Interplay of metagenomics and in vitro compartmentalization

Microbial Biotechnology

Volumn 2, Issue 1, 2009, Pages 31-39

  Ferrer, Manuel ^a   Beloqui, Ana ^a   Vieites, José María ^a   Guazzaroni, María Eugenia ^b   Berger, Ilana ^c   Aharoni, Amir ^c  

^a INSTITUTO DE CATÁLISIS Y PETROLEOQUÍMICA   (Spain)

^b CSIC   (Spain)

^c BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL ENZYME;

BACTERIAL GENOME; BACTERIUM CULTURE; BIOCATALYST; BIOTRANSFORMATION; CELL COMPARTMENTALIZATION; COMPUTER MODEL; DIRECTED MOLECULAR EVOLUTION; DNA EXTRACTION; EMULSION; ENZYME ACTIVITY; FLUORESCENCE ACTIVATED CELL SORTING; GENE LIBRARY; GENE SEQUENCE; GENETIC VARIABILITY; HIGH THROUGHPUT SCREENING; IN VITRO STUDY; METAGENOMICS; MICROBIAL COMMUNITY; MINING; MOLECULAR CLONING; NONHUMAN; PROTEIN ENGINEERING; SHORT SURVEY; SITE DIRECTED MUTAGENESIS;

ENVIRONMENTAL MICROBIOLOGY; GENE LIBRARY; HIGH-THROUGHPUT SCREENING ASSAYS; METAGENOMICS;

EID: 67349240597     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/j.1751-7915.2008.00057.x     Document Type: Short Survey

References (46)

1. Aharoni, A., Amitai, G., Bernath, K., Magdassi, S., and Tawfik, D.S. (2005a) High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments. Chem Biol 12: 1281-1289. (Pubitemid 41779468)
2. Aharoni, A., Griffiths, A.D., and Tawfik, D.S. (2005b) High-throughput screens and selections of enzyme encoding genes. Curr Opin Chem Biol 9: 210-216. (Pubitemid 40462492)
3. Amitai, G., Gupta, R.D., and Tawfik, D.S. (2007) Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J 1: 67-78.
4. Andexer, J., Guterl, J.K., Pohl, M., and Eggert, T. (2006) A high-throughput screening assay for hydroxynitrile lyase activity. Chem Commun (Camb) 40: 4201-4203. (Pubitemid 44556358)
5. Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., et al. (2006) The marine viromes of four oceanic regions. PLoS Biol 4: e368. (Pubitemid 44760026)
6. Beloqui, A., de María, P.D., Golyshin, P.N., and Ferrer, M. (2008) Recent trends in industrial microbiology. Curr Opin Microbiol 11: 240-248.
7. Bernath, K., Hai, M., Mastrobattista, E., Griffiths, A.D., Magdassi, S., and Tawfik, D.S. (2004) In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. Anal Biochem 325: 151-157. (Pubitemid 38050278)
8. Bernath, K., Magdassi, S., and Tawfik, D.S. (2005) Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nano-droplet delivery. J Mol Biol 345: 1015-1026. (Pubitemid 40092221)
9. Bornscheuer, U.T. (2002) Methods to increase enantioselectivity of lipases and esterases. Curr Opin Biotechnol 13: 543-547. (Pubitemid 35452578)
10. Doi, N., Kumadaki, S., Oishi, Y., Matsumura, N., and Yanagawa, H. (2004) In vitro selection of restriction endonucleases by in vitro compartmentalization. Nucleic Acids Res 32: e95.
11. Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., et al. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7: 57. (Pubitemid 43983121)
12. Ferrer, M., Golyshina, O., Beloqui, A., and Golyshin, P.N. (2007) Mining enzymes from extreme environments. Curr Opin Microbiol 10: 207-214.
13. Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, C., Jones, R., et al. (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73: 7059-7066. (Pubitemid 350076828)
14. Fox, R.J., Davis, S.C., Mundorff, E.C., Newman, L.M., Gavrilovic, V., Ma, S.K., et al. (2007) Improving catalytic function by ProSAR-driven enzyme evolution. Nature Biotechnol 25: 338-344. (Pubitemid 46398768)
15. Frias-Lopez, J., Shi, Y., Tyson, G.W., Coleman, M.L., Schuster, S.C., Chisholm, S.W., and Delong, E.F. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 10: 3805-3810. (Pubitemid 351723480)
16. Gabor, E., Liebeton, K., Niehaus, F., Eck, J., and Lorenz, P. (2007) Updating the metagenomics toolbox. Biotechnol J 2: 201-206.
17. Galvao, T.C., Mohn, W.W., and de Lorenzo, V. (2005) Exploring the microbial biodegradation and biotransformation gene pool. Trends Biotechnol 23: 497-506. (Pubitemid 41317913)
18. Geddie, M.L., Rowe, L.A., Alexander, O.B., and Matsumura, I. (2004) High throughput microplate screens for directed protein evolution. Methods Enzymol 388: 134-145. (Pubitemid 39061061)
19. Ghadessy, F.J., Ong, J.L., and Holliger, P. (2001) Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci USA 98: 4552-4557. (Pubitemid 32295014)
20. Ghadessy, F.J., Ramsay, N., Boudsocq, F., Loakes, D., Brown, A., Iwai, S., et al. (2004) Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol 22: 755-759. (Pubitemid 38702833)
21. Goddard, J.P., and Reymond, J.L. (2004) Enzyme assays for high-throughput screening. Curr Opin Biotechnol 15: 314-322.
22. Griffiths, A.D., and Tawfik, D.S. (2003) Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization. EMBO J 22: 24-35. (Pubitemid 36091266)
23. Griffiths, A.D., and Tawfik, D.S. (2006) Miniaturising the laboratory in emulsion droplets. Trends Biotechnol 24: 395-402.
24. Hallin, P.F., Binnewies, T.T., and Ussery, D.W. (2008) The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst 5: 363-371. (Pubitemid 351543601)
25. Khalameyzer, V., Fischer, I., Bornscheuer, U.T., and Altenbuchner, J. (1999) Screening, nucleotide sequence, and biochemical characterization of an esterase from Pseudomonas fluorescens with high activity towards lactones. Appl Environ Microbiol 65: 477-482. (Pubitemid 29075086)
26. Khersonsky, O., and Tawfik, D.S. (2006) Chromogenic and fluorogenic assays for the lactonase activity of serum paraoxonases. Chembiochem 7: 49-53. (Pubitemid 43076285)
27. Krause, L., Diaz, N.N., Goesmann, A., Kelley, S., Nattkemper, T.W., Rohwer, F., Edwards, R.A., and Stoye, J. (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 36: 2230-2239. (Pubitemid 351566997)
28. Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., et al. 2006. Archaea predominant among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809. (Pubitemid 44258909)
29. Liolios, K., Mavromatis, K., Tavernarakis, N., and Kyrpides, N.C. (2008) The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36: D475-D479. (Pubitemid 351149769)
30. Mastrobattista, E., Taly, V., Chanudet, E., Treacy, P., Kelly, B.T., and Griffiths, A.D. (2005) High-throughput screening of enzyme libraries: in vitro evolution of a b-galactosidase by fluorescence-activated sorting of double emulsions. Chem Biol 12: 1291-1300. (Pubitemid 41779469)
31. Miller, O.J., Bernath, K., Agresti, J.J., Amitai, G., Kelly, B.T., Mastrobattista, E., et al. (2006) Directed evolution by in vitro compartmentalization. Nat Methods 3: 561-570.
32. Park, S.J., Kang, C.H., Chae, J.C., and Rhee, S.K. (2008) Metagenome microarray for screaning of fosmid clones containing specific genes. FEMS Microbiol Lett 284: 28-34. (Pubitemid 351776892)
33. Raes, J., Foerstner, K.U., and Bork, P. (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol 10: 490-498. (Pubitemid 350052690)
34. Riesenfeld, C.S., Goodman, R.M., and Handelsman, J. (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6: 981-989. (Pubitemid 39123252)
35. Rusch, D.B., Halpern, A.L., Sutton, G., Heidelberg, K.B., Williamson, S., Yooseph, S., et al. (2007) The Sorcerer II Global Ocean Sampling Expedition: Northwest. Atlantic through Eastern Tropical Pacific. PLoS Biol 5: e77. (Pubitemid 46422965)
36. Schloss, P.D., and Handelsman, J. (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14: 303-310.
37. Sebat, J.L., Colwell, F.S., and Crawford, R.L. (2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Appl Environ Microbiol 8: 4927-4934. (Pubitemid 36992958)
38. Segota, I., Bartonicek, N., and Vlahovicek, K. (2008) MADNet: microarray database network web server. Nucleic Acids Res 36: w332-w335.
39. Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D., Huse, S.M., Neal, P.R., et al. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere' Proc Natl Acad Sci USA 103: 12115-12120. (Pubitemid 44215820)
40. Tawfik, D.S., and Griffiths, A.D. (1998) Man-made cell-like compartments for molecular evolution. Nat Biotechnol 16: 652-656. (Pubitemid 28334323)
41. Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43. (Pubitemid 38332350)
42. Uchiyama, T., and Watanabe, K. (2008) Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nat Protoc 3: 1202-1212.
43. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., and Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74. (Pubitemid 38451457)
44. Wegley, L., Edwards, R., Rodriguez-Brito, B., Liu, H., and Rohwer, F. (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9: 2707-2719. (Pubitemid 47547539)
45. Williamson, S.J., Rusch, D.B., Yooseph, S., Halpern, A.L., Heidelberg, K.B., Glass, J.I., et al. (2008) The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS ONE 1: e1456. (Pubitemid 351791355)
46. Yooseph, S., Sutton, G., Rusch, D.B., Halpern, A.L., Williamson, S.J., Remington, K., et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16. (Pubitemid 46422966)