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(12) United States Patent (10) Patent No.: US 8,962,800 B2 Mathur Et Al

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(12) United States Patent (10) Patent No.: US 8,962,800 B2 Mathur Et Al USOO89628OOB2 (12) United States Patent (10) Patent No.: US 8,962,800 B2 Mathur et al. (45) Date of Patent: Feb. 24, 2015 (54) NUCLEICACIDS AND PROTEINS AND USPC .......................................................... 530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Naperville, IL (US) PUBLICATIONS (*) Notice: Subject to any disclaimer, the term of this Nolling etal (J. Bacteriol. 183: 4823 (2001).* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 0 days. Isolates of Pseudomonas aeruginosa J. Bacteriol. (2003) 185: 1316-1325. (21) Appl. No.: 13/400,365 2002.Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (22) Filed: Feb. 20, 2012 bor New York, 2001, pp. 382-393. O O Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (65) Prior Publication Data toxicology” Toxicol. Lett. (2000) 1.12: 365-370. US 2012/O266329 A1 Oct. 18, 2012 * cited by examiner Related U.S. Application Data - - - Primary Examiner — James Martinell (62) Division of application No. 1 1/817,403, filed as (74) Attorney, Agent, or Firm — DLA Piper LLP (US) application No. PCT/US2006/007642 on Mar. 3, 2006, now Pat. No. 8,119,385. (57) ABSTRACT (60) Provisional application No. 60/658,984, filed on Mar. The invention provides polypeptides, including enzymes, 4, 2005. structural proteins and binding proteins, polynucleotides encoding these polypeptides, and methods of making and (51) Int. Cl. using these polynucleotides and polypeptides. Polypeptides, CI2N 9/00 (2006.01) including enzymes and antibodies, and nucleic acids of the C07K I4/00 (2006.01) invention can be used in industrial, experimental, food and CI2N 9/34 (2006.01) feed processing, nutritional and pharmaceutical applications, CI2N 9/42 (2006.01) e.g., for food and feed Supplements, colorants, neutraceuti (52) U.S.AV e. Clwe CalS,1 COSmet1Cic anand ph armaceut1calical needneeds. CPC ................ CI2N 9/00 (2013.01); C12N 9/2428 (2013.01); C12N 9/2445 (2013.01) 18 Claims, 4 Drawing Sheets U.S. Patent Feb. 24, 2015 Sheet 1 of 4 US 8,962,800 B2 COMPUTER SYSTEM PROCESSOR | s. - - 15 - - NERNA. 110 A / SrAGE / her CRY / 4 120 Refers SPAY EWC, GRE U.S. Patent Feb. 24, 2015 Sheet 2 of 4 US 8,962,800 B2 2 N SORE NEW SEGENCE O AMOY - E AAAS OF SES --a-a-a-we-a-W-----& M-- mo M-m----------- 28 READ FRS SELENCE MAASASE |- PERFORM comparison OF NEW SEQUENCEAN SORE SECUENCE —ss| YES O. EX SCE 2 is AAAS - ore SES AAEASE E. E. U.S. Patent Feb. 24, 2015 Sheet 3 of 4 US 8,962,800 B2 252 SAR 254 STORE AFRS SQUENCEO A MeMORY H M. 256 SOREA SECONSEQUENCE O AMEMORY l/ -- 260 READ FRST CHARACER OF FIRS SEQUENCE --- m 262 READ FIRST CHARACTER OF SECOND SEQUENCE -- SAME? stm- ------ YES 268 READ NEXTCHARACTER OF FIRST AND second YES SECUENCES NO NO -itsORE 274 YES <CHARACTERSsRap. to p 26 SPAYHOMOOGY EVE 3ETWEEN HE FRS ANd SECOND SEQUENCES END FIGURE 3 U.S. Patent Feb. 24, 2015 Sheet 4 of 4 US 8,962,800 B2 302 30 3.4 SOREA FRS SEQUENCE O MEMORY - 306 OEN AABAS OF SEC ENCE FEATURE3 -xH-xx-xx-wx -mwo-www.www. 38 READ FIRST FEATURE FROM dAAbASE |- -M www.www.xm:-Xx-w- www 3. CC Are FAREA TreuS With the FRS SECENCE a---reco- Wexor w -as- s is ty s 3.18 ------- --d SPAY FOUND FEATURE TO EuSER &-------------------- REAs NEX FAUREN 3. AABASE - r FATRES ---own----YES-- AAEASE FIU US 8,962,800 B2 1. 2 NUCLECACDS AND PROTEINS AND Table 2 or Table 3, below. The enzymes and proteins of the METHODS FOR MAKING AND USING THEMI invention have utility in a variety of applications. CROSS-REFERENCE TO RELATED SUMMARY APPLICATIONS The invention provides isolated or recombinant nucleic This application is a divisional of U.S. patent application acids comprising a nucleic acid sequence having at least Ser. No. 1 1/817,403, filed Aug. 29, 2007, now U.S. Pat. No. about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 8,119,385; which is the U.S. national phase, pursuant to 35 59%, 60%, 61%, 62%, 63%, 64%. 65%, 66%, 67%, 68%, 10 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, U.S.C. S371, of international application number PCT/ 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, US2006/007642, filed Mar. 3, 2006, designating the United 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, States and published on Sep. 14, 2006 as publication number 99%, or more, or complete (100%) sequence identity to an WO 2006/096527, which claims priority under 35 USC S 119 exemplary nucleic acid of the invention, e.g., including SEQ (e)(1) of prior U.S. provisional application No. 60/658,984, 15 ID NO:1, SEQID NO:3, SEQID NO:5, SEQID NO:7, SEQ filed Mar. 4, 2005, all of which are hereby incorporated by ID NO:9, SEQID NO:11, SEQID NO:13, SEQID NO:15, reference. SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQID NO:25, and all nucleic acids disclosed in the FIELD OF THE INVENTION SEQ ID listing, which include all odd numbered SEQ ID NO:s from SEQID NO:1 through SEQID NO:26,897, over a This invention relates to molecular and cellular biology region of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, and biochemistry. In one aspect, the invention provides 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, polypeptides, including enzymes, structural proteins and 700, 750, 800, 850, 900,950, 1000, 1050, 1100, 1150, 1200, binding proteins (e.g., ligands, receptors), polynucleotides 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, encoding these polypeptides, and methods of making and 25 1750, 1800, 1850, 1900, 1950, 2000, 2050,2100,2200,2250, using these polynucleotides and polypeptides. In one aspect, 2300, 2350, 2400, 2450, 2500, or more residues, encodes at the invention is directed to polypeptides, e.g., enzymes, struc least one polypeptide having an enzyme, structural or binding tural proteins and binding proteins, including thermostable activity, and the sequence identities are determined by analy and thermotolerant activity, and polynucleotides encoding sis with a sequence comparison algorithm or by a visual these enzymes, structural proteins and binding proteins and 30 inspection. In one aspect, the enzymes and proteins of the making and using these polynucleotides and polypeptides. invention include, e.g. aldolases, alpha-galactosidases, ami The polypeptides of the invention can be used in a variety of dases, e.g. secondary amidases, amylases, catalases, caro pharmaceutical, agricultural and industrial contexts, includ tenoid pathway enzymes, dehalogenases, endoglucanases, ing the manufacture of cosmetics and nutraceuticals. epoxide hydrolases, esterases, hydrolases, glucosidases, gly 35 cosidases, inteins, isomerases, laccases, lipases, monooxyge Additionally, the polypeptides of the invention can be used nases, nitroreductases, nitrilases, P450 enzymes, pectate in food processing, brewing, bath additives, alcohol produc lyases, phosphatases, phospholipases, phytases, polymerases tion, peptide synthesis, enantioselectivity, hide preparation in and Xylanases. In another aspect, the isolated and recombi the leather industry, waste management and animal degrada nant polypeptides of the invention, including enzymes, struc tion, silver recovery in the photographic industry, medical 40 tural proteins and binding proteins, and polynucleotides treatment, silk degumming, biofilm degradation, biomass encoding these polypeptides, of the invention have activity as conversion to ethanol, biodefense, antimicrobial agents and described in Table 1, Table 2 or Table 3, below. disinfectants, personal care and cosmetics, biotech reagents, In one aspect, the invention also provides isolated or in corn wet milling and pharmaceuticals such as digestive recombinant nucleic acids with a common novelty in that they aids and anti-inflammatory (anti-phlogistic) agents. 45 are all derived from a common Source, e.g., an environmental Source, mixed environmental sources or mixed cultures. The BACKGROUND invention provides isolated or recombinant nucleic acids iso lated from a common Source, e.g. an environmental source, The invention provides isolated and recombinant polypep mixed environmental sources or mixed cultures comprising a tides, including enzymes, structural proteins and binding pro 50 polynucleotide of the invention, e.g., an exemplary sequence teins, polynucleotides encoding these polypeptides, and of the invention, including SEQ ID NO:1, SEQ ID NO:3, methods of making and using these polynucleotides and SEQID NO:5, SEQID NO:7, SEQIDNO:9, SEQID NO:11, polypeptides. The polypeptides of the invention, and the SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID polynucleotides encoding the polypeptides of the invention, NO:19, SEQID NO:21, SEQID NO:23, SEQID NO:25, and encompass many classes of enzymes, structural proteins and 55 all nucleic acids disclosed in the SEQ ID listing, which binding proteins. In one aspect, the enzymes and proteins of include all odd numbered SEQID NO:s from SEQID NO:1 the invention include, e.g. aldolases, alpha-galactosidases, through SEQID NO:26,897, over a region of at least about amidases, e.g. secondary amidases, amylases, catalases, caro 10, 15, 20, 25, 30, 35, 40, 45,50, 75, 100, 150, 200, 250,300, tenoid pathway enzymes, dehalogenases, endoglucanases, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, epoxide hydrolases, esterases, hydrolases, glucosidases, gly 60 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, cosidases, inteins, isomerases, laccases, lipases, monooxyge 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, nases, nitroreductases, nitrilases, P450 enzymes, pectate 1950, 2000, 2050,2100, 2200,2250,2300, 2350,2400, 2450, lyases, phosphatases, phospholipases, phytases, polymerases 2500, or more residues, encodes at least one polypeptide and Xylanases.
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