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( 12 ) United States Patent US010167482B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 , 167, 482 B2 Coffin (45 ) Date of Patent: Jan . 1 , 2019 ( 54 ) GENES AND USES FOR PLANT WO WO - 2008153927 A3 12 / 2008 WO W O - 2009091518 A2 7 / 2009 ENHANCEMENT WO WO - 2009134339 A2 11 / 2009 (71 ) Applicant : Monsanto Technology LLC , St. Louis , MO (US ) OTHER PUBLICATIONS ( 72 ) Inventor: Marie Coffin , Cary , NC (US ) Weigel et al 2000 (Plant Physiology 122 : p . 1003 - 1013 ). * Theologis et al 2000 (Nature 408 : p . 816 - 820 ) . * ( 73 ) Assignee : Monsanto Technology LLC , St. Louis , “ European Application Serial No . 14181041. 6 , Communication Pursuant to Article 94 ( 3 ) EPC dated Feb . 13 , 2017 ” , 3 pgs. MO (US ) “ European Application Serial No . 14181041 . 6 , Office Action dated Mar . 2 , 2015 ” , 2 pgs. ( * ) Notice : Subject to any disclaimer, the term of this “ European Application Serial No . 14181041. 6 , Response filed Aug . patent is extended or adjusted under 35 25 , 2015 to Office Action dated Mar . 2 , 2015 ” , 10 pgs. U . S . C . 154 (b ) by 266 days . “ U . S . Appl. No . 12 / 157 , 153 , Non Final Office Action dated Oct . 17 , 2011” , 17 pgs . (21 ) Appl. No. : 14 /757 ,273 “ U . S . Appl. No. 12 / 157 ,153 , Response filed Aug . 22 , 2011 to Restriction Requirement dated Jun . 21 , 2011” , 11 pgs. (22 ) Filed : Dec . 10 , 2015 “ U . S . Appl. No . 12 / 157 , 153 , Restriction Requirement dated Jun . 21, 2011” , 11 pgs . (65 ) Prior Publication Data “ U . S . Appl. No . 13/ 385 , 376 , Final Office Action dated Sep . 10 , 2015 ” , 17 pgs. US 2016 /0244777 A1 Aug. 25 , 2016 “ U . S . Appl. No . 13/ 385 , 376 , Non Final Office Action dated Feb . 27 , 2015 ” , 18 pgs . “ U . S . Appl. No . 13/ 385, 376 , Preliminary Amendment filed Feb . 16 , Related U . S . Application Data 2012 ” , 7 pgs. “ U . S . Appl. No . 13 /385 , 376 , Response filed Feb . 13, 2015 to (63 ) Continuation of application No. 13 / 385, 376 , filed on Restriction Requirement dated Dec . 16 , 2014 ” , 8 pgs . Feb . 16 , 2012 , which is a continuation of application “ U . S . Appl. No. 13 / 385 ,376 , Response filed Jun . 26 , 2015 to Non No. 12 / 157 , 153 , filed on Jun . 5 , 2008 . Final Office Action dated Feb . 27 , 2015 ” , 8 pgs. “ U . S . Appl . No. 13 / 385 , 376 , Restriction Requirement dated Dec . (60 ) Provisional application No . 60 /933 , 428, filed on Jun . 16 , 2014 ” , 6 pgs . 6 , 2007 . “ European Application Application Serial No. 08768181 . 3 , Com munication dated Sep . 9 , 2010 " , 1 pg . (51 ) Int . Ci. “ European Application Application Serial No . 08768181. 3 , Response filed Mar. 16 , 2011 to Communication dated Sep . 9 , 2010 ” , 8 pgs. C12N 15 / 82 ( 2006 . 01 ) “ European Application Serial No. 08768181. 3 , Communication C12Q 1 /6895 ( 2018 . 01 ) dated Jan . 19 , 2010 ” , 2 pgs. ( 52 ) U . S . CI. “ European Application Serial No . 08768181. 3 , Communication CPC .. C12N 15/ 8261 ( 2013 .01 ) ; C12N 15 /8247 noting loss of rights dated Sep . 11 , 2012 ” , 1 pg . ( 2013 . 01 ) ; C12N 15 /8251 ( 2013 .01 ) ; C12N “ European Application Serial No. 08768181. 3 , Extended European 15 / 8262 ( 2013 .01 ) ; C12N 15 / 8267 ( 2013 .01 ) ; Search Report dated Aug . 23 , 2010 ” , 6 pgs . C12N 15 /8271 (2013 .01 ) ; C12N 15 /8273 “ European Application Serial No . 08768181. 3 , Office Action dated Jan . 26 , 2012" , 4 pgs. ( 2013 .01 ) ; C12N 15 /8274 ( 2013 .01 ) ; C12N “ European Application Serial No . 08768181. 3 , Response filed Feb . 15 /8275 ( 2013 .01 ) ; C12Q 1 /6895 ( 2013 .01 ) ; 16 , 2010 to Communication dated Jan . 19 , 2010 ” , 10 pgs. YO2A 40 / 146 ( 2018 .01 ) “ European Application Serial No . 12179231, Communication not (58 ) Field of Classification Search ing of loss of rights dated Aug. 19 , 2013 ” , 1 pg . None See application file for complete search history. (Continued ) Primary Examiner — Matthew R Keogh (56 ) References Cited ( 74 ) Attorney , Agent, or Firm — Schwegman Lundberg & U . S . PATENT DOCUMENTS Woessner , P . A . 6 ,096 , 953 A 8 / 2000 Hoffbeck (57 ) ABSTRACT 2003 /0140380 A1 7 / 2003 Henkes et al . 2003 /0233067 A1 12 / 2003 Yongwei et al . Transgenic seed for crops with enhanced agronomic traits 2003 / 0233675 Al 12 / 2003 Cao et al. are provided by trait - improving recombinant DNA in the 2004 /0123343 AL 6 / 2004 La Rosa et al. nucleus of cells of the seed where plants grown from such 2004 / 0216190 A1 10 / 2004 Kovalic 2006 /0048240 A1 3 / 2006 Alexandrov et al . transgenic seed exhibit one or more enhanced traits as 2006 /0150283 A1 7 / 2006 Alexandrov et al . compared to a control plant . Of particular interest are 2011/ 0214199 AL 9 / 2011 Coffin transgenic plants that have increased yield . The present 2013 / 0305398 A1 11 / 2013 Coffin invention also provides recombinant DNA molecules for expression of a protein , and recombinant DNA molecules FOREIGN PATENT DOCUMENTS for suppression of a protein . WO WO - 2006076423 A2 7 / 2006 WO WO - 2007044043 A2 4 / 2007 13 Claims, 7 Drawing Sheets WO W O - 2008153927 A2 12 / 2008 Specification includes a Sequence Listing . US 10 ,167 ,482 B2 Page 2 ( 56 ) References Cited Geelen , et al. , “ ”) , Genbank Accession # AF044313 , ( 1998 ) . Geelen , et al ., “ ” ), The Plant Journal 21: 3 , (2000 ) , 259 - 267 . Guo , H . H . , et al . , “ Protein tolerance to random amino acid change ” , OTHER PUBLICATIONS Proc. Natl . Acad . Sci. USA , 101, ( 2004 ) , 9205 - 9210 . Hechenberger, “ A family of putative chloride channels from Arabidopsis “ European Application Serial No . 12179231, European Search and functional complementation of a yeast strain with a CLC gene Report dated Dec . 10 , 2012 ” , 6 pgs. disruption ” , Journal of Biological Chemistry , vol . 271, No . 52 (Dec . “ European Application Serial No. 12179231, Invitation to Remedy 1 , 1996 ) , 33632 - 33638 . Deficiencies dated Aug . 16 , 2012 ” , 1 pg . Keskin , O ., et al ., “ A new , structurally nonredundant, diverse data “ European Application Serial No . 12179231, Reply filed Oct. 19 , set of protein - protein interfaces and its implications ” , Protein Sci 2012 to Invitation to Remedy Deficiencies dated Aug . 16 , 2012” , 4 ence , 13 , ( 2004 ) , 1043 - 1055 . pgs . Lorkovic , Z . J ., et al ., “Genome analysis : RNA recognition motif “ European Application Serial No . 13174081. 3 , European Search ( RRM ) and K homology (KH ) domain RNA -binding proteins from Report dated Jan . 17 , 2014 ” , 6 pgs . the flowering plant Arabidopsis thaliana ” , Nucleic Acids Research , “ European Application Serial No . 13174081 . 3 , Invitation to Rem 30 , ( 2002 ) , 623 -635 . edy Deficiencies dated Jul. 17 , 2013 ” , 1 pg. Mitchell, R A , et al. , “ A novel bioinformatics approach identifies “ European Application Serial No. 13174081. 3 , Reply filed Sep . 25 , candidate genes for the synthesis and feruloylation of arabinoxylan ” , 2013 to Invitation to Remedy Deficiencies dated Jul. 17 , 2013 ” , 5 Plant Physiol . , 144 ( 1 ) , (May 2007 ) , 43 -53 . pgs . Mitchell , Rowan A , et al ., “ A Novel Bioinformatics Approach " European Application Serial No. 14181041 . 6 , Extended European Identifies Candidate Genes for the Synthesis and Feruloylation of Search Report dated Jan . 26 , 2015 ” , 7 pgs . Arabinoxylan ” , Plant Physiology, 144 ( 1 ) , ( 2007 ) , 43 -53 . “ International Application Serial No . PCT/ US2008 / 007105 , Inter Ngo , J . Thomas , et al. , “ In the Protein Folding Problem and Tertiary national Preliminary Report on Patentability dated Dec. 17 , 2009 ” , Structure Prediction ” , Merz , et al ., ( ed .) , Birkhauser, Boston , MA , 10 pgs. ( 1994 ) , 492 -495 . " International Application Serial No . PCT/ US2008 /007105 , Inter Nishimura , A . , et al. , “ Over - expression of tobacco knotted 1 - type national Search Report dated Jan . 30 , 2009 ” , 5 pgs. class1 homeobox genes alters various leaf morphology ” , Plant Cell “ International Application Serial No. PCT /US2008 / 007105 , Inter Physiol. , 41 ( 5 ) , ( 2000 ) , 583 - 590 . national Written Opinion dated Jan . 30 , 2009 ” , 6 pgs. Saisho , D , et al. , “ Characterization of the gene family for alternative “ RNA Recognition Motif - Containing Protein ( Arabidopsis thaliana ) oxidase from Arabidopsis thaiana ” , Plant Mol Biol ., 35 ( 5 ) , (Nov . ( AEE75400 ) ” , http : // www .ncbi . nlm .nih .gov ( submitted Feb . 18 , 1997 ) , 585 - 96 . 2011) , (Feb . 18 , 2011 ) , 2 pgs . Salanoubat , et al. , “ NCBI” , GenBank Accession No . NP _ 187983 , " RNA Recognition Motif - Containing Protein ( Arabidopsis thaliana ) ( Aug. 13 , 2001 ) , 1 - 2 . (NP _ 187983 ) ” , http : // www .ncbi . nlm .nih . gov ( submitted Feb . 18 , Sivasankar, et al. , " > , Plant Physiology 114 , ( 1997 ) , 583 -589 . 2011) , ( Feb . 18 , 2011 ) , 2 pgs. Smith , Temple F , et al . , “ The Challenges of Genome Sequence “ RNA Recognition Motif -Containing Protein ( B3H4PO _ ARATH ) ” , Annotation or “ The Devil is in the Details " , Nature Biotechnology , http :/ /www .uniprot . org ( last modified Jul. 22, 2008 ), ( Jul. 22 , 2008 ) , 15 ( 12 ) , (Nov . 1997 ) , 1222 - 1223 . 2 pgs . Sonnhammer , E . L , et al ., “ Pfam : a comprehensive database of “ RNA - Binding Protein, Putative ( IP100523019 . 1 ) ” , http :/ /www . ebi. protein domain families based on seed alignments ." , Proteins, 28 ( 3 ) , ac .uk ( created Jan . 5 , 2005 ) , ( Jan . 5 , 2005 ) , 1 pg . ( Jul. 1997 ) , 405 - 420 . “ Subname: Full = Transducin /WD40 domaining - containing protein ; Thornton , J . M ., et al ., “ From structure to function : Approaches and Subname: Full -WD40
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