Direct cloning and expression of putative esterase genes from environmental DNA

Enzyme and Microbial Technology

Volumn 47, Issue 1-2, 2010, Pages 17-23

  Terahara, Takeshi ^a,c   Yamada, Kazutaka ^b   Kurata, Shinya ^b   Yokomaku, Toyokazu ^b   Tsuneda, Satoshi ^a   Harayama, Shigeaki ^c,d  

^a WASEDA UNIVERSITY   (Japan)

^b NIPPON STEEL CORPORATION   (Japan)

^c NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

^d CHUO UNIVERSITY   (Japan)

Author keywords

Esterase; Inverse PCR; Metagenome; Sequence based approach

Indexed keywords

ACTIVITY-BASED; AMINO ACID SEQUENCE; DIRECT CLONING; INDUSTRIAL ENZYMES; INSOLUBLE PROTEINS; INVERSE PCR; METAGENOMES; OPTIMAL TEMPERATURE; OPTIMUM ACTIVITY; P-NITROPHENYL ACETATE; PUBLIC DATABASE; RECOMBINANT ESCHERICHIA COLI; SEQUENCE ANALYSIS; SUBSTRATE SPECIFICITY; THERMAL STABILITY;

AMINO ACIDS; CATALYSTS; CLONING; DNA; ENZYMES; ESCHERICHIA COLI; OPTIMIZATION; ORGANIC ACIDS;

GENE EXPRESSION;

ESTERASE; P NITROPHENYL ACETATE; P NITROPHENYL DECANOATE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; DNA ISOLATION; ENZYMATIC ASSAY; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME STABILITY; ESCHERICHIA COLI; GENE EXPRESSION; INVERSE POLYMERASE CHAIN REACTION; METAGENOMICS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; SEQUENCE ANALYSIS;

ESCHERICHIA COLI;

EID: 77953616535     PISSN: 01410229     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.enzmictec.2010.04.005     Document Type: Article

References (33)

1. Jaeger K.E., Dijkstra B.W., Reetz M.T. Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu Rev Microbiol 1999, 53:315-351.
2. Bornscheuer U.T. Microbial carboxyl esterases: classification, properties and application in biocatalysis. FEMS Microbiol Rev 2002, 26:73-81.
3. Akoh C.C., Lee G.C., Liaw Y.C., Huang T.H., Shaw J.F. GDSL family of serine esterases/lipases. Prog Lipid Res 2004, 43:534-552.
4. Arpigny J.L., Jaeger K.E. Bacterial lipolytic enzymes: classification and properties. Biochem J 1999, 343:177-183.
5. Shankaranand V.S., Ramesh M.V., Lonsane B.K. Idiosyncrasies of solid-state fermentation systems in the biosynthesis of metabolites by some bacterial and fungal cultures. Process Biochem 1992, 27:33-36.
6. Panda T., Gowrishankar B.S. Production and applications of esterases. Appl Microbiol Biotechnol 2005, 67:160-169.
7. Rappe M.S., Giovannoni S.J. The uncultured microbial majority. Annu Rev Microbiol 2003, 57:369-394.
8. Schloss P.D., Handelsman J. Biotechnological prospects from metagenomics. Curr Opin Biotechnol 2003, 14:303-310.
9. Christen R. Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes Environ. 2008, 23:253-268.
10. Simon C., Daniel R. Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 2009, 85:265-276.
11. Okuta A., Ohnishi K., Harayama S. PCR isolation of catechol 2,3-dioxygenase gene fragments from environmental samples and their assembly into functional genes. Gene 1998, 212:221-228.
12. Eschenfeldt W.H., Stols L., Rosenbaum H., Khambatta Z.S., Quaite-Randall E., Wu S., et al. DNA from uncultured organisms as a source of 2,5-diketo-d-gluconic acid reductases. Appl Environ Microbiol 2001, 67:4206-4214.
13. Sunna A., Bergquist P.L. A gene encoding a novel extremely thermostable 1,4-beta-xylanase isolated directly from an environmental DNA sample. Extremophiles 2003, 7:63-70.
14. Uchiyama T., Watanabe K. Improved inverse PCR scheme for metagenome walking. Biotechniques 2006, 41:183-188.
15. Yamada K., Terahara T., Kurata S., Yokomaku T., Tsuneda S., Harayama S. Retrieval of entire genes from environmental DNA by inverse PCR with pre-amplification of target genes using primers containing locked nucleic acids. Environ Microbiol 2008, 10:978-987.
16. Bell P.J., Sunna A., Gibbs M.D., Curach N.C., Nevalainen H., Bergquist P.L. Prospecting for novel lipase genes using PCR. Microbiology 2002, 148:2283-2291.
17. Ro H.S., Hong H.P., Kho B.H., Kim S., Chung B.H. Genome-wide cloning and characterization of microbial esterases. FEMS Microbiol Lett 2004, 233:97-105.
18. Davis G.D., Elisee C., Newham D.M., Harrison R.G. New fusion protein systems designed to give soluble expression in Escherichia coli. Biotechnol Bioeng 1999, 65:382-388.
19. Akbari N., Khajeh K., Rezaie S., Mirdamadi S., Shavandi M., Ghaemi N. High-level expression of lipase in Escherichia coli and recovery of active recombinant enzyme through in vitro refolding. Protein Expr Purif 2009, 70:75-80.
20. Ferrer M., Beloqui A., Timmis K.N., Golyshin P.N. Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 2009, 16:109-123.
21. Kirk O., Borchert T.V., Fuglsang C.C. Industrial enzyme applications. Curr Opin Biotechnol 2002, 13:345-351.
22. Cherry J.R., Fidantsef A.L. Directed evolution of industrial enzymes: an update. Curr Opin Biotechnol 2003, 14:438-443.
23. Morimoto S., Fujii T. A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking. Appl Microbiol Biotechnol 2009, 83:389-396.
24. Meyer Q.C., Burton S.G., Cowan D.A. Subtractive hybridization magnetic bead capture: a new technique for the recovery of full-length ORFs from the metagenome. Biotechnol J 2007, 2:36-40.
25. Jiang C., Wu B. Molecular cloning and functional characterization of a novel decarboxylase from uncultured microorganisms. Biochem Biophys Res Commun 2007, 357:421-426.
26. Banik J.J., Brady S.F. Cloning and characterization of new glycopeptide gene clusters found in an environmental DNA megalibrary. Proc Natl Acad Sci USA 2008, 105:17273-17277.
27. Jogler C., Lin W., Meyerdierks A., Kube M., Katzmann E., Flies C., et al. Toward cloning of the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments. Appl Environ Microbiol 2009, 75:3972-3979.
28. Rose T.M., Schultz E.R., Henikoff J.G., Pietrokovski S., McCallum C.M., Henikoff S. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res 1998, 26:1628-1635.
29. Jeon J.H., Kim J.T., Kang S.G., Lee J.H., Kim S.J. Characterization and its potential application of two esterases derived from the arctic sediment metagenome. Mar Biotechnol (NY) 2009, 11:307-316.
30. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004, 68:669-685.
31. Gabor E.M., Alkema W.B., Janssen D.B. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol 2004, 6:879-886.
32. Lemercier G., Bakalara N., Santarelli X. On-column refolding of an insoluble histidine tag recombinant exopolyphosphatase from Trypanosoma brucei overexpressed in Escherichia coli. J Chromatogr B Analyt Technol Biomed Life Sci 2003, 786:305-309.
33. Kotik M. Novel genes retrieved from environmental DNA by polymerase chain reaction: current genome-walking techniques for future metagenome applications. J Biotechnol 2009, 144:75-82.