicide tolerance activity are well known in the art and exemplary methods are described herein.
  • a fragment of the invention will be tolerant to the same dose of an HPPD inhibitor herbicide, or tolerant to lx, 2x, 3x, 4x, or higher dose of an HPPD inhibitor herbicide, or the fragments will be as or more tolerant based on ki between the fragment and SEQ ID NO:2 to NO:69.
  • a fragment of a polynucleotide that encodes a biologically active portion of a polypeptide of the invention will encode at least about 150, 175, 200, 250, 300, 350 contiguous amino acids, or up to the total number of amino acids present in a full-length polypeptide of the invention.
  • a fragment of a polynucleotide that encodes a biologically active portion of an HPPD polypeptide having (a) a glutamine or a lysine at the amino acid position corresponding to amino acid position 315 of SEQ ID NO:l, (b) a proline at the amino acid position corresponding to amino acid position 335 of SEQ ID NO: l,
  • the invention also encompasses variant polynucleotides as described supra. "Variants" of the polynucleotide also include those sequences that encode the HPPD of the invention but that differ conservatively because of the degeneracy of the genetic code, as well as those that are sufficiently identical. Variants of the present invention will retain HPPD polypeptide activity and HPPD herbicide inhibitor tolerance.
  • polypeptide or polynucleotide sequence that has at least about 53%, at least about 60% or 65% sequence identity, about 70% or 75% sequence identity, about 80% or 85% sequence identity, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%), 98%) or 99% sequence identity compared to a reference sequence using one of the alignment programs using standard parameters.
  • sequence identity compared to a reference sequence using one of the alignment programs using standard parameters.
  • polynucleotides by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like.
  • Bacterial genes quite often possess multiple methionine initiation codons in proximity to the start of the open reading frame. Often, translation initiation at one or more of these start codons will lead to generation of a functional protein. These start codons can include ATG codons. However, bacteria such as Bacillus sp. also recognize the codon GTG as a start codon, and proteins that initiate translation at GTG codons contain a methionine at the first amino acid. Furthermore, it is not often determined a priori which of these codons are used naturally in the bacterium.
  • variants that confer herbicide tolerance.
  • These herbicide tolerance proteins are encompassed in the present invention and may be used in the methods of the present invention.
  • Naturally occurring allelic variants can be identified with the use of well-known molecular biology techniques, such as polymerase chain reaction (PCR) and hybridization techniques as outlined below.
  • Variant polynucleotides also include synthetically derived polynucleotides that have been generated, for example, by using site-directed or other mutagenesis strategies but which still encode the polypeptide having the desired biological activity.
  • variant isolated polynucleotides can be created by introducing one or more additional nucleotide substitutions, additions, or deletions into the corresponding polynucleotide encoding the HPPD of the invention, such that 3-5, 1- 7, 1-9, 1-11, 1-13, 1-15, or 1-17 amino acid substitutions, additions or deletions, or 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 amino acid substitutions, additions or deletions, are introduced into the encoded polypeptide.
  • Further mutations can be introduced by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis, or gene shuffling techniques. Such variant polynucleotides are also encompassed by the present invention.
  • Variant polynucleotides can be made by introducing mutations randomly along all or part of the coding sequence, such as by saturation mutagenesis or permutational mutagenesis, and the resultant mutants can be screened for the ability to confer herbicide tolerance activity to identify mutants that retain activity.
  • Additional methods for generating variants include subjecting a cell expressing a protein disclosed herein (or library thereof) to a specific condition that creates a stress to the activity of the protein.
  • Specific conditions can include (but are not limited to) changes in temperature, changes in pH, changes in the concentrations of substrates or inhibitors, and changes in the buffer composition or their concentrations.
  • the protein library can be subjected to these conditions during the time of protein expression (e.g. in E. coli or other host) or following creation of a protein extract, or following protein purification.
  • the functional or enzymatic activity of the protein library that has been subjected to a stress condition can then be compared to the reference protein to identify proteins with improved properties.
  • This activity comparison can be carried out as part of a growth screen or alternatively as part of an enzymatic assay that quantifies the activity of the protein.
  • the properties that can be identified as improved can include HPPD inhibitor herbicide tolerance, changes in kinetic constants (including KM, Ki, kcat), protein stability, protein thermostability, or protein temperature and pH optimum.
  • Herbicide tolerance polypeptides are also encompassed within the present invention.
  • a herbicide tolerance polypeptide includes preparations of polypeptides having less than about 30%, 20%, 10%), or 5% (by dry weight) of non-herbicide tolerance polypeptide (also referred to herein as a "contaminating protein").
  • contaminating protein also referred to herein as a "contaminating protein”
  • herbicide tolerance protein is intended an HPPD polypeptide disclosed herein. Fragments, biologically active portions, and variants thereof are also provided, and may be used to practice the methods of the present invention.
  • “Fragments” or “biologically active portions” include polypeptide fragments comprising a portion of an amino acid sequence encoding an herbicide tolerance protein and that retains herbicide tolerance activity.
  • a biologically active portion of an herbicide tolerance protein can be a polypeptide that is, for example, 10, 25, 50, 100 or more amino acids in length. Such biologically active portions can be prepared by recombinant techniques and evaluated for herbicide tolerance activity.
  • variants proteins or polypeptides having an amino acid sequence that is at least about 53%, 60%, 65%, about 70%, 75%, about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any of the exemplary SEQ ID NO:2 to NO:69, wherein said variant has HPPD polypeptide activity and HPPD inhibitor herbicide tolerance.
  • HPPD polypeptide activity HPPD polypeptide activity and HPPD inhibitor herbicide tolerance.
  • conservative amino acid substitutions may be made at one or more nonessential amino acid residues.
  • a “nonessential” amino acid residue is a residue that can be altered from the reference sequence of a polypeptide without altering the biological activity, whereas an "essential” amino acid residue is required for biological activity.
  • a “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain.
  • Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g. lysine, arginine, histidine), acidic side chains (e.g. aspartic acid, glutamic acid), uncharged polar side chains (e.g. glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g. alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g. threonine, valine, isoleucine) and aromatic side chains (e.g.
  • basic side chains e.g. lysine, arginine, histidine
  • acidic side chains e.g. aspartic acid, glutamic acid
  • uncharged polar side chains e.g. glycine, as
  • amino acid substitutions may be made in non-conserved regions that retain function. In general, such substitutions would not be made for conserved amino acid residues, or for amino acid residues residing within a conserved motif, where such residues are essential for polypeptide activity. However, one of skill in the art would understand that functional variants may have minor conserved or non-conserved alterations in the conserved residues.
  • Antibodies to the HPPD of the present invention, or to variants or fragments thereof, are also encompassed.
  • Methods for producing antibodies are well known in the art (see, for example, Harlow and Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY; U.S. Patent No. 4,196,265).
  • one aspect of the invention concerns antibodies, single-chain antigen binding molecules, or other proteins that specifically bind to one or more of the protein or peptide molecules of the invention and their homologs, fusions or fragments.
  • the antibody specifically binds to a protein having the amino acid sequence set forth in SEQ ID NO:2 to NO:69 or a fragment thereof.
  • Antibodies of the invention may be used to quantitatively or qualitatively detect the protein or peptide molecules of the invention, or to detect post translational modifications of the proteins.
  • an antibody or peptide is said to "specifically bind" to a protein or peptide molecule of the invention if such binding is not competitively inhibited by the presence of non-related molecules.
  • weeds unwanted plants
  • An ideal treatment would be one which could be applied to an entire field but which would eliminate only the unwanted plants while leaving the crop plants unaffected.
  • One such treatment system would involve the use of crop plants which are tolerant to an herbicide so that when the herbicide is sprayed on a field of herbicide-tolerant crop plants, the crop plants would continue to thrive while non-herbicide-tolerant weeds are killed or severely damaged.
  • such treatment systems would take advantage of varying herbicide properties so that weed control could provide the best possible combination of flexibility and economy.
  • herbicides have different longevities in the field, and some herbicides persist and are effective for a relatively long time after they are applied to a field while other herbicides are quickly broken down into other and/or non-active compounds.
  • An ideal treatment system would allow the use of different herbicides so that growers could tailor the choice of herbicides for a particular situation.
  • HPPD protein or nucleotide sequence of the invention is advantageously combined in plants with other genes which encode proteins or RNAs that confer useful agronomic properties to such plants.
  • genes which encode proteins or RNAs that confer useful agronomic properties on the transformed plants mention can be made of the DNA sequences encoding proteins which confer tolerance to one or more herbicides that, according to their chemical structure, differ from HPPD inhibitor herbicides, and others which confer tolerance to certain insects, those which confer tolerance to certain diseases, DNAs that encodes RNAs that provide nematode or insect control, and the like.
  • EPSPS EPSPS which confer tolerance to the herbicides which have EPSPS as a target
  • sequence encoding these enzymes is advantageously preceded by a sequence encoding a transit peptide, in particular the "optimized transit peptide" described in US Patent 5,510,471 or 5,633,448.
  • Exemplary herbicide tolerance traits that can be combined with the nucleic acid sequence of the invention further include at least one ALS (acetolactate synthase) inhibitor (WO2007/024782); a mutated Arabidopsis ALS/AHAS gene (U.S. Patent 6,855,533); genes encoding 2,4-D-monooxygenases conferring tolerance to 2,4-D (2,4-dichlorophenoxyacetic acid) by metabolization (U.S. Patent
  • the HPPD of the invention is stacked with one or more herbicide tolerant genes, including one or more additional HPPD inhibitor herbicide tolerant genes, and/or one or more genes tolerant to glyphosate and/or glufosinate. In one embodiment, the HPPD of the invention is combined with 2mEPSPS and bar.
  • the CrylA-type proteins or toxic fragments thereof preferably the Cryl Ac protein or hybrids derived from the Cryl Ac protein (e.g., the hybrid Cryl Ab-Cryl Ac protein described in US 5,880,275) or the Cryl Ab or Bt2 protein or insecticidal fragments thereof as described in EP451878, the Cry2Ae, Cry2Af or Cry2Ag proteins as described in WO2002/057664 or toxic fragments thereof, the CrylA.105 protein described in WO 2007/140256 (SEQ ID No.
  • Photorhabdus as described in WO98/08932 e.g., Waterfield et al., 2001, Appl Environ Microbiol. 67(11):5017-24; Ffrench-Constant and Bowen, 2000, Cell Mol Life Sci.; 57(5):828-33.
  • any variants or mutants of any one of these proteins differing in some (1-10, preferably 1-5) amino acids from any of the above sequences, particularly the sequence of their toxic fragment, or which are fused to a transit peptide, such as a plastid transit peptide, or another protein or peptide, is included herein.
  • the HPPD sequence of the invention can be combined in plants with one or more genes conferring a desirable trait, such as herbicide tolerance, insect tolerance, drought tolerance, nematode control, water use efficiency, nitrogen use efficiency, improved nutritional value, disease resistance, improved photosynthesis, improved fiber quality, stress tolerance, improved reproduction, and the like.
  • a desirable trait such as herbicide tolerance, insect tolerance, drought tolerance, nematode control, water use efficiency, nitrogen use efficiency, improved nutritional value, disease resistance, improved photosynthesis, improved fiber quality, stress tolerance, improved reproduction, and the like.
  • Particularly useful transgenic events which may be combined with the genes of the current invention in plants of the same species (e.g., by crossing or by re-transforming a plant containing another transgenic event with a chimeric gene of the invention), include Event 531/ PV-GHBK04 (cotton, insect control, described in WO2002/040677), Event 1143-14A (cotton, insect control, not deposited, described in WO2006/128569); Event 1143-51B (cotton, insect control, not deposited, described in WO2006/128570); Event 1445 (cotton, herbicide tolerance, not deposited, described in US- A 2002-120964 or WO2002/034946Event 17053 (rice, herbicide tolerance, deposited as PTA-9843, described in WO2010/117737); Event 17314 (rice, herbicide tolerance, deposited as PTA-9844, described in WO2010/117735); Event 281-24-236 (cotton, insect control - herbicide tolerance, deposited as PTA-6233, described in
  • Event B16 corn, herbicide tolerance, not deposited, described in US-A 2003- 126634
  • Event BPS-CV127-9 soybean, herbicide tolerance, deposited as NCIMB No. 41603, described in WO2010/080829
  • Event BLR1 oileed rape, restoration of male sterility, deposited as NCIMB 41193, described in WO2005/074671
  • Event CE43-67B cotton, insect control, deposited as DSM ACC2724, described in US-A 2009-217423 or WO2006/128573
  • Event CE44-69D cotton, insect control, not deposited, described in US-A 2010-0024077
  • Event CE44-69D cotton, insect control, not deposited, described in WO2006/128571
  • Event CE46-02A cotton, insect control, not deposited, described in WO2006/128572
  • Event COT102 cotton, insect control, not deposited, described in US-A 2006-130175 or
  • Event MON87460 corn, stress tolerance, deposited as ATCC PTA-8910, described in WO2009/111263 or US-A 2011-0138504; Event MON87701 (soybean, insect control, deposited as ATCC PTA-8194, described in US-A 2009-130071 or WO2009/064652); Event MON87705 (soybean, quality trait - herbicide tolerance, deposited as ATCC PTA-9241, described in US-A 2010-0080887 or WO2010/037016); Event MON87708 (soybean, herbicide tolerance, deposited as ATCC PTA-9670, described in WO2011/034704); Event MON87712 (soybean, yield, deposited as PTA-10296, described in WO2012/051199), Event MON87754 (soybean, quality trait, deposited as ATCC PTA-9385, described in WO2010/024976); Event MON87769 (
  • Event MON88017 corn, insect control - herbicide tolerance, deposited as ATCC PTA-5582, described in US-A 2008-028482 or
  • Event MON88913 cotton, herbicide tolerance, deposited as ATCC PTA-4854, described in WO2004/072235 or US-A 2006-059590
  • Event MON88302 (oilseed rape, herbicide tolerance, deposited as PTA-10955, described in WO2011/153186)
  • Event MON88701 cotton, herbicide tolerance, deposited as PTA-11754, described in WO2012/134808)
  • Event MON89034 corn, insect control, deposited as ATCC PTA-7455, described in WO 2007/140256 or US-A 2008-260932)
  • Event MON89788 sibean, herbicide tolerance, deposited as ATCC PTA-6708, described in US-A 2006-282915 or WO2006/130436
  • Event MSI 1 (oilseed rape, pollination control - herbicide tolerance, deposited as ATCC PTA-850 or PTA-2485, described in WO2001/031042)
  • Event MSI 1 (o
  • Event T304-40 cotton, insect control - herbicide tolerance, deposited as ATCC PTA-8171, described in US-A 2010-077501 or WO2008/122406); Event T342-142 (cotton, insect control, not deposited, described in WO2006/128568); Event TC1507 (corn, insect control - herbicide tolerance, not deposited, described in US-A 2005-039226 or WO2004/099447); Event VIP1034 (corn, insect control - herbicide tolerance, deposited as ATCC PTA-3925., described in WO2003/052073), Event 32316 (corn, insect control-herbicide tolerance, deposited as PTA-11507, described in
  • Event 4114 corn, insect control-herbicide tolerance, deposited as PTA-11506, described in WO2011/084621
  • event EE-GM3 / FG72 sibean, herbicide tolerance, ATCC Accession N° PTA-11041
  • event EE-GM2/LL55 optionally stacked with event EE-GM1/LL27 or event EE-GM2/LL55
  • event DAS-68416-4 sibean, herbicide tolerance, ATCC Accession N° PTA- 10442, WO2011/066360A1
  • event DAS-68416-4 sibean, herbicide tolerance, ATCC Accession N° PTA-10442, WO2011/066384A1
  • event DP-040416-8 corn, insect control, ATCC Accession N° PTA- 11508, WO2011/075593A1
  • event DP-043A47-3 corn, insect control, ATCC Accession N° PTA- 11509, WO2011/075595A1
  • event DP-004114-3 corn, insect control, ATCC Accession N° PTA-
  • event DP-032316-8 corn, insect control, ATCC Accession N° PTA-
  • MON87411 (Maize, ATCC Accession N° PTA-12669) WO2013169923, event A26-5 (Cotton, insect control) WO2013170398, event A2-6 (Cotton, insect control ) WO2013/170399, event 9582.816.15.1 (Soybean, insect control, herbicide tolerance), ATCC Accession N° PTA-12588) WO2014/004458, event 33121 (Maize, insect control, herbicide tolerance, ATCC Accession N° PTA-13392)
  • the polynucleotides encoding the HPPD polypeptides of the present invention may be modified to obtain or enhance expression in plant cells.
  • the polynucleotides encoding the polypeptides identified herein may be provided in expression cassettes for expression in the plant of interest.
  • a "plant expression cassette” includes a DNA construct, including a recombinant DNA construct, that is capable of resulting in the expression of a polynucleotide in a plant cell.
  • the cassette can include in the 5 '-3' direction of transcription, a transcriptional initiation region (i.e. promoter, particularly a heterologous promoter) operably- linked to one or more polynucleotides of interest, and/or a translation and transcriptional termination region (i.e.
  • the cassette may additionally contain at least one additional polynucleotide to be introduced into the organism, such as a selectable marker gene.
  • the additional polynucleotide(s) can be provided on multiple expression cassettes.
  • Such an expression cassette is provided with a plurality of restriction sites for insertion of the polynucleotide(s) to be under the transcriptional regulation of the regulatory regions.
  • the present invention relates to a chimeric gene comprising a coding sequence comprising heterologous the nucleic acid of the invention operably linked to a plant- expressible promoter and optionally a transcription termination and polyadenylation region.
  • Heterologous generally refers to the polynucleotide or polypeptide that is not endogenous to the cell or is not endogenous to the location in the native genome in which it is present, and has been added to the cell by infection, transfection, microinjection, electroporation, microprojection, or the like.
  • operably linked is intended a functional linkage between two polynucleotides. For example, when a promoter is operably linked to a DNA sequence, the promoter sequence initiates and mediates transcription of the DNA sequence. It is recognized that operably linked polynucleotides may or may not be contiguous and, where used to reference the joining of two polypeptide coding regions, the polypeptides are expressed in the same reading frame.
  • the promoter may be any polynucleotide sequence which shows transcriptional activity in the chosen plant cells, plant parts, or plants.
  • the promoter may be native or analogous, or foreign or heterologous, to the plant host and/or to the DNA sequence of the invention. Where the promoter is
  • the promoter is found in the native plant into which the promoter is introduced. Where the promoter is “foreign” or “heterologous” to the DNA sequence of the invention, it is intended that the promoter is not the native or naturally occurring promoter for the operably linked DNA sequence of the invention.
  • the promoter may be inducible or constitutive. It may be naturally- occurring, may be composed of portions of various naturally- occurring promoters, or may be partially or totally synthetic. Guidance for the design of promoters is provided by studies of promoter structure, such as that of Harley and Reynolds (1987) Nucleic Acids Res. 15:2343- 2361. Also, the location of the promoter relative to the transcription start may be optimized. See, e.g., Roberts et al. (1979) Proc. Natl. Acad. Sci. USA, 76:760-764. Many suitable promoters for use in plants are well known in the art.
  • suitable constitutive promoters for use in plants include: the promoters from plant viruses, such as the peanut chlorotic streak caulimovirus (PC1SV) promoter (U.S. Pat. No. 5,850,019); the 35S promoter from cauliflower mosaic virus (CaMV) (Odell et al. (1985) Nature 313:810-812); the 35S promoter described in Kay et al. (1987) Science 236: 1299-1302; promoters of Chlorella virus methyltransferase genes (U.S. Pat. No. 5,563,328) and the full-length transcript promoter from figwort mosaic virus (FMV) (U.S. Pat. No.
  • PC1SV peanut chlorotic streak caulimovirus
  • CaMV cauliflower mosaic virus
  • FMV figwort mosaic virus
  • Patent 5,510,474 maize H3 histone (Lepetit et al. (1992) Mol. Gen. Genet. 231 :276-285 and Atanassova et al. (1992) Plant J. 2(3):291-300); Brassica napus ALS3 (PCT application W097/41228); a plant ribulose-biscarboxylase/oxygenase (RuBisCO) small subunit gene; the circovirus (AU 689 311) or the Cassava vein mosaic virus (CsVMV, US 7,053,205); and promoters of various Agrobacterium genes (see U.S. Pat. Nos. 4,771,002; 5,102,796; 5,182,200; and 5,428,147).
  • Suitable inducible promoters for use in plants include: the promoter from the ACE1 system which responds to copper (Mett et al. (1993) PNAS 90:4567-4571); the promoter of the maize In2 gene which responds to benzenesulfonamide herbicide safeners (Hershey et al. (1991) Mol. Gen. Genetics 227:229-237 and Gatz et al. (1994) Mol. Gen. Genetics 243:32-38); and the promoter of the Tet repressor from TnlO (Gatz et al. (1991) Mol. Gen. Genet. 227:229-237).
  • Another inducible promoter for use in plants is one that responds to an inducing agent to which plants do not normally respond.
  • An exemplary inducible promoter of this type is the inducible promoter from a steroid hormone gene, the transcriptional activity of which is induced by a glucocorticosteroid hormone (Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421) or the recent application of a chimeric transcription activator, XVE, for use in an estrogen receptor-based inducible plant expression system activated by estradiol (Zuo et al. (2000) Plant J., 24:265-273).
  • inducible promoters for use in plants are described in EP 332104, WO 93/21334 and WO 97/06269 which are herein incorporated by reference in their entirety. Promoters composed of portions of other promoters and partially or totally synthetic promoters can also be used. See, e.g., Ni et al. (1995) Plant J. 7:661-676 and WO 95/14098 describing such promoters for use in plants.
  • a promoter sequence specific for particular regions or tissues of plants can be used to express the HPPD proteins of the invention, such as promoters specific for seeds (Datla, R. et al., 1997, Biotechnology Ann. Rev. 3, 269-296), especially the napin promoter (EP 255 378 Al), the phaseolin promoter, the glutenin promoter, the helianthinin promoter
  • an inducible promoter advantageously chosen from the phenylalanine ammonia lyase (PAL), HMG-CoA reductase (HMG), chitinase, glucanase, proteinase inhibitor (PI), PR1 family gene, nopaline synthase (nos) and vspB promoters (US 5,670,349, Table 3), the HMG2 promoter (US 5,670,349), the apple beta-galactosidase (ABG1) promoter and the apple aminocyclopropane carboxylate synthase (ACC synthase) promoter (W098/45445).
  • Multiple promoters can be used in the constructs of the invention, including in succession.
  • the promoter may include, or be modified to include, one or more enhancer elements.
  • the promoter may include a plurality of enhancer elements. Promoters containing enhancer elements provide for higher levels of transcription as compared to promoters that do not include them. Suitable enhancer elements for use in plants include the PC1SV enhancer element (U.S. Pat. No. 5,850,019), the CaMV 35S enhancer element (U.S. Pat. Nos. 5,106,739 and 5,164,316) and the FMV enhancer element (Maiti et al. (1997) Transgenic Res.
  • constructs can contain 5' and 3' untranslated regions.
  • Such constructs may contain a "signal sequence” or “leader sequence” to facilitate co-translational or post-translational transport of the peptide of interest to certain intracellular structures such as the chloroplast (or other plastid), endoplasmic reticulum, or Golgi apparatus, or to be secreted.
  • the construct can be engineered to contain a signal peptide to facilitate transfer of the peptide to the endoplasmic reticulum.
  • signal sequence is intended a sequence that is known or suspected to result in co-translational or post-translational peptide transport across the cell membrane.
  • leader sequence is intended any sequence that, when translated, results in an amino acid sequence sufficient to trigger co- translational transport of the peptide chain to a sub-cellular organelle.
  • leader sequences targeting transport and/or glycosylation by passage into the endoplasmic reticulum, passage to vacuoles, plastids including chloroplasts, mitochondria, and the like. It may also be preferable to engineer the plant expression cassette to contain an intron, such that mRNA processing of the intron is required for expression.
  • 3' untranslated region is intended a polynucleotide located downstream of a coding sequence.
  • Polyadenylation signal sequences and other sequences encoding regulatory signals capable of affecting the addition of polyadenylic acid tracts to the 3' end of the mRNA precursor are 3' untranslated regions.
  • 5' untranslated region is intended a polynucleotide located upstream of a coding sequence.
  • Enhancers are polynucleotides that act to increase the expression of a promoter region. Enhancers are well known in the art and include, but are not limited to, the SV40 enhancer region and the 35S enhancer element.
  • the termination region may be native with the transcriptional initiation region, may be native with the sequence of the present invention, or may be derived from another source.
  • Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141- 144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen ei a/. (1990) Plant Cell 2:1261-1272; Mumoc et al.
  • synthetic DNA sequences are designed for a given polypeptide, such as the polypeptides of the invention. Expression of the open reading frame of the synthetic DNA sequence in a cell results in production of the polypeptide of the invention.
  • Synthetic DNA sequences can be useful to simply remove unwanted restriction endonuclease sites, to facilitate DNA cloning strategies, to alter or remove any potential codon bias, to alter or improve GC content, to remove or alter alternate reading frames, and/or to alter or remove intron/exon splice recognition sites, polyadenylation sites, Shine-Delgarno sequences, unwanted promoter elements and the like that may be present in a native DNA sequence.
  • synthetic DNA sequences may be utilized to introduce other improvements to a DNA sequence, such as introduction of an intron sequence, creation of a DNA sequence that is expressed as a protein fusion to organelle targeting sequences, such as chloroplast transit peptides, apoplast/vacuolar targeting peptides, or peptide sequences that result in retention of the resulting peptide in the endoplasmic reticulum.
  • organelle targeting sequences such as chloroplast transit peptides, apoplast/vacuolar targeting peptides, or peptide sequences that result in retention of the resulting peptide in the endoplasmic reticulum.
  • Synthetic genes can also be synthesized using host cell- preferred codons for improved expression, or may be synthesized using codons at a host-preferred codon usage frequency. See, for example, Campbell and Gowri (1990) Plant Physiol. 92: 1-11 ; U.S. Patent Nos.
  • the polynucleotides of interest are targeted to the chloroplast for expression.
  • the expression cassette will additionally contain a polynucleotide encoding a transit peptide to direct the nucleotide of interest to the chloroplasts.
  • transit peptides are known in the art. See, for example, Von Heijne et al. (1991) Plant Mol. Biol. Rep. 9:104-126; Clark et al. (1989) J. Biol. Chem. 264:17544- 17550; Della-Cioppa et al. (1987) Plant Physiol. 84:965-968; Romer et al. (1993) Biochem. Biophys. Res. Commun. 196:1414-1421; and Shah et al. (1986) Science 233:478-481.
  • the polynucleotides of interest to be targeted to the chloroplast may be optimized for expression in the chloroplast to account for differences in codon usage between the plant nucleus and this organelle. In this manner, the polynucleotides of interest may be synthesized using chloroplast-preferred codons. See, for example, U.S. Patent No. 5,380,831, herein incorporated by reference.
  • This plant expression cassette can be inserted into a plant transformation vector.
  • transformation vector is intended a DNA molecule that allows for the transformation of a cell. Such a molecule may consist of one or more expression cassettes, and may be organized into more than one vector DNA molecule.
  • binary vectors are plant transformation vectors that utilize two noncontiguous DNA vectors to encode all requisite cis- and trans-acting functions for transformation of plant cells (Hellens and Mullineaux (2000) Trends in Plant Science 5:446-451).
  • Vector refers to a polynucleotide construct designed for transfer between different host cells.
  • Expression vector refers to a vector that has the ability to incorporate, integrate and express heterologous DNA sequences or fragments in a foreign cell.
  • the plant transformation vector comprises one or more DNA vectors for achieving plant transformation.
  • DNA vectors for achieving plant transformation.
  • These vectors are often referred to in the art as binary vectors.
  • Binary vectors as well as vectors with helper plasmids are most often used for
  • Binary vectors typically contain a plasmid vector that contains the cis-acting sequences required for T-DNA transfer (such as left border and right border), a selectable marker that is engineered to be capable of expression in a plant cell, and a "polynucleotide of interest" (a polynucleotide engineered to be capable of expression in a plant cell for which generation of transgenic plants is desired). Also present on this plasmid vector are sequences required for bacterial replication.
  • the cis- acting sequences are arranged in a fashion to allow efficient transfer into plant cells and expression therein.
  • the selectable marker sequence and the sequence of interest are located between the left and right borders.
  • a second plasmid vector contains the trans-acting factors that mediate T- DNA transfer from Agrobacterium to plant cells.
  • This plasmid often contains the virulence functions (Vir genes) that allow infection of plant cells by Agrobacterium, and transfer of DNA by cleavage at border sequences and vir-mediated DNA transfer, as is understood in the art (Hellens and Mullineaux (2000) Trends in Plant Science, 5:446-451).
  • Agrobacterium strains e.g., LBA4404, GV3101, EHA101, EHA105, etc.
  • the second plasmid vector is not necessary for introduction of polynucleotides into plants by other methods such as microprojection, microinjection, electroporation, polyethylene glycol, etc.
  • Methods of the invention involve introducing a nucleotide construct into a plant.
  • introducing is intended to present to the plant the nucleotide construct in such a manner that the construct gains access to the interior of a cell of the plant.
  • the methods of the invention do not require that a particular method for introducing a nucleotide construct to a plant is used, only that the nucleotide construct gains access to the interior of at least one cell of the plant.
  • Methods for introducing nucleotide constructs into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods. See, for example, the methods for transforming plant cells and regenerating plants described in: US 4,459,355, US 4,536,475,
  • WO2012/015039A1 WO2012/019660A1
  • WO2012/021494A1 WO2012/064827A1
  • WO2013/033308A2 WO2013/066007A1, WO2013/077420A1, WO2013/090734A1,
  • WO2014/200842A2 WO2015/051083A1, WO2015/077620A1, WO2015/085990A1,
  • plant transformation methods involve transferring heterologous DNA into target plant cells (e.g. immature or mature embryos, suspension cultures, undifferentiated callus, protoplasts, etc.), followed by applying a maximum threshold level of appropriate selection (depending on the selectable marker gene) to recover the transformed plant cells from a group of untransformed cell mass. Explants are typically transferred to a fresh supply of the same medium and cultured routinely.
  • the transformed cells are differentiated into shoots after placing on regeneration medium supplemented with a maximum threshold level of selecting agent.
  • the shoots are then transferred to a selective rooting medium for recovering rooted shoot or plantlet.
  • the transgenic plantlet then grow into mature plants and produce fertile seeds (e.g. Hiei et al. (1994) The Plant Journal 6:271-282; Ishida et al. (1996) Nature Biotechnology 14:745-750). Explants are typically transferred to a fresh supply of the same medium and cultured routinely.
  • Transgenic plants may be performed by one of several methods, including, but not limited to, introduction of heterologous DNA by Agrobacterium into plant cells (Agrobacterium- mediated transformation), bombardment of plant cells with heterologous foreign DNA adhered to particles, and various other non-particle direct-mediated methods (e.g. Hiei et al. (1994) The Plant Journal 6:271-282; Ishida et al. (1996) Nature Biotechnology 14:745-750; Ayres and Park (1994) Critical Reviews in Plant Science 13:219-239; Bommineni and Jauhar (1997) Maydica 42:107-120) to transfer DNA.
  • Agrobacterium- mediated transformation introduction of heterologous DNA by Agrobacterium into plant cells
  • bombardment of plant cells with heterologous foreign DNA adhered to particles and various other non-particle direct-mediated methods (e.g. Hiei et al. (1994) The Plant Journal 6:271-282; Ishida et al. (1996) Nature Biotechnology 14:745-7
  • plastid transformation can be accomplished by transactivation of a silent plastid-borne transgene by tissue-preferred expression of a nuclear-encoded and plastid- directed RNA polymerase.
  • tissue-preferred expression of a nuclear-encoded and plastid- directed RNA polymerase Such a system has been reported in McBride et al. (1994) Proc. Natl. Acad. Sci. USA 91 :7301-7305.
  • the plant 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 hybrid 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.
  • the present invention provides transformed seed (also referred to as "transgenic seed") having a nucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • the seed can be coated with at least one fungicide and/or at least one insecticide, at least one herbicide, and/or at least one safener, or any combination thereof.
  • heterologous foreign DNA Following introduction of heterologous foreign DNA into plant cells, the transformation or integration of the heterologous gene in the plant genome is confirmed by various methods such as analysis of nucleic acids, proteins and metabolites associated with the integrated gene.
  • PCR analysis is a rapid method to screen transformed cells, tissue or shoots for the presence of incorporated gene at the earlier stage before transplanting into the soil (Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY)). PCR is carried out using oligonucleotide primers specific to the gene of interest or Agrobacterium vector background, etc.
  • Plant transformation may be confirmed by Southern blot analysis of genomic DNA (Sambrook and Russell (2001) supra).
  • total DNA is extracted from the transformant, digested with appropriate restriction enzymes, fractionated in an agarose gel and transferred to a nitrocellulose or nylon membrane.
  • the membrane or "blot" can then be probed with, for example, radiolabeled 32 P target DNA fragment to confirm the integration of the introduced gene in the plant genome according to standard techniques (Sambrook and Russell, 2001, supra).
  • RNA is isolated from specific tissues of transformant, fractionated in a formaldehyde agarose gel, and blotted onto a nylon filter according to standard procedures that are routinely used in the art (Sambrook and Russell (2001) supra). Expression of RNA encoded by nucleotide sequences of the invention is then tested by hybridizing the filter to a radioactive probe derived by methods known in the art (Sambrook and Russell (2001) supra). RNA can also be detected and/or quantified using reverse transcriptase PCR as known in the art (e.g., Green and Sambrook (2012) Molecular Cloning: A Laboratory Manual, 4 th Edition, Cold Spring Harbor Laboratory Press,
  • Western blot, ELISA, lateral flow testing, and biochemical assays and the like may be carried out on the transgenic plants to determine the presence of protein encoded by the herbicide tolerance gene by standard procedures (Sambrook and Russell (2001) supra) using antibodies that bind to one or more epitopes present on the herbicide tolerance protein.
  • the HPPD genes described herein are useful as markers to assess transformation of bacterial or plant cells.
  • the invention also relates to the use, in a method for transforming plants, of a nucleic acid which encodes an HPPD according to the invention as a marker gene or as a coding sequence which makes it possible to confer to the plant tolerance to herbicides which are HPPD inhibitors, and the use of one or more HPPD inhibitor(s) on plants comprising a nucleic acid sequence encoding an HPPD according to the invention.
  • a nucleic acid which encodes an HPPD according to the invention as a marker gene or as a coding sequence which makes it possible to confer to the plant tolerance to herbicides which are HPPD inhibitors
  • one or more HPPD inhibitor(s) on plants comprising a nucleic acid sequence encoding an HPPD according to the invention.
  • an HPPD inhibitor can be introduced into the culture medium of the competent plant cells so as to bleach said cells before the transformation step.
  • the bleached competent cells are then transformed with the gene for tolerance to HPPD inhibitors, as a selection marker, and the transformed cells which have integrated said selection marker into their genome become green, enabling them to be selected.
  • Such a process makes it possible to decrease the time required for selecting the transformed cells.
  • one embodiment of the present invention consists of a method for transforming plant cells by introducing a heterologous gene into said plant cells with a gene for tolerance to HPPD inhibitors as selection markers, wherein the method comprises preparing and culturing competent plant cells capable of receiving the heterologous gene in a suitable medium and introducing a suitable amount of HPPD inhibitor into the suitable culture medium of the competent plant cells.
  • the competent cells are then transformed with the heterologous gene and the selection marker, and the transformed cells comprising the heterologous gene are grown in a suitable medium and transformants selected therefrom.
  • the transformed cells can then be regenerated into a fertile transformed plant.
  • plant is intended whole plants, plant organs (e.g., leaves, stems, roots, etc.), seeds, plant cells, propagules, embryos and progeny of the same.
  • Plant cells can be differentiated or undifferentiated (e.g., callus, suspension culture cells, protoplasts, leaf cells, root cells, phloem cells, pollen).
  • the present invention may be used for introduction of polynucleotides into any plant species, including, but not limited to, monocots and dicots.
  • plants of interest include, but are not limited to, corn (maize), sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugar beet, sugarcane, tobacco, barley, and oilseed rape, Brassica sp., alfalfa, rye, millet, safflower, peanuts, sweet potato, cassava, coffee, coconut, pineapple, citrus trees, cocoa, tea, banana, avocado, fig, guava, mango, olive, papaya, cashew, macadamia, almond, oats, vegetables, ornamentals, and conifers.
  • Vegetables include, but are not limited to tomatoes, lettuce, green beans, lima beans, peas, and members of the genus Curcumis such as cucumber, cantaloupe, and musk melon. Ornamentals include, but are not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum Crop plants are also of interest, including, for example, maize, sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugar beet, sugarcane, tobacco, barley, oilseed rape, etc.
  • This invention is suitable for any member of the monocot plant family including, but not limited to, maize, rice, barley, oats, wheat, sorghum, rye, sugarcane, pineapple, yams, onion, banana, coconut, and dates.
  • the methods comprise providing a plant comprising, or introducing into a plant or plant cell, a polynucleotide comprising a nucleotide sequence encoding an HPPD of the invention, growing the plant or a seed thereof in a field, and producing a harvest from said plants or seeds.
  • the “yield” of the plant refers to the quality and/or quantity of biomass produced by the plant.
  • biomass is intended any measured plant product.
  • An increase in biomass production is any improvement in the yield of the measured plant product.
  • increasing plant yield has several commercial applications. For example, increasing plant leaf biomass may increase the yield of leafy vegetables for human or animal consumption. Additionally, increasing leaf biomass can be used to increase production of plant-derived pharmaceutical or industrial products.
  • An increase in yield can comprise any statistically significant increase including, but not limited to, at least a 1% increase, at least a 3% increase, at least a 5% increase, at least a 10% increase, at least a 20%> increase, at least a 30%>, at least a 50%, at least a 70%, at least a 100%) or a greater increase.
  • the plant comprising an HPPD sequence of the invention is treated with an effective concentration of an HPPD inhibitor herbicide, such as one or more HPPD inhibitor herbicide(s) selected from the group consisting of HPPD inhibitor herbicides of the class of triketones (preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole), hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3- yl)benzamides, N-(l ,3,4-oxadiazol-2-yl)benzamides (preferably 2-methyl-N-(5-methyl-l,3,4-oxadiazol- 2-yl)-3-(
  • Plants produced via this method can be treated with an effective concentration of an herbicide (such as one or more HPPD inhibitor herbicide(s) selected from the group consisting of HPPD inhibitor herbicides of the class of triketones (preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole), hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3- yl)benzamides, N-(l ,3,4-oxadiazol-2-yl)benzamides (preferably 2-methyl-N-(5-methyl-l,3,4-oxadiazol- 2-yl)-3 -(methylsulfonyl)-4
  • the present invention therefore also relates to a method of controlling undesired plants or for regulating the growth of plants in crops of plants comprising a nucleotide sequence encoding an HPPD polypeptide according to the invention, where one or more HPPD inhibitor herbicides, for example, one or more HPPD inhibitor herbicides selected from the class of triketones (preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole), hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3-yl)benzamides, N-(l ,3,4- oxadiazol-2-yl)benzamides (preferably 2-methyl-
  • an effective concentration of one or more HPPD inhibitor herbicide(s) for example, one or more HPPD inhibitor herbicides selected from the group consisting of HPPD inhibitor herbicides of the class of triketones (preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole), hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3-yl)benzamides, N-(l ,3,4-oxadiazol-2-yl)benzamides (preferably 2-methyl-N-(5-methyl-l,3,4-oxadiazol-2-yl)-3-(methylsulfonyl)-4-(triketones
  • pre-emergent and post-emergent are used with reference to a weed in an area of interest, and in some instances these terms are used with reference to a crop plant in an area of interest. When used with reference to a weed, these terms may apply to a particular type of weed or species of weed that is present or believed to be present in the area of interest.
  • Pre-plant incorporation of an herbicide involves the incorporation of compounds into the soil prior to planting.
  • the present invention comprises a method of controlling weeds in a field comprising planting in a field a plant or a seed thereof comprising an HPPD polypeptide of present invention and applying to said plant or area surrounding said plant an effective concentration of one or more HPPD inhibitor herbicides.
  • a field to be planted with plants (such as soybean, cotton, corn, or wheat plants, e.g.) containing an HPPD nucleotide sequence of the invention
  • plants such as soybean, cotton, corn, or wheat plants, e.g.
  • an HPPD inhibitor herbicide such as isoxaflutole (IFT)
  • IFT isoxaflutole
  • the residual activity of IFT will also protect the emerging and growing plants from competition by weeds in the early growth stages.
  • a field in which seeds containing an HPPD nucleotide sequence of the invention were sown can be treated with an HPPD inhibitor herbicide, such as IFT, before the plants emerge but after the seeds are sown (the field can be made weed- free before sowing using other means, typically conventional tillage practices such as ploughing, chissel ploughing, or seed bed preparation), where residual activity will keep the field free of weeds killed by the herbicide so that the emerging and growing plants have no competition by weeds (pre- emergence application of an HPPD inhibitor herbicide).
  • an HPPD inhibitor herbicide such as IFT
  • plants containing an HPPD nucleotide sequence of the invention can be treated with an HPPD inhibitor herbicide, over the top of the plants that have emerged from the seeds that were sown, which cleans the field of weeds killed by the HPPD inhibitor herbicide, which application can be together with (e.g., in a spray tank mix), followed by or preceded by a treatment with glyphosate or glufosinate as post-emergent herbicide over the top of the plants (post- emergence application of an HPPD inhibitor herbicide (with or without glyphosate)), when such plants are tolerant to such herbicides.
  • an HPPD inhibitor herbicide e.g., glyphosate or glufosinate
  • Examples of individual representatives of the monocotyledonous and dicotyledonous weeds which can be controlled with an HPPD inhibitor herbicide include:
  • Monocotyledonous harmful plants of the genera Aegilops, Agropyron, Agrostis, Alopecurus, Apera, Avena, Brachiaria, Bromus, Cenchrus, Commelina, Cynodon, Cyperus, Dactyloctenium, Digitaria, Echinochloa, Eleocharis, Eleusine, Eragrostis, Eriochloa, Festuca, Fimbristylis, Heteranthera, Imperata, Ischaemum, Leptochloa, Lolium, Monochoria, Panicum, Paspalum, Phalaris, Phleum, Poa, Rottboellia, Sagittaria, Scirpus, Setaria, Sorghum.
  • HPPD inhibitor herbicides useful in the present invention including but not limited to HPPD inhibitor herbicides of the class of triketones (preferably benzobicyclon, sulcotrione, mesotrione, tembotrione, tefuryltrione, bicyclopyrone, fenquinotrione), diketonitriles, isoxazoles (preferably isoxaflutole), hydroxypyrazoles (preferably pyrazoxyfen, benzofenap, pyrazolynate, pyrasulfotole, topramezone, tolpyralate), N-(l ,2,5-oxadiazol-3-yl)benzamides, N-(l ,3,4-oxadiazol-2-yl)benzamides (preferably 2-methyl-N-(5-methyl-l,3,4-oxadiazol-2-yl)-3-(methylsulfonyl)-4-
  • HPPD inhibitor herbicides of the class of triketones preferably benzobicyclon
  • WP wettable powders
  • SP water-soluble powders
  • EC emulsifiable concentrates
  • EW emulsions
  • SC suspension concentrates
  • CS oil- or water- based dispersions
  • DP dusts
  • seed-dressing products granules for application by broadcasting and on the soil
  • granules GR
  • WG water-dispersible granules
  • SG water-soluble granules
  • HPPD nucleotide sequence of the invention can be introduced into second plant by recurrent selection, backcrossing, pedigree breeding, line selection, mass selection, mutation breeding and/or genetic marker enhanced selection.
  • the methods of the invention comprise crossing a first plant comprising an HPPD nucleotide sequence of the invention with a second plant to produce Fl progeny plants and selecting Fl progeny plants that are tolerant to an HPPD inhibitor herbicide or that comprise the HPPD nucleotide sequence of the invention.
  • the methods may further comprise crossing the selected progeny plants with the first plant comprising the HPPD nucleotide sequence of the invention to produce backcross progeny plants and selecting backcross progeny plants that are tolerant to an HPPD inhibitor herbicide or that comprise the HPPD nucleotide sequence of the invention.
  • Methods for evaluating HPPD inhibitor herbicide tolerance are provided elsewhere herein.
  • the methods may further comprise repeating these steps one or more times in succession to produce selected second or higher backcross progeny plants that are tolerant to an HPPD inhibitor herbicide or that comprise the HPPD nucleotide sequence of the invention.
  • the Fl plants may be self-pollinated to produce a segregating F2 generation. Individual plants may then be selected which represent the desired phenotype (e.g., HPPD inhibitor herbicide tolerance) in each generation (F3, F4, F5, etc.) until the traits are homozygous or fixed within a breeding population.
  • desired phenotype e.g., HPPD inhibitor herbicide tolerance
  • the second plant can be a plant having a desired trait, such as herbicide tolerance, insect tolerance, drought tolerance, nematode control, water use efficiency, nitrogen use efficiency, improved nutritional value, disease resistance, improved photosynthesis, improved fiber quality, stress tolerance, improved reproduction, and the like.
  • the second plant may be an elite event as described elsewhere herein.
  • plant parts whole plants, plant organs (e.g., leaves, stems, roots, etc.), seeds, plant cells, propagules, embryos, and the like
  • N Methods of obtaining a plant product
  • the present invention also relates to a process for obtaining a commodity product, comprising harvesting and/or milling the grains from a crop comprising an HPPD sequence of the invention to obtain the commodity product.
  • a process for obtaining a commodity product comprising harvesting and/or milling the grains from a crop comprising an HPPD sequence of the invention to obtain the commodity product.
  • compositions of matter including but not limited to animal feed, commodities, and plant products and by-products that are intended for use as food for human consumption or for use in compositions and commodities that are intended for human consumption, particularly devitalized seed/grain products, including a (semi-)processed products produced from such grain/seeds, wherein said product is or comprises whole or processed seeds or grain, animal feed, corn or soy meal, corn or soy flour, corn, corn starch, soybean meal, soy flour, flakes, soy protein concentrate, soy protein isolates, texturized soy protein concentrate, cosmetics, hair care products, soy nut butter, natto, tempeh, hydrolyzed soy protein, whipped topping, shortening, lecithin, edible whole soybeans (raw, roasted, or as edamame), soy yogurt, soy cheese, tofu, yuba, as well as cooked, polished, steamed, baked or parboiled grain, and the like are intended to be within the scope of the present invention
  • Example 1 Creation of mutated HPPD polypeptides by site-directed mutagenesis
  • Example 3 HPPD enzyme assay to analyse mutant HPPD polypeptides with improved HPPD inhibitor herbicide tolerance
  • the Pseudomonas fluorescens HPPD nucleotide sequence (SEQ ID NO:70) as described in
  • WO2009/144079 encoding the HPPD polypeptide corresponding to SEQ ID NO: l was cloned according to well known methods in the art and as described in WO2014/043435. Subsequent site-saturated mutagenesis, site-directed mutagenesis and combinatorial variants with one or more mutations of the nucleic acid encoding sequence of wild-type PfHPPD polypeptide encoding the recombinant HPPD polypeptide corresponding to SEQ ID NO: 1 were carried out using standard PCR-based technologies well known in the art (and as described likewise in WO2014/043435). All designed and synthesized mutant clones were confirmed by DNA sequencing using plasmid specific oligonucleotides. Table 2, below, summarizes the exemplary mutant HPPD polypeptides (SEQ ID NO:2 to NO:69).
  • Table 2 Overview of exemplary amino acid exchanges corresponding to amino acid position in SEQ ID NO:l.
  • mutant HPPD polypeptides represented here are examples by a way of illustration, not by a way of limitation.
  • this starter culture were added to 600 ⁇ LB medium containing 100 ⁇ g/ml ampicillin and 150 mM Hepes (Merck, Darmstadt, Germany) as inoculum for the expression culture in 96 well plates (2 ml deep wells; HJ Bioanalytik, Erkelenz, Germany).
  • the plates were sealed by an aluminium foil, and cells were incubated for 5 h at 37°C on a plate shaker at 750 rpm.
  • the expression was induced by addition of IPTG in a final concentration of 1 mM followed by further sealed incubation for about 18 h at 30°C on a plate shaker at 750 rpm.
  • HPPD polypeptides The activity of HPPD polypeptides was determined in absence or presence of HPPD inhibitors using the coupled HPPD activity assay ( Figure 1).
  • the apparent kinetic constant (k app ) of the determined substrate conversion was measured as kinetic changes in absorbance (OD) at 320 nm in a coupled assay, in that homogentisate (HGA) formed by HPPD from HPP is directly converted into the well absorbing molecule maleylacetoacetate (MAA) by a second enzyme homogentisate dioxygenase (HGD), applied in excess uniformly in all assays (see Figure 1).
  • HGA homogentisate formed by HPPD from HPP is directly converted into the well absorbing molecule maleylacetoacetate (MAA) by a second enzyme homogentisate dioxygenase (HGD), applied in excess uniformly in all assays (see Figure 1).
  • HGA homogentisate formed by HPPD from HPP is directly converted into the well absorbing molecule maleylacetoacetate (MAA) by a second enzyme homogentisate dioxygenase (HGD), applied in excess uniformly in all assays (see Figure 1).
  • HGA homo
  • a competitive inhibitor exhibits an apparent increase in kM and thereby a reciprocal decrease in k app at non- saturating substrate concentrations.
  • the enzyme concentration eliminates from the calculation of residual activity and the ratio of both k app directly indicates the change of kM due to the inhibition.
  • the assay solution used for determination of residual activities in raw HPPD polypeptide samples was composed by 200 mM sodium phosphate (Merck, Darmstadt, Germany, pH 7.0), 5 mM MgCL (Merck, Darmstadt, Germany), 20 mM ascorbate (Sigma- Aldrich, St. Louis, USA), 1 mM DTT (Sigma- Aldrich, St. Louis, USA), 0.1% Pluronic F-68 (Sigma-Aldrich, St. Louis, USA), 40 ⁇ FeS0 4 (Sigma- Aldrich, St. Louis, USA), about 8mg/ml purified HGD and 500 ⁇ substrate HPP from a 1 M stock solution in DMSO (Sigma-Aldrich, St.
  • HPPD polypeptide sample were mixed firstly with 5 ⁇ 1 buffer (lx BugBuster®; (Merck, Darmstadt, Germany); in 140 mM Tris, pH7.8, with 1 : 25000 diluted BNase®; Qiagen, Hilden, Germany)) or 5 ⁇ inhibitor diluted in the same buffer from a 0.1 M stock solution in DMSO 200 ⁇ resulting in 100 ⁇ in the HPPD
  • polypeptide/inhibitor sample in the reference and inhibition assay, respectively, and subsequently with ⁇ assay solution .
  • the change in absorbance at 320 nm was followed in 1 min intervals for 30 min.
  • the k ap p values were calculated as signal slope over time in the early phase of the kinetic reaction, usually for the first 5 - 10 minutes of the measurements.
  • the total conversion, i.e. the absolute change in signal, in the 30 min timeframe was monitored as measure of turnover, and a residual turnover was calculated by dividing the change in signal in the presence of inhibitor by the change in signal in the reference sample without inhibitor.
  • the assay solutions used for determination of ki values were composed in the same way containing six different concentrations of HPP substrate (0 - 1350 ⁇ ) for each of the four inhibitor concentrations tested.
  • the inhibitors were diluted in 140 mM Tris, 0.05% Pluronic F-68 (Sigma-Aldrich, St. Louis, USA) and applied in concentrations adopted for the respective HPPD polypeptide/inhibitor pairs to generate dynamic data; generally, their concentrations in the HPPD polypeptide/ inhibitor sample were in the range from 0 to 0.001 M.
  • Example 4 Improved herbicide tolerance mediated by residue exchanges in HPPD polypeptides
  • prior art mutant HPPD polypeptides corresponding to SEQ ID NO:2 in this invention contains residue exchanges at position 335, 336, 339 and 340.
  • the introduction of further residue exchanges at position 213, 215, 264, 268, 270, 340, 344 and/or 345 generated mutant HPPD polypeptides showing strongly improved tolerance (Table 3), concerning applied HPPD inhibitor in a sequence context specific manner.
  • HPPD inhibitor herbicides appear to be reversible inhibitors against the new mutant HPPD polypeptides, in contrast to the slow and tight binding inhibitor characteristic of the wild-type HPPD polypeptide corresponding to SEQ ID NO: l (see Figure 2). These behaviors provide a better and versatile potential for tolerances in crop plants to HPPD inhibitor herbicides.
  • Table 3 Tolerance of mutant HPPD polypeptides against HPPD inhibitor herbicides.
  • Residual turnover were determined according to Example 3 by measuring total change in signal in the presence and absence of Cmpd. 1 (2-chloro-3-(methylsulfanyl)-N-(l-methyl-lH-tetrazol-5-yl)-4- (trifluoromethyl)benzamide).
  • total change in signal without HPPD inhibitor herbicides served for normalization of total change in signal in the presence of the herbicide.
  • values for the turnover are medians of measurements in quadruplets with an average standard deviation of 5%.
  • empty cells at the respective amino acid position in SEQ ID NO:2 to NO:69 are defined as identical to the amino acids corresponding to SEQ ID NO:l, highlighting only the exchanges in the HPPD polypeptide variant.
  • WO2014/043435 with SEQ ID NO:2 do not exhibit any significant kinetic changes in absorbance at 320 nm (Abs320) in the coupled HPPD activity assay compared to the values measured with the knockout HPPD polypeptide.
  • the value for the knock-out HPPD polypeptide without inhibitor was at 0.045 (changes in absorbance at 320 nm) and the values of the HPPD polypeptides corresponding to SEQ ID NO:l and SEQ ID NO:2 were 0.042 and 0.041 at a inhibitor concentration of ⁇ , respectively (Table 3).
  • the knock-out HPPD polypeptide was obtained by exchanging a histidine to an alanine at the amino acid position corresponding to amino acid position 162 of SEQ ID NO:l. This position is well known for its importance due to its involvement in the coordinated binding of the iron atom in the active site of the HPPD polypeptide (Serre et al. (1999), Structure, 7, 977-988).
  • Several exemplary mutants listed in Table 3 with the amino acids glutamine or lysine at position 315 improve the residual turnover of the mutant HPPD polypeptide in a context dependent manner.
  • mutant HPPD polypeptide from SEQ ID NO: 38 with amino acid exchanges at positions 268, 270, 335, 336, 337, 340, 344 and 345 relative to HPPD polypeptide according to SEQ ID NO:l, does not show a significant turnover.
  • an glutamine (SEQ ID NO:36) or a lysine (SEQ ID NO: 35) at position 315 relative to HPPD polypeptide according to SEQ ID NO:38 increases significantly the turnover and residual turnover compared to mutant HPPD polypeptide SEQ ID NO:38 or the prior art (WO2014/043435) mutant HPPD polypeptide corresponding to SEQ ID NO:2.
  • mutant HPPD polypeptide SEQ ID NO: 57 has an additional combinatorial residue exchange at position 213 and it increases significantly the absolute turnover in the absence and presence of the HPPD inhibitor Cmpd. 1 (Table 3).
  • Exemplary mutant HPPD polypeptides e.g. SEQ ID NO: 62 has amino acid exchanges at positions 213, 215, 264, 268, 270, 315, 335, 336, 337, 340, 344 and 345 relative to HPPD polypeptide according to SEQ ID NO: l. These changes increase significantly the turnover and the residual turnover in the presence of HPPD inhibitor Cmpd. l (Table 3) compared to the prior art (WO2014/043435) mutant HPPD polypeptide corresponding to SEQ ID NO:2 in this invention.
  • Improved HPPD tolerance are also seen by the significantly improved ki values (Table 4) of several exemplary mutant HPPD polypeptides (SEQ ID NO:18, SEQ ID NO:36, SEQ ID NO:43, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, and SEQ ID NO: 69) compared to the prior art mutant HPPD polypeptide (WO2014/043435) corresponding to SEQ ID NO:2 in this invention.
  • the level of improvement might differ concerning the HPPD polypeptides employed in such assay, with a level of up to 50 fold, compared to SEQ ID NO: 2 (Table 4).
  • Table 4 Evaluation of tolerance of mutated HPPD polypeptides against HPPD inhibitor herbicide Cmpd.l by the determination of the ki values
  • mutant HPPD polypeptides represented here are examples by a way of illustration, not by a way of limitation.
  • Soybean transformation was achieved by using methods well known in the art, such as the one described using the Agrobacterium tumefaciens mediated transformation soybean half-seed explants using essentially the method described by Paz et al. (2006), Plant cell Rep. 25:206.
  • Transformants were identified by using the HPPD inhibitor herbicide "tembotrione" as selection marker.
  • the appearance of green shoots was observed, and documented as an indicator of tolerance to the HPPD inhibitor herbicide tembotrione.
  • the tolerant transgenic shoots showed normal greening comparable to wild-type soybean shoots not treated with HPPD inhibitor herbicide tembotrione, whereas wild-type soybean shoots treated with the same amount of HPPD inhibitor herbicide tembotrione were entirely bleached. This indicated that the presence of the respective HPPD polypeptide enabled the tolerance to HPPD inhibitor herbicides, like tembotrione.
  • Tolerant green shoots were transferred to rooting media or grafted. Rooted plantlets were transferred to the greenhouse after an acclimation period. Plants containing the transgene were then sprayed with HPPD inhibitor herbicides, as for example with mesotrione at a rate of 300 - 600 g Al/ha, or with Cmpd. 1 (2-chloro-3-(methylsulfanyl)-N-(l-methyl-lH-tetrazol-5-yl)-4- (trifluoromethyl)benzamide) at a rate of 150g - 300g Al/ha supplemented with ammonium sulfate and methyl ester rapeseed oil.
  • HPPD inhibitor herbicides as for example with mesotrione at a rate of 300 - 600 g Al/ha, or with Cmpd. 1 (2-chloro-3-(methylsulfanyl)-N-(l-methyl-lH-tetrazol-5-yl)-4- (trifluoromethyl
  • Table 5 presents the distribution of the HPPD inhibitor herbicide damage score data as percentile for exemplary mutant HPPD inhibitor herbicide tolerant polypeptides (SEQ ID NOs).
  • the percentiles normalize ranks of the damage score from an individual plant in a population.
  • the value of the 25th percentile is the damage score where 25% of the soybean events in the given population had a lower and 75%) higher damage scores.
  • the median is the 50th percentile.
  • Half the values had higher damage scores; half had lower damage scores.
  • the value of the 75th and 90th percentile is the damage score where 75%> and 90%> of the soybean events had lower damage scores, respectively.
  • the difference between the 75th and 25th percentile is called the interquartile range and a marker to quantify scattering in the population. All constructs had only one single cassette insertion in the soybean genome.
  • the exemplary HPPD polypeptide variant is better in all percentile analyses than the prior art mutant HPPD polypeptide (WO2014/043435) corresponding to SEQ ID NO:2 in this invention.
  • the scoring of the prior art mutant HPPD polypeptide (WO2014/043435) corresponding to SEQ ID NO:2 in this invention is listed in the bottom row of Table 5.
  • Table 5 Evaluation of leaf area damage from transgenic soybean TO events five days after the application of Cmpd. 1 at a rate of 300 g ⁇ /ha by percentile distribution.
  • Cotton transformation is achieved by using methods well known in the art, especially preferred method in the one described in the PCT patent publication WO 00/71733. Regenerated plants are transferred to the greenhouse. Following an acclimation period, sufficiently grown plants are sprayed with HPPD inhibitor herbicides as for example tembotrione equivalent to 100 or 200 gAI/ha supplemented with ammonium sulfate and methyl ester rapeseed oil. Seven days after the spray application, the symptoms due to the treatment with the HPPD inhibitor herbicide are evaluated and compared to the symptoms observed on wild-type cotton plants subjected to the same treatment under the same conditions.
  • Example 7 Transformation of Maize Plant Cells by Agrobacterium-Mediated Transformation
  • Constructing the plant expression cassette for stable expression in the maize plant and maize transformation are well known in the art and in this particular example the methods were described and used from W02014/043435 and WO2008/100353.
  • the polynucleotide sequences encoding the mutant HPPD polypeptides in this application are stacked with a polynucleotide sequence encoding an EPSPS protein variant to confer tolerance to herbicides, which target the EPSPS.
  • the EPSPS gene was isolated and mutated from Arthrobacter globiformis (WO2008/100353) and joined in- frame to a transit peptide sequence to guide translocation of the translated protein to the chloroplast.
  • Stable expression is achieved with a ubiquitous promoter (Ubiquitin 4 promoter from sugarcane, U.S. Patent 6,638,766), and a 35S terminator sequence from Cauliflower Mosaic Virus, which is cloned upstream and downstream of the EPSPS gene, respectively.
  • a ubiquitous promoter Ubiquitin 4 promoter from sugarcane, U.S. Patent 6,638,766
  • a 35S terminator sequence from Cauliflower Mosaic Virus
  • the corresponding mutant HPPD polypeptide will be cloned with the same promoter, chloroplast transit peptide, and terminator sequence as described for the EPSPS gene expression cassette.
  • the coding sequences for both genes are codon optimized for maize expression.
  • ears are best collected 8-12 days after pollination. Embryos are isolated from the ears, and those embryos 0.8-1.5 mm in size are preferred for use in transformation. Embryos are plated scutellum side-up on a suitable incubation media, and incubated overnight at 25°C in the dark.
  • Embryos are contacted with an Agrobacterium strain containing the appropriate vectors having a nucleotide sequence of the present invention for Ti plasmid mediated transfer for about 5-10 min, and then plated onto co- cultivation media for about 3 days (25°C in the dark). After co-cultivation, explants are transferred to recovery period media for about five days (at 25°C in the dark). Explants are incubated in selection media with glyphosate for up to eight weeks, depending on the nature and characteristics of the particular selection utilized. After the selection period, the resulting callus is transferred to embryo maturation media, until the formation of mature somatic embryos is observed.
  • the resulting mature somatic embryos are then placed under low light, and the process of regeneration is initiated as known in the art.
  • the resulting shoots are allowed to root on rooting media, and the resulting plants are transferred to nursery pots and propagated as transgenic plants.
  • Plants are routinely analyzed for the expression and presence of the transgenes using the ELISA protein detection method. Only plants recovering in the selection media and having a detectable HPPD transgene protein expression are used for the herbicide tolerance analysis.

Abstract

La présente invention concerne des polypeptides de la HPPD et des plantes les contenant présentant une tolérance totale vis-à-vis d'un ou plusieurs herbicides inhibiteurs de la HPPD appartenant à différentes classes de composés chimiques. Un ensemble de polypeptides de la HPPD mutante a été conçu, lesdits polypeptides ne présentant aucune affinité ou seulement une affinité significativement réduite envers les herbicides inhibiteurs de la HPPD et, simultanément, la vitesse de dissociation des inhibiteurs de la HPPD du polypeptide de la HPPD mutante est augmentée dans une mesure telle que les inhibiteurs de la HPPD n'agissent plus comme des inhibiteurs à interaction lente ou comme des inhibiteurs à interaction à forte affinité et lente, mais plutôt comme des inhibiteurs totalement réversibles. L'invention concerne en particulier des polynucléotides isolés codant pour des polypeptides de la HPPD mutante conférant une tolérance aux herbicides inhibiteurs de la HPPD appartenant à différentes classes de composés chimiques. De plus, l'invention concerne des séquences d'acides aminés correspondant aux polynucléotides.
PCT/EP2018/055102 2017-03-07 2018-03-01 Variants de la hppd et procédé d'utilisation WO2018162330A1 (fr)

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WO2015078828A2 (fr) * 2013-11-28 2015-06-04 Bayer Cropscience Ag Utilisation de 2-chloro-3-(méthylsulfanyl)-n-(1-méthyl-1h-tétrazol-5-yl)-4-(trifluorométhyl)benzamide ou de ses sels pour lutter contre les plantes indésirables dans des zones de culture de plantes transgéniques tolérantes aux herbicides à base d'inhibiteurs de l'hppd
WO2015135881A1 (fr) * 2014-03-11 2015-09-17 Bayer Cropscience Ag Variants d'hppd et procédés d'utilisation

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