A wide host-range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase

Environmental Microbiology

Volumn 7, Issue 12, 2005, Pages 1917-1926

  Wexler, Margaret ^a   Bond, Philip L ^a   Richardson, David J ^a   Johnston, Andrew W B ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE; ALDEHYDE DEHYDROGENASE;

ARTICLE; BIOREACTOR; BIOREMEDIATION; COSMID; GENE LIBRARY; GENETICS; METABOLISM; MICROBIOLOGY; SEWAGE;

ALCOHOL DEHYDROGENASE; ALDEHYDE DEHYDROGENASE; BIODEGRADATION, ENVIRONMENTAL; BIOREACTORS; COSMIDS; ENVIRONMENTAL MICROBIOLOGY; GENOMIC LIBRARY; SEWAGE;

CLOSTRIDIUM ACETOBUTYLICUM; ESCHERICHIA COLI; PSEUDOMONAS AERUGINOSA; RHIZOBIUM LEGUMINOSARUM;

EID: 28644431563     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00854.x     Document Type: Article

References (43)

1. Arnau, J., Jorgensen, F., Madsen, S.M., Vrang, A., and Israelsen, H. (1998) Cloning of the Lactococcus lactis adhE gene, encoding a multifunctional alcohol dehydrogenase, by complementation of a fermentative mutant of Escherichia coli. J Bacteriol 180: 3049-3055.
2. Beringer, J.E. (1974) R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 84: 188-198.
3. Bond, P.L., Hugenholtz, P., Keller, J., and Blackall, L.L. (1995) Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol 61: 1910-1916.
4. Bond, P.L., Smriga, S.P., and Banfield, J.F. (2000) Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl Environ Microbiol 66: 3842-3849.
5. Clark, D.P., and Cronan, J.E. (1980) Escherichia coli mutants with altered control of alcohol dehydrogenase and nitrate reductase. J Bacteriol 141: 177-183.
6. Cornillot, E., Nair, R.V., Papoutsakis, E.T., and Soucaille, P. (1997) The genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 reside on a large plasmid whose loss leads to degeneration of the strain. J Bacteriol 179: 5442-5447.
7. Courtois, S., Cappellano, C.M., Ball, M., Francou, F.X., Normand, P., Helynck, G., et al. (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69: 49-55.
8. Dailly, Y., Mat-Jan, F., and Clark, D.J. (2001) Novel alcohol dehydrogenase activity in a mutant of Salmonella able to use ethanol as sole carbon source. FEMS Microbiol Lett 201: 41-45.
9. Echave, P., Tamarit, J., Cabiscol, E., and Ros, J. (2003) Novel antioxidant role of alcohol dehydrogenase E from Escherichia coli. J Biol Chem 278: 49-55.
10. Ficker, M., Krastel, K., Orlicky, S., and Edwards, E. (1999) Molecular characterization of a toluene-degrading methanogenic consortium. Appl Environ Microbiol 65: 5576-5585.
11. Figurski, D.H., and Helinski, D.R. (1979) Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in. Trans Proc Natl Acad Sci USA 76: 1648-1652.
12. Gupta, S., and Clark, D.P. (1989) Escherichia coli derivatives lacking both alcohol dehydrogenase and phosphotransacetylase grow anaerobically by lactate fermentation. J Bacteriol 171: 3650-3655.
13. Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J., and Goodman, R.M. (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5: 245-249.
14. Holland-Staley, C.A., Lee, K., Clark, D.P., and Cunningham, P.R. (2000) Aerobic activity of Escherichia coli alcohol dehydrogenase is determined by a single amino acid. J Bacteriol 182: 6049-6054.
15. Holloway, B.W. (1955) Genetic recombination in Pseudomonas aeruginosa. J Gen Microbiol 13: 572-581.
16. Ishihama, A. (2000) Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 54: 499-518.
17. Kaga, N., Umitsuki, G., Clark, D.P., Nagai, K., and Wachi, M. (2002) Extensive overproduction of the AdhE protein by rng mutations depends on mutations in the cra gene or in the Cra-box of the adhE promoter. Biochem Biophys Res Comm 295: 92-97.
18. Knietsch, A., Waschkowitz, T., Bowien, S., Henne, A., and Daniel, R. (2003) Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli. J Mol Microbiol Biotechnol 5: 46-56.
19. Li, Y.-Y., Fang, H.H.P., Chen, T., and Chui, H.-K. (1995) UASB Treatment of wastewater containing concentrated benzoate. J Env Engineering 121: 748-751.
20. Li, Y.G., Wexler, M., Richardson, D.J., Bond, P.L., and Johnston, A.W.B. (2005) Screening a wide host-range, waste-water metagenomic library in tryptophan auxotrophs of Rhizobium leguminosarum and of Escherichia coli reveals different classes of cloned trp genes. Environ Microbiol (in press). doi:10.1111/j.1462-2920.2005.00853.x
21. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, L., et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
22. Martinez, A., Kolvek, S.J., Yip, C.L., Hopke, J., Brown, K.A., MacNeil, I.A., and Osburne, M.S. (2004) Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl Environ Microbiol 70: 2452-2463.
23. Martinez-Bueno, M.A., Tobes, R., Rey, M., and Ramos, J.L. (2002) Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01. Environ Microbiol 4: 842-855.
24. Membrillo-Hernandez, J., Echave, P., Cabiscol, E., Tamarit, J., Ros, J., and Lin, E.C. (2000) Evolution of the adhE gene product of Escherichia coli from a functional reductase to a dehydrogenase. Genetic and biochemical studies of the mutant proteins. J Biol Chem 275: 33869-33875.
25. Riesenfeld, C.S., Schloss, P.D., and Handelsman, J. (2004) METAGENOMICS: genomic analysis of microbial communities. Ann Rev Genet 38: 525-552.
26. Rondon, M.R., Raffel, S.J., Goodman, R.J., and Handelsman, J. (1999) Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. Proc Natl Acad Sci USA 96: 6451-6455.
27. Rondon, M.R., August, P.R., Bettermann, A.D., Brady, S.F., Grossman, T.H., Liles, M.R., et al. (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66: 2541-2547.
28. Schink, B. (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61: 262-280.
29. Sekiguchi, Y., Kamagata, Y., Syutsubo, K., Ohashi, A., Harada, H., and Nakamura, K. (1998) Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144: 2655-2665.
30. Simon, R., O'Connell, M., Labes, M., and Puhler, A. (1986) Plasmid vectors for the genetic analysis and manipulation of rhizobia and other Gram negative bacteria. Methods Enzymol 118: 640-659.
31. Staskawicz, B., Dahlbeck, D., Keen, N., and Napoli, C. (1987) Molecular characterization of cloned avirulence genes from race 0 and race 1 of Pseudomonas syringae pv. Glycinea. J Bacteriol 169: 5789-5794.
32. Streit, W.R., and Schmitz, R.A. (2004) Metagenomics - the key to the uncultured microbes. Curr Opin Microbiol 7: 492-498.
33. Tchobanoglous, G., and Burton, F.L. (1991) Wastewater Engineering: Treatment, Disposal, and Reuse, 3rd edn. New York: Metcalf and Eddy, McGraw-Hill International Edition.
34. Thormann, K., Feustel, L., Lorenz, K., Nakotte, S., and Durre, P. (2002) Control of butanol formation in Clostridium acetobutylicum by transcriptional activation. J Bacteriol 184: 1966-1973.
35. 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.
36. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
37. Wagner, M., Loy, A., Nogueira, R., Purkhold, U., Lee, N., and Daims, H. (2002) Microbial community composition and function in wastewater treatment plants. Antonie Van Leeuwenhoek 81: 665-680.
38. Ward, D.M., Weller, R., and Bateson, M.M. (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345: 63-65.
39. Wexler, M., Yeoman, K.H., Stevens, J.B., de Luca, N.G., Sawers, G., and Johnston, A.W.B. (2001) The Rhizobium leguminosarum tonB gene is required for the uptake of siderophore and haem as sources of iron. Mol Microbiol 41: 801-816.
40. Wood, W.B. (1966) Host specificity of DNA produced by Escherichia coli; bacterial mutations affecting the restriction and modification of DNA. J Mol Biol 16: 118-133.
41. Wyborn, N.R., Messenger, S.L., Henderson, R.A., Sawers, G., Roberts, R.E., Attwood, M.M., and Green, J. (2002) Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products. Microbiology 148: 1015-1026.
42. Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103-119.
43. Yong, T.S., Li, E., Clark, D., and Stanley, S.L. Jr (1996) Complementation of an Escherichia coli adhE mutant by the Entamoeba histolytica EhADH2 gene provides a method for the identification of new antiamebic drugs. Proc Natl Acad Sci USA 93: 6464-6469.