Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1

Applied Microbiology and Biotechnology

Volumn 68, Issue 5, 2005, Pages 580-587

  Rabus, Ralf ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BENZENE; BIODEGRADATION; GENES; GENETIC ENGINEERING; METABOLISM; SOILS; SUBSTRATES; TOLUENE; WATER;

METABOLIC VERSATILITY; NITRATE-REDUCING BACTERIA; PARALOGOUS GENE CLUSTERS; PHYLOGENETIC GROUPS;

BACTERIOLOGY;

ALKYLBENZENE; ETHYLBENZENE; TOLUENE;

BIODEGRADATION; DENITRIFICATION; PHYLOGENETICS;

ANAEROBIC BACTERIUM; AZOARCUS; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL STRAIN; BETAPROTEOBACTERIA; BIODEGRADATION; BIOINFORMATICS; DENITRIFICATION; DNA MICROARRAY; FUNCTIONAL GENOMICS; GENE CLUSTER; GENE EXPRESSION; GENE SEQUENCE; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PLASMID; PROTEOMICS; SHORT SURVEY; THAUERA;

ANAEROBIOSIS; BETAPROTEOBACTERIA; BIODEGRADATION, ENVIRONMENTAL; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; HYDROCARBONS, AROMATIC; PROTEOME;

AZOARCUS; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; THAUERA;

EID: 27644578460     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-005-0030-x     Document Type: Short Survey

References (60)

1. Anders HJ, Kaetzke A, Kämpfer P, Ludwig W, Fuchs G (1995) Taxonomic position of aromatic-degrading denitrifying pseudomonad strains K 172 and KB 740 and description as new members of the genera Thauera, as Thauera aromatica sp. nov., and Azoarcus, as Azoarcus evansii sp. nov., respectively, members of the beta subclass of the Proteobacteria. Int J Syst Bacteriol 45:327-333
2. Barragán MJL, Blázquez B, Zamarro MT, Mancheño JM, García JL, Díaz E, Carmona M (2005) BzdR, a repressor that controls the anaerobic catabolism of benzoate in Azoarcus sp. CIB, is the first member of a new subfamily of transcriptional regulators. J Biol Chem 280:10683-10694
3. Boll M, Fuchs G, Heider J (2002) Anaerobic oxidation of aromatic compounds and hydrocarbons. Curr Opin Chem Biol 6:604-611
4. Breinig S, Schiltz E, Fuchs G (2000) Genes involved in anaerobic metabolism of phenol in the bacterium Thauera aromatica. J Bacteriol 182:5849-5863
5. Champion KM, Zengler K, Rabus R (1999) Anaerobic degradation of ethylbenzene and toluene in denitrifying strain EbN1 proceeds via independent substrate-induced pathways. J Mol Microbiol Biotechnol 1:157-164
6. Coschigano PW, Bishop BJ (2004) Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1. FEMS Microbiol Lett 231:261-266
7. Cunningham JA, Rahme H, Hopkins GD, Lebron C, Reinhard M (2001) Enhanced in situ bioremediation of BTEX-contaminated groundwater by combined injection of nitrate and sulfate. Environ Sci Technol 35:1663-1670
8. Dejonghe W, Boon N, Seghers D, Top EM, Verstraete W (2001) Bioaugmentation of soils by increasing microbial richness: missing links. Environ Microbiol 3:649-657
9. Dörr J, Hurek T, Reinhold-Hurek B (1998) Type IV pili are involved in plant-microbe and fungus-microbe interactions. Mol Microbiol 30:7-17
10. Egland PG, Pelletier DA, Dispensa M, Gibson J, Harwood CS (1997) A cluster of bacterial genes for anaerobic benzene ring biodegradation. Proc Natl Acad Sci U S A 94:6484-6489
11. Gersberg RM, Dawsey WJ, Bradley MD (1993) Nitrate enhancement of in situ bioremediation of monoaromatic compounds in groundwater. Remediation 3:233-245
12. Gibson J, Harwood CS (2002) Metabolic diversity in aromatic compound utilization by anaerobic microbes. Annu Rev Microbiol 56:345-369
13. Gibson DT, Parales RE (2000) Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11:236-243
14. Greated A, Lambertsen L, Williams PA, Thomas CM (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol 4:856-871
15. Harayama S, Kok M, Neidle EL (1992) Functional and evolutionary relationships among diverse oxygenases. Annu Rev Microbiol 46:565-601
16. Harwood CS, Burchhardt G, Hermann H, Fuchs G (1999) Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway. FEMS Microbiol Rev 22:439-458
17. Hayes F (2003) Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301:1496-1499
18. Heider J, Fuchs G (1997) Anaerobic metabolism of aromatic compounds. Eur J Biochem 243:577-596
19. Heider J, Boll M, Breese K, Breinig S, Ebenau-Jehle C, Feil U, Gadón N, Laempe D, Leuthner B, Mohamed ME, Schneider S, Burchhardt G, Fuchs G (1998) Differential induction of enzymes involved in anaerobic metabolism of aromatic compounds in the denitrifying bacterium Thauera aromatica. Arch Microbiol 170:120-131
20. Hess A, Zarda B, Hahn D, Häner A, Stax D, Höhener P, Zeyer J (1997) In situ analysis of denitrifying toluene- and m-xylene-degrading bacteria in a diesel fuel-contaminated laboratory aquifer column. Appl Environ Microbiol 63:2136-2141
21. Hurek T, Reinhold-Hurek B (2003) Azoarcus sp. strain BH72 as a model for nitrogen-fixing grass endophytes. J Biotechnol 106:169-178
22. Jiménez JI, Miñambres B, García JL, Díaz E (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4:824-841
23. Johnson HA, Pelletier DA, Spormann AM (2001) Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J Bacteriol 183:4536-4542
24. Kniemeyer O, Heider J (2001a) Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J Biol Chem 276:21381-21386
25. Kniemeyer O, Heider J (2001b) (S)-1-Phenylethanol dehydrogenase of Azoarcus sp. strain EbN1, an enzyme of anaerobic ethyl-benzene catabolism. Arch Microbiol 176:129-135
26. Körner H, Sofia HJ, Zumft WG (2003) Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol Rev 27:559-592
27. Kube M, Heider J, Amann J, Hufnagel P, Kühner S, Beck A, Reinhardt R, Rabus R (2004) Genes involved in the anaerobic degradation of toluene in a denitrifying bacterium, strain EbN1. Arch Microbiol 181:182-194
28. Kube M, Beck A, Meyerdierks A, Amann R, Reinhardt R, Rabus R (2005) A catabolic gene cluster for anaerobic benzoate degradation in methanotrophic microbial Black Sea mats. Syst Appl Microbiol 28:287-294
29. Kuhn EP, Zeyer J, Eicher P, Schwarzenbach RP (1985) Anaerobic degradation of alkylated benzenes in denitrifying laboratory aquifer columns. Appl Environ Microbiol 54:490-496
30. Kühner S, Wöhlbrand L, Fritz I, Wruck W, Hultschig C, Hufnagel P, Kube M, Reinhardt R, Rabus R (2005) Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol 187:1493-1503
31. Kumagai H, Fujiwara T, Matsubara H, Saeki K (1997) Membrane localization, topology, and mutual stabilization of the rnfABC gene products in Rhodobacter capsulatus and implications for a new family of energy-coupling NADH oxidoreductases. Biochemistry 36:5509-5521
32. Laempe D, Jahn M, Breese K, Schägger H, Fuchs G (2001) Anaerobic metabolism of 3-hydroxybenzoate by the denitrifying bacterium Thauera aromatica. J Bacteriol 183:968-979
33. Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres y Torres JL, Peres C, Harrison FH, Gibson J, Harwood CS (2004) Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 22:55-61
34. Leuthner B, Leutwein C, Schulz H, Hörth P, Haehnel W, Schlitz E, Schägger H, Heider J (1998) Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Mol Microbiol 28:615-628
35. Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VAP, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen J, Timmis KN, Düsterhöft A, Tümmler B, Fraser CM (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4:799-808
36. Pelz O, Chatzinotas A, Andersen N, Bernasconi SM, Hesse C, Abraham W-R, Zeyer J (2001) Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations. Arch Microbiol 175:270-281
37. 3 oxidase from Pseudomonas stutzeri. J Biol Chem 277:31474-31483
38. Rabus R (2005) Biodegradation of hydrocarbons under anoxic conditions. In: Ollivier B, Magot M (eds) Petroleum microbiology. ASM, Washington DC, pp. 277-299
39. Rabus R, Heider J (1998) Initial reactions of anaerobic metabolism of alkylbenzenes in denitrifying and sulfate-reducing bacteria. Arch Microbiol 170:377-384
40. Rabus R, Widdel F (1995) Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch Microbiol 163:96-103
41. Rabus R, Widdel F (1996) Utilization of alkylbenzenes during anaerobic growth of pure cultures of denitrifying bacteria on crude oil. Appl Environ Microbiol 62:1238-1241
42. Rabus R, Wilkes H, Schramm A, Harms G, Behrends A, Amann R, Widdel F (1999) Anaerobic utilization of alkylbenzenes and n-alkanes from crude oil in an enrichment culture of denitrifying bacteria affiliating with the β-subclass of Proteobacteria. Environ Microbiol 1:145-157
43. Rabus R, Kube M, Beck A, Widdel F, Reinhardt R (2002) Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch Microbiol 178:506-516
44. Rabus R, Kube M, Heider J, Beck A, Heitmann K, Widdel F, Reinhardt R (2005) The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 183:27-36
45. Ramos JL, Marqués S, Timmis KN (1997) Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Ann Rev Microbiol 51:341-372
46. Reinhold-Hurek B, Hurek T (2000) Reassessment of the taxonomic structure of the diazotrophic genus Azoarcus sensu lato and description of three new genera and new species, Azovibrio restrictus gen. nov., sp. nov., Azospira oryzae gen. nov., sp. nov. and Azonexus fungiphilus gen. nov., sp. nov. Int J Syst Evol Microbiol 50:649-659
47. Schmeling S, Narmandakh A, Schmitt O, Gad'on N, Schuhle K, Fuchs G (2004) Phenylphosphate synthase: a new phosphotransferase catalyzing the first step in anaerobic phenol metabolism in Thauera aromatica. J Bacteriol 186:8044-8057
48. Schmid A, Dordick JS, Hauer B, Kiener A, Wubbolts M, Witholt B (2001) Industrial biocatalysis today and tomorrow. Nature 409:258-268
49. Sluis MK, Larsen RA, Krum JG, Anderson R, Metcalf WW, Ensign SA (2002) Biochemical, molecular, and genetic analyses of the acetone carboxylase from Xanthobacter autotrophicus strain Py2 and Rhodobacter capsulatus strain B10. J Bacteriol 184:2969-2977
50. Smolenski WJ, Suflita JM (1987) Biodegradation of cresol isomers in anoxic aquifers. Appl Environ Microbiol 53:710-716
51. Song B, Häggblom MM, Zhou J, Tiedje JM, Palleroni NJ (1999) Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov. Int J Syst Bacteriol 49:1129-1140
52. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41
53. 2 and reducing conditions. J Mol Microbiol Biotechnol 4:263-268
54. Wackett LP, Hershberger CD (2001) Biocatalysis and biodegradation: microbial transformation of organic compounds. ASM, Washington DC
55. Weinel C, Nelson KE, Tümmler B (2002) Global features of the Pseudomonas putida KT2440 genome sequence. Environ Microbiol 4:809-818
56. Widdel F, Rabus R (2001) Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr Opin Biotechnol 12:259-276
57. Williams PA, Murray K (1974) Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol 120:416-423
58. Zaar A, Gescher J, Eisenreich W, Bacher A, Fuchs G (2004) New enzymes involved in aerobic benzoate metabolism in Azoarcus evansii. Mol Microbiol 54:223-238
59. Zhou J, Fries MR, Chee-Sanford JC, Tiedje JM (1995) Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 45:500-506
60. Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61:533-616