(12) United States Patent (10) Patent No.: US 7,795,503 B2 Apuya Et Al
Total Page:16
File Type:pdf, Size:1020Kb
US007795.503B2 (12) United States Patent (10) Patent No.: US 7,795,503 B2 Apuya et al. (45) Date of Patent: Sep. 14, 2010 (54) MODULATING PLANT ALKALOIDS 6,013,863 A 1/2000 Lundquist et al. 6,087,558 A 7/2000 Howard et al. (75) Inventors: Nestor Apuya, Culver City, CA (US); 6,093,874 A 7/2000 Jofuku et al. Steven Craig Bobzin, Malibu, CA (US); 6,136,320 A 10/2000 Arntzen et al. Joon-Hyun Park, Oak Park, CA (US) 6,235,975 B1 5, 2001 Harada et al. 6.255,562 B1 7/2001 Heyer et al. (73) Assignee: Ceres, Inc., Thousand Oaks, CA (US) 6,271,016 B1 8/2001 Anderson et al. 6,294,717 B1 9, 2001 Xie (*) Notice: Subject to any disclaimer, the term of this 6,303,341. B1 102001 Hiatt et al. patent is extended or adjusted under 35 6,326,527 B1 12/2001 Kirihara et al. U.S.C. 154(b) by 824 days. 6,329,567 B1 12/2001 Jofuku et al. 6,329,571 B1 12/2001 Hiei (21) Appl. No.: 11/360,459 6,417,429 B1 7/2002 Hein et al. 6,423,885 B1 7/2002 Waterhouse et al. (22) Filed: Feb. 22, 2006 6,452,067 B1 9, 2002 Bedbrook et al. 6,518,066 B1 2/2003 Oulmassov et al. (65) Prior Publication Data 6,573,099 B2 6/2003 Graham 6,645,765 B1 1 1/2003 Anderson et al. US 2006/O195934 A1 Aug. 31, 2006 6,664,446 B2 12/2003 Heard et al. 6,706,470 B2 3/2004 Choo et al. Related U.S. Application Data 6,753,139 B1 6/2004 Baulcombe et al. (60) Provisional application No. 60/654,927, filed on Feb. 6,777,588 B2 8, 2004 Waterhouse et al. 6,835,540 B2 12/2004 Broun 22, 2005. 6,846,669 B1 1/2005 Jofuku et al. 6,906.244 B2 6/2005 Fischer et al. (51) Int. Cl. - WW CI2N 15/29 (2006.01) SA, SSEord et al. CI2N 5/82 (2006.01) 2003/OO37355 A1 2/2003 Barbas et al. AOIH 5/00 (2006.01) 2003/006 1637 A1 3/2003 Jiang et al. (52) U.S. Cl. ....................... 800/298; 800/287: 800/312: 2003/0131386 A1 7/2003 Samaha et al. 800/317; 800/321 2003. O135887 A1 7, 2003 Brandle et al. (58) Field of Classification Search ....................... None 2003. O140381 A1 7, 2003 Bate et al. See application file for complete search history. 2003/0153097 A1 8/2003. Deshaies et al. 2003/017O656 A1 9, 2003 Cen et al. (56) References Cited 2003/0175783 Al 9, 2003 Waterhouse et al. U.S. PATENT DOCUMENTS 4,654,465. A 3, 1987 Brar et al. (Continued) 4,727,219 A 2f1988 Brar et al. 4,801,340 A 1, 1989 Inoue et al. FOREIGN PATENT DOCUMENTS 4,801,540 A 1, 1989 Hiatt et al. 4,936,904. A 6/1990 Carlson CA 2316036 8, 2000 4.946,778 A 8, 1990 Ladner et al. 4,987,071 A 1/1991 Cech et al. 5,034.323 A 7/1991 Jorgensen et al. (Continued) 5,188,958 A 2/1993 Moloney et al. 5,204.253 A 4, 1993 Sanford et al. OTHER PUBLICATIONS 5,231,020 A 7, 1993 Jorgensen et al. Grasser, K. Plant Molecular Biology 2003, vol. 53: pp. 281-295.* 5,254,678 A 10, 1993 Haseloff et al. 5,283,184 A 2/1994 Jorgensen et al. (Continued) 5,380,831 A 1/1995 Adang et al. 5,410,270 A 4/1995 Rybicki et al. Primary Examiner Russell Kallis 5.432,068 A 7, 1995 Albertsen et al. (74) Attorney, Agent, or Firm Fish & Richardson P.C. 5,445,934 A 8, 1995 Fodor et al. 5,538,880 A 7, 1996 Lundquist et al. (57) ABSTRACT 5,723,766 A 3/1998 Theologis et al. 5,766,847 A 6, 1998 Jackle et al. 5,777,079 A 7, 1998 Tsien et al. Materials and methods are provided for identifying regula 5,824,779 A 10/1998 Koegel et al. tory region-regulatory protein associations and modulating 5,824.798. A 10, 1998 Tallberg et al. expression of a sequence of interest. For example, a plant cell 5,859,330 A 1/1999 Bestwicket al. is provided containing a regulatory protein that can modulate 5,900,5255,880,333 A 3,5/1999 1999 GoffetAustin-Phillips al. et al. expression of one or more genes involved in alkaloid biosyn 5,925,806 A 7, 1999 McBride et al. thesis in plants, which, in turn, can modulate the amount 5,958,745 A 9/1999 Gruys et al. and/or rate of biosynthesis of one or more alkaloid com 5,994,622 A 1 1/1999 Jofuku et al. pounds. 6,004,804 A 12/1999 Kumar et al. 6,010,907 A 1/2000 Kmiec et al. 21 Claims, 57 Drawing Sheets US 7,795,503 B2 Page 2 U.S. PATENT DOCUMENTS WO O2/O55669 T 2002 WO O2/10.1052 12/2002 2003/0175965 A1 9, 2003 Lowe et al. WO O3,O13227 2, 2003 2003. O180945 A1 9/2003 Wang et al. WO O3,O25172 3, 2003 2003/0229915 A1 12/2003 Keddie et al. WO 03/034812 5, 2003 2004/OO 19927 A1 1/2004 Sherman et al. WO O3/O57877 T 2003 2004.0034.888 A1 2/2004 Liu et al. WO O3,060476 T 2003 2004/0045049 A1 3/2004 Zhang et al. WO 2004/O27038 4/2004 2004.0053876 A1 3, 2004 Turner et al. WO 2004/035798 4/2004 2004/OO72159 A1 4/2004 Takaiwa et al. WO 2004/O39956 5, 2004 2004/OO73972 A1 4/2004 Beachy et al. WO 2004/041170 5, 2004 2004f0078852 A1 4/2004 Thomashow et al. WO 2004/043361 5, 2004 2004/0203109 A1 10, 2004 Lal et al. WO 2005/047516 5, 2005 2004/0214330 A1 10, 2004 Waterhouse et al. WO 2005/054453 6, 2005 2004/0216190 A1 10, 2004 Kovalic WO 2006/005O23 1, 2006 2005.00091.87 A1 1/2005 Shinozaki et al. WO 2006/009922 1, 2006 2005/0081261 A1 4/2005 Pennell et al. 2005, 0108791 A1 5/2005 Edgerton et al. 2005/0223434 A1 10, 2005 Alexandrov et al. OTHER PUBLICATIONS 2005.0246785 A1 11, 2005 Cook et al. Stemmer et al. European Journal of Biochemistry; 1997, vol. 250, pp. 2005/0257293 A1 11, 2005 Mascia 646-652. 2006, OO1597O A1 1/2006 Pennell et al. Grasser KD, et al., FEBS Letters, Jul 26, 1993; vol. 327, No. 2: pp. 2006.0143729 A1 6/2006 Alexandrov et al. 141-144. 2006, O194959 A1 8/2006 Alexandrov et al. Hauschild K. et al. In Plant Molecular Biology: 1998, vol. 36; pp. 2006/0195934 A1 8/2006 Apuya et al. 473.478.* 2006/0272060 A1 11/2006 Heard et al. U.S. Appl. No. 60/121,700, filed Feb. 25, 1999, Bouckaert et al. 2007/0022495 A1 1/2007 Reuber et al. GenBank Accession No. U93215, dated Feb. 27, 2002. FOREIGN PATENT DOCUMENTS GenBank Accession No. AF129516, dated Apr. 6, 1999. GenBank Accession No. AFO96096, dated Jan. 25, 1999. DE 102 12703 10, 2003 GenBank Accession No. L05934, dated Oct. 22, 1993. EP O 329 308 8, 1989 GenBank Accession No. AAB57606, dated May 14, 1997. EP 1033 405 9, 2000 Abler et al. “Isolation and characterization of a genomic sequence EP O 625 572 4/2001 encoding the maize Cat3 catalase gene' Plant Mol. Biol., 22:1031 EP O 320500 11, 2004 1038 (1993). JP 5-219974 8, 1993 Ahn et al., “Homoeologous relationships of rice, wheat and maize JP O9-224672 9, 1997 chromosomes' Molecular and General Genetics, 241:483-490 KR 2004 OO8459 1, 2004 (1993). WO 90,08828 8, 1990 Alexandrov et al. “Features of Arabidopsis genes and genome dis WO 95/35505 12/1995 covered using full-length cDNAs' Plant Molecular Biology, 60:69 WO 96.34981 11, 1996 85 (2006). WO 96.36693 11, 1996 Allen et al. “RNAi-mediated replacement of morphine with the non WO 97/O1952 1, 1997 narcotic alkaloid reticuline in opium poppy' Nature Biotechnology, WO 97.31064 8, 1997 22(12): 1559-1566 (2004). WO 98,07842 2, 1998 Baerson et al., “Developmental regulation of an acyl carrier protein WO 98.36083 8, 1998 gene promoter in vegetative and reproductive tissues' Plant Mol. WO 98.53O83 11, 1998 Biol., 22(2):255-267 (1993). WO 99.04117 1, 1999 Bateman et al., “Pfam 3.1: 1313 multiple alignments and profile WO 99.07865 2, 1999 HMMs match the majority of proteins' Nucl. Acids Res. 27(1):260 WO 99.24574 5, 1999 262 (1999). WO 99.32619 7, 1999 Bechtold et al., “In planta Agrobacterium mediated gene transfer by WO 99.34663 7, 1999 infiltration of adult Arabidopsis thaliana plants' C.R. Acad. Sci. WO 99,38977 8, 1999 Paris, 3.16:1194-1199 (1993). WO 99.53050 10, 1999 BD Matchmaker One-Hybrid Library construction & Screening Kit, WO 99.58723 11, 1999 Clonetechniques, 2003. WO OO34318 6, 2000 Bird etal. "Atale of three cell types: alkaloid biosynthesis is localized WO OO34319 6, 2000 to sieve elements in opium poppy” The Plant Cell, 15:2626-2635 WO OO34320 6, 2000 (2003). WO OO34321 6, 2000 Broun et al. “Catalytic plasticity of fatty acid modification enzymes WO OO34322 6, 2000 underlying chemical diversity of plant lipids' Science, 282:1315 WO OO34323 6, 2000 1317 (1998).