Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H 2-oxidizing bacteria

Applied and Environmental Microbiology

Volumn 77, Issue 17, 2011, Pages 6027-6035

  Constant, Philippe ^a,b   Chowdhury, Soumitra Paul ^a,c   Hesse, Laura ^a   Pratscher, Jennifer ^a   Conrad, Ralf ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b INRS INSTITUT ARMAND FRAPPIER   (Canada)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

[NIFE]-HYDROGENASE; ACTINOBACTERIA; DRY WEIGHT; ENERGY REQUIREMENTS; GENE CLUSTERS; GENE SEQUENCES; GENES ENCODING; GENOME DATA MINING; HYDROGENASES; MIXOTROPHIC; OPEN READING FRAME; OXIDATION ACTIVITIES; POPULATION SIZES; PROTEOBACTERIA; QUANTITATIVE PCR; STRUCTURAL COMPONENT; TAXONOMIC DIVERSITY;

BACTERIOLOGY; DATA MINING; ECOLOGY; ENCODING (SYMBOLS); FUNCTIONAL GROUPS; GENE ENCODING; OXIDATION; POLYMERASE CHAIN REACTION; POPULATION STATISTICS; SOIL SURVEYS; SOILS;

BACTERIA;

HYDROGEN; HYDROGENASE; NICKEL IRON HYDROGENASE; NICKEL-IRON HYDROGENASE;

ABUNDANCE; BACTERIUM; DATA MINING; ENZYME ACTIVITY; FUNCTIONAL GROUP; GENOME; METABOLISM; MICROBIAL COMMUNITY; PHYLOGENETICS; POLYMERASE CHAIN REACTION; POPULATION SIZE; QUANTITATIVE ANALYSIS; SOIL SURVEY; SPECIES DIVERSITY; TAXONOMY;

ARTICLE; BACTERIUM; BIODIVERSITY; BIOLOGY; CLASSIFICATION; ENZYMOLOGY; GENETIC VARIABILITY; GENETICS; METABOLISM; METAGENOME; MICROBIOLOGY; OXIDATION REDUCTION REACTION;

BACTERIA; BIODIVERSITY; COMPUTATIONAL BIOLOGY; GENETIC VARIATION; HYDROGEN; HYDROGENASE; METAGENOME; OXIDATION-REDUCTION; SOIL MICROBIOLOGY;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); CHLOROFLEXI; CHLOROFLEXI (CLASS); PROTEOBACTERIA; STREPTOMYCES;

EID: 80052722488     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00673-11     Document Type: Article

References (61)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Appel, J., S. Phunpruch, K. Steinmüller, and R. Schulz. 2000. The bidirectional hydrogenase of Synechocystis sp. PCC 6803 works as an electron valve during photosynthesis. Arch. Microbiol. 173:333-338.
3. Bendtsen, J. D., H. Nielsen, G. von Heijne, and S. Brunak. 2004. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340:783-795.
4. Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and E. W. Sayers. 2009. GenBank. Nucleic Acids Res. 37:D26-D31.
5. Berney, M., and G. M. Cook. 2010. Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia. PLoS One 5:e8614.
6. Bleijlevens, B., T. Buhrke, E. van der Linden, B. Friedrich, and S. P. J. Albracht. 2004. The auxiliary protein HypX provides oxygen tolerance to the soluble [NiFe]-hydrogenase of Ralstonia eutropha H16 by way of a cyanide ligand to nickel. J. Biol. Chem. 279:46686-46691.
7. Böck, A., P. W. King, M. Blokesch, and M. C. Posewitz. 2006. Maturation of hydrogenases. Adv. Microb. Physiol. 51:1-71.
8. Chivers, P. T., K. E. Prehoda, and R. T. Raines. 1997. The CXXC motif: a rheostat in the active site. Biochemistry 36:4061-4066.
9. 2 uptake activity in soils. Soil Biol. Biochem. 42:1574-1580.
10. 2, NO). Indian J. Microbiol. 39:193-203.
11. Conrad, R., M. Aragno, and W. Seiler. 1983. The inability of hydrogen bacteria to utilize atmospheric hydrogen is due to threshold and affinity for hydrogen. FEMS Microbiol. Lett. 18:207-210.
12. 2-oxidizing bacteria in non-axenic soil and sterile soil amended with Streptomyces sp. PCB7. Soil Biol. Biochem. doi:10.1016/j.soilbio.2011.05.009.
13. Constant, P., S. P. Chowdhury, J. Pratscher, and R. Conrad. 2010. Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase. Environ. Microbiol. 12:821-829.
14. 2. ISME J. 2:1066-1076.
15. 2 budget and the response of its soil uptake under the changing environment. Sci. Total Environ. 407:1809-1823.
16. Crooks, G. E., G. Hon, J.-M. Chandonia, and S. E. Brenner. 2004. WebLogo: a sequence logo generator. Genome Res. 14:1188-1190.
17. Degelmann, D. M., W. Borken, H. L. Drake, and S. Kolb. 2010. Different atmospheric methane-oxidizing communities in European beech and Norway spruce soils. Appl. Environ. Microbiol. 76:3228-3235.
18. 2: a critical review. Tellus 61B:500-535.
19. Emanuelsson, O., S. Brunak, G. von Heijne, and H. Nielsen. 2007. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2:953-971.
20. Fontecilla-Camps, J. C., A. Volbeda, C. Cavazza, and Y. Nicolet. 2007. Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem. Rev. 107:4273-4303.
21. Frey, M. 2002. Hydrogenases: hydrogen-activating enzymes. Chembiochem 3:153-160.
22. Gödde, M., K. Meuser, and R. Conrad. 2000. Hydrogen consumption and carbon monoxide production in soils with different properties. Biol. Fertil. Soils 32:129-134.
23. Hube, M., M. Blokesch, and A. Böck. 2002. Network of hydrogenase maturation in Escherichia coli: role of accessory proteins HypA and HybF. J. Bacteriol. 184:3879-3885.
24. Jacobi, A., R. Rossmann, and A. Böck. 1992. The hyp operon gene products are required for the maturation of catalytically active hydrogenase isoenzymes in Escherichia coli. Arch. Microbiol. 158:444-451.
25. Juhas, M., et al. 2009. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol. Rev. 33:376-393.
26. Kiessling, M., and O. Meyer. 1982. Profitable oxidation of carbon monoxide or hydrogen during heterotrophic growth of Pseudomonas carboxydoflava. FEMS Microbiol. Lett. 13:333-338.
27. Kim, J. Y. H., B. H. Jo, and H. J. Cha. 2010. Production of biohydrogen by recombinant expression of [NiFe]-hydrogenase 1 in Escherichia coli. Microb. Cell Fact. 9:54.
28. King, G. M. 2003. Uptake of carbon monoxide and hydrogen at environmentally relevant concentrations by mycobacteria. Appl. Environ. Microbiol. 69:7266-7272.
29. King, G. M., and C. F. Weber. 2007. Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat. Rev. Microbiol. 5:107-118.
30. 2 sensor of Ralstonia eutropha is a member of the subclass of regulatory [NiFe] hydrogenases. J. Bacteriol. 182:2716-2724.
31. Krogh, A., B. Larsson, G. von Heijne, and E. L. L. Sonnhammer. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580.
32. Lallo, M., T. Aalto, T. Laurila, and J. Hatakka. 2008. Seasonal variations in hydrogen deposition to boreal forest soil in southern Finland. Geophys. Res. Lett. 35:L04402.
33. Lawrence, J. 1999. Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9:642-648.
34. 2 as performed by the membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. Chemphyschem 11:1107-1119.
35. 2 sensing in Alcaligenes eutrophus. Proc. Natl. Acad. Sci. U. S. A. 95:12474-12479.
36. Leul, M., P. Normand, and A. Sellstedt. 2007. The organization, regulation and phylogeny of uptake hydrogenase genes in Frankia. Physiol. Plant. 130: 464-470.
37. Ludwig, W., et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
38. Maier, T., U. Binder, and A. Böck. 1996. Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism. Arch. Microbiol. 165:333-341.
39. Mattsson, U., and A. Sellstedt. 2000. Hydrogenase in Frankia KB5: expression of and relation to nitrogenase. Can. J. Microbiol. 46:1091-1095.
40. 4 uptake by altering biomass and activity but not composition of high-affinity methanotrophs. Global Change Biol. 14: 2405-2419.
41. Menyailo, O. V., B. A. Hungate, and W. Zech. 2002. Tree species mediated soil chemical changes in a Siberian artificial afforestation experiment. Plant Soil 242:171-182.
42. Mulrooney, S. B., and R. P. Hausinger. 2003. Nickel uptake and utilization by microorganisms. FEMS Microbiol. Rev. 27:239-261.
43. Olson, J. W., N. S. Mehta, and R. J. Maier. 2001. Requirement of nickel metabolism proteins HypA and HypB for full activity of both hydrogenase and urease in Helicobacter pylori. Mol. Microbiol. 39:176-182.
44. Pruesse, E., et al. 2007. SILVA: a comprehensive online resource for quality checked and aligned rRNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188-7196.
45. 10-formyltetrahydrofolate-dependent enzyme family and is required for nickel-dependent hydrogenase processing and activity. Mol. Gen. Genet. 252:237-248.
46. Rittenberg, S. C., and N. S. Goodman. 1969. Mixotrophic growth of Hydrogenomonas eutropha. J. Bacteriol. 98:617-622.
47. Sawers, G. 1994. The hydrogenases and formate dehydrogenases of Escherichia coli. Antonie Van Leeuwenhoek 66:57-88.
48. Schmitt, S., A. Hanselmann, U. Wollschläger, S. Hammer, and I. Levin. 2009. Investigation of parameters controlling the soil sink of atmospheric molecular hydrogen. Tellus 61B:416-423.
49. Schuler, S., and R. Conrad. 1990. Soils contain two different activities for oxidation of hydrogen. FEMS Microbiol. Lett. 73:77-83.
50. 2-based lithoautotrophy and anaerobiosis. J. Mol. Biol. 332:369-383.
51. 2 storage. Annu. Rev. Biochem. 79:507-536.
52. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
53. Tibazarwa, C., et al. 2001. A microbial biosensor to predict bioavailable nickel in soil and its transfer to plants. Environ. Pollut. 113:19-26.
54. Tijhuis, L., M. C. M. Van Loosdrecht, and J. J. Heijnen. 1993. A thermodynamically based correlation for maintenance Gibbs energy requirements in aerobic and anaerobic chemotrophic growth. Biotechnol. Bioeng. 42:509-519.
55. Vignais, P. M., and B. Billoud. 2007. Occurrence, classification, and biological function of hydrogenases: an overview. Chem. Rev. 107:4206-4272.
56. Vignais, P. M., B. Billoud, and J. Meyer. 2001. Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25:455-501.
57. Vignais, P. M., and A. Colbeau. 2004. Molecular biology of microbial hydrogenases. Curr. Issues Mol. Biol. 6:159-188.
58. Vincent, K. A., et al. 2005. Electrocatalytic hydrogen oxidation by an enzyme at high carbon monoxide or oxygen levels. Proc. Natl. Acad. Sci. U. S. A. 102:16951-16954.
59. Weber, C. F., and G. M. King. 2010. Distribution and diversity of carbon monoxide-oxidizing bacteria and bulk bacterial communities across a succession gradient on a Hawaiian volcanic deposit. Environ. Microbiol. 12: 1855-1867.
60. Wu, D., et al. 2009. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One 4:e4207.
61. Yanai, I., J. C. Mellor, and C. DeLisi. 2002. Identifying functional links between genes using conserved proximity. Trends Genet. 18:176-179.