Bioprospecting in the Genomic Age

Advances in Applied Microbiology

Volumn 87, Issue , 2014, Pages 111-146

  Hicks, Michael A ^a   Prather, Kristala L J ^a,b  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Biocatalysts; Enzyme engineering; Function based bioprospecting; Gene based bioprospecting; Protein similarity networks

Indexed keywords

DNA POLYMERASE; ENZYME; MANDELATE RACEMASE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOCATALYSIS; COST; DNA REPLICATION; DNA SHUFFLING; ENZYME ENGINEERING; GENOME ANALYSIS; GENOMICS; HETEROLOGOUS EXPRESSION; HUMAN; METAGENOME; METAGENOMICS; MICROFLORA; MOLECULAR LIBRARY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ENGINEERING; PYROSEQUENCING; SCREENING; STRUCTURE ACTIVITY RELATION;

BIOCATALYSTS; ENZYME ENGINEERING; FUNCTION-BASED BIOPROSPECTING; GENE-BASED BIOPROSPECTING; PROTEIN SIMILARITY NETWORKS;

CATALYSIS; GENOMICS; METAGENOMICS; PROTEIN ENGINEERING; PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 84894461463     PISSN: 00652164     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-800261-2.00003-7     Document Type: Chapter

References (148)

1. Aharoni A., Gaidukov L., Yagur S., Toker L., Silman I., Tawfik D.S. Directed evolution of mammalian paraoxonases PON1 and PON3 for bacterial expression and catalytic specialization. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(2):482-487.
2. Allen K.N., Dunaway-Mariano D. Phosphoryl group transfer: Evolution of a catalytic scaffold. Trends in Biochemical Sciences 2004, 29(9):495-503.
3. Almonacid D.E., Babbitt P.C. Toward mechanistic classification of enzyme functions. Current Opinion in Chemical Biology 2011, 15(3):435-442.
4. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology 1990, 215(3):403-410.
5. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 1997, 25(17):3389-3402.
6. +. FEBS Journal 2008, 275(15):3859-3869.
7. Aneja P., Charles T.C. Poly-3-hydroxybutyrate degradation in Rhizobium (Sinorhizobium) meliloti: Isolation and characterization of a gene encoding 3-hydroxybutyrate dehydrogenase. Journal of Bacteriology 1999, 181(3):849-857.
8. Aneja P., Dziak R., Cai G.-Q., Charles T.C. Identification of an acetoacetyl coenzyme a synthetase-dependent pathway for utilization of l-(+)-3-hydroxybutyrate in Sinorhizobium meliloti. Journal of Bacteriology 2002, 184(6):1571-1577.
9. Anton B.P., Chang Y.C., Brown P., Choi H.-P., Faller L.L., Guleria J., et al. The COMBREX project: Design, methodology, and initial results. PLoS Biology 2013, 11(8):e1001638.
10. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene Ontology: Tool for the unification of biology. Nature Genetics 2000, 25(1):25-29.
11. Atkinson H.J., Babbitt P.C. An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Computational Biology 2009, 5(10):e1000541.
12. Atkinson H.J., Babbitt P.C. Glutathione transferases are structural and functional outliers in the thioredoxin fold. Biochemistry 2009, 48(46):11108-11116.
13. Atkinson H.J., Babbitt P.C., Sajid M. The global cysteine peptidase landscape in parasites. Trends in Parasitology 2009, 25(12):573-581.
14. Atkinson H.J., Morris J.H., Ferrin T.E., Babbitt P.C. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One 2009, 4(2):e4345.
15. Axarli I., Prigipaki A., Labrou N.E. Engineering the substrate specificity of cytochrome P450 CYP102A2 by directed evolution: Production of an efficient enzyme for bioconversion of fine chemicals. Biomolecular Engineering 2005, 22(1-3):81-88.
16. Babbitt P.C., Hasson M.S., Wedekind J.E., Palmer D.R.J., Barrett W.C., Reed G.H., et al. The enolase superfamily: A general strategy for enzyme-catalyzed abstraction of the α-protons of carboxylic acids. Biochemistry 1996, 35(51):16489-16501.
17. Baker D., Sali A. Protein structure prediction and structural genomics. Science 2001, 294(5540):93-96.
18. Barber A.E., Babbitt P.C. Pythoscape: A framework for generation of large protein similarity networks. Bioinformatics 2012, 28(21):2845-2846.
19. Bar-Even A., Noor E., Savir Y., Liebermeister W., Davidi D., Tawfik D.S., et al. The moderately efficient enzyme: Evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 2011, 50(21):4402-4410.
20. Benson D.A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., et al. GenBank. Nucleic Acids Research 2013, 41(D1):D36-D42.
21. Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59.
22. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Brice M.D., Rodgers J.R., et al. The protein data bank: A computer-based archival file for macromolecular structures. Archives of Biochemistry and Biophysics 1978, 185(2):584-591.
23. Binga E.K., Lasken R.S., Neufeld J.D. Something from (almost) nothing: The impact of multiple displacement amplification on microbial ecology. ISME Journal 2008, 2(3):233-241.
24. Bitar A.P., Cao M., Marquis H. The metalloprotease of Listeria monocytogenes is activated by intramolecular autocatalysis. Journal of Bacteriology 2008, 190(1):107-111.
25. Blaby-Haas C.E., Merchant S.S. The ins and outs of algal metal transport. Biochimica et Biophysica Acta 2012, 1823(9):1531-1552.
26. Bloom J.D., Labthavikul S.T., Otey C.R., Arnold F.H. Protein stability promotes evolvability. Proceedings of the National Academy of Sciences of the United States of America 2006, 103(15):5869-5874.
27. Bommarius A.S. Protein engineering: Check nature first, then evolve. Nature Chemical Biology 2010, 6(11):793-794.
28. Bornscheuer U.T., Kazlauskas R.J. Other hydrolases. Hydrolases in organic synthesis 2006, 241-248. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG (Federal Republic of Germany).
29. Brown S.D., Babbitt P.C. Inference of functional properties from large-scale analysis of enzyme superfamilies. Journal of Biological Chemistry 2012, 287(1):35-42.
30. Brown S., Gerlt J., Seffernick J., Babbitt P. A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biology 2006, 7(1):R8.
31. Calamia J., Manoil C. lac permease of Escherichia coli: Topology and sequence elements promoting membrane insertion. Proceedings of the National Academy of Sciences of the United States of America 1990, 87(13):4937-4941.
32. Chaisson M., Pevzner P., Tang H. Fragment assembly with short reads. Bioinformatics 2004, 20(13):2067-2074.
33. Chan W.Y., Wong M., Guthrie J., Savchenko A.V., Yakunin A.F., Pai E.F., et al. Sequence- and activity-based screening of microbial genomes for novel dehalogenases. Microbial Biotechnology 2010, 3(1):107-120.
34. Charles T.C., Cai G.-Q., Aneja P. Megaplasmid and chromosomal loci for the PHB degradation pathway in Rhizobium (Sinorhizobium) meliloti. Genetics 1997, 146(4):1211-1220.
35. Charuvaka A., Rangwala H. Evaluation of short read metagenomic assembly. BMC Genomics 2011, 12(Suppl. 2):S8.
36. Chin C.-S., Alexander D.H., Marks P., Klammer A.A., Drake J., Heiner C., et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods 2013, 10(6):563-569.
37. Christianson D.W. Structural biology and chemistry of the terpenoid cyclases. Chemical Reviews 2006, 106(8):3412-3442.
38. Chuang Y.C., Chang T.M., Chang M.C. Cloning and characterization of the gene (empV) encoding extracellular metalloprotease from Vibrio vulnificus. Gene 1997, 189(2):163-168.
39. Cobb R.E., Si T., Zhao H. Directed evolution: An evolving and enabling synthetic biology tool. Current Opinion in Chemical Biology 2012, 16(3-4):285-291.
40. Das R., Baker D. Macromolecular modeling with Rosetta. Annual Review of Biochemistry 2008, 77(1):363-382.
41. Delavat F., Phalip V., Forster A., Plewniak F., Lett M.-C., Lièvremont D. Amylases without known homologues discovered in an acid mine drainage: Significance and impact. Scientific Reports 2012, 2.
42. Der B.S., Kluwe C., Miklos A.E., Jacak R., Lyskov S., Gray J.J., et al. Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. PLoS One 2013, 8(5):e64363.
43. Durani V., Magliery T.J. Protein engineering and stabilization from sequence statistics: Variation and covariation analysis. Methods in enzymology 2013, Vol. 523:237-256. Academic Press, Waltham, Massachusetts, (chapter 11). E.K. Amy (Ed.).
44. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323(5910):133-138.
45. Ekkers D., Cretoiu M., Kielak A., Elsas J. The great screen anomaly-A new frontier in product discovery through functional metagenomics. Applied Microbiology and Biotechnology 2012, 93(3):1005-1020.
46. Esvelt K.M., Carlson J.C., Liu D.R. A system for the continuous directed evolution of biomolecules. Nature 2011, 472(7344):499-503.
47. Fernández-Arrojo L., Guazzaroni M.-E., López-Cortés N., Beloqui A., Ferrer M. Metagenomic era for biocatalyst identification. Current Opinion in Biotechnology 2010, 21(6):725-733.
48. Ferrer M., Ghazi A., Beloqui A., Vieites J.M., López-Cortés N., Marín-Navarro J., et al. Functional metagenomics unveils a multifunctional glycosyl hydrolase from the family 43 catalysing the breakdown of plant polymers in the calf rumen. PLoS One 2012, 7(6):e38134.
49. Fields G.B., Alonso D.O.V., Stigter D., Dill K.A. Theory for the aggregation of proteins and copolymers. The Journal of Physical Chemistry 1992, 96(10):3974-3981.
50. Fink A.L. Protein aggregation: Folding aggregates, inclusion bodies and amyloid. Folding and Design 1998, 3(1):R9-R23.
51. Frickey T., Lupas A. CLANS: A Java application for visualizing protein families based on pairwise similarity. Bioinformatics 2004, 20(18):3702-3704.
52. Furnham N., de Beer T.A.P., Thornton J.M. Current challenges in genome annotation through structural biology and bioinformatics. Current Opinion in Structural Biology 2012, 22(5):594-601.
53. Gabor E.M., Alkema W.B.L., Janssen D.B. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environmental Microbiology 2004, 6(9):879-886.
54. Gerlt J.A., Allen K.N., Almo S.C., Armstrong R.N., Babbitt P.C., Cronan J.E., et al. The Enzyme Function Initiative. Biochemistry 2011, 50(46):9950-9962.
55. Gerlt J.A., Babbitt P.C. Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies. Annual Review of Biochemistry 2001, 70(1):209-246.
56. Gerlt J.A., Babbitt P.C., Jacobson M.P., Almo S.C. Divergent evolution in enolase superfamily: Strategies for assigning functions. Journal of Biological Chemistry 2012, 287(1):29-34.
57. Gilks W.R., Audit B., De Angelis D., Tsoka S., Ouzounis C.A. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 2002, 18(12):1641-1649.
58. Gilks W.R., Audit B., de Angelis D., Tsoka S., Ouzounis C.A. Percolation of annotation errors through hierarchically structured protein sequence databases. Mathematical Biosciences 2005, 193(2):223-234.
59. Glenn T.C. Field guide to next-generation DNA sequencers. Molecular Ecology Resources 2011, 11(5):759-769.
60. Godoy-Ruiz R., Perez-Jimenez R., Ibarra-Molero B., Sanchez-Ruiz J.M. A stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization. Biophysical Journal 2005, 89(5):3320-3331.
61. Goldsmith M., Ashani Y., Simo Y., Ben-David M., Leader H., Silman I., et al. Evolved stereoselective hydrolases for broad-spectrum G-type nerve agent detoxification. Chemistry & Biology 2012, 19(4):456-466.
62. Goldsmith M., Tawfik D.S. Enzyme engineering by targeted libraries. Methods in enzymology 2013, Vol. 523:257-283. Academic Press, Waltham, Massachusetts, (chapter 12). E.K. Amy (Ed.).
63. Graham J.E., Clark M.E., Nadler D.C., Huffer S., Chokhawala H.A., Rowland S.E., et al. Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment. Nature Communications 2011, 2:375.
64. Haft D.H., Selengut J.D., Richter R.A., Harkins D., Basu M.K., Beck E. TIGRFAMs and Genome Properties in 2013. Nucleic Acids Research 2013, 41(D1):D387-D395.
65. Hasan F., Shah A.A., Hameed A. Industrial applications of microbial lipases. Enzyme and Microbial Technology 2006, 39(2):235-251.
66. Häse C.C., Finkelstein R.A. Bacterial extracellular zinc-containing metalloproteases. Microbiological Reviews 1993, 57(4):823-837.
67. Heinzelman P., Komor R., Kanaan A., Romero P., Yu X., Mohler S., et al. Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination. Protein Engineering Design and Selection 2010, 23(11):871-880.
68. Henson J., Tischler G., Ning Z. Next-generation sequencing and large genome assemblies. Pharmacogenomics 2012, 13(8):901-915.
69. Herman A., Tawfik D.S. Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): A versatile tool for generating targeted libraries. Protein Engineering Design and Selection 2007, 20(5):219-226.
70. Heurgue-Hamard V., Champ S., Engstrom A., Ehrenberg M., Buckingham R.H. The hemK gene in Escherichia coli encodes the N5-glutamine methyltransferase that modifies peptide release factors. EMBO Journal 2002, 21(4):769-778.
71. Hicks M.A., Barber A.E., Giddings L.-A., Caldwell J., O'Connor S.E., Babbitt P.C. The evolution of function in strictosidine synthase-like proteins. Proteins: Structure, Function, and Bioinformatics 2011, 79(11):3082-3098.
72. Höhne M., Schätzle S., Jochens H., Robins K., Bornscheuer U.T. Rational assignment of key motifs for function guides in silico enzyme identification. Nature Chemical Biology 2010, 6(11):807-813.
73. Huang Y.-F., Chen S.C., Chiang Y.-S., Chen T.-H., Chiu K.-P. Palindromic sequence impedes sequencing-by-ligation mechanism. BMC Systems Biology 2012, 6(Suppl. 2):S10.
74. Hunter S., Jones P., Mitchell A., Apweiler R., Attwood T.K., Bateman A., et al. InterPro in 2011: New developments in the family and domain prediction database. Nucleic Acids Research 2012, 40(D1):D306-D312.
75. Hwang C.-S., Choi E.-S., Han S.-S., Kim G.-J. Screening of a highly soluble and oxygen-independent blue fluorescent protein from metagenome. Biochemical and Biophysical Research Communications 2012, 419(4):676-681.
76. Jenney F., Adams M.W. The impact of extremophiles on structural genomics (and vice versa). Extremophiles 2008, 12(1):39-50.
77. Kanehisa M., Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 2000, 28(1):27-30.
78. Kanehisa M., Goto S., Sato Y., Furumichi M., Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research 2012, 40(D1):D109-D114.
79. Kim S.-K., Yang J.-Y., Cha J. Cloning and sequence analysis of a novel metalloprotease gene from Vibrio parahaemolyticus 04. Gene 2002, 283(1-2):277-286.
80. Kirk O., Borchert T.V., Fuglsang C.C. Industrial enzyme applications. Current Opinion in Biotechnology 2002, 13(4):345-351.
81. Kristensen D.M., Kannan L., Coleman M.K., Wolf Y.I., Sorokin A., Koonin E.V., et al. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 2010, 26(12):1481-1487.
82. Labrou N.E. Random mutagenesis methods for in vitro directed enzyme evolution. Current Protein & Peptide Science 2010, 11(1):91-100.
83. Lämmle K., Zipper H., Breuer M., Hauer B., Buta C., Brunner H., et al. Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. Journal of Biotechnology 2007, 127(4):575-592.
84. Lawrence M.S., Phillips K.J., Liu D.R. Supercharging proteins can impart unusual resilience. Journal of the American Chemical Society 2007, 129(33):10110-10112.
85. Leaver-Fay A., Tyka M., Lewis S.M., Lange O.F., Thompson J., Jacak R., et al. Rosetta3: An object-oriented software suite for the simulation and design of macromolecules. Methods in enzymology 2011, Vol. 487:545-574. Academic Press, Waltham, Massachusetts, (chapter 19). L.J. Michael, B. Ludwig (Eds.).
86. Leis B., Angelov A., Liebl W. Screening and expression of genes from metagenomes. Advances in applied microbiology 2013, Vol. 83:1-68. Academic Press, Waltham, Massachusetts, (chapter 1). S. Sima, M.G. Geoffrey (Eds.).
87. Li W., Kinch L.N., Grishin N.V. Pclust: Protein network visualization highlighting experimental data. Bioinformatics 2013, 29(20):2647-2648.
88. Liebl W. Metagenomics. Encyclopedia of geobiology 2011, 553-558. Springer, The Netherlands. J. Reitner, V. Thiel (Eds.).
89. Liu L., Li Y., Li S., Hu N., He Y., Pong R., et al. Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology 2012, 2012:11.
90. Lorenz P., Eck J. Metagenomics and industrial applications. Nature Reviews. Microbiology 2005, 3(6):510-516.
91. Madison L.L., Huisman G.W. Metabolic engineering of poly(3-hydroxyalkanoates): From DNA to plastic. Microbiology and Molecular Biology Reviews 1999, 63(1):21-53.
92. Malik M.S., Park E.-S., Shin J.-S. Features and technical applications of ω-transaminases. Applied Microbiology and Biotechnology 2012, 94(5):1163-1171.
93. Mardis E.R. The impact of next-generation sequencing technology on genetics. Trends in Genetics 2008, 24(3):133-141.
94. Maurer K.-H. Detergent proteases. Current Opinion in Biotechnology 2004, 15(4):330-334.
95. McMahon M.D., Guan C., Handelsman J., Thomas M.G. Metagenomic analysis of Streptomyces lividans reveals host-dependent functional expression. Applied and Environmental Microbiology 2012, 78(10):3622-3629.
96. Metzker M.L. Sequencing technologies-The next generation. Nature Reviews. Genetics 2010, 11(1):31-46.
97. Mi H., Muruganujan A., Casagrande J.T., Thomas P.D. Large-scale gene function analysis with the PANTHER classification system. Nature Protocols 2013, 8(8):1551-1566.
98. Mi H., Muruganujan A., Thomas P.D. PANTHER in 2013: Modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Research 2013, 41(D1):D377-D386.
99. Miyoshi S., Kawata K., Tomochika K., Shinoda S., Yamamoto S. The C-terminal domain promotes the hemorrhagic damage caused by Vibrio vulnificus metalloprotease. Toxicon 2001, 39(12):1883-1886.
100. Nakahigashi K., Kubo N., Narita S.-I., Shimaoka T., Goto S., Oshima T., et al. HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(3):1473-1478.
101. Nakayashiki T., Nishimura K., Inokuchi H. Cloning and sequencing of a previously unidentified gene that is involved in the biosynthesis of heme in Escherichia coli. Gene 1995, 153(1):67-70.
102. Nordeste R., Trainer M., Charles T. Methods for the isolation of genes encoding novel PHB cycle enzymes from complex microbial communities. Metagenomics 2010, Vol. 668:235-246. Humana Press, New York. W.R. Streit, R. Daniel (Eds.).
103. O'Boyle N.M., Holliday G.L., Almonacid D.E., Mitchell J.B.O. Using reaction mechanism to measure enzyme similarity. Journal of Molecular Biology 2007, 368(5):1484-1499.
104. Pegg S.C.H., Brown S.D., Ojha S., Seffernick J., Meng E.C., Morris J.H., et al. Leveraging enzyme structure-function relationships for functional inference and experimental design: The structure-function linkage database. Biochemistry 2006, 45(8):2545-2555.
105. Pelletier E., Kreimeyer A., Bocs S., Rouy Z., Gyapay G., Chouari R., et al. "Candidatus Cloacamonas acidaminovorans": Genome sequence reconstruction provides a first glimpse of a new bacterial division. Journal of Bacteriology 2008, 190(7):2572-2579.
106. Perret A., Lechaplais C., Tricot S., Perchat N., Vergne C., Pellé C., et al. A novelacyl-CoA beta-transaminase characterized from a metagenome. PLoS One 2011, 6(8):e22918.
107. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., et al. UCSF Chimera-A visualization system for exploratory research and analysis. Journal of Computational Chemistry 2004, 25(13):1605-1612.
108. Pieper U., Chiang R., Seffernick J., Brown S., Glasner M., Kelly L., et al. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. Journal of Structural and Functional Genomics 2009, 10(2):107-125.
109. Pirie C.M., De Mey M., Prather K.L.J., Ajikumar P.K. Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis. ACS Chemical Biology 2013, 8(4):662-672.
110. Punta M., Coggill P.C., Eberhardt R.Y., Mistry J., Tate J., Boursnell C., et al. The Pfam protein families database. Nucleic Acids Research 2012, 40(D1):D290-D301.
111. Quail M., Smith M., Coupland P., Otto T., Harris S., Connor T., et al. A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012, 13(1):341.
112. Radivojac P., Clark W.T., Oron T.R., Schnoes A.M., Wittkop T., Sokolov A., et al. A large-scale evaluation of computational protein function prediction. Nature Methods 2013, 10(3):221-227.
113. Roberts R.J. Identifying protein function-A call for community action. PLoS Biology 2004, 2(3):e42.
114. Roberts R.J., Chang Y.-C., Hu Z., Rachlin J.N., Anton B.P., Pokrzywa R.M., et al. COMBREX: A project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Research 2011, 39(Suppl. 1):D11-D14.
115. Rothberg J.M., Hinz W., Rearick T.M., Schultz J., Mileski W., Davey M., et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475(7356):348-352.
116. Sanchez S., Demain A.L. Enzymes and bioconversions of industrial, pharmaceutical, and biotechnological significance. Organic Process Research & Development 2010, 15(1):224-230.
117. Sanger F., Coulson A.R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology 1975, 94(3):441-448.
118. Savile C.K., Janey J.M., Mundorff E.C., Moore J.C., Tam S., Jarvis W.R., et al. Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science 2010, 329(5989):305-309.
119. Schallmey M., Ly A., Wang C., Meglei G., Voget S., Streit W.R., et al. Harvesting of novel polyhydroxyalkanoate (PHA) synthase encoding genes from a soil metagenome library using phenotypic screening. FEMS Microbiology Letters 2011, 321(2):150-156.
120. Schipper C., Hornung C., Bijtenhoorn P., Quitschau M., Grond S., Streit W.R. Metagenome-derived clones encoding two novel lactonase family proteins involved in biofilm inhibition in Pseudomonas aeruginosa. Applied and Environmental Microbiology 2009, 75(1):224-233.
121. Schnoes A.M., Brown S.D., Dodevski I., Babbitt P.C. Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies. PLoS Computational Biology 2009, 5(12):e1000605.
122. Schnoes A.M., Ream D.C., Thorman A.W., Babbitt P.C., Friedberg I. Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Computational Biology 2013, 9(5):e1003063.
123. Schomburg I., Chang A., Placzek S., Söhngen C., Rother M., Lang M., et al. BRENDA in 2013: Integrated reactions, kinetic data, enzyme function data, improved disease classification: New options and contents in BRENDA. Nucleic Acids Research 2013, 41(D1):D764-D772.
124. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13(11):2498-2504.
125. Shokralla S., Spall J.L., Gibson J.F., Hajibabaei M. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 2012, 21(8):1794-1805.
126. Simon C., Daniel R. Achievements and new knowledge unraveled by metagenomic approaches. Applied Microbiology and Biotechnology 2009, 85(2):265-276.
127. Singh R. Facts, growth, and opportunities in industrial biotechnology. Organic Process Research & Development 2010, 15(1):175-179.
128. Steipe B., Schiller B., Plückthun A., Steinbacher S. Sequence statistics reliably predict stabilizing mutations in a protein domain. Journal of Molecular Biology 1994, 240(3):188-192.
129. Stemmer W.P. DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proceedings of the National Academy of Sciences of the United States of America 1994, 91(22):10747-10751.
130. Sullivan B.J., Nguyen T., Durani V., Mathur D., Rojas S., Thomas M., et al. Stabilizing proteins from sequence statistics: The interplay of conservation and correlation in triosephosphate isomerase stability. Journal of Molecular Biology 2012, 420(4-5):384-399.
131. Sundquist A., Ronaghi M., Tang H., Pevzner P., Batzoglou S. Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS One 2007, 2(5):e484.
132. The_UniProt_Consortium Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Research 2013, 41(D1):D43-D47.
133. Thompson J., Milos P. The properties and applications of single-molecule DNA sequencing. Genome Biology 2011, 12(2):217.
134. Tishkov V.I., Popov V.O. Protein engineering of formate dehydrogenase. Biomolecular Engineering 2006, 23(2-3):89-110.
135. Tufvesson P., Lima-Ramos J., Jensen J.S., Al-Haque N., Neto W., Woodley J.M. Process considerations for the asymmetric synthesis of chiral amines using transaminases. Biotechnology and Bioengineering 2011, 108(7):1479-1493.
136. Uberto R., Moomaw E.W. Protein similarity networks reveal relationships among sequence, structure, and function within the cupin superfamily. PLoS One 2013, 8(9):e74477.
137. Uchiyama T., Abe T., Ikemura T., Watanabe K. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nature Biotechnology 2005, 23(1):88-93.
138. Uchiyama T., Watanabe K. The SIGEX scheme: High throughput screening of environmental metagenomes for the isolation of novel catabolic genes. Biotechnology and Genetic Engineering Reviews 2007, 24:107-116.
139. Vieites J.M., Guazzaroni M.-E., Beloqui A., Golyshin P.N., Ferrer M. Metagenomics approaches in systems microbiology. FEMS Microbiology Reviews 2009, 33(1):236-255.
140. Voget S., Leggewie C., Uesbeck A., Raasch C., Jaeger K.-E., Streit W.R. Prospecting for novel biocatalysts in a soil metagenome. Applied and Environmental Microbiology 2003, 69(10):6235-6242.
141. Wang Y., Hayatsu M., Fujii T. Extraction of bacterial RNA from soil: Challenges and solutions. Microbes and Environments 2012, 27(2):111-121.
142. Wang M., Si T., Zhao H. Biocatalyst development by directed evolution. Bioresource Technology 2012, 115:117-125.
143. Waschkowitz T., Rockstroh S., Daniel R. Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries. Applied and Environmental Microbiology 2009, 75(8):2506-2516.
144. Wieczorek S.J., Kalivoda K.A., Clifton J.G., Ringe D., Petsko G.A., Gerlt J.A. Evolution of enzymatic activities in the enolase superfamily: Identification of a "new" general acid catalyst in the active site of d-galactonate dehydratase from Escherichia coli. Journal of the American Chemical Society 1999, 121(18):4540-4541.
145. Willis L.B., Walker G.C. The phbC (poly-β-hydroxybutyrate synthase) gene of Rhizobium (Sinorhizobium) meliloti and characterization of phbC mutants. Canadian Journal of Microbiology 1998, 44(6):554-564.
146. Wilson D., Pethica R., Zhou Y., Talbot C., Vogel C., Madera M., et al. SUPERFAMILY-Sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Research 2009, 37(Suppl. 1):D380-D386.
147. Zerbino D.R., Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 2008, 18(5):821-829.
148. Zhao S., Kumar R., Sakai A., Vetting M.W., Wood B.M., Brown S., et al. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature 2013, 502:698-702.