Metagenomic era for biocatalyst identification

Current Opinion in Biotechnology

Volumn 21, Issue 6, 2010, Pages 725-733

  Fernández Arrojo, Lucía ^a   Guazzaroni, María Eugenia ^a   López Cortés, Nieves ^a   Beloqui, Ana ^a   Ferrer, Manuel ^a  

^a INSTITUTO DE CATÁLISIS Y PETROLEOQUÍMICA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCATALYSIS; CATALYTIC POTENTIAL; COMPREHENSIVE ANALYSIS; COMPUTATIONAL FRAMEWORK; CURRENT CAPABILITY; METAGENOMES; METAGENOMICS; MICROBIAL ENZYMES; MICROBIAL POPULATIONS; SEQUENCE DATABASE;

ENZYMES;

HYDROLASE; ISOMERASE; LIGASE; LYASE; OXIDOREDUCTASE; TRANSFERASE;

BIOCATALYSIS; BIOCATALYST; BIOINFORMATICS; CONCEPTUAL FRAMEWORK; DNA DETERMINATION; ENZYME ACTIVITY; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC DATABASE; INTERNET; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; ONLINE ANALYSIS; ONLINE SYSTEM; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN ANALYSIS; REVIEW; SEQUENCE ANALYSIS; WEB BROWSER;

BIOCATALYSIS; METAGENOMICS;

EID: 78349308978     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2010.09.006     Document Type: Review

References (55)

1. Glueck S.M., Gümüs S., Fabian W.M., Faber K. Biocatalytic carboxylation. Chem Soc Rev 2010, 39:313-328.
2. Beloqui A., de Maria P.D., Golyshin P.N., Ferrer M. Recent trends in industrial microbiology. Curr Opin Microbiol 2008, 11:240-248.
3. Vieites J.M., Guazzaroni M.E., Beloqui A., Golyshin P.N., Ferrer M. Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 2009, 33:236-255.
4. Lee H.S., Kwon K.K., Kang S.G., Cha S.S., Kim S.J., Lee J.H. Approaches for novel enzyme discovery from marine environments. Curr Opin Biotechnol 2010, 21:353-357.
5. Warnecke F., Hess M. A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 2009, 142:91-95.
6. Sommer M.O., Church G.M., Dantas G. A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Mol Syst Biol 2010, 6:360.
7. Tuffin M., Anderson D., Health C., Cowan D.A. Metagenomic gene discovery: how far we moved into novel sequence space?. Biotechnol J 2009, 4:1671-1683.
8. Feist A.M., Herrgard M.J., Thiele I., Reed J.L., Palsson B.O. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 2009, 7:129-143.
9. Uchiyama T., Miyazaki M. Functional metagenomics for enzyme discovery: challenges of efficient screening. Curr Opin Biotechnol 2009, 20:616-622.
10. Steele H.L., Jaeger K.-E., Daniel R., Streit W.R. Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 2009, 16:25-37.
11. Kalyuzhnaya M.G., Lapidus A., Ivanova N., Copeland A.C., McHardy A.C., Szeto E., Salamov A., Grigoriev I.V., Suciu D., Levine S.R., et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 2008, 26:1029-1034.
12. Hoff K.J. The effect of sequencing errors on metagenomic gene prediction. BMC Genomics 2009, 10:520.
13. Schnoes A.M., Brown S.D., Babbitt P.C. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 2009, 5:e1000605.
14. Harrington E.D., Singh A.H., Doerks T., Letunic I., von Mering C., Jensen L.J., Raes J., Borj P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci USA 2007, 104:13913-13918.
15. Rentzsch R., Orengo C.A. Protein function prediction-the power of multiplicity. Trends Biotechnol 2009, 27:210-219.
16. Sharma V.K., Kumar N., Prakash T., Taylor T.D. MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. Nucleic Acids Res 2010, 38:D468-472.
17. Cardenas E., Tiedje J.M. New tools for discovering and characterizing microbial diversity. Curr Opin Biotechnol 2008, 19:544-549.
18. Benndorf D., Vogt C., Jehmlich N., Schmidt Y., Thomas H., Woffendin G., Shevchenko A., Richnow H.H., von Bergen M. Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation 2009, 20:737-750.
19. Wilmes P., Andersson A.F., Lefsrud M.G., Wexler M., Shah M., Zhang B., Hettich R.L., Bond P.L., VerBerkmoes N.C., Banfield J.F. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J 2008, 2:853-864.
20. Wilmes P., Wexler M., Bond P.L. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 2008, 3:e1778.
21. Warnecke F., Hess M. A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 2009, 142:91-95.
22. Demaneche S., David M.M., Navarro E., Simonet P., Vogel T.M. Evaluation of functional gene enrichment in a soil metagenomic clone library. J Microbiol Methods 2009, 76:105-107.
23. Li T.L., Mazeas L., Sghir A., Leblon G., Bouchez T. Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions. Environ Microbiol 2009, 11:889-904.
24. Sorek R., Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 2010, 11:9-16.
25. Ansorge W.J. Next-generation DNA sequencing techniques. New Biotech 2009, 25:195-203.
26. Liolios K., Chen I., Mavromatis K., Tavernarakis N., Hugenholtz P., Markowitz V., Kyrpides N.C. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010, D346-D354.
27. Li L.-L., McCorkle S.R., Monchy S., Taghavi S., van der Lelie D. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuels 2009, 2:10.
28. Allgaier M., Reddy A., Park J.I., Ivanova N., D'haeseleer P., Lowry S., Sapra R., Hazen T.C., Simmons B.A., VanderGheynst J.S., Hugenholtz P. Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 2010, 5:e8812.
29. Brulc J.M., Antonopoulos D.A., Miller M.E., Wilson M.K., Yannarell A.C., Dinsdale E.A., Edwards R.E., Frank E.D., Emerson J.B., Wacklin P., et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 2009, 106:1948-1953.
30. Gomez-Alvarez V., Teal T.K., Schmidt T.M. Systematic artifacts in metagenomes from complex microbial communities. ISME J 2009, 3:1314-1317.
31. Mou X.Z., Sun S.L., Edwards R.A., Hodson R.E., Moran M.A. Bacterial carbon processing by generalist species in the coastal ocean. Nature 2008, 451:708-711.
32. Jehmlich N., Schmidt F., von Bergen M., Richnow H.H., Vogt C. Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures. ISME J 2008, 2:1122-1133.
33. Gibson D.T., Parales R.E. Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 2000, 11:236-243.
34. Parales R.E., Resnick S.M., Yu C.L., Boyd D.R., Sharma N.D., Gibson D.T. Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis dihydroxylation: control by phenylalanine 352 in the alpha subunit. J Bacteriol 2000, 182:5495-5504.
35. Ferrer M., Beloqui A., Vieites J.M., Guazzaroni M.-E., Berger I., Aaron A. Interplay of metagenomics and in vitro compartmentalization. Microb Biotechnol 2008, 2:31-39.
36. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., et al. The Pfam protein families database. Nucleic Acids Res 2004, 32:D138-141.
37. He Z., Gentry T.J., Schadt C.W., Wu L., Liebich J., Chong S.C., Huang Z., Wu W., Gu B., Jardine P., et al. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 2007, 1:67-77.
38. Iwai S., Kurisu F., Urakawa H., Yagi O., Kasuga I., Furumai H. Development of an oligonucleotide microarray to detect di- and monooxygenase genes for benzene degradation in soil. FEMS Microbiol Lett 2008, 285:111-121.
39. Liang Y., He Z., Wu L., Deng Y., Li G., Zhou J. Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Appl Environ Microbiol 2010, 76:1088-1094.
40. Brennerova M.V., Josefiova J., Brenner V., Pieper D.H., Junca H. Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation. Environ Microbiol 2009, 11:2216-2227.
41. Suenaga H., Ohnuki T., Miyazaki K. Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ Microbiol 2007, 9:2289-2297.
42. Suenaga H., Mizuta S., Miyazaki K. The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome. FEMS Microbiol Ecol 2009, 69:472-480.
43. van Hellemond E.W., Janssen D.B., Fraaije M.W. Discovery of a novel styrene monooxygenase originating from the metagenome. Appl Environ Microbiol 2007, 73:5832-5839.
44. Beloqui A., Polaina J., Vieites J.M., Reyes-Duarte D., Torres R., Golyshina O.V., Chernikova T.N., Waliczek A., Aharoni A., Yakimov M.M., et al. Novel hybrid esterase-haloacid dehalogenase enzyme. Chembiochem 2010, 10.1002/cbic.201000258.
45. Ferrer M. The microbial reactome. Microbial Biotechnol 2009, 2:133-135.
46. Galvao T.C., de Lorenzo V. Transcriptional regulators a la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol 2006, 17:34-42.
47. Mohn W.W., Garmendia J., Galvao T.C., de Lorenzo V. Surveying biotransformations with a la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes. Environ Microbiol 2006, 8:546-555.
48. Uchiyama T., Watanabe K. Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nat Protoc 2008, 3:1202-1212.
49. Northen T.R., Lee J.C., Hoang L., Raymond J., Hwang D.R., Yannone S.M., Wong C.H., Siuzdak G. A nanostructure-initiator mass spectrometry-based enzyme activity assay. Proc Natl Acad Sci USA 2008, 105:3678-3683.
50. Bairoch A. The ENZYME database in 2000. Nucleic Acids Res 2000, 28:304-305.
51. Freilich S., Kreimer A., Borenstein E., Yosef N., Sharan R., Gophna U., Ruppin E. Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol 2009, 10:R61.
52. Gernaey K.V., Lantz A.E., Tufvesson P., Woodley J.M., Sin G. Application of mechanistic models to fermentation and biocatalysis for next-generation processes. Trends Biotechnol 2010, 28:346-354.
53. Fernandes P. Miniaturization in biocatalysis. Int J Mol Sci 2010, 11:585-879.
54. de Lorenzo V. Systems biology approaches to bioremediation. Curr Opin Biotechnol 2008, 19:579-589.
55. Faber K. Biotransformations in Organic Chemistry 2000, Springer, Berlin. 4th ed.