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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.
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    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
  • 1 AMINO ACIDS Commonly, 21 L-Amino Acids Encoded by DNA Represent the Building Blocks of Animal, Plant, and Microbial Proteins

    1 AMINO ACIDS Commonly, 21 L-Amino Acids Encoded by DNA Represent the Building Blocks of Animal, Plant, and Microbial Proteins

    1 AMINO ACIDS Commonly, 21 L-amino acids encoded by DNA represent the building blocks of animal, plant, and microbial proteins. The basic amino acids encountered in proteins are called proteinogenic amino acids 1.1). Biosynthesis of some of these amino acids proceeds by ribosomal processes only in microorganisms and plants and the ability to synthesize them is lacking in animals, including human beings. These amino acids have to be obtained in the diet (or produced by hydrolysis of body proteins) since they are required for normal good health and are referred to as essential amino acids. The essential amino acids are arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The rest of encoded amino acids are referred to as non-essential amino acids (alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine). Arginine and histidine are classified as essential, sometimes as semi-essential amino acids, as their amount synthesized in the body is not sufficient for normal growth of children. Although it is itself non-essential, cysteine (classified as conditionally essential amino acid) can partly replace methionine, which is an essential amino acid. Similarly, tyrosine can partly replace phenylalanine. 1.1 The glutamic acid group 1.1.1 Glutamic acid and glutamine Free ammonium ions are toxic to living cells and are rapidly incorporated into organic compounds. One of such transformations is the reaction of ammonia with 2-oxoglutaric acid from the citric acid cycle to produce L-glutamic acid. This reaction is known as reductive amination. Glutamic acid is accordingly the amino acid generated first as both constituent of proteins and a biosynthetic precursor.