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(12) United States Patent (10) Patent No.: US 7,868,155 B2 Lu Et Al

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(12) United States Patent (10) Patent No.: US 7,868,155 B2 Lu Et Al US007868155B2 (12) United States Patent (10) Patent No.: US 7,868,155 B2 Lu et al. (45) Date of Patent: Jan. 11, 2011 (54) PROMOTER, PROMOTER CONTROL OTHER PUBLICATIONS ELEMENTS, AND COMBINATIONS, AND Kim et al., “A 20 Nucleotide Upstream Element is Essential for the USES THEREOF Nopaline Synthase (nos) Promoter Activity.” Plant Molecular Biol (75) Inventors: Yu-Ping Lu, Camarillo, CA (US); Roger ogy, vol. 24, pp. 105-117, 1994. Donald et al., “Mutation of Either G Box or I Box Sequences Pro Pennell, Malibu, CA (US); Jack foundly Affects Expression From the Arabidopsis rbcS-1A Pro Okamuro, Oak Park, CA (US); Richard moter.” EMBO Journal, vol. 9, No. 6, pp. 1717-1726, 1990. Schneeberger, Carlsbad, CA (US); Dolferus et al., “Differential Interactions of Promoter Elemtns in Yiwen Fang, Los Angeles, CA (US); Stress Responses of the Arabidopsis Adh Gene.” Plant Physiology, Shing Kwok, Woodland Hills, CA (US) vol. 105, pp. 1075-1087, 1994. Database Genbank Online Feb. 14, 2004, "Arabidopsis thaliana (73) Assignee: Ceres, Inc., Thousand Oaks, CA (US) genomic DNA, chromosome 5, P1 clone: MNC 17” retrieved from NCBI accession No. AB016890 BA000015. (*) Notice: Subject to any disclaimer, the term of this Database EMBL Nov. 24, 2004 WiscDsLox 262D09 Arabidopsis patent is extended or adjusted under 35 thaliana T-DNA insertion flanking sequences XP002372669. U.S.C. 154(b) by 574 days. Database EMBL Mar. 21, 2002 Arabadopsis thaliana cDNA clone: RAFL09-89-K19,5-end. XPO02372670. (21) Appl. No.: 11/603,542 Database EMBL Apr. 23, 2002, Arabidopsis thaliana putative photoassimilate-responsive protein PAR (At5g52390) mRNA, com (22) Filed: Nov. 22, 2006 plete cds. XP002372671. Database Geneseq Oct. 18, 2000 Arabadopsis thaliana protein frag (65) Prior Publication Data ment SEQ ID No. 62052, XP002372672. Shahmuradov I A et al., PlantProm: a database of plant promoter US 2008/OO44898A1 Feb. 21, 2008 sequences, Nucleic Acids Research, Oxford University Press, Surrey GB vol. 31, No. 1, 2003, pp. 114-117 XP002993034. (51) Int. Cl. Database EMBLNov. 16, 1998 Arabidopsis thaliana genomic DNA, CI2N 15/82 (2006.01) chromosome 5, TAC clone: K24M7 XP002372668 retrieved from CI2N 15/63 (2006.01) EBI accession No. EM PRO: AB019226 Database accession No. ABO 19226. CI2N IS/II (2006.01) Benfey, et al. Science, (1990), vol. 250, pp. 959-966. AOIH 5/00 (2006.01) Sato, etal, NCBI GenBank Sequence Accession No. AB022216, pp. (52) U.S. Cl. ..................... 536/24.1:536/23.1: 800/278: 1-31 (Dec. 27, 2000). 800/287; 435/320.1 Tyagi, et al. Current Science, (2001), vol. 80. pp. 161-169. (58) Field of Classification Search ........... ... None Maniatis, et al. Molecular Cloning: A Laboratory Manual, Cold See application file for complete search history. Spring Harbor Laboratory (1982). GenBank Accession No. NM 112618 (Apr. 20, 2007). (56) References Cited Goto, et al., Genes Genet. Syst., (2002), vol. 77, pp. 89-95. Shen, et al., Plant J. (2002), vol. 29(3), pp. 371-380. U.S. PATENT DOCUMENTS Doerks, et al., TIG, (1998), vol. 14, pp. 248-250. Smith, et al., Nature Biotechnology, (1997), vol. 15, pp. 1222-1223. 5,362,865 A 11/1994 Austin Bork, et al., TIG, (1996), vol. 12, pp. 425-427. 5,424,412 A 6, 1995 Brown Guo, et al., PNAS, (2004), vol. 101, pp. 9205-9210. 5,659,122 A 8, 1997 Austin Keskin, et al., Protein Science, (2004), vol. 13, pp. 1043-1055. 5,754,888 A 5/1998 Yang et al. Thornton, et al., Nature structural Biology, structural genomics 5,764,903. A 6, 1998 Yu supplement, (Nov. 2000). 5,857,208 A 1, 1999 Ofek Wells, Biochemistry, (1990), vol. 29, pp. 8509-8517. 5,974,563 A 10/1999 Beeler, Jr. Miyoshi, et al., Plant J, (2003), vol. 36, pp. 532-540. 6,092,066 A 7, 2000 Ofek Ngo, et al., The Protein Folding Problem and Tertiary Structure 6,448.476 B1 9/2002 Barry Prediction, K. Merz and S. LeGrand (eds.), (1994), pp. 492-495. 2003,0226166 A1 12, 2003 Falco Office Action dated Jul. 28, 2008 in U.S. Appl. No. 11/058,689. 2004/0163144 A1* 8, 2004 Kriz et al. ................... 800,279 Office Action dated May 7, 2009 in U.S. Appl. No. 1 1/097.589. 2005/004.8556 A1 3, 2005 Heck Office Action dated May 13, 2009 in U.S. Appl. No. 11/058,689. 2005, OO86718 A1 4/2005 Heard 2006, OOO881.6 A1 1/2006 Lu * cited by examiner 2006,004 1952 A1 2/2006 Cook Primary Examiner Michele KJoike 2006, O137034 A1 6/2006 Schneeberger (74) Attorney, Agent, or Firm Birch, Stewart, Kolasch and 2006, O150283 A1 7/2006 Alexandrov Birch, LLP 2006, O150285 A1 7/2006 Nadzan 2006, O168696 A1 7/2006 Feldmann (57) ABSTRACT 2006/0195934 A1 8/2006 Apuya 2006/0195943 A1 8, 2006 Feldmann The present invention is directed to promoter sequences and 2006/0236421 A1 10, 2006 Pennell promoter control elements, polynucleotide constructs com 2007,0006335 A1 1, 2007 Cook prising the promoters and control elements, and methods of 2007,0006345 A1 1/2007 Alexandrov identifying the promoters, control elements, or fragments 2007/O199090 A1 8/2007 Apuya thereof. The invention further relates to the use of the present promoters or promoter control elements to modulate tran FOREIGN PATENT DOCUMENTS script levels. EP 1033405 9, 2000 WO WOO1f9848O 12/2001 10 Claims, 2 Drawing Sheets U.S. Patent Jan. 11, 2011 Sheet 2 of 2 US 7,868,155 B2 Figure 2 Upstream TATA RNA promoter elements box initation XYXYXY US 7,868,155 B2 1. 2 PROMOTER, PROMOTER CONTROL (3) a polynucleotide having a nucleotide sequence which ELEMENTS, AND COMBINATIONS, AND hybridizes to those shown in Table 1 under a condition USES THEREOF establishing a Tm-20°C. It is another object of the present invention to provide This non-provisional application claims priority under 35 5 isolated polynucleotides that are promoter control element U.S.C. S 119(e) on U.S. to Application No: 10-981,334, filed sequences. These promoter control element sequences com Nov. 4, 2004, and Application No. 60/518,075 filed on Nov. 6, prise, for example, 2003 and Provisional Application No. 60/527,611 filed on (1) a polynucleotide having a nucleotide sequence accord Dec. 4, 2003, the entire contents of which are hereby incor ing to Table 1 or fragment thereof; porated by reference. 10 (2) a polynucleotide having a nucleotide sequence having at least 80% sequence identity to those shown in Table 1 FIELD OF THE INVENTION or fragment thereof, and (3) a polynucleotide having a nucleotide sequence which The present invention relates to promoters and promoter hybridizes to those shown in Table 1 under a condition control elements that are useful for modulating transcription 15 establishing a Tm-20°C. of a desired polynucleotide. Such promoters and promoter Promoter or promoter control element sequences of the control elements can be included in a polynucleotide con present invention are capable of modulating preferential tran struct, expression cassettes, vectors, or inserted into the chro Scription. mosome or as an exogenous element, to modulate in Vivo and In another embodiment, the present promoter control ele in vitro transcription of a polynucleotide. Host cells, includ- 20 ments are capable of Serving as or fulfilling the function, for ing plant cells, and organisms, such as regenerated plants example, as a core promoter, a TATA box, a polymerase therefrom, with desired traits or characteristics using poly binding site, an initiator site, a transcription binding site, an nucleotides comprising the promoters and promoter control enhancer, an inverted repeat, a locus control region, or a elements of the present invention. scaffold/matrix attachment region. 25 It is yet another object of the present invention to provide a BACKGROUND OF THE INVENTION polynucleotide that includes at least a first and a second promoter control element. The first promoter control element This invention relates to the field of biotechnology and, in is a promoter control element sequence as discussed above, particular, to specific promoter sequences and promoter con and the second promoter control element is heterologous to trol element sequences which are useful for the transcription 30 the first control element. Moreover, the first and second con of polynucleotides in a host cell or transformed host organ trol elements are operably linked. Such promoters may modu 1S late transcript levels preferentially in a tissue or under par One of the primary goals of biotechnology is to obtain ticular conditions. organisms, such as plants, mammals, yeast, and prokaryotes In another embodiment, the present isolated polynucle having particular desired characteristics or traits. Examples 35 otide comprises a promoter or a promoter control element as of these characteristic or traits abound and may include, for described above, wherein the promoter or promoter control example, in plants, virus resistance, insect resistance, herbi element is operably linked to a polynucleotide to be tran cide resistance, enhanced Stability or additional nutritional scribed. value. Recent advances in genetic engineering have enabled In another embodiment of the present vector, the promoter researchers in the field to incorporate polynucleotide 40 and promoter control elements of the instant invention are sequences into host cells to obtain the desired qualities in the operably linked to a heterologous polynucleotide that is a organism of choice. This technology permits one or more regulatory sequence. polynucleotides from a source different than the organism of It is another object of the present invention to provide a host choice to be transcribed by the organism of choice. If desired, cell comprising an isolated polynucleotide or vector as the transcription and/or translation of these new polynucle 45 described above or fragment thereof.
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