US 20150240226A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur et al. (43) Pub. Date: Aug. 27, 2015 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/16 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/02 (2006.01) CI2N 9/78 (2006.01) (71) Applicant: BP Corporation North America Inc., CI2N 9/12 (2006.01) Naperville, IL (US) CI2N 9/24 (2006.01) CI2O 1/02 (2006.01) (72) Inventors: Eric J. Mathur, San Diego, CA (US); CI2N 9/42 (2006.01) Cathy Chang, San Marcos, CA (US) (52) U.S. Cl. CPC. CI2N 9/88 (2013.01); C12O 1/02 (2013.01); (21) Appl. No.: 14/630,006 CI2O I/04 (2013.01): CI2N 9/80 (2013.01); CI2N 9/241.1 (2013.01); C12N 9/0065 (22) Filed: Feb. 24, 2015 (2013.01); C12N 9/2437 (2013.01); C12N 9/14 Related U.S. Application Data (2013.01); C12N 9/16 (2013.01); C12N 9/0061 (2013.01); C12N 9/78 (2013.01); C12N 9/0071 (62) Division of application No. 13/400,365, filed on Feb. (2013.01); C12N 9/1241 (2013.01): CI2N 20, 2012, now Pat. No. 8,962,800, which is a division 9/2482 (2013.01); C07K 2/00 (2013.01); C12Y of application No. 1 1/817,403, filed on May 7, 2008, 305/01004 (2013.01); C12Y 1 1 1/01016 now Pat. No. 8,119,385, filed as application No. PCT/ (2013.01); C12Y302/01004 (2013.01); C12Y US2006/007642 on Mar. 3, 2006. 303/02009 (2013.01); C12Y402/02002 (60) Provisional application No. 60/658,984, filed on Mar. (2013.01); C12Y 401/02 (2013.01); C12Y 4, 2005. 301/03 (2013.01) Publication Classification (57) ABSTRACT The invention provides polypeptides, including enzymes, (51) Int. Cl. structural proteins and binding proteins, polynucleotides CI2N 9/88 (2006.01) encoding these polypeptides, and methods of making and CI2O I/04 (2006.01) using these polynucleotides and polypeptides. Polypeptides, CI2N 9/80 (2006.01) including enzymes and antibodies, and nucleic acids of the CI2N 9/26 (2006.01) invention can be used in industrial, experimental, food and CI2N 9/08 (2006.01) feed processing, nutritional and pharmaceutical applications, C07K 2/00 (2006.01) e.g., for food and feed Supplements, colorants, neutraceuti CI2N 9/14 (2006.01) cals, cosmetic and pharmaceutical needs. Patent Application Publication Aug. 27, 2015 Sheet 1 of 4 US 2015/0240226A1 100 COMPUTER SYSTEM INTERNAL STORAGE 118 120 DATA RETREVING DISPLAY DEVICE FIGURE Patent Application Publication Aug. 27, 2015 Sheet 2 of 4 US 2015/0240226A1 201 200 NY START 2O2 STORE NEW SEQUENCE TO A MEMORY - - 4. OPEN DATABASE OF SECRUENCES 20 6 READ FIRST SEQUENCE IN DATABASE 21 O PERFORM COMPARISON OF NEW SEQUENCE AND STORED SEQUENCE YES 214 DISPLAY STORED SEQUENCE NAME TO USER NO 224 GO TO NEXT SEQUENCE IN DATABASE MORE SEQUENCES IN YES DATABASEP NO 220 END FIGURE 2 Patent Application Publication Aug. 27, 2015 Sheet 3 of 4 US 2015/0240226A1 252 250 NY START 254 STORE A FIRST SEQUENCE TO A MEMORY 256 STORE ASECOND SEQUENCE TO A MEMORY 260 READ FIRST CHARACTER OF FIRST SEQUENCE 262 READ FIRST CHARACTER OF SECOND SEQUENCE 264 SAME? - YES 268 y YES READ NEXT CHARACTER OF FIRST AND SECOND SEQUENCES NO 270 NO 274. YES CHARACTERS TO NO -y 276 DSPLAY HOMOLOGY EVEL BE WEEN THE FRST ANE) SECOND SECRUENCES FTGURE 3 Patent Application Publication Aug. 27, 2015 Sheet 4 of 4 US 2015/0240226A1 302 300 Na STAR 304 STORE AFRS SEQUENCE TO MEMORY 306 OPEN DATABASE OF SEQUENCE FEATURES -/ 308 READ FIRST FEATURE FROM DATABASE - 31 O cours FEATUREATTRIBUTESSEQUENCE WITH THE rary YES 318 y- -l DISPLAY FOUND FEATURE TO THE USER NO 326 READ NEXT FEATURE IN DATABASE MORE FEATURES IN YES DAABASE NO 324 END FIGURE A US 2015/0240226 A1 Aug. 27, 2015 NUCLECACDS AND PROTEINS AND these polypeptides, having the activities described in Table 1, METHODS FOR MAKING AND USING THEMI Table 2 or Table 3, below. The enzymes and proteins of the invention have utility in a variety of applications. CROSS-REFERENCE TO RELATED APPLICATIONS SUMMARY OF THE INVENTION 0001. This application is a divisional application of U.S. 0007. The invention provides isolated or recombinant application Ser. No. 13/400,365 filed Feb. 20, 2012, now nucleic acids comprising a nucleic acid sequence having at issued as U.S. Pat. No. 8,962,800; which is a divisional appli least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, cation of U.S. application Ser. No. 1 1/817.403 filed May 7, 58%, 59%, 60%, 61%. 62%, 63%, 64%. 65%, 66%, 67%, 2008, now issued as U.S. Pat. No. 8,119,385; which is a 35 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, USC S371 National Stage application of International Appli 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, cation No. PCT/US2006/007642 filed Mar. 3, 2006; which 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, claims the benefit under 35 USC S 119(e) to U.S. Application 98%, 99%, or more, or complete (100%) sequence identity to Ser. No. 60/658,984 filed Mar. 4, 2005, now expired. The an exemplary nucleic acid of the invention, e.g., including disclosure of each of the prior applications is considered part SEQID NO:1, SEQID NO:3, SEQID NO:5, SEQID NO:7, of and is incorporated by reference in the disclosure of this SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID application. NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, and all nucleic acids dis BACKGROUND OF THE INVENTION closed in the SEQID listing, which include all odd numbered SEQID NO:s from SEQ ID NO:1 through SEQ ID NO:26, 0002 1. Field of the Invention 897, over a region of at least about 10, 20, 25, 30, 35, 40, 45, 0003. This invention relates to molecular and cellular biol 50, 75, 100, 150, 200,250, 300,350, 400, 450, 500,550, 600, ogy and biochemistry. In one aspect, the invention provides 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, polypeptides, including enzymes, structural proteins and 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, binding proteins (e.g., ligands, receptors), polynucleotides 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050,2100, 2200, encoding these polypeptides, and methods of making and 2250, 2300, 2350, 2400, 2450, 2500, or more residues, using these polynucleotides and polypeptides. In one aspect, encodes at least one polypeptide having an enzyme, structural the invention is directed to polypeptides, e.g., enzymes, struc orbinding activity, and the sequence identities are determined tural proteins and binding proteins, including thermostable by analysis with a sequence comparison algorithm or by a and thermotolerant activity, and polynucleotides encoding visual inspection. In one aspect, the enzymes and proteins of these enzymes, structural proteins and binding proteins and the invention include, e.g., aldolases, alpha-galactosidases, making and using these polynucleotides and polypeptides. amidases, e.g., secondary amidases, amylases, catalases, The polypeptides of the invention can be used in a variety of carotenoid pathway enzymes, dehalogenases, endogluca pharmaceutical, agricultural and industrial contexts, includ nases, epoxide hydrolases, esterases, hydrolases, glucosi ing the manufacture of cosmetics and nutraceuticals. dases, glycosidases, inteins, isomerases, laccases, lipases, 0004 Additionally, the polypeptides of the invention can monooxygenases, nitroreductases, nitrilases, P450 enzymes, be used in food processing, brewing, bath additives, alcohol pectate lyases, phosphatases, phospholipases, phytases, poly production, peptide synthesis, enantioselectivity, hide prepa merases and Xylanases. In another aspect, the isolated and ration in the leather industry, waste management and animal recombinant polypeptides of the invention, including degradation, silver recovery in the photographic industry, enzymes, structural proteins and binding proteins, and poly medical treatment, silk degumming, biofilm degradation, nucleotides encoding these polypeptides, of the invention biomass conversion to ethanol, biodefense, antimicrobial have activity as described in Table 1, Table 2 or Table 3, agents and disinfectants, personal care and cosmetics, biotech below. reagents, in corn wet milling and pharmaceuticals such as 0008. In one aspect, the invention also provides isolated or digestive aids and anti-inflammatory (anti-phlogistic) agents. recombinant nucleic acids with a common novelty in that they 0005 2. Background Information are all derived from a common Source, e.g., an environmental 0006. The invention provides isolated and recombinant Source, mixed environmental sources or mixed cultures. The polypeptides, including enzymes, structural proteins and invention provides isolated or recombinant nucleic acids iso binding proteins, polynucleotides encoding these polypep lated from a common Source, e.g., an environmental source, tides, and methods of making and using these polynucleotides mixed environmental sources or mixed cultures comprising a and polypeptides. The polypeptides of the invention, and the polynucleotide of the invention, e.g., an exemplary sequence polynucleotides encoding the polypeptides of the invention, of the invention, including SEQ ID NO:1, SEQ ID NO:3, encompass many classes of enzymes, structural proteins and SEQID NO:5, SEQID NO:7, SEQIDNO:9, SEQID NO:11, binding proteins. In one aspect, the enzymes and proteins of SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID the invention include, e.g., aldolases, alpha-galactosidases, NO:19, SEQID NO:21, SEQID NO:23, SEQID NO:25, and amidases, e.g., secondary amidases, amylases, catalases, all nucleic acids disclosed in the SEQ ID listing, which carotenoid pathway enzymes, dehalogenases, endogluca include all odd numbered SEQID NO:s from SEQID NO:1 nases, epoxide hydrolases, esterases, hydrolases, glucosi through SEQID NO:26,897, over a region of at least about dases, glycosidases, inteins, isomerases, laccases, lipases, 10, 15, 20, 25, 30, 35, 40, 45,50, 75, 100, 150, 200, 250,300, monooxygenases, nitroreductases, nitrilases, P450 enzymes, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, pectate lyases, phosphatases, phospholipases, phytases, poly 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, merases and Xylanases.