( 12 ) United States Patent
`Wright et al .
`
`US 11,371,055 B2
`( 10 ) Patent No .:
`( 45 ) Date of Patent :
`* Jun . 28 , 2022
`
`US011371055B2
`
`( 54 ) HERBICIDE RESISTANCE GENES
`( 71 ) Applicant : CORTEVA AGRISCIENCE LLC ,
`Indianapolis , IN ( US )
`( 72 ) Inventors : Terry R. Wright , Carmel , IN ( US ) ;
`Justin M. Lira , Zionsville , IN ( US ) ;
`Terence Anthony Walsh , Zionsville , IN
`( US ) ; Donald Merlo , Carmel , IN ( US ) ;
`Jayakumar Pon Samuel , Carmel , IN
`( US ) ; Gaofeng Lin , Zionsville , IN ( US )
`( 73 ) Assignee : Corteva Agriscience LLC ,
`Indianapolis , IN ( US )
`Subject to any disclaimer , the term of this
`patent is extended or adjusted under 35
`U.S.C. 154 ( b ) by 217 days .
`This patent is subject to a terminal dis
`claimer .
`( 21 ) Appl . No .: 15 / 468,494
`( 22 ) Filed :
`Mar. 24 , 2017
`( 65 )
`Prior Publication Data
`Jul . 27 , 2017
`US 2017/0211087 A1
`
`( * ) Notice :
`
`( 63 )
`
`( 60 )
`
`Related U.S. Application Data
`Continuation of application No. 14 / 491,197 , filed on
`Sep. 19 , 2014 , now Pat . No. 10,167,483 , which is a
`continuation of application No. 13 / 647,081 , filed on
`Oct. 8 , 2012 , now Pat . No. 8,916,752 , which is a
`continuation of application No. 12 / 091,896 , filed as
`application No. PCT / US2006 / 042133 on Oct. 27 ,
`2006 , now Pat . No. 8,283,522 .
`sional application No. 60 / 731,044 , filed on Oct.
`28 , 2005 .
`( 51 ) Int . Ci .
`C12N 15/82
`C12N 9/02
`( 52 ) U.S. CI .
`CPC
`
`( 2006.01 )
`( 2006.01 )
`
`C12N 15/8274 ( 2013.01 ) ; C12N 9/0069
`( 2013.01 ) ; C12N 9/0071 ( 2013.01 ) ; C12N
`15/8275 ( 2013.01 ) ; CI2Y 113/11 ( 2013.01 )
`( 58 ) Field of Classification Search
`???
`C12N 9/0071
`See application file for complete search history .
`References Cited
`
`( 56 )
`
`U.S. PATENT DOCUMENTS
`
`4,683,195 A
`4,761,373 A
`5,135,867 A
`5,273,894 A
`5,316,931 A
`5,463,175 A
`5,500,360 A
`5,561,236 A
`5,589,367 A
`
`7/1987 Mullis et al .
`8/1988 Anderson et al .
`8/1992 Payne et al .
`12/1993 Strauch et al .
`5/1994 Donson et al .
`10/1995 Barry et al .
`3/1996 Ahlquist et al .
`10/1996 Leemans et al .
`12/1996 Donson et al .
`
`5,608,147 A *
`5,637,489 A
`5,646,024 A
`5,648,477 A
`5,656,422 A
`5,879,903 A
`5,910,626 A
`6,087,563 A
`6,107,549 A
`6,153,401 A
`6,268,547 B1
`6,518,222 B2
`6,645,497 B2
`6,664,384 B1
`7,112,665 B1
`7,205,561 B2 *
`7,405,074 B2
`
`C12N 9/0004
`435/410
`
`B41J 11/0095
`250 / 559.16
`
`3/1997 Kaphammer
`6/1997 Strauch et al .
`7/1997 Leemans et al .
`7/1997 Leemans et al .
`8/1997 Crawford
`3/1999 Strauch et al .
`6/1999 Haselkorn
`7/2000 DellaPenna
`8/2000 Feng et al .
`11/2000 Streber et al .
`7/2001 Weeks
`2/2003 Arndt et al .
`11/2003 Malvar et al .
`12/2003 Xu
`9/2006 Leemans et al .
`4/2007 Chelvayohan
`7/2008 Castle et al .
`( Continued )
`FOREIGN PATENT DOCUMENTS
`1471533
`1/2004
`5/1999
`1025250
`( Continued )
`
`CN
`EP
`
`OTHER PUBLICATIONS
`Schleinitz et al , Applied and Environmental Microbiology 70 ( 9 ) :
`5357-5365 ( Year : 2004 ) . *
`Fourgoux - Nicol et al . , Isolation of rapeseed genes expressed early
`and specifically during development of the male gametophyte , Plant
`Biology , 1999 , vol . 40 , p . 857-872 .
`Gressel , Jonathan , Molecular biology of weed control , Transgenic
`Research 2000 , vol . 9 , p . 355-382 .
`Halford et al . , Weed Technology , 2001 , vol . 15 , p . 737-744 .
`Hegg , Eric L. et al . , Herbicide - Degrading a - Keto Acid - Dependent
`Enzyme TfdA : Metal Coordination Environment and Mechanistic
`Insights , Biochemistry , 1999 , vol . 38 , p . 16714-16726 .
`( Continued )
`Primary Examiner — David H Kruse
`( 74 ) Attorney , Agent , or Firm Barnes & Thornburg
`LLP
`
`ABSTRACT
`( 57 )
`The subject invention provides novel plants that are not only
`resistant to 2,4 - D , but also to pyridyloxyacetate herbicides .
`Heretofore , there was no expectation or suggestion that a
`plant with both of these advantageous properties could be
`produced by the introduction of a single gene . The subject
`invention also includes plants that produce one or more
`enz nes of the subject invention " stacked ” together with
`one or more other herbicide resistance genes . The subject
`invention enables novel combinations of herbicides to be
`used in new ways . Furthermore , the subject invention pro
`vides novel methods of preventing the development of , and
`controlling , strains of weeds that are resistant to one or more
`herbicides such as glyphosate . The preferred enzyme and
`gene for use according to the subject invention are referred
`to herein as AAD - 12 ( AryloxyAlkanoate Dioxygenase ) .
`This highly novel discovery is the basis of significant
`herbicide tolerant crop trait and selectable marker opportu
`nities .
`
`33 Claims , 3 Drawing Sheets
`Specification includes a Sequence Listing .
`
`Inari Ex. 1001
`Inari Agric. v. Corteva Agriscience
`PGR2023-00022
`Page 00001
`
`

`

`US 11,371,055 B2
`Page 2
`
`( 56 )
`
`References Cited
`U.S. PATENT DOCUMENTS
`
`12/2008 Castle et al .
`7,462,481 B2
`2/2010 Ahrens et al .
`7,659,448 B2
`11/2010 Wright et al .
`7,838,733 B2
`1/2011 Castle et al .
`7,863,503 B2
`8/2011 Castle et al .
`7,998,703 B2
`7/2012 Castle et al .
`8,222,489 B2
`8,278,505 B2 10/2012 Lira
`8,283,522 B2 * 10/2012 Wright
`98,413 B2 12/2013 Cui et al .
`8,916,752 B2 * 12/2014 Wright
`9,062,284 B2
`6/2015 Lira
`9,074,007 B2
`7/2015 Danilevskaya et al .
`9,127,289 B2
`9/2015 Wright
`9,944,944 B2 *
`4/2018 Cui
`1/2019 Wright
`10,167,483 B2 *
`10,174,337 B2
`1/2019 Wright
`2002/0059659 Al
`5/2002 Stemmer
`2003/0041357 A1
`2/2003 Jepson
`2003/0056245 Al
`3/2003 Chatterjee et al .
`2003/0135879 Al
`7/2003 Weeks et al .
`2009/0069182 Al
`3/2009 Castle et al .
`2012/0245339 Al
`9/2012 Castle et al .
`2014/0325713 Al 10/2014 Kovalic et al .
`2016/0108422 A1
`4/2016 Ellis
`
`C12N 9/0071
`800/300
`C12N 9/0071
`800/300
`
`C12N 9/0069
`C12N 9/0069
`
`FOREIGN PATENT DOCUMENTS
`
`EP
`EP
`EP
`JP
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`
`1167531
`1695983 B1
`1740039
`2005/287415
`87/05629
`96/33270
`97/13402
`98/02562
`9808963
`98/20144
`9820144
`9838294
`9838336
`9844139
`9910513
`1999/063092
`2000/006757
`0009727
`0066748
`2001/038513
`03/013224
`WO 2003/034813
`2003/056904
`WO 2005/107437
`WO 2007/053482
`
`1/2002
`8/2006
`6/2012
`10/2005
`9/1987
`10/1996
`4/1997
`1/1998
`3/1998
`5/1998
`5/1998
`9/1998
`9/1998
`10/1998
`3/1999
`12/1999
`2/2000
`2/2000
`11/2000
`5/2001
`2/2003
`5/2003
`7/2003
`11/2005
`5/2007
`
`OTHER PUBLICATIONS
`Iowa State University Extension 2005 Herbicide manual for Agri
`cultural Professionals , p . 50-72 .
`Kasuga , Mie , Improving Plant Drought , Salt , and Freezing Toler
`ance by Gene Transfer of a Single Stress - Inducible Transcription
`Factor , Nature Biotechnology , Mar. 1999 , vol . 17 , p . 287-291 .
`Maliga , Current Opinion in Plant Biology , 5 : 164-172 ( 2002 ) .
`Perlack , Frederick J. , Modification of the Coding Sequence Enhances
`Plant Expression of Insect Control Protein Genes , Proc . Natl . , Acad .
`Sci . , USA , Biochemistry , Apr. 1991 , vol . 88 , p . 3324-3328 .
`Schleinitz , et al . , Localization and Characterization of two Novel
`Genes Encoding Stereospecific Diosygenases Catalyzing 2 ( 2,4
`Dichlorophenoxy ) propionate Cleavage in Delftia acidovorans MCI ,
`Applied and Environmental Microbiology , Sep. 2004 , vol . 70 , p .
`5357-5365 .
`
`Verdaguer , Bertrand , Isolation and Expression in Transgenic Tobacco
`and Rice Plants , of the Cassava Vein Mosaic Virus ( CVMV )
`Promoter , Plant Molecular Biology , 1996 , vol . 31 , p . 1129-1139 .
`Westendorf et al . , Purification and Characterisation of the Enantiospecific
`Dioxygenases from Delftia acidovorans MC1 Initiating the Degra
`dation of Phenoxypropionate and Phenoxyacetate Herbicides , Acta
`Biotechnol . 2003 , vol . 23 , p . 3-17 .
`Hotopp et al , Biochemistry 2002 , 41 , 9787-9794 .
`Kohler , Genbank Accession No. Q8KSC8 first published on Oct. 1 ,
`2002 ( Year : 2002 ) .
`Hogan et al , The Journal of Biological Chemistry , 275 ( 17 ) : 12400
`12409 ( Year : 2000 ) .
`Genbank Accession No. M16730 , Apr. 1993 .
`Horvath , M. et al . , Isolation and characterization of a 2- ( 2,4
`dichlorophenoxy ) propionic acid - degrading .
`, Appl . Microbiol
`Biotechnol . , 1990 , pp . 33 , 213-216 , ( Abstract only ) .
`Kohler , Sphingomonas herbicidovorans tnpA gene for transposase
`and rdpA gene for ( R ) -2- ( 2,4 - dichlorophenoxy ) propionate ,
`2 - oxoglutarate dioxygenase , Database EMBI , Accesion No. AJ628859 ,
`Mar. 3 , 2004 , pp . 1-2 .
`Kohler , “ Sphinogomonas herbicidovorans MH : A versitle
`phenoxyalkanoic acid herbicide degrader , " J. Industrial Microbiol
`ogy & Biotechnology , vol . 23 , No. 4-5 : 336-340 ( Oct. 1999 ) .
`Lyon , B.R. , et al . , “ Cotton plants transformed with a bacterial
`degradation gene are protected from accidental spray drift damage
`by the herbicide 2,4 - dichlorophenoxyacetic acid , ” Transgenic Res . ,
`1993 , pp . 2 : 166-169 .
`Lyon , B.R. , et al . , Expression of a bacterial gene in transgenic
`tobacco confers resistance to the herbicide 2,4 - dichlorophenoxyacetic
`acid , Transgenic Res . , 1989 , pp . 33 : 166-169 .
`Schleinitz , K.M. , Localization and Characterization of Two Novel
`Genes Encoding Sterospecific Diosygenases Catalyzing 2 ( 2,4
`Dichlrophenoxy ) propionate cleavage in Delftia acidovorans MCI ,
`Applied and Environmental Microbiology , Sep. 2004 , pp . 5357
`5365 , vol . 70 , No. 9 .
`Smejkal , C.W. et al . , “ Substrate specificity of chlorophenoxyalkanoic
`acid - degrading bacteria is not dependent upon phylogenetically
`related tfdA gene types , ” Biol . Fertil . , 2001 , pp . 33 : 507-513 .
`Spencer et al . , Segregation of transgenes in maize , Plant Molecular
`Biology , Jan. 1992 , pp . 201-210 , vol . 18 , Issue 2 .
`Streber et al . , Analysis , cloning , and high - level expression of
`2,4 - dichlorophenixyacetic monooxygenase gene tfdA of Alcaligenes
`eutrophus JMP134 , J. Bacteriol . , 1987 , pp . 169 : 2950-2955 .
`Streber et al . , Transgenic tobacco plants expressing a bacterial
`detoxifying enzyme are resistant to 2,4 - D , Bio / Technology , 1989 ,
`pp . 7 : 811-816 ( Abstract only ) .
`Van der Meer , Genbank Accession No. AJ628859 , NCBI — National
`Library of Medicine USA , Bethesda , Maryland ( Mar. 3 , 2004 ) .
`Westendorf et al . , The two enantiospecific dichlorprop / .alpha.
`ketoglutarate - dioxygenases from Delftia acidovorans MC1
`protein and sequence data of RdpA and SdpA , Microbiol . Res . ,
`2002 , pp . 157 : 317-322 ( Abstract only ) .
`Muller et al , Protein Science ( 2006 ) , 15 : 1356-1368 .
`Bayley et al . , Engineering 2,4 - D resistance into cotton , Theoretical
`and Applied Genetics ( 1992 ) , 83 ( 5 ) , 645-9 .
`Bhat et al . , Purification of 3,5 - dichlorocatechol 1,2 - dioxygenase , a
`nonheme iron dioxygenase and a key enzyme in the biodegradation
`of a herbicide , 2,4 - dichlorophenoxyacetic acid ( 2,4 - D ) , from
`Pseudomonas cepacia CSV90 , Archives of Biochemistry and Bio
`physics ( 1993 ) , 300 ( 2 ) , 738-46 .
`Chaudhry and Huang , Isolation and characterization of a new
`plasmid from a Flavobacterium sp . which carries the genes for
`degradation of 2,4 - dichlorophenoxyacetate , Journal of Bacteriology
`( 1988 ) , 170 ( 9 ) , 3897-902 .
`Chen and Martin , Reasons for the acclimation for 2,4 - D biodegra
`dation in lake water , Journal of Environmental Quality ( 1989 ) ,
`18 ( 2 ) , 153-6 .
`Cosper et al . , X - ray absorption spectroscopic analysis of Fe ( II ) and
`Cu ( II ) forms of a herbicide - degrading ketoglutarate dioxygenase ,
`JBIC , Journal of Biological Inorganic Chemistry ( 1999 ) , 4 ( 1 ) ,
`122-129 .
`
`> >
`
`PGR2023-00022 Page 00002
`
`

`

`US 11,371,055 B2
`Page 3
`
`( 56 )
`
`References Cited
`OTHER PUBLICATIONS
`De Lipthay et al . , Enhanced degradation of phenoxyacetic acid in
`soil by horizontal transfer of the tfdA gene encoding a 2,4
`dichlorophenoxyacetic acid dioxygenase , FEMS Microbiology Ecol
`ogy ( 2001 ) , 35 ( 1 ) , 75-84 .
`De Lipthay et al . , Expression of tfdA genes in aquatic microbial
`communities during acclimation to 2,4 - dichlorophenoxyacetic acid ,
`FEMS Microbiology Ecology ( 2002 ) , 40 ( 3 ) , 205-214 .
`De Lipthay et al . , In situ exposure to low herbicide concentrations
`affects microbial population composition and catabolic gene fre
`quency in an aerobic shallow aquifer , Applied and Environmental
`Microbiology ( 2003 ) , 69 ( 1 ) , 461-467 .
`Feng and Kennedy , Biodegradation and plant protection from the
`herbicide 2,4 - D by plant - microbial associations in cotton produc
`tion systems , Biotechnology and Bioengineering ( 1997 ) , 54 ( 6 ) ,
`513-519 .
`Fuechslin et al . , Effect of integration of a GFP reporter gene on
`fitness of Ralstonia eutropha during growth with 2,4
`dichlorophenoxyacetic acid , Environmental Microbiology ( 2003 ) ,
`5 ( 10 ) , 878-887 .
`Harker et al . , Phenoxyacetic acid degradation by the 2,4
`dichlorophenoxyacetic acid ( TFD ) pathway of plasmid PJP4 : map
`ping and characterization of the TFD regulatory gene , tfdR , Journal
`of Bacteriology ( 1989 ) , 171 ( 1 ) , 314-20 .
`Hawkins and Harwood , Chemotaxis of Ralstonia eutropha
`JMP134 ( pJP4 ) to the herbicide 2,4 - dichlorophenoxyacetate , Applied
`and Environmental Microbiology ( 2002 ) , 68 ( 2 ) , 968-972 .
`Hoffmann et al . , A transposon encoding the complete 2,4
`dichlorophenoxyacetic acid degradation pathway in the alkalitoler
`ant strain Delftia acidovorans P4a , Microbiology ( Reading , United
`Kingdom ) ( 2003 ) , 149 ( 9 ) , 2545-2556 .
`Hogan et al . , Distribution of the tfdA gene in soil bacteria that do
`not degrade 2,4 - dichlorophenoxyacetic acid ( 2,4 - D ) , Microbial Ecol
`ogy ( 1997 ) , 34 ( 2 ) , 90-96 .
`Hogan et al . , Site - directed mutagenesis of 2,4 - dichlorophenoxyacetic
`acid / ketoglutarate dioxygenase . Identification of residues involved
`in metallocenter formation and substrate binding , Journal of Bio
`logical Chemistry ( 2000 ) , 275 ( 17 ) , 12400-12409 .
`Jackman et al . , Electrokinetic movement and biodegradation of
`2,4 - dichlorophenoxyacetic acid in silt soil , Biotechnology and Bio
`engineering ( 2001 ) , 74 ( 1 ) , 40-48 .
`Ka and Tiedje , Integration and excision of a 2,4 - dichlorophenoxyacetic
`acid - degradative plasmid in Alcaligenes paradoxus and evidence of
`its natural intergeneric transfer , Journal of Bacteriology ( 1994 ) ,
`176 ( 17 ) , 5284-9 .
`Ka et al . , Use of gene probes to aid in recovery and identification
`of functionally dominant 2,4 - dichlorophenoxyacetic acid - degrading
`populations in soil , Applied and Environmental Microbiology ( 1994 ) ,
`60 ( 4 ) , 1116-20 .
`Kitagawa et al . , Novel 2,4 - dichlorophenoxyacetic acid degradation
`genes from oligotrophic Bradyrhizobium sp . strain HW13 isolated
`from a pristine environment , Journal of Bacteriology ( 2002 ) , 184 ( 2 ) ,
`509-518 .
`Kleinsteuber et al . , Expression of the 2,4 - D degradative pathway of
`PJP4 in an alkaliphilic , moderately halophilic soda lake isolate ,
`Halomonas sp . EF43 , Extremophiles ( 2001 ) , 5 ( 6 ) , 375-384 .
`Laemmli et al . , Mutation analysis of the different tfd genes for
`degradation of chloroaromatic compounds in Ralstonia eutropha
`JMP134 , Archives of Microbiology ( 2004 ) , 181 ( 2 ) , 112-121 . (
`Published online : Dec. 16 , 2003 ) .
`Laurent et al . , 2,4 - Dichlorophenoxyacetic Acid Metabolism in
`Transgenic Tolerant Cotton ( Gossypium hirsutum ) , Journal of Agri
`cultural and Food Chemistry ( 2000 ) , 48 ( 11 ) , 5307-5311 .
`Loos et al . , Phenoxyacetate herbicide detoxication by bacterial
`enzymes , Journal of Agricultural and Food Chemistry ( 1967 ) , 15 ( 5 ) ,
`858-60 .
`Ludwig et al . , Chromatographic separation of the enantiomers of
`marine pollutants . Part 5 : enantioselective degradation of
`phenoxycarboxylic acid herbicides by marine microorganisms ,
`Chemosphere ( 1992 ) , 24 ( 10 ) , 1423-9 .
`
`Mae et al . , Characterization of a new 2,4 - dichlorophenoxyacetic
`acid degrading plasmid pEST4011 : physical map and localization of
`catabolic genes , Journal of General Microbiology ( 1993 ) , 139 ( 12 ) ,
`3165-70 .
`Maltseva et al . , Degradation of 2,4 - dichlorophenoxyacetic acid by
`haloalkaliphilic bacteria , Microbiology ( Reading , United Kingdom )
`( 1996 ) , 142 ( 5 ) , 1115-1122 .
`Marriott et al . , Biodegradation of mixtures of chlorophenoxyalkanoic
`acid herbicides by Alcaligenes denitrificans , Journal of Industrial
`Microbiology & Biotechnology ( 2000 ) , 25 ( 5 ) , 255-259 .
`Matheson et al . , Evidence for acquisition in nature of a chromo
`somal 2,4 - dichlorophenoxyacetic acid / ketoglutarate dioxygenase
`gene by different Burkholderia spp , Applied and Environmental
`Microbiology ( 1996 ) , 62 ( 7 ) , 2457-2463 .
`McGowan et al . , Evidence for interspecies gene transfer in the
`evolution of 2,4 - dichlorophenoxyacetic acid degraders , Applied and
`Environmental Microbiology ( 1998 ) , 64 ( 10 ) , 4089-4092 .
`Muller and Babel , Pseudo - recalcitrance of chlorophenoxyalkanoate
`herbicides — correlation to the availability of ketoglutarate , Acta
`Biotechnologica ( 2001 ) , 21 ( 3 ) , 227-242 .
`Muller and Babel , Separation of two dichlorprop / ketoglutarate
`dioxygenases with enantiospecific properties from Comamonas
`acidovorans MC1 , Acta Biotechnologica ( 1999 ) , 19 ( 4 ) , 349-355 .
`Muller et al . , Comamonas acidovorans strain MC1 . A new isolate
`capable of degrading the chiral herbicides dichlorprop and mecoprop
`and the herbicides 2,4 - D and MCPA , Microbiological Research
`( 1999 ) , 154 ( 3 ) , 241-246 .
`Nickel et al . , Involvement of two ketoglutarate - dependent dioxygenases
`in enantioselective degradation of ( R ) - and ( S ) -mecoprop by
`Sphingomonas herbicidovorans MH , Journal of Bacteriology ( 1997 ) ,
`179 ( 21 ) , 6674-6679 .
`Ohkouchi et al . , Cloning and expression of DL - 2 - haloacid dehalogenase
`gene from Burkholderia cepacia , Water Science and Technology
`( 2000 ) , 42 ( 7-8 , Hazard Assessment and Control of Environmental
`Contaminants ( Ecohazard 99 ) ) , 261-268 .
`Parker and Doxtader , Kinetics of microbial decomposition of 2,4 - D
`in soil : effects of herbicide concentration , Journal of Environmental
`Quality ( 1982 ) , 11 ( 4 ) , 679-84 .
`genes for
`Perkins et al . , Use of Alcaligenes eutrophus as a source of
`2,4 - D resistance in plants , Weed Science ( 1987 ) , 35 ( Suppl . 1 ) ,
`12-18 .
`Plumeier et al . , Importance of different tfd genes for degradation of
`chloroaromatics by Ralstonia eutropha JMP134 , Journal of Bacte
`riology ( 2002 ) , 184 ( 15 ) , 4054-4064 .
`Poh et al . , Complete characterization of Tn5530 from Burkholderia
`cepacia strain 2a ( pIJB1 ) and studies of 2,4 - dichlorophenoxyacetate
`uptake by the organism , Plasmid ( 2002 ) , 48 ( 1 ) , 1-12 .
`Preston et al . , Multiple resistance to dissimilar herbicide chemistries
`in a biotype of Lolium rigidum due to enhanced activity of several
`herbicide degrading enzymes , Pesticide Biochemistry and Physiol
`ogy ( 1996 ) , 54 ( 2 ) , 123-134 .
`Saari et al . , Stereospecific degradation of the phenoxypropionate
`herbicide dichlorprop , Journal of Molecular Catalysis B : Enzymatic
`( 1999 ) , 6 ( 4 ) , 421-428 .
`Schneiderheinze et al . , Plant and soil enantioselective biodegrada
`tion of racemic phenoxyalkanoic herbicides , Chirality ( 1999 ) , 11 ( 4 ) ,
`330-337 .
`Shaw and Burns , Enhanced mineralization of [ U - 14C ] 2,4
`dichlorophenoxyacetic acid in soil from the rhizosphere of Trifolium
`pratense , Applied and Environmental Microbiology ( 2004 ) , 70 ( 8 ) ,
`4766-4774 .
`Tett et al . , Enantioselective degradation of the herbicide mecoprop
`[ 2- ( 2 - methyl - 4 - chlorophenoxy ) propionic acid ] by mixed and pure
`bacterial cultures , FEMS Microbiology Ecology ( 1994 ) , 14 ( 3 ) ,
`191-200 .
`Top et al . , Capture of a catabolic plasmid that encodes only
`2,4 - dichlorophenoxyacetic acid : ketoglutaric acid dioxygenase ( TfdA )
`by genetic complementation , Applied and Environmental Microbi
`ology ( 1996 ) , 62 ( 7 ) , 2470-2476 .
`Top et al . , Methane oxidation as a method to evaluate the removal
`of 2,4 - dichlorophenoxyacetic acid ( 2,4 - D ) from soil by plasmid
`mediated bioaugmentation , FEMS Microbiology Ecology ( 1999 ) ,
`28 ( 3 ) , 203-213 .
`
`PGR2023-00022 Page 00003
`
`

`

`US 11,371,055 B2
`Page 4
`
`2
`
`( 56 )
`
`References Cited
`OTHER PUBLICATIONS
`Travkin et al . , Characterization of an intradiol dioxygenase involved
`in the biodegradation of the chlorophenoxy herbicides 2,4 - D and
`2,4,5 - T , FEBS Letters ( 1997 ) , 407 ( 1 ) , 69-72 .
`Vallaeys et al . , PCR - RFLP analysis of 16S rRNA , tfdA and tfdB
`genes reveals a diversity of 2,4 - D degraders in soil aggregates ,
`FEMS Microbiology Ecology ( 1997 ) , 24 ( 3 ) , 269-278 .
`Vallaeys et al . , The metabolic pathway of 2,4 - dichlorophenoxyacetic
`acid degradation involves different families of tfdA and tfdB genes
`according to PCR - RFLP analysis , FEMS Microbiology Ecology
`( 1996 ) , 20 ( 3 ) , 163-172 .
`Vedler et al . , Analysis of the 2,4 - dichlorophenoxyacetic acid
`degradative plasmid PEST4011 of Achromobacter xylosoxidans
`subsp . denitrificans strain EST4002 , Gene ( 2000 ) , 255 ( 2 ) , 281-288 .
`Vedler et al . , TfdR , the LysR - type transcriptional activator , is
`responsible for the activation of the tfdCB operon of Pseudomonas
`putida 2,4 - dichlorophenoxyacetic acid degradative plasmid PEST4011 ,
`Gene ( 2000 ) , 245 ( 1 ) , 161-168 .
`Zhang et al . , In vitro assay for 2,4 - D resistance in transgenic cotton ,
`in Vitro Cellular & Developmental Biology : Plant ( 2001 ) , 37 ( 2 ) ,
`300-304 .
`Zipper et al . , Complete microbial degradation of both enantiomers
`of the chiral herbicide mecoprop [ ( RS ) -2- ( 4 - chloro - 2
`methylphenoxy ) propionic acid ] in an enantioselective manner by
`Sphingomonas herbicidovorans sp . Nov , Applied and Environmen
`tal Microbiology ( 1996 ) , 62 ( 12 ) , 4318-4322 .
`Zipper et al . , Enantioselective uptake and degradation of the chiral
`herbicide dichlorprop [ ( RS ) -2- ( 2,4 - dichlorophenoxy ) propanoic acid ]
`by Sphingomonas herbicidovorans MH , Journal of Bacteriology
`( 1998 ) , 180 ( 13 ) , 3368-3374 .
`Cho et al , Agricultural Chemistry and Biotechnology ( English
`Edition ) ( 1999 ) , 42 ( 2 ) , 57-61 , Isolation and characterization of
`2 - methyl - 4 - chlorophenoxyacetic acid - degrading bacteria from agri
`cultural soils .
`Lim et al , Journal of Microbiology ( Seoul , Republic of Korea )
`( 2004 ) , 42 ( 2 ) , 87-93 Genetic and phenotypic diversity of ( R / S )
`mecoprop [ 2- ( 2 - methyl - 4 - chlorophenoxy ) propionic acid ]
`degrading bacteria isolated from soils .
`Tamura et al , Nippon Noyaku Gakkaishi ( 2001 ) , 26 ( 3 ) , 309-314 ,
`Microbial pesticide degradations and evolutionary analysis of degrad
`ing enzymes .
`Vallaeys et al , Biotechnology Letters ( 1998 ) , 20 ( 11 ) , 1073-1076 ,
`Isolation and characterization of a stable 2,4 - dichlorophenoxyacetic
`acid degrading bacterium , Variovorax paradoxus , using chemostat
`culture .
`Fukamori and Hausinger , JBC ( 268 ) 24311 ( 1993 ) , Purification and
`characterization of 2,4 - Dichlorophenoxyacetate / a - ketogutarate
`dioxygenase
`Fukamori and Hausinger , JBacterioloogy ( 175 ) 2083 ( 1993 ) , Alcaligenes
`eutrophus JMP134 “ 2,4 - Dichlorophenoxyacetate monooxygenase ”
`is an a - ketoglutarate - dependent dioxygenase .
`Ehrig et al . , Acta Biotechologica ( 17 ) 351-356 ( 1997 ) , Isolation of
`phenoxyherbicidedegrading rhodoferax species from contaminated
`building material .
`Hausinger , Critical Reviews in Biochemsitry ( 39 ) 21-68 ( 2004 ) , Fe ( II ) .
`alpha . - Ketoglutarate - Dependent Hydroxylases and Related Enzymes .
`Hausinger and Fukamori , Env Health Perspectives ( 103 ) 37
`39 ( 1995 ) , Characterization of the first enzyme in 2,4
`Dichlorphenoxyacetic acid metabolism .
`Don et al . , J Bacteriol ( 161 ) 85 ( 1985 ) , Transposon Mutagenesis and
`Cloning Analysis of the Pathways for Degradation of 2,4
`Dichlorophenoxyacetic Acid and 3 - Chlorobenzoate in Alcaligenes
`eutrophus JMP134 ( pJP4 ) .
`Don et al . , J Bacteriol ( 161 ) 466 ( 1985 ) , Genetic and Physical Map of
`the 2,4 - Dichlorophenoxyacetic Acid - Degradative Plasmid pJP4 .
`Hotopp et al . , J. Molec . Catalysis B : Enzymatic ( 15 ) 155-162 ( 2001 ) ,
`Alternative substrates of 2,4 - dichlorophenoxyacetate / -ketoglutarate
`dioxygenase .
`
`9
`
`2
`
`Park et al , Journal of Microbiology and Biotechnology ( 2003 ) ,
`13 ( 2 ) , 243-250 , Isolation and characterization of 4- ( 2,4
`dichlorophenoxy ) butyric acid - degrading bacteria from agricultural
`soils .
`Mueller RH , Babel W. Degradability and recalcitrance of
`phenoxyalkanoic acid herbicides — traits of the microbial metabo
`lism . InSecond International Conference on Remediation of Chlo
`rinated and Racalcitrant Compounds 2000 ( pp . 229-236 ) .
`Tett , Biodegradation ( 1997 ) , 8 ( 1 ) , 43-52 , Biodegradation of the
`chlorophenoxy herbicide ( R ) - ( + ) - mecoprop by Alcaligenes denitrificans .
`Llewellyn et al , Herbicide - Resistant Crops ( 1996 ) , 159-74 , Genetic
`engineering of crops for tolerance to 2,4 - D .
`Baelum et al . , Appl . Environ . Microbiol . ( 72 ) 1476-1486 ( 2006 ) ,
`Degradation of 4 - Chloro - 2 - Methylphenoxyacetic Acid in Top- and
`Subsoil is Quantitatively Linked to the Class III tfdA Gene .
`Baelum et al . , Appl . Environ . Microbiol . ( 75 ) 2969-2972 ( 2009 ) ,
`TaqMan Probe - Based Real - Time PCR Assay for Detection and
`Discrimination of Class I , II , and III tfdA Genes in Soils Treated
`with Phenoxy Acid Herbicides .
`Griffin et al . , J Agric Food Chem ( 61 ) 6589-6596 ( 2013 ) , Character
`ization of Aryloxyalkanoate Dioxygenase - 12 , a Nonheme Fe ( II ) / .
`alpha . - Ketoglutarate - Dependent Dioxygenase , Expressed in Trans
`genic Soybean and Pseudomonas fluorescens .
`Hausinger , RSC Metallobiology ( 2015 ) Chapter 1 of 2 - Oxoglutarate
`dependent oxygenases , Biochemical diversity of 2 - oxoglytarate
`dependent oxygenases .
`Leibeling et al , Eng Life Sci ( 13 ) 278 ( 2013 ) , Posttranslational
`oxidative modification of ( R ) -2- ( 2,4 - dichlorophenoxy ) propionate / .
`alpha . - ketoglutarate - dependent dioxygenases ( RdpA ) leads to improved
`degradation of 2,4 - dichlorophenoxyacetate ( 2,4 - D ) .
`Muller et al . , Applied and Environmental Microbiology ( 72 ) 4853 ( 2006 ) ,
`Purification and Characterization of Two Enantioselective
`a - Ketoglutarate - Dependent Dioxygenases , RdpA and SdpA , from
`Sphingomonas herbicidovorans MH .
`Zaprasis et al , Appl . Environ . Microbiol . ( 76 ) 119 ( 2010 ) , Abundance
`of Novel and Diverse tfdA - Like Genes , Encoding Putative
`Phenoxyalkanoic Acid Herbicide - Degrading Dioxygenases , in Soil .
`Zhang et al . Journal of Agricultural and Food Chemistry ( 2020 ) ,
`68 ( 26 ) , 6967-6976 CODEN : JAFCAU ; ISSN : 0021-8561 Enantioselec
`tive Catabolism of the Two Enantiomers of the Phenoxyalkanoic
`Acid Herbicide Dichlorprop by Sphingopyxis sp . DBS4 .
`Krausse et al . , 4th biotechnology symposium of the University of
`Leipzig ( abstract ) p . 60 ( 2005 ) , Crystal structure of the 2 - oxoglutarate
`dependent dioxygenase RdpA .
`Mueller et al . , Un Mich ICBIC 2005 abstract , Insights into the
`enantiospecificities of ( R ) - and ( S ) -dichlorprop / a - ketoglutarate
`dioxygenases .
`Krausse et al . , Freiberg Un Deutschen Gesellschaft fur Kristal
`lographie ( 2006 ) , ( Poster title 72L ) Structure of the 2 - Oxoglutarate
`Dependent Dioxygenase RdpA by X - ray Crystallography and Small
`Angle X - ray Scattering .
`Gazitua et al . , Environ Microbiol ( 12 ) 2411 ( 2010 ) , Novel .alpha.
`ketoglutarate dioxygenase tfdA - related genes are found in soil DNA
`after exposure to phenoxyalkanoic herbicides .
`Chekan et al . , Proceedings of the National Academy of Sciences
`( 116 ) 13299-13304 ( 2019 ) , Molecular basis for enantioselective her
`bicide degradation imparted by aryloxyalkanoate dioxygenases in
`transgenic plants .
`Larue et al , Pest Manag Sci ( 75 ) 2086 ( 2019 ) , Development of
`enzymes for robust aryloxyphenoxypropionate and synthetic auxin
`herbicide tolerance traits in maize and soybean crops .
`Liu et al . , FEMS Microbiol Ecol ( 86 ) 114-129 ( 2013 ) , Consumers of
`4 - chloro - 2 - methylpheoxyacetic acid from agricultural soil and
`drilosphere harbor cadA , r / sdpA , and tfdA - like gene encoding
`oxygenases .
`Muller et al . , Protein Science ( 15 ) prot1356 ( 2006 ) , Structural basis
`for the enantiospecificities of R- and S - specific phenoxypropionate /
`a - ketoglutarate dioxygenases .
`Muller , Eng Life Sci ( 7 ) 311-321 ( 2007 ) , Activity and Reaction
`Mechanism of the Initial Enzymatic Step Specifying the Microbial
`Degradation of 2,4 - Dichlorophenoxyacetate .
`
`PGR2023-00022 Page 00004
`
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`

`US 11,371,055 B2
`Page 5
`
`( 56 )
`
`References Cited
`OTHER PUBLICATIONS
`Westendorf , Eng Life Sci ( 6 ) 552-559 ( 2006 ) , Kinetic Traits and
`Enzyme Form Patterns of ( R ) -2- ( 2,4 - Dichlorophenoxy ) propionate /
`a - Ketoglutarate Dioxygenase ( RdpA ) after Expression in Different
`Bacterial Strains .
`Wright et al . , Proc Natl Acad Sci ( 107 ) 20240 ( 2010 ) , Robust crop
`resistance to broadleaf and grass herbicides provided by aryloxyalkano
`ate dioxygenase transgenes .
`GenBank accession No. AAA21983.1 tfdA Cupriavidus necator
`( replaced Ralstonia eutropha ) , Apr. 23 , 1993 .
`GenBank accession No. AAK81681.1 tfdA Burkholderia cepacia ,
`Aug. 24 , 2020 , Jul . 23 , 2016 .
`UniProtKB accession No. 045423.1 tfdA Burkholderia sp . RASC ,
`Nov. 1 , 1996 .
`GenBank accession No. AAS49436 tfdAAchromobacter denitrificans ,
`Apr. 3 , 2020 .
`GenBank accession No. AAB47567.1 tfd?Burkholderia cepacia
`PIJB , Jul . 26 , 2016 .
`GenBank accession No. AAM76772.1 tfd?Delftia acidovorans_
`287 aaProtein _ - _ NCBI Jul . 26 , 2016 .
`GenBank accession No. BAB92965.1 tfdA alpha proteobacterium
`HWK12 , Jul . 2 , 2002 .
`GenBank accession No. BAB92966.1 tfdA alpha proteobacterium
`HW13 , Jul . 2 , 2002 .
`NCBI accession No. WP_011084309.1 tfdA Bradyrhizobium diazoef
`ficiens ( replaced B. japonicum ) , Jul . 27 , 2019 .
`UniProtKB accession No. P83309.2 sdpA MC1 Delftia aciovorans ,
`Sep. 18 , 2019 .
`UniProtKB accession No. 0700X4.1 sdpA MH Shingobium
`herbicidovorans , Nov. 1 , 1996 .
`GenBank accession No. ABD67501.1 sdpA P230 Rhodoferax sp .
`P230 , Mar. 14 , 2006 .
`Muller , Swiss Federal Institute of Technology thesis ( Nov. 2004 ) ,
`Metabolism of phenoxyalkanoic acid herbicides in Sphingomonas
`herbicidovorans MH cloning and characterization oftwo enantiospecific
`.alpha . - ketoglutarate - dependent dioxygenases and degradation path
`way analysis .
`Westendorf Universitat Leipzig thesis – German ( 2005 ) ,
`Enantioselektive Verwertung von Phenoxyalkanoat - Herbiziden durch
`Bakterien - Eine Charakterisierung der Dioxygenasen des initialen
`Abbau - Schrittes .
`Baelum et al . , System Appl Microbiol . ( 33 ) 67 ( 2010 ) , Supplemental
`Material to Comparison of 16S rRNA gene phylogeny and func
`tional tfdA gene distribution in thirty - one different 2,4
`dichlorophenoxyacetic acid and 4 - chloro - 2 - methylphenoxyacetic
`acid degraders .
`Han et al , World Journal of Microbiology & Biotechnology ( 2014 ) ,
`30 ( 10 ) 2567-2576 , 16S rRNA gene phylogeny and tfdA gene
`analysis of 2,4 - D - degrading bacteria isolated in China .
`Zhang et al . , J. Agric . Food Chem . ( 58 ) 12878 ( 2010 ) , Enantioselec
`tive Environmental Behavior of the Chiral Herbicide Fenoxaprop
`ethyl and Its Chiral MetaboliteFenoxaprop in Soil .
`Wu et al . , J. Agric . Food Chem . ( 65 ) 3711 ( 2017 ) , Rapid Biodegra
`dation of the Herbicide 2,4 - Dichlorophenoxyacetic Acid by Cupriavidus
`gilardii T - 1 .
`Zabaloy et al . , Ann Microbiol ( 64 ) 969 ( 2014 ) , Isolation and char
`acterization of indigenous 2,4 - D herbicide degrading bacteria from
`an agricultural soil in proximity of Sauce Grande River , Argentina .
`Nielsen et al . , PLOS One 8 ( 12 ) e83346 ( 2013 ) , Novel Insight into the
`Genetic Context of the cadAB Genes from a 4 - chloro - 2
`methylphenoxyacetic Acid - Degrading Sphingomonas .
`Mierzejewska et al , Bulletin Env Contam Tox ( 104 ) 200 ( 2020 ) ,
`Biodegradation Potential and Ecotoxicity Assessment in Soil Extracts
`Amended with Phenoxy Acid Herbicide ( 2,4 - D ) and a Structurally
`Similar Plant Secondary Metabolite ( Ferulic Acid ) .
`Shimojo et al . , J Biosc Bioengin . ( 108 ) 56 ( 2009 ) , Analysis of genes
`encoding the 2,4 - dichlorophenoxyacetic acid degrading enzyme
`from Sphingomonas agrestis 58-1 .
`
`2
`
`9
`
`Han et al , World Journal of Microbiology & Biotechnology ( 2015 ) ,
`31 ( 7