Anaerobic catabolism of aromatic compounds: A genetic and genomic view

Microbiology and Molecular Biology Reviews

Volumn 73, Issue 1, 2009, Pages 71-133

  Carmona, Manuel ^a   Zamarro, María Teresa ^a   Biázquez, Bias ^a   Durante Rodríguez, Gonzalo ^a   Juárez, Javier F ^a   Valderrama, J Andrés ^a   Barragán, María J L ^a   García, José Luis ^a   Díaz, Eduardo ^a,b  

^a CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^b NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1,2,4 BENZENETRIOL; 3 HYDROXYBENZOIC ACID; 3 METHYLBENZOIC ACID; 4 ETHYLPHENOL; ANTHRANILIC ACID; AROMATIC COMPOUND; BACTERIAL PROTEIN; BENZENE; BENZOATE COA LIGASE; BENZOIC ACID DERIVATIVE; BIOLOGICAL MARKER; ETHYLBENZENE; LIGASE; NICOTINIC ACID; PARA COUMARIC ACID; PARA CRESOL; PHENYLACETIC ACID; PHENYLALANINE; PHLOROGLUCINOL; POLYCYCLIC AROMATIC HYDROCARBON; RESORCINOL; RNA 16S; TOLUENE; UNCLASSIFIED DRUG; XYLENE;

ANAEROBIC METABOLISM; AZOARCUS; CATABOLISM; CHEMICAL REACTION; ECOPHYSIOLOGY; FATTY ACID OXIDATION; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENETIC VARIABILITY; MAGNETOSPIRILLUM; METAGENOMICS; NUCLEOTIDE SEQUENCE; REVIEW; STRAIN DIFFERENCE; STREPTOMYCES; THAUERA AROMATICA; UNINDEXED SEQUENCE;

AMINO ACIDS, AROMATIC; ANAEROBIOSIS; BACTERIA, ANAEROBIC; BIODEGRADATION, ENVIRONMENTAL; ECOSYSTEM; ENVIRONMENTAL POLLUTANTS; FERMENTATION; GENOMICS; HYDROCARBONS, AROMATIC; MULTIGENE FAMILY; PHOTOPHOSPHORYLATION;

EID: 63849112848     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/MMBR.00021-08     Document Type: Review

References (389)

1. Achong, G. R., A. M. Rodríguez, and A. M. Spormann. 2001. Benzylsucci-nate synthase of Azoarcus sp. strain T: cloning, sequencing, transcriptional rganization, and its role in anaerobic toluene and m-xylene mineralization. J. Bacteriol. 183:6763-6770.
2. Aitken, C. M., D. M. Jones, and S. R. Larter. 2004. Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs. Nature 431:291-294.
3. Alder, E. 1977. Lignin chemistry past, present and future. Wood Sci. Technol. 11:169-218.
4. Alhapel, A., D. J. Darley, N. Wagener, E. Eckel, N. Elsner, and A. J. Pierik. 2006. Molecular and funcional analysis of nicotinate catabolism in Eubac-terium barkeri. Proc. Natl. Acad. Sci. USA 103:12341-12346.
5. Altenschmidt, U., B. Oswald, and G. Fuchs. 1991. Purification and characterization of benzoate-coenzyme A ligase and 2-aminobenzoate-coenzyme A ligase from a denitrifying Pseudomonas sp. J. Bacteriol. 173:5494-5501.
6. Andreesen, J. R., and S. Fetzner. 2002. The molybdenum-containing hy-droxylases of nicotinate, isonicotinate, and nicotine. Met. Ions Biol. Syst. 39:405-430.
7. Annweiler, E., A. Materna, M. Safinowski, A. Kappler, H. H. Richnow, W. Michaelis, and R. U.Meckenstock. 2000. Anaerobic degradation of2-methyl-naphthalene by a sulfate-reducing enrichment culture. Appl. Environ. Microbiol. 66:5329-5333.
8. Annweiler, E., W. Michaelis, and R. U. Meckenstock. 2002. Identical ring cleavage products during anaerobic degradation of naphthalene, 2-methyl-naphthalene, and tetralin indicate a new metabolic pathway. Appl. Environ. Microbiol. 68:852-858.
9. Auburger, G., and J. Winter. 1992. Purification and characterization of benzoyl-CoA ligase from a syntrophic, benzoate-degrading, anaerobic mixed culture. Appl. Microbiol. Biotechnol. 37:789-795.
10. Auburger, G., and J. Winter. 1996. Activation and degradation of benzoate, 3-phenylpropionate and crotonate by Syntrophus buswettii strain GA. Evidence for electron-transport phosphorylation during crotonate respiration. Appl. Microbiol. Biotechnol. 44:807-815.
11. Baas, D., and J. Retey. 1999. Cloning, sequencing and heterologous expression of pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. Eur. J. Biochem. 265:896-901.
12. Ball, H. A., H. A. Johnson, M. Reinhard, and A. M. Spormann. 1996. Initial reactions in anaerobic ethylbenzene oxidation by a denitrifying bacterium, strain EB1. J. Bacteriol. 178:5755-5761.
13. Barker, H. A. 1981. Amino acid degradation by anaerobic bacteria. Annu. Rev. Biochem. 50:23-40.
14. Barragán, M. J. L., B. Blázquez, M. T. Zamarro, J. M. Mancheño,J.L. García, E. Díaz, and M. Carmona. 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.
15. Beatrix, B., O. Zelder, D. Linder, and W. Buckel. 1994. Cloning, sequencing and expression of the gene encoding the coenzyme B12-dependent 2-methyl-eneglutarate mutase from Clostridium barkeri in Escherichia coli. Eur. J. Biochem. 221:101-109.
16. Beller, H. R., W. H. Ding, and M. Reinhard. 1995. Byproducts of anaerobic alkylbenzene metabolism useful as indicators of in situ bioremediation. Environ. Sci. Technol. 29:286-2869.
17. Beller, H. R., S. R. Kane, T. C. Legler, and P. J. J. Alvarez. 2002. A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene. Environ. Sci. Technol. 36:3977-3984.
18. Beller, H.R.,andA.M.Spormann.1998. Analysisofthenovelbenzylsuccinate synthase reaction for anaerobic toluene activation based on structural studies of the product. J. Bacteriol. 180:5454-5457.
19. Beller, H. R., and A. M. Spormann. 1999. Substrate range of benzylsucci-nate synthase from Azoarcus sp. strain T. FEMS Microbiol. Lett. 178:147-153.
20. Berman-Frank, I., P. Lundgren, and P. Falkowski. 2003. Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria. Res. Microbiol. 154: 157-164.
21. Berry, D. F., A. J. Francis, and J. M. Bollag. 1987. Microbial metabolism of homocyclic and heterocyclic aromatic compounds under anaerobic conditions. Microbiol. Rev. 51:43-59.
22. Beuerle, T., and E. Pichersky. 2002. Enzymatic synthesis and purification of aromatic coenzyme A esters. Anal. Biochem. 302:305-312.
23. Bhandare, R., M. Calabro, and P. Coschigano. 2006. Site-directed mutagenesis of the Thauera aromatica strain T1 tutE tutFDGH gene cluster. Biochem. Biophys. Res. Commun. 346:992-998.
24. Biegert, T., U. Altenschmidt, C. Eckerskorn, and G. Fuchs. 1993. Enzymes of anaerobic metabolism of phenolic compounds. 4-Hydroxybenzoate-CoA ligase from a denitrifying Pseudomonas species. Eur. J. Biochem. 213:555-561.
25. Biegert, T., U. Altenschmidt, C. Eckerskorn, and G. Fuchs. 1995. Purification and properties of benzyl alcohol dehydrogenase from a denitrifying Thauera sp. Arch. Microbiol. 163:418-423.
26. Biegert, T., G. Fuchs, and J. Heider. 1996. Evidence that anaerobic oxidation of toluene in the denitrifying bacterium Thauera aromatica is initiated by formation of benzylsuccinate from toluene and fumarate. Eur. J. Bio-chem. 238:661-668.
27. Blake, C. K., and G. D. Hegeman. 1987. Plasmid pCBI carries genes for anaerobic benzoate catabolism in Alcaligenes xylosoxidans subsp. denitrifi-cans PN-1. J. Bacteriol.169:4878-4883.
28. Blakley, E. R. 1978. The microbial degradation of cyclohexanecarboxylic acid by a β-oxidation pathway with simultaneous induction to the utilisation of benzoate. Can. J. Microbiol. 24:847-855.
29. Blázquez, B., M. Carmona, J. L. García, and E. Díaz. 2008. Identification and analysis of a glutaryl-CoA dehydrogenase-encoding gene and its cognate transcriptional regulator from Azoarcus sp. CIB. Environ. Microbiol. 10:474-482.
30. Boll, M. 2005. Dearomatizing benzene ring reductases. J. Mol. Microbiol. Biotechnol. 10:132-142.
31. Boll, M. 2005. Key enzymes in the anaerobic aromatic metabolism catalysing Birch-like reductions. Biochim. Biophys. Acta 1707:34-50.
32. Boll, M., and G. Fuchs. 1998. Identification and characterization of the natural electron donor ferredoxin and of FAD as a possible prosthetic group of benzoyl-CoA reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism. Eur. J. Biochem. 251:946-954. 33. Boll, M., G. Fuchs, and J. Heider. 2002. Anaerobic oxidation of aromatic compounds and hydrocarbons. Curr. Opin. Chem. Biol. 6:604-611.
33. Boll, M., G. Fuchs, C. Meier, A. Trautwein, A. El Kasmi, S. W. Ragsdale, G. Buchanan, and D. J. Lowe. 2001. Redox centers of 4-hydroxybenzoyl-CoA reductase, a member of the xanthine oxidase family of molybdenum-containing enzymes. J. Biol. Chem. 276:47853-47862.
34. Boll, M., D. Laempe, W. Eisenreich, A. Bacher, T. Mittelberger, J. Heinze, and G. Fuchs. 2000. Nonaromatic products from anoxic conversion of benzoyl-CoA with benzoyl-CoA reductase and cyclohexa-1,5-diene-1-carbonyl-CoA hydratase. J. Biol. Chem. 275:21889-21895.
35. Bonin, I., B. M. Martins, V. Purvanov, S. Fetzner, R. Huber, and H. Dobbek. 2004. Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase. Structure 12:1425-1435.
36. Bonting, C. F., and G. Fuchs. 1996. Anaerobic metabolism of 2-hydroxy-benzoic acid (salicylic acid) by a denitrifying bacterium. Arch. Microbiol. 165:402-408.
37. Bossert, I. D., G. Whited, D. T. Gibson, and L. Y. Young. 1989. Anaerobic oxidation of p-cresol mediated by a partially purified methylhydroxylase from a denitrifying bacterium. J. Bacteriol. 171:2956-2962.
38. Breese, K., M. Boll, J. Alt-Mörbe, H. Scha7die;gger, and G. Fuchs. 1998. Genes coding for the benzoyl-CoA pathway of anaerobic aromatic metabolism in the bacterium Thauera aromatica. Eur. J. Biochem. 256:148-154.
39. Breese, K., and G. Fuchs. 1998. 4-Hydroxybenzoyl-CoA reductase (dehy-droxylating) from the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 251:916-923.
40. Breining, S., E. Schiltz, and G. Fuchs. 2000. Genes involved in anaerobic metabolism of phenol in the bacterium Thauera aromatica. J. Bacteriol. 182:5849-5863.
41. Brune, A., E. Miambi, and J. A. Breznak. 1995. Roles of oxygen and the intestinal microflora in the metabolism of lignin-derived phenylpropanoids and other monoaromatic compounds by termites. Appl. Environ. Micro-biol. 61:2688-2695.
42. Brune, A., S. Schnell, and B. Schink. 1992. Sequential transhydroxylations converting hydroxyhydroquinone to phloroglucinol in the strictly anaerobic, fermentative bacterium Pelobacter massiliensis. Appl. Environ. Microbiol. 58:1861-1868.
43. Buckel, W., and R. Semmler. 1983. Purification, characterisation and re-constitution of glutaconyl-CoA decarboxylase, a biotin-dependent sodium pump from anaerobic bacteria. Eur. J. Biochem. 136:427-434.
44. Bunge, M., L. Adrian, A. Kraus, M. Opel, W. G. Lorenz, J. R. Andreesen, H. G̈risch, and U. Lechner. 2003. Reductive dehalogenation of chlorinated dioxins by an anaerobic bacterium. Nature 421:357-360.
45. Burland, S. M., and E. A. Edwards. 1999. Anaerobic benzene biodegrada-tion linked to nitrate reduction. Appl. Environ. Microbiol. 65:529-533.
46. Busch, A., J. Lacal, A. Martos, J. L. Ramos, and T. Krell. 2007. Bacterial sensor kinase TodS interacts with agonistic and antagonistic signals. Proc. Natl. Acad. Sci. USA 104:13774-13779.
47. Butler, J. E., Q. He, K. P. Nevin, Z. He, J. Zhou, and D. R. Lovley. 2007. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genomics 8:180.
48. Caldwell, M. E., and J. M. Suflita 2000. Detection ofphenol and benzoate as intermediates of anaerobic benzene biodegradation under different terminal electron-accepting conditions. Environ. Sci. Technol. 34:1216-1220.
49. Callaghan, A. V., B. Wawrik, S. M. N. Chadhain, L. Y. Young, and G. J. Zylstra. 2008. Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes. Biochem. Biophys. Res. Commun. 366:142-148.
50. Canosa, I., J. M. Sánchez-Romero, L. Yuste, and F. Rojo. 2000. A positive feedback mechanism controls expression of AlkS, the transcriptional regulator of the Pseudomonas oleovorans alkane degradation pathway. Mol. Microbiol. 35:791-799.
51. Carmona, M., and E. Díaz. 2005. Iron-reducing bacteria unravel novel strategies for the anaerobic catabolism of aromatic compounds. Mol. Mi-crobiol. 58:1210-1215.
52. Carmona, M., M. A. Prieto, B. Galán, J. L. Garcia, and E. Díaz. 2008. Signaling networks and design of pollutants biosensors, p. 97-143. In E. Díaz (ed.), Microbial biodegradation: genomics and molecular biology. Caister Academic Press, Norfolk, United Kingdom.
53. Cases, I., and V. de Lorenzo. 2001. The black cat/white cat principle of signal integration in bacterial promoters. EMBO J. 20:1-11.
54. Cases, I., and V. de Lorenzo. 2005. Promoters in the environment: tran-scriptional regulation in its natural context. Nat. Rev. Microbiol. 3:105-118.
55. Cases, I., D. W. Ussery, and V. de Lorenzo. 2003. The sigma54 regulon (sigmulon) of Pseudomonas putida. Environ. Microbiol. 5:1281-1293.
56. Cerniglia, C. E. 1992. Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351-368.
57. Cervin, M. A., R. J. Lewis, J. A. Brannigan, and G. B. Spiegelman. 1998. The Bacillus subtilis regulator SinR inhibits spoIIG promoter transcription in vitro without displacing RNA polymerase. Nucleic Acids Res. 26:38063812.
58. Chakraborty, R., and J. D. Coates. 2004. Anaerobic degradation of mono-aromatic hydrocarbons. Appl. Microbiol. Biotechnol. 64:437-446.
59. Chakraborty, R., and J. D. Coates. 2005. Hydroxylation and carboxylation-two crucial steps of anaerobic benzene degradation by Dechlowmonas strain RCB. Appl. Environ. Microbiol. 71:5427-5432.
60. Chakraborty, R., S. M. O'Connor, E. Chan, and J. D. Coates. 2005. Anaerobic degradation of benzene, toluene, ethylbenzene, and xylene compounds by Dechloromonas strain RCB. Appl. Environ. Microbiol. 71:8649-8655.
61. Chalmers, R. M., J. N. Keen, and C. A. Fewson. 1991. Comparison of benzyl alcohol dehydrogenases and benzaldehyde dehydrogenases from the benzyl alcohol and mandelate pathways in Acinetobacter calcoaceticus and from the TOL-plasmid-encoded toluene pathway in Pseudomonas putida.N-terminal amino acid sequences, amino acid compositions and immunolog-ical cross-reactions. Biochem. J. 273:99-107.
62. Champion, K. M., K. Zengler, and R. Rabus. 1999. Anaerobic degradation of ethylbenzene and toluene in denitrifying strain EbN1 proceeds via independent substrate-induced pathways. J. Mol. Microbiol. Biotechnol. 1:157-164.
63. Coates, J. D., R. Chakraborty, J. G. Lack, S. M. O'Connor, K. A. Cole, K. S. Bender, and L. A. Achenbach. 2001. Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411:1039-1043.
64. Coates, J. D., R. Chakraborty, and M. J. Mclnerney. 2002. Anaerobic benzene biodegradation-a new era. Res. Microbiol. 153:621-628.
65. Collier, D. N., P. W. Hager, and P. V. Phibbs, Jr. 1996. Catabolite repression control in the pseudomonads. Res. Microbiol. 147:551-561.
66. Collier, L. S., N. N. Nichols, and E. L. Neidle. 1997. benK encodes a hydrophobic permease-like protein involved in benzoate degradation by Acinetobacter sp. strain ADP1. J. Bacteriol. 179:5943-5946.
67. Coschigano, P. W. 2000. Transcriptional analysis of the tutE tutFDGH gene cluster from Thauera aromatica strain T1. Appl. Environ. Microbiol. 66:1147-1151.
68. Coschigano, P. W. 2002. Construction and characterization of insertion/deletion mutations of the tutF, tutD, and tutG genes of Thauera aromatica strain T1. FEMS Microbiol. Lett. 217:37-42.
69. Coschigano, P. W., and B. J. Bishop. 2004. Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1. FEMS Microbiol. Lett. 16:261-266.
70. Coschigano, P. W., M. M. Häggblom, and L. Y. Young. 1994. Metabolism of both 4-chlorobenzoate and toluene under denitrifying conditions by a constructed bacterial strain. Appl. Environ. Microbiol. 60:989-995.
71. Coschigano, P. W., T. S. Wehrman, and L. Y. Young. 1998. Identification and analysis of genes involved in anaerobic toluene metabolic by strain T1: putative role of a glycine free radical. Appl. Environ. Microbiol. 64:1650-1656.
72. Coschigano, P. W., and L. Y. Young. 1997. Identification and sequence analysis of two regulatory genes involved in anaerobic toluene metabolismby strain T1. Appl. Environ. Microbiol. 63:652-660.
73. Crawford, J. J., G. K. Sims, R. L. Mulvaney, and M. Radosevich. 1998. Biodegradation of atrazine under denitrifying conditions. Appl. Microbiol. Biotechnol. 49:618-623.
74. Cunane, L. M., Z. W. Chen, N. Shamala, F. S. Mathews, C. N. Cronin, and W. S. Mclntire. 2000. Structures of the flavocytochrome p-cresol methyl-hydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism. J. Mol. Biol. 295:357-374.
75. Dagley, S. 1978. Determinants of biodegradability. Q. Rev. Biophys. 11:577-602.
76. Darley, P. I., J. A. Hellstern, J. I. Medina-Bellver, S. Marqués, B. Schink, and B. Philipp. 2007. Heterologous expression and identification of the genes involved in anaerobic degradation of 1,3-dihydroxybenzene (resor-cinol) in Azoarcus anaerobius. J. Bacteriol. 189:3824-3833.
77. Da Silva, M. L. B., and P. J. J. Alvarez. 2004. Enhanced anaerobic biodeg-radation of benzene-toluene-ethylbenzene-xylene-ethanol mixtures in bio-augmented aquifer columns. Appl. Environ. Microbiol. 70:4720-4726.
78. Da Silva, M. L. B., and P. J. J. Alvarez. 2007. Assessment of anaerobic benzene degradation potential using 16S rRNA gene-targeted real-time PCR. Environ. Microbiol. 9:72-80.
79. Dayan, F. E., S. B. Watson, and N. P. Nanayakkara. 2007. Biosynthesis of lipid resorcinols and benzoquinones in isolated secretory plant root hairs. J. Exp. Bot. 58:3263-3272.
80. de Lorenzo, V., and J. Pérez-Martín. 1996. Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals. Mol. Microbiol. 19:1177-1184.
81. del Peso-Santos, T., D. Bartolomé-Martín, C. Fernández, S. Alonso, J. L. García, E. Díaz, V. Shingler, and J. Perera. 2006. Coregulation by phenyl-acetyl-coenzyme A-responsive PaaX integrates control of the upper and lower pathways for catabolism of styrene by Pseudomonas sp. strain Y2. J. Bacteriol. 188:4812-4821.
82. Denef, V. J., J. A. Klappenbach, M. A. Patrauchan, C. Florizone, J. L. Rodrigues, T. V. Tsoi, W. Verstraete, L. D. Eltis, and J. M. Tiedje. 2006. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl. Environ. Microbiol. 72:585-595.
83. Díaz, E. 2004. Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int. Microbiol. 7:173-180.
84. Díaz, E., A. Ferrández, M. A. Prieto, and J. L. García. 2001. Biodegradation of aromatic compounds by Escherichia coli. Microbiol. Mol. Biol. Rev. 65:523-569.
85. Díaz, E., and M. A. Prieto. 2000. Bacterial promoters triggering biodegra-dation of aromatic pollutants. Curr. Opin. Biotechnol. 11:467-475.
86. Dickert, S., A. J. Pierik, D. Linder, and W. Buckel. 2000. The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cin-namate by Clostridium sporogenes. Eur. J. Biochem. 267:3874-3884.
87. Dilling, S., F. Imkamp, S. Schmidt, and V. Mualler. 2007. Regulation of caffeate respiration in the acetogenic bacterium Acetobacterium woodii. Appl. Environ. Microbiol. 73:3630-3636.
88. Dimroth, P., and B. Schink. 1998. Energy conservation in the decarbox-ylation of dicarboxylic acids by fermenting bacteria. Arch. Microbiol. 170:69-77.
89. Ding, B., S. Schmeling, and G. Fuchs. 2008. Anaerobic metabolism of catechol by the denitrifying bacterium Thauera aromatica-a result of promiscuous enzymes and regulators? J. Bacteriol. 190:1620-1630.
90. Dispensa, M., C. T. Thomas, M. K. Kim, J. A. Perrotta, J. Gibson, and C. S. Harwood. 1992. Anaerobic growth of Rhodopseudomonas palustris on 4-hy-droxybenzoate is dependent on AadR, a member of the cyclic AMP receptor protein family of transcriptional regulators. J. Bacteriol. 174:5803- 5813.
91. Dobrindt, U., B. Hochhut, U. Hentschel, and J. Hacker. 2004. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Micro-biol. 2:414-424.
92. Dominguez-Cuevas, P., J. E. Gonzaalez-Pastor, S. Marquaes, J. L. Ramos, and V. de Lorenzo. 2006. Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J. Biol. Chem. 281:11981-11991.
93. Daorner, E., and M. Boll. 2002. Properties of 2-oxoglutarate: ferredoxin oxidoreductase from Thauera aromatica and its role in enzymatic reduction of the aromatic ring. J. Bacteriol. 184:3975-3983.
94. Duetz, W. A., S. Marquaés, B. Wind, J. L. Ramos, and J. G. van Andel. 1996. Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation in chemostat culture. Appl. Environ. Microbiol. 62:601-606.
95. Duldhardt, I., I. Nijenhuis, F. Schauer, and H. J. Heipieper. 2007. Anaer-obically grown Thauera aromatica, Desulfococcus multivorans, Geobacter sulfurreducens are more sensitive towards organic solvents than aerobic bacteria. Appl. Microbiol. Biotechnol. 77:705-711.
96. Durante-Rodríguez, G., M. T. Zamarro, J. L. García, E. Diaz, and M. Carmona. 2006. Oxygen-dependent regulation of the central pathway for the anaerobic catabolism of aromatic compounds in Azoarcus sp. strain CIB. J. Bacteriol. 188:2343-2354.
97. Durante-Rodríguez, G., M. T. Zamarro, J. L. García, E. Diaz, and M. Carmona. 2008. New insights into the BzdR-mediated transcriptional regulation of the anaerobic catabolism of benzoate in Azoarcus sp. CIB. Microbiology 154:306-316.
98. +oxidoreductase in Azoarcus evansii: properties and function in electron transfer reactions in aromatic ring reduction. J. Bacteriol. 185:6119-6129.
99. Egland, P. G., J. Gibson, and C. S. Harwood. 1995. Benzoate-coenzyme A ligase, encoded by badA, is one of three ligases able to catalyze benzoyl-coenzyme A formation during anaerobic growth of Rhodopseudomonas palustris on benzoate. J. Bacteriol. 177:6545-6551.
100. Egland, P. G., J. Gibson, and C. S. Harwood. 2001. Reductive, coenzyme A-mediated pathway for 3-chlorobenzoate degradation in the phototrophic bacterium Rhodopseudomonas palustris. Appl. Environ. Microbiol. 67: 1396-1399.
101. Egland, P. G., and C. S. Harwood. 1999. BadR, a new MarR family member, regulates anaerobic benzoate degradation by Rhodopseudomonas palustris in concert with AadR, an FNR family member. J. Bacteriol. 181:2102-2109.
102. Egland, P. G., and C. S. Harwood. 2000. HbaR, a 4-hydroxybenzoate sensor and FNR-CRP superfamily member, regulates anaerobic 4-hydroxybenzo-ate degradation by Rhodopseudomonas palustris. J. Bacteriol. 182:100-106.
103. Egland, P. G., D. A. Pelletier, M. Dispensa, J. Gibson, and C. S. Harwood. 1997. A cluster of bacterial genes for anaerobic benzene ring biodegrada-tion. Proc. Natl. Acad. Sci. USA 94:6484-6489.
104. El Fantroussi, S., H. Naveau, and S. N. Agathos. 1998. Anaerobic dechlo-rinating bacteria. Biotechnol. Prog. 14:167-188.
105. 2-using microorganisms. Appl. Environ. Microbiol. 67:1728-1738.
106. Elshahed, M. S., and M. J. McInerney. 2001. Benzoate fermentation by the anaerobic bacterium Syntrophus aciditrophicus in the absence of hydrogen-using microorganisms. Appl. Environ. Microbiol. 67:5520-5525.
107. Esteve-Núñiez, A., A. Caballero, and J. L. Ramos. 2001. Biological degradation of 2,4,6-trinitrotoluene. Microbiol. Mol. Biol. Rev. 65:335-352.
108. Esteve-Nuñez, A., G. Lucchesi, B. Philipp, B. Schink, and J. L. Ramos. 2000. Respirationof2,4,6-trinitrotoluene byPseudomonassp. strainJLR11. J. Bacteriol. 182:1352-1355.
109. Evans, W. C., and G. Fuchs. 1988. Anaerobic degradation of aromatic compounds. Annu. Rev. Microbiol. 42:289-317.
110. Fetzner, S. 1998. Bacterial degradation of pyridine, indole, quinoline, and their derivatives under different redox conditions. Appl. Microbiol. Bio-technol. 49:237-250.
111. Fetzner, S. 2002. Enzymes involved in the aerobic bacterial degradation of N-heteroaromatic compounds: molybdenum hydroxylases and ring-opening 2,4-dioxygenases. Naturwissenschaften 87:59-69.
112. Fischer, A., I. Herklotz, S. Herrmann, M. Thullner, S. A. Weelink, A. J. Stams, M. Schlömann, H. H. Richnow, and C. Vogt. 2008. Combined carbon and hydrogen isotope fractionation investigations for elucidating benzene biodegradation pathways. Environ. Sci. Technol. 42:4356-4363.
113. Friedrich, M. W. 2006. Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metage-nomes. Curr. Opin. Biotechnol. 17:59-66.
114. Fu, Z., M. Wang, R. Paschke, S. Rao, F. E. Frerman, and J. J. P. Kim. 2004. Crystal structures of human glutaryl-CoA dehydrogenases with and without an alternate substrate: structural bases of dehydrogenation and decarbox-ylation reactions. Biochemistry 43:9674-9684.
115. Fuchs, G. 2008. Anaerobic metabolism of aromatic compounds. Ann. N. Y. Acad. Sci. 1125:82-99.
116. Gallegos, M. T., A. J. Molina-Henares, X. Zhang, W. Teran, P. Bernal, Y. Alguel, M. E. Guazzaroni, T. Krell, A. Segura, and J. L. Ramos. 2008. Genomic insights into solvent tolerance and pumps that extrude toxic chemicals, p. 189-217. In E. Díz (ed.), Microbial biodegradation: genomics and molecular biology. Caister Academic Press, Norfolk, United Kingdom.
117. Gallus, C., and B. Schink. 1994. Anaerobic degradation of pimelate by newly isolated denitrifying bacteria. Microbiology 140:409-416.
118. Gallus, C., and B. Schink. 1998. Anaerobic degradation of a-resorcylate by Thauera aromatica strain AR-1 proceeds via oxidation and decarboxylation to hydroxyhydroquinone. Arch. Microbiol. 169:333-338.
119. Galushko, A., D. Minz, B. Schink, and F. Widdel. 1999. Anaerobic degradation of naphthalene by a pure culture of a novel type of marine sulphate-reducing bacterium. Environ. Microbiol. 1:415-420.
120. Galushko, A. S., and B. Schink. 2000. Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture. Arch. Microbiol. 174:314-321.
121. Gasson, M. J., Y. Kitamura, W. R. McLauchlan, A. Narbad, A. J. Parr, E. L. Parsons, J. Payne, M. J. Rhodes, and N. J. Walton. 1998. Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester. J. Biol. Chem. 273:4163-4170.
122. Geissler, J. F., C. S. Harwood, and J. Gibson. 1988. Purification and properties of benzoate-coenzyme A ligase, a Rhodopseudomonas palustris enzyme involved in the anaerobic degradation of benzoate. J. Bacteriol. 170:1709-1714.
123. Gescher, J., W. Ismail, E. Olgeschläger, W. Eisenreich, J. Wo6rth, and G. Fuchs. 2006. Aerobic benzoyl-coenzyme A (CoA) catabolic pathway in Azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase. J. Bacteriol. 188:2919-2927.
124. Gescher, J., A. Zaar, M. Mohamed, H. Schägger, and G. Fuchs. 2002. Genes coding for a new pathway of aerobic benzoate metabolism in Azo-arcus evansii. J. Bacteriol. 184:6301-6315.
125. Gibson, J., M. Dispensa, G. C. Fogg, D. T. Evans, and C. S. Harwood. 1994. 4-Hydroxybenzoate-coenzyme A ligase from Rhodopseudomonas palustris:purification, gene sequence, and role in anaerobic degradation. J. Bacteriol. 176:634-641.
126. Gibson, J., M. Dispensa, and C. S. Harwood. 1997. 4-Hydroxybenzoyl coenzyme A reductase (dehydroxylating) is required for anaerobic degradation of 4-hydroxybenzoate by Rhodopseudomonas palustris and shares features with molybdenum-containing hydroxylases. J. Bacteriol. 179:634-642.
127. Gibson, J., and C. S. Harwood. 2002. Metabolic diversity in aromatic compound utilization by anaerobic microbes. Annu. Rev. Microbiol. 56:345-369.
128. Gibson, K. J., and J. Gibson. 1992. Potential early intermediates in anaerobic benzoate degradation by Rhodopseudomonas palustris. Appl. Environ. Microbiol. 58:696-698.
129. Giel, J. L., D. Rodionov, M. Liu, F. R. Blattner, and P. J. Kiley. 2006. IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli. Mol. Microbiol. 60:1058-1075.
130. Gillooly, D. J., A. G. Robertson, and C. A. Fewson. 1998. Molecular char-acterization of benzyl alcohol dehydrogenase and benzaldehyde dehydro-genase II of Acinetobacter calcoaceticus. Biochem. J. 330:1375-1381.
131. Gladyshev, V. N., S. V. Khangulov, and T. C. Stadtman. 1996. Properties of the selenium- and molybdenum-containing nicotinic acid hydroxylase from Clostridium barkeri. Biochemistry 35:212-223.
132. Glo6ckler, R., A. Tschech, and G. Fuchs. 1989. Reductive dehydroxylationof 4-hydroxybenzoyl-CoA to benzoyl-CoA in a denitrifying, phenol-degrading Pseudomonas species. FEBS Lett. 251:237-240.
133. Gomes, B., G. Fendrich, and R. H. Abeles. 1981. Mechanism of action of glutaryl-CoA and butyryl-CoA dehydrogenases. Purification of glutaryl-CoA dehydrogenase. Biochemistry 20:1481-1490.
134. Gorny, N., and B. Schink. 1994. Anaerobic degradation of catechol by Desulfobacterium sp. strain Cat2 proceeds via carboxylation to protocate-chuate. Appl. Environ. Microbiol. 60:3396-3400.
135. Gorny, N., G. Wahl, A. Brune, and B. Schink. 1992. A strictly anaerobic nitrate-reducing bacterium growing with resorcinol and other aromatic compounds. Arch. Microbiol. 158:48-53.
136. Green, J., B. Bennett, P. Jordan, E. T. Ralph, A. J. Thomson, and J. R. Guest. 1996. Reconstitution of the [4Fe-4S] cluster in FNR and demonstration of the aerobic-anaerobic transcription switch in vitro. Biochem. J. 316:887-892.
137. Gu, Y., L. Reshetnikova, Y. Li, Y. Wu, H. Yan, S. Singh, and X. Ji. 2002. Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis. J. Mol. Biol. 319:779-789.
138. Gulensoy, N., and P. J. Alvarez. 1999. Diversity and correlation of specific aromatic hydrocarbon biodegradation capabilities. Biodegradation 10:331-340.
139. Harrison, F. H., and C. S. Harwood. 2005. The pimFABCDEoperon from Rhodopseudomonas palustris mediates dicarboxylic acid degradation and participates in anaerobic benzoate degradation. Microbiology 151:727-736.
140. Härtel, U., E. Eckel, J. Koch, G. Fuchs, D. Linder, and W. Buckel. 1993. Purification of glutaryl-CoA dehydrogenase from Pseudomonas sp., an enzyme involved in the anaerobic degradation of benzoate. Arch. Microbiol. 159:174-181.
141. Harwood, C. S., G. Burchhardt, H. Herrmann, and G. Fuchs. 1999. Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway. FEMS Microbiol. Rev. 22:439-458.
142. Harwood, C. S., and J. Gibson. 1988. Anaerobic and aerobic metabolism of diverse aromatic compounds by the photosynthetic bacterium Rhodopseu-domonas palustris. Appl. Environ. Microbiol. 54:712-717.
143. Harwood, C. S., and J. Gibson. 1997. Shedding light on anaerobic benzene ring degradation: a process unique to prokaryotes? J. Bacteriol. 179:301-309.
144. Harwood, C. S., and R. E. Parales. 1996. The beta-ketoadipate pathwayand the biology of self-identity. Annu. Rev. Microbiol. 50:553-590.
145. He, Z., T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, Z. Huang, W. Wu, B. Gu, P. Jardine, C. Criddle, and J. Zhou. 2007. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J. 1:67-77.
146. Head, I. M., D. M. Jones, and S. R. Larter. 2003. Biological activity in the deep subsurface and the origin of heavy oil. Nature 426:344-352.
147. Hearn, E. M., D. R. Patel, and B. van den Berg. 2008. Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation. Proc. Natl. Acad. Sci. USA 105:8601-8606.
148. Heider, J. 2007. Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms. Curr. Opin. Chem. Biol. 11:188-194.
149. Heider, J., M. Boll, K. Breese, S. Breinig, C. Ebenau-Jehle, U. Feil, N. Gad'on, D. Laempe, B. Leuthner, M. El-Said Mohamed, S. Schneider, G. Burchhardt, and G. Fuchs. 1998. Differential induction of enzymes involved in anaerobic metabolism of aromatic compounds in the denitrifying bacterium Thauera aromatica. Arch. Microbiol. 170:120-131.
150. Heider, J., and G. Fuchs. 1997. Anaerobic metabolism of aromatic compounds. Eur. J. Biochem. 243:577-596.
151. Heider, J., and R. Rabus. 2008. Genomic insights in the anaerobic biodeg-radation of organic pollutants, p. 25-54. In E. Díaz (ed.), Microbial bio-degradation: genomics and molecular biology. Caister Academic Press, Norfolk, United Kingdom.
152. Heider, J., A. M. Spormann, H. R. Beller, and F. Widdel. 1999. Anaerobic bacterial metabolism of hydrocarbons. FEMS Microbiol. Rev. 22:459-473.
153. Heipieper, H. J., G. Neumann, S. Cornelissen, and F. Meinhardt. 2007. Solvent-tolerant bacteria for biotransformations in two-phase fermentation systems. Appl. Microbiol. Biotechnol. 74:961-973.
154. Hermuth, K., B. Leuthner, and J. Heider. 2002. Operon structure and expression of the genes for benzylsuccinate synthase in Thauera aromatica strain K172. Arch. Microbiol. 177:132-138.
155. Hess, A., B. Zarda, D. Hahn, A. H6aner, D. Stax, P. H6ohener, and J. Zeyer. 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.
156. + oxidoreductase (CoA benzoylating), a new enzyme of anaerobic phenylalanine metabolism in the denitrifying bacterium Azoarcus evansii. Eur. J. Biochem. 251:907-915.
157. Höaffken, H. W., M. Duong, T. Friedrich, M. Breuer, B. Hauer, R. Rein-hardt, R. Rabus, and J. Heider. 2006. Crystal structure and enzyme kinetics of the (S)-specific 1-phenylethanol dehydrogenase of the denitrifying bacterium strain EbN1. Biochemistry 45:82-93.
158. Holcenberg, J. S., and L. Tsai. 1969. Nicotinic acid metabolism. IV. Ferre-doxin-dependent reduction of 6-hydroxynicotinic acid to 6-oxo-1,4,5,6-tetra-hydronicotinic acid. J. Biol. Chem. 244:1204-1211.
159. Holliger, C., G. Wohlfarth, and G. Dieckert. 1999. Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol. Rev. 22:383-398.
160. Holm, L., and C. Sander. 1997. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 28:72-82.
161. Hopper, D. J., I. D. Bossert, and M. E. Rhodes-Roberts. 1991. p-Cresol methylhydroxylase from a denitrifying bacterium involved in anaerobic degradation of p-cresol. J. Bacteriol. 173:1298-1301.
162. Hosoda, A., Y. Kasai, N. Hamamura, Y. Takahata, and K. Watanabe.
163. Huang, J., Z. He, and J. Wiegel. 1999. Cloning, characterization, and expression of a novel gene encoding a reversible 4-hydroxybenzoate decar-boxylase from Clostridium hydroxybenzoicum. J. Bacteriol. 181:5119-5122.
164. Huffman, J. L., and R. G. Brennan. 2002. Prokaryotic transcription regulators: more than just the helix-turn-helix motif. Curr. Opin. Struct. Biol. 12:98-106.
165. Hughes, M. N. 1999. Relationships between nitric oxide, nitroxyl ion, ni-trosonium cation and peroxynitrite. Biochim. Biophys. Acta 1411:263-272.
166. Ismail, W., M. El-Said Mohamed, B. L. Wanner, K. A. Datsenko, W. Eisenreich, F. Rohdich, A. Bacher, and G. Fuchs. 2003. Functional genom-ics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli Eur. J. Biochem. 270:3047-3054.
167. Jackson, B. E., and M. J. McInerney. 2002. Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature 415:454-456.
168. Jannsen, D. B., J. E. Oppentocht, and G. J. Poelarends. 2001. Microbial dehalogenation. Curr. Opin. Biotechnol. 12:254-258.
169. Jimenéz, J. I., B. Miñambres, J. L. Garcia, and E. Diaz. 2002. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol. 4:824-841.
170. Johannes, J., A. Bluschke, N. Jehmlich, M. von Bergen, and M. Boll. 2008. Purification and characterization of active-site components of the putative p-cresol methylhydroxylase membrane complex from Geobacter metallire-ducens. J. Bacteriol. 190:6493-6500.
171. Johannes, J., M. C. Unciuleac, T. Friedrich, E. Warkentin, U. Ermler, and M. Boll. 2008. Inhibitors of the molybdenum cofactor containing 4-hydroxy-benzoyl-CoA reductase. Biochemistry 47:4964-4972.
172. Johnson, H. A., D. A. Pelletier, and A. M. Spormann. 2001. Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J. Bacteriol. 183:4536-4542.
173. Johnson, H. A., and A. M. Spormann. 1999. In vitro studies on the initial reactions of anaerobic ethylbenzene mineralization. J. Bacteriol. 181:5662-5668.
174. Jones, D. M., I. M. Head, N. D. Gray, J. J. Adams, A. K. Rowan, C. M. Aitken, B. Bennett, H. Huang, A. Brown, B. F. J. Bowler, T. Oldenburg, M. Erdmann, and S. R. Larter. 2007. Crude-oil biodegradation via methano-genesis in subsurface petroleum reservoirs. Nature 451:176-180.
175. Kaiser, J. P., Y. Feng, and J. M. Bollag. 1996. Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions. Microbiol. Rev. 60:483-498.
176. Kane, S. R., H. R. Beller, T. C. Legler, and R. T. Anderson. 2002. Biochemical and genetic evidence of benzylsuccinate synthase in toluene-degrading, ferric iron-reducing Geobacter metallireducens. Biodegradation 13:149-154.
177. Karns, J. S. 1999. Gene sequence and properties of an s-triazine ring-cleavage enzyme from Pseudomonas sp. strain NRRLB-12227. Appl. Environ. Microbiol. 65:3512-3517.
178. Kasai, Y., Y. Kodama, Y. Takahata, T. Hoaki, and K. Watanabe. 2007. Degradative capacities and bioaugmentation potential of an anaerobic benzene-degrading bacterium strain DN11. Environ. Sci. Technol. 41:6222-6227.
179. Kasai, Y., Y. Takahata, M. Manefield, and K. Watanabe. 2006. RNA-based stable isotope probing and isolation of anaerobic benzene-degrading bacteria from gasoline-contaminated groundwater. Appl. Environ. Microbiol. 72:3586-3592.
180. Kawaguchi, K., Y. Shinoda, H. Yurimoto, Y. Sakai, and N. Kato. 2006. Purification and characterization of benzoate-CoA ligase from Magnetospi-rillum sp. strain TS-6 capable of aerobic and anaerobic degradation of aromatic compounds. FEMS Microbiol. Lett. 257:208-213.
181. Kazumi, J., M. E. Caldwell, J. M. Suflita, D. R. Lovley, and L. Y. Young. 1997. Anaerobic degradation of benzene in diverse anoxic environments. Environ. Sci. Technol. 31:813-818.
182. Keat, M. J., and D. J. Hopper. 1978. p-Cresol and 3,5-xylenol methylhy-droxylases in Pseudomonas putida N.C.I.B. 9896. Biochem. J. 175:649-658.
183. Kerkhof, L. J., and M. M. Haaggblom. 2008. Detecting active bacteria involved in biodegradation in the environment, p. 55-70. In E. Díaz (ed.), Microbial biodegradation: genomics and molecular biology. Caister Academic Press, Norfolk, United Kingdom.
184. Kiley, P. J., and W. S. Reznikoff. 1991. Fnr mutants that activate gene expression in the presence of oxygen. J. Bacteriol. 173:16-22.
185. Kim, T. S., H. Y. Kim, and B. H. Kim. 1990. Petroleum desulfurization by Desulfovibrio desulfuricans M6 using electrochemically supplied reducing equivalent. Biotechnol. Lett. 12:757-761.
186. Kitts, C. L., J. P. Lapointe, V. T. Lam, and R. A. Ludwig. 1992. Elucidation of the complete Azorhizobium nicotinate catabolism pathway. J. Bacteriol. 174:7791-7797.
187. Kloer, D. P., C. Hagel, J. Heider, and G. E. Schulz. 2006. Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum. Structure 14:1377-1388.
188. Kluge, C., A. Tschech, and G. Fuchs. 1990. Anaerobic metabolism of res-orcyclic acids (m-dihydroxybenzoic acids) and resorcinol (1,3-benzenediol) in a fermenting and in a denitrifying bacterium. Arch. Microbiol. 155:68-74.
189. Kniemeyer, O., T. Fischer, H. Wilkes, F. O. Glaockner, and F. Widdel. 2003. Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl. Environ. Microbiol. 69:760-768.
190. Kniemeyer, O., and J. Heider. 2001. (S)-1-Phenylethanol dehydrogenase of Azoarcus sp. strain EbN1, an enzyme of anaerobic ethylbenzene catabolism. Arch. Microbiol. 176:129-135.
191. Kniemeyer, O., and J. Heider. 2001. Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J. Biol. Chem. 276:21381-21386.
192. Koizumi, Y., J. J. Nelly, T. Nakagawa, H. Urakawa, S. El-Fantroussi, S. Al-Muzaini, M. Fukui, Y. Urushigawa, and D. A. Stahl. 2002. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading micro-bial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Appl. Environ. Microbiol. 68:3215-3225.
193. Kollmann-Koch, A., and H. Eggerer. 1984. Nicotinic acid metabolism. Di-methylmaleate hydratase. Hoppe Syler's Z. Physiol. Chem. 365:847-857.
194. Korner, H., H. J. Sofia, and W. G. Zumft. 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.
195. Koudelka, G. B., and C. Y. Lam. 1993. Differential recognition of OR1 and OR3 by bacteriophage 434 repressor and Cro. J. Biol. Chem. 268:23812-23817.
196. Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
197. Krell, T., J. R. Coggins, and A. J. Lapthorn. 1998. The three-dimensional structure of shikimate kinase. J. Mol. Biol. 278:983-987.
198. Krieger, C. J., H. R. Beller, M. Reinhard, and A. M. Spormann. 1999. Initial reactions in anaerobic oxidation of m-xylene by the denitrifying bacterium Azoarcus sp. strain T. J. Bacteriol. 181:6403-6410.
199. Krieger, C. J., W. Roseboom, S. P. Albracht, and A. M. Spormann. 2001. A stable organic free radical in anaerobic benzylsuccinate synthase of Azo-arcus sp. strain T. J. Biol. Chem. 276:12924-12927.
200. Kube, M., A. Beck, A. Meyerdierks, R. Amann, R. Reinhardt, and R. Rabus. 2005. A catabolic gene cluster for anaerobic benzoate degradation in meth-anotrophic microbial Black Sea mats. Syst. Appl. Microbiol. 28:287-294.
201. Kube, M., J. Heider, J. Amann, P. Hufnagel, S. Kuahner, A. Beck, R. Reinhardt, and R. Rabus. 2004. Genes involved in the anaerobic degradation of toluene in a denitrifying bacterium, strain EbN1. Arch. Microbiol. 181:182-194.
202. Kauhner, S., L. Woahlbrand, I. Fritz, W. Wruck, C. Hultschig, P. Hufnagel, M. Kube, R. Reinhardt, and R. Rabus. 2005. Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J. Bacteriol. 187:1493-1503.
203. Kunapuli, U., C. Griebler, H. R. Beller, and R. U. Meckenstock. 2008. Identification of intermediates formed during anaerobic benzene degradation by an iron-reducing enrichment culture. Environ. Microbiol. 10:1703-1712.
204. Kunapuli, U., T. Lueders, and R. U. Meckenstock. 2007. The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation. ISME J. 1:643-653.
205. Kuntze, K., Y. Shinoda, H. Moutakki, M. J. McInerney, C. Vogt, H. H. Richnow, and M. Boll. 2008. 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes. Environ. Microbiol. 10:1547-1556.
206. Küver, J., Y. Xu, and J. Gibson. 1995. Metabolism of cyclohexane carboxylic acid by the photosynthetic bacterium Rhodopseudomonas palustris. Arch. Microbiol. 164:337-345.
207. Lacal, J., A. Busch, M. E. Guazzaroni, T. Krell, and J. L. Ramos. 2006. The TodS-TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins. Proc. Natl. Acad. Sci. USA 103:8191-8196.
208. Lack, A., and G. Fuchs. 1992. Carboxylation of phenylphosphate by phenol carboxylase, an enzyme system of anaerobic phenol metabolism. J. Bacte- riol. 174:3629-3636.
209. Laempe, D., W. Eisenreich, A. Bacher, and G. Fuchs. 1998. Cyclohexa-1,5-diene-1-carbonyl-CoA hydratase, an enzyme involved in anaerobic metabolism of benzoyl-CoA in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 255:618-627.
210. Laempe, D., M. Jahn, K. Breese, H. Schaagger, and G. Fuchs. 2001. Anaerobic metabolism of 3-hydroxybenzoate by the denitrifying bacterium Thauera aromatica. J. Bacteriol. 183:968-979.
211. Laempe, D., M. Jahn, and G. Fuchs. 1999. 6-Hydroxycyclohex-1-ene- 1-carbonyl-CoA dehydrogenase and 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, enzymes of the benzoyl-CoA pathway of anaerobic aromatic metabolism in the denitrifying bacterium Thauera aromatica. Eur. J. Bio-chem. 263:420-429.
212. Larimer, F. W., P. Chain, L. Hauser, J. Lamerdin, S. Malfatti, L. Do, M. L. Land, D. A. Pelletier, J. T. Beatty, A. S. Lang, F. R. Tabita, J. L. Gibson, T. E. Hanson, C. Bobst, J. L. Torres, C. Peres, F. H. Harrison, J. Gibson, and C. S. Harwood. 2004. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat. Bio-technol. 22:55-61.
213. Lau, P. C., Y. Wang, A. Patel, D. Labbaé, H. Bergeron, R. Brousseau, Y. Konishi, and M. Rawlings. 1997. A bacterial basic region leucine zipper histidine kinase regulating toluene degradation. Proc. Natl. Acad. Sci. USA 18:1453-1458.
214. Leuthner, B., and J. Heider. 1998. A two-component system involved in regulation of anaerobic toluene metabolism in Thauera aromatica. FEMS Microbiol. Lett. 166:35-41.
215. Leuthner, B., and J. Heider. 2000. Anaerobic toluene catabolism of Thauera aromatica: the bbs operon codes for enzymes of β-oxidation of the intermediate benzylsuccinate. J. Bacteriol. 182:272-277.
216. Leuthner, B., C. Leutwein, H. Schulz, P. Höarth, W. Haehnel, E. Schiltz, H. Schägger, and J. Heider. 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.
217. Leutwein, C., and J. Heider. 2001. Succinyl-CoA:(R)- benzylsuccinate CoA- transferase: an enzyme of the anaerobic toluene catabolic pathway in denitrifying bacteria. J. Bacteriol. 183:4288-4295.
218. Leutwein, C., and J. Heider. 2002.(R)-Benzylsuccinyl-CoA dehydrogenase of Thauera aromatica, an enzyme of the anaerobic toluene catabolic pathway. Arch. Microbiol. 178:517-524.
219. Lochmeyer, C., J. Koch, and G. Fuchs. 1992. Anaerobic degradation of 2-aminobenzoic acid (anthranilic acid) via benzoyl-coenzyme A (CoA) and cyclohex-1-enecarboxyl-CoA in a denitrifying bacterium. J. Bacteriol. 174:3621-3628.
220. London, J., and M. Knight. 1966. Concentrations of nicotinamide nucleo-tide coenzymes in microorganisms. J. Gen. Microbiol. 44:241-254.
221. Londry, K. L., J. M. Suflita, and R. S. Tanner. 1999. Cresol metabolism by the sulfate-reducing bacterium Desulfotomaculum sp. strain Groll. Can. J. Microbiol. 45:458-463.
222. Lonetto, M. A., V. Rhodius, K. Lamberg, P. Kiley, S. Busby, and C. Gross. 1998. Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase sigma70 subunit. J. Mol. Biol. 284:1353-1365.
223. Laópez-Barragán, M. J., M. Carmona, M. T. Zamarro, B. Thiele, M. Boll, G. Fuchs, J. L. Garcia, and E. Dí az. 2004. The bzd gene cluster, coding for anaerobic benzoate catabolism, in Azoarcus sp. strain CIB. J. Bacteriol. 186:5762-5774.
224. Lóapez-Barragaan, M. J., E. Díaz, J. L. Garcia, and M. Carmona. 2004. Genetic clues on the evolution of anaerobic catabolism of aromatic compounds. Microbiology 150:2018-2021.
225. Lovley, D. R. 2001. Bioremediation. Anaerobes to the rescue. Science 293:1444-1446.
226. Lovley, D. R. 2003. Cleaning up with genomics: applying molecular biology to bioremediation. Nat. Rev. Microbiol. 1:35-44.
227. Lovley, D. R., J. D. Coates, J. C. Woodward, and E. Phillips. 1995. Benzene oxidation coupled to sulfate reduction. Appl. Environ. Microbiol. 61:953-958.
228. Lovley, D. R., J. C. Woodward, and F. H. Chapelle. 1996. Rapid anaerobic benzene oxidation with a variety of chelated Fe(III) forms. Appl. Environ. Microbiol. 62:288-291.
229. Lupa, B., D. Lyon, M. D. Gibbs, R. A. Reeves, and J. Wiegel. 2005. Distribution of genes encoding the microbial non-oxidative reversible hydroxy-arylic acid decarboxylases/phenol carboxylases. Genomics 86:342-351.
230. Mancini, S. A., A. C. Ulrich, G. Lacrampe-Couloume, B. Sleep, E. A. Edwards, and B. S. Lollar. 2003. Carbon and hydrogen isotopic fraction- ation during anaerobic biodegradation of benzene. Appl. Environ. Micro-biol. 69:191-198.
231. Mandic-Mulec, I., L. Doukhan, and I. Smith. 1995. The Bacillus subtilis SinR protein is a repressor of the key sporulation gene spoOA. J. Bacteriol. 177:4619-4627.
232. Marqueas, S., I. Aranda-Olmedo, and J. L. Ramos. 2006. Controlling bacterial physiology for optimal expression of gene reporter constructs. Curr. Opin. Biotechnol. 17:50-56.
233. Martin, R. G., and J. L. Rosner. 1995. Binding of purified multiple antibiotic-resistance repressor protein (MarR) to mar operator sequences. Proc. Natl. Acad. Sci. USA 92:5456-5460.
234. Mascher, T., J. D. Helmann, and G. Unden. 2006. Stimulus perception in bacterial signal-transducing histidine kinases. Microbiol. Mol. Biol. Rev. 70:910-938.
235. Matsunaga, T., Y. Okamura, Y. Fukuda, A. T. Wahyudi, Y. Murase, and H. Takeyama. 2005. Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1. DNA Res. 12:157-166.
236. McInerney, M., L. Rohlin, H. Mouttaki, U. Kim, R. S. Krupp, L. Rios-Hernández, J. Sieber, C. G. Struchtemeyer, A. Bhattacharyya, J. W. Campbell, and R. P. Gunsalus. 2007. The genome of Syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth. Proc. Natl. Acad. Sci. USA 104:7600-7605.
237. McLeod, M. P., and L. D. Eltis. 2008. Genomic insights into the aerobic pathways for degradation of organic pollutants, p. 1-23. In E. Diaz (ed.), Microbial biodegradation: genomics and molecular biology. Caister Academic Press, Norfolk, United Kingdom.
238. Mechichi, T., E. Stackebrandt, N. Gad'on, and G. Fuchs. 2002. Phyloge-netic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckelii sp. nov. Arch. Microbiol. 178:26-35.
239. Meckenstock, R. U., M. Safinowski, and C. Griebler. 2004. Anaerobic degradation of polycyclic aromatic hydrocarbons: a review. FEMS Micro- biol. Ecol. 49:27-36.
240. Medina-Bellver, J. I., P. Marín, A. Delgado, A. Rodríguez-Sánchez, E. Reyes, J. L. Ramos, and S. Marquaés. 2005. Evidence for in situ crude oil biodegradation after the Prestige oil spill. Environ. Microbiol. 7:773-779.
241. Melville, S. B., and R. P. Gunsalus. 1990. Mutations in fnr that alter anaerobic regulation of electron transport-associated genes in Escherichia coli. J. Biol. Chem. 265:18733-18736.
242. Merritt, E. A., and M. E. Murphy. 1994. Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 1:869-873.
243. Messerschmidt, A., H. Niessen, D. Abt, O. Einsle, B. Schink, and P. M. Kroneck. 2004. Crystal structure of pyrogallol-phloroglucinol transhydroxy-lase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols. Proc. Natl. Acad. Sci. USA 101:11571-11576.
244. Maöbitz, H., and M. Boll. 2002. A Birch-like mechanism in enzymatic ben-zoyl-CoA reduction: a kinetic study of substrate analogues combined with an ab initio model. Biochemistry 41:1752-1758.
245. Mohamed, M. E. 2000. Biochemical and molecular characterization of phenylacetate-coenzyme A ligase, an enzyme catalyzing the first step in aerobic metabolism of phenylacetic acid in Azoarcus evansii. J. Bacteriol. 182:286-294.
246. Mohamed, M. E., and G. Fuchs. 1993. Purification and characterization of phenylacetate-coenzyme A ligase from a denitrifying Pseudomonas sp., an enzyme involved in the anaerobic degradation of phenylacetate. Arch. Mi-crobiol. 159:554-562.
247. 2 in denitrifying Pseudomonas sp. Arch. Microbiol. 159:563-573.
248. Morales, G., J. F. Linares, A. Beloso, J. P. Albar, J. L. Martinez, and F. Rojo. 2004. The Pseudomonas putida Crc global regulator controls the expression of genes from several chromosomal catabolic pathways for aromatic compounds. J. Bacteriol. 186:1337-1344.
249. Morales, G., A. Ugidos, and F. Rojo. 2006. Inactivation of the Pseudomonas putida cytochrome o ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases. Environ. Microbiol. 8:1764-1774.
250. Morasch, B., and R. U. Meckenstock. 2005. Anaerobic degradation of p-xylene by a sulfate-reducing enrichment culture. Curr. Microbiol. 51:127-130.
251. Morasch, B., H. H. Richnow, A. Vieth, B. Schink, and R. U. Meckenstock. 2004. Stable isotope fractionation caused by glycyl radical enzymes during bacterial degradation of aromatic compounds. Appl. Environ. Microbiol. 70:2935-2940.
252. Morasch, B., B. Schink, C. C. Tebbe, and R. U. Meckenstock. 2004. Degradation of o-xylene and m-xylene by a novel sulphate-reducer belonging to the genus Desulfatomaculum. Arch. Microbiol. 181:407-417.
253. Moreno, R., and F. Rojo. 2008. The target for the Pseudomonas putida Crc global regulator in the benzoate degradation pathway is the BenR tran-scriptional regulator. J. Bacteriol. 190:1539-1545.
254. Mosqueda, G., M. I. Ramos-Gonzaalez, and J. L. Ramos. 1999. Toluene metabolism by the solvent-tolerant Pseudomonas putida DOT-T1 strain, and its role in solvent impermeabilization. Gene 232:69-76.
255. Mouttaki, H., M. A. Nanny, and M. J. McInerney. 2007. Cyclohexane carboxylate and benzoate formation from crotonate in Syntrophus aciditro-phicus. Appl. Environ. Microbiol. 73:930-938.
256. Müller, C., L. Petruschka, H. Cuypers, G. Burchhardt, and H. Herrmann. 1996. Carbon catabolite repression of phenol degradation in Pseudomonas putida is mediated by the inhibition of the activator protein PhlR. J. Bacteriol. 178:2030-2036.
257. Müller, J. A., A. S. Galushko, A. Kappler, and B. Schink. 2001. Initiation of anaerobic degradation of p-cresol by formation of 4-hydroxybenzylsucci-nate in Desulfobacterium cetonicum. J. Bacteriol. 183:752-757.
258. Mu6ller, J. A., and B. Schink. 2000. Initial steps in the fermentation of 3-hydroxybenzoate bySporotomaculum hydroxybenzoicum. Arch. Microbiol. 173:288-295.
259. Musat, F., A. Galushko, J. Jacob, F. Widdel, M. Kube, R. Reinhardt, H. Wilkes, B. Schink, and R. Rabus. 22 September 2008. Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria. Environ. Microbiol. [Epub ahead of print.] doi:10.1111/j.1462-2920. 2008.01756.x
260. Narasingarao, P., and M. M. Häggblom. 2006. Sedimenticola selenatiredu-cens, gen. nov., sp. nov., an anaerobic selenate-respiring bacterium isolated from estuarine sediment. Syst. Appl. Microbiol. 29:382-388.
261. Narmandakh, A., N. Gad'on, F. Drepper, B. Knapp, W. Haehnel, and G. Fuchs. 2006. Phosphorylation of phenol by phenylphosphate synthase: role of histidine phosphate in catalysis. J. Bacteriol. 188:7815-7822.
262. Oda, Y., W. G. Meijer, J. L. Gibson, J. C. Gottschal, and L. J. Forney. 2004. Analysis of diversity among 3-chlorobenzoate-degrading strains of Rhodo-pseudomonas palustris. Microb. Ecol. 47:68-79.
263. Ohtsubo, Y., H. Goto, Y. Nagata, T. Kudo, and M. Tsuda. 2006. Identification of a response regulator gene for catabolite control from a PCB-degrading beta-proteobacteria, Acidovorax sp. KKS102. Mol. Microbiol. 60:1563-1575.
264. Olivera, E. R., B. Miñambres, B. García, C. Muńiz, M. A. Moreno, A. Ferraandez, E. Díaz, J. L. García, and J. M. Luengo. 1998. Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon. Proc. Natl. Acad. Sci. USA 95:6419-6424.
265. Ostermann, A., C. Gallus, and B. Schink. 1997. Decarboxylation of 2,3-dihydroxybenzoate to catechol supports growth of fermenting bacteria. Curr. Microbiol. 35:270-273.
266. Pan, C., Y. Oda, P. K. Lankford, B. Zhang, N. F. Samatova, D. A. Pelletier, C. S. Harwood, and R. L. Hettich. 2008. Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics. Mol. Cell. Proteomics 7:938-948.
267. Parales, R. E., and C. S. Harwood. 2002. Bacterial chemotaxis to pollutants and plant-derived aromatic molecules. Curr. Opin. Microbiol. 5:266-273.
268. Parales, R. E., K. S. Ju, J. B. Rollefson, and J. L. Ditty. 2008. Bioavailabil-ity, chemotaxis, and transport of organic pollutants, p. 145-187. In E. Diaz (ed.), Microbial biodegradation: genomics and molecular biology. Caister Academic Press, Norfolk, United Kingdom.
269. Parales, R. E., and S. M. Resnick. 2006. Aromatic ring hydroxylating di-oxygenases, p. 287-340. In J. L. Ramos and R. C. Levesque (ed.), Pseudo-monas, vol. 4. Molecular biology of emerging issues. Springer, New York, NY.
270. Parke, D., M. A. García, and L. N. Ornston. 2001. Cloning and genetic characterization of dca genes required for β-oxidation of straight-chain dicarboxylic acids in Acinetobacter sp. strain ADP1. Appl. Environ. Micro-biol. 67:4817-4827.
271. Parke, D., and L. N. Ornston. 2004. Toxicity caused by hydroxycinnamoyl-coenzyme A thioester accumulation in mutants of Acinetobacter sp. strain ADP1. Appl. Environ. Microbiol. 70:2974-2983.
272. Pelletier, D. A., and C. S. Harwood. 1998. 2- Ketocyclohexanecarboxyl co-enzyme A hydrolase, the ring cleavage enzyme required for anaerobic benzoate degradation by Rhodopseudomonas palustris. J. Bacteriol. 180:2330-2336.
273. Pelletier, D. A., and C. S. Harwood. 2000. 2- Hydroxycyclohexanecarboxyl coenzyme A dehydrogenase, an enzyme characteristic of the anaerobic benzoate degradation pathway used by Rhodopseudomonas palustris. J. Bac-teriol. 182:2753-2760.
274. Pelz, O., A. Chatzinotas, N. Andersen, S. M. Bernasconi, C. Hesse, W. R. Abraham, and J. Zeyer. 2001. Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifers microcosms to specific microbial populations. Arch. Microbiol. 175:270-281.
275. Peres, C., and C. S. Harwood. 2006. BadM is a transcriptional regulator and one of three regulators that control benzoyl coenzyme A reductase gene expression in Rhodopseudomonas palustris. J. Bacteriol. 188:8662-8665.
276. Peters, F., D. Heintz, J. Johannes, A. V. Dorsselaer, and M. Boll. 2007. Genes, enzymes, and regulation of para-cresol metabolism in Geobacter metallireducens. J. Bacteriol. 189:4729-4738.
277. Peters, F., M. Rother, and M. Boll. 2004. Selenocysteine- containing pro-teins in anaerobic benzoate metabolism of Desulfococcus multivorans.J. Bacteriol. 186:2156-2163.
278. Peters, F., Y. Shinoda, M. J. McInerney, and M. Boll. 2007. Cyclohexa-1,5-diene-1-carbonyl-coenzyme A (CoA) hydratases of Geobacter metalliredu-cens and Syntrophus aciditrophicus: evidence for a common benzoyl-CoA degradation pathway in facultative and strict anaerobes. J. Bacteriol. 189: 1055-1060.
279. Petruschka, L., G. Burchhardt, C. Müller, C. Weihe, and H. Herrmann. 2001. The cyo operon of Pseudomonas putida is involved in carbon catab-olite repression of phenol degradation. Mol. Genet. Genomics 266:199-206.
280. Pflüger, K., and V. de Lorenzo. 2008. Evidence of in vivo cross talk between the nitrogen-related and fructose-related branches of the carbohydrate phosphotransferase system of Pseudomonas putida. J. Bacteriol. 190:3374-3380.
281. Philipp, B., D. Kemmler, J. Hellstern, N. Gorny, A. Caballero, and B. Schink. 2002. Anaerobic degradation of protocatechuate (3,4-dihydroxy- benzoate) by Thauera aromatica strain AR-1. FEMS Microbiol. Lett. 212:139-143.
282. Philipp, B., and B. Schink. 1998. Evidence of two oxidative reaction steps initiating anaerobic degradation of resorcinol (1,3-dihydroxybenzene) by the denitrifying bacterium Azoarcus anaerobius. J. Bacteriol. 180:3644-3649.
283. Pieper, D. H., V. A. P. Martins dos Santos, and P. N. Golyshin. 2004. Genomic and mechanistic insights into the biodegradation of organic pollutants. Curr. Opin. Biotechnol. 15:215-224.
284. Pop, S. M., N. Gupta, A. S. Raza, and S. W. Ragsdale. 2006. Transcriptional activation of dehalorespiration. Identification of redox-active cysteines regulating dimerization and DNA binding. J. Biol. Chem. 281:26382-26390.
285. Pop, S. M., R. J. Kolarik, and S. W. Ragsdale. 2004. Regulation of anaerobic dehalorespiration by the transcriptional activator CprK. J. Biol. Chem. 26:49910-49918.
286. Prieto, M., B. Galán, B. Torres, A. Ferrández, C. Fernández, B. Miñambres, J. L. Garc a, and E. Díaz. 2004. Aromatic metabolism versus carbon availability: the regulatory network that controls catabolism of less-preferred carbon sources in Escherichia coli. FEMS Microbiol. Rev. 28:503-518.
287. Qiu, Y. L., Y. Sekiguchi, S. Hanada. H. Imachi, I. C. Tseng, S. S. Cheng, A. Ohashi, H. Harada, and Y. Kamagata. 2006. Pelotomaculum terephtalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydro-genotrophic methanogens. Arch. Microbiol. 185:172-182.
288. Qiu, Y. L., Y. Sekiguchi, H. Imachi, Y. Kamagata, I. C. Tseng, S. S. Cheng, A. Ohashi, and H. Harada. 2003. Sporotomaculum syntrophicum sp. nov., a novel anaerobic, syntrophic benzoate-degrading bacterium isolated from methanogenic sludge treating wastewater from terephthalate manufacturing. Arch. Microbiol. 179:242-249.
289. Rabus, R. 2005. Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Appl. Microbiol. Biotechnol. 68:580-587.
290. Rabus, R., and J. Heider. 1998. Initialreactions of anaerobic metabolism of alkylbenzenes in denitrifying and sulfate-reducing bacteria. Arch. Micro-biol. 170:377-384.
291. Rabus, R., M. Kube, A. Beck, F. Widdel, and R. Reinhardt. 2002. Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch. Microbiol. 178:506-516.
292. Rabus, R., M. Kube, J. Heider, A. Beck, K. Heitmann, F. Widdel, and R. Reinhardt. 2005. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch. Microbiol. 183:27-36.
293. Rabus, R., and F. Widdel. 1995. Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch. Mi-crobiol. 163:96-103.
294. Rabus, R., H. Wilkes, A. Behrends, A. Armstroff, T. Fischer, A. J. Pierik,and F. Widdel. 2001. Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: evidence for
295. (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism. Appl. Environ. Microbiol. 183:1707-1715.
296. Ramos, J. L., S. Marquaés, and K. N. Timmis. 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu. Rev. Microbiol. 51:341-373.
297. Reams, A. B., and E. L. Neidle. 2004. Selection for gene clustering by tandem duplication. Annu. Rev. Microbiol. 58:119-142.
298. Reeve, C. D., M. A. Carver, and D. J. Hopper. 1989. The purification and characterization of 4-ethylphenol methylenehydroxylase, a flavocytochrome from Pseudomonas putida JD1. Biochem. J. 263:431-437.
299. Reichenbecher, W., B. Philipp, M. J. Suter, and B. Schink. 2000. Hydroxy-hydroquinone reductase, the initial enzyme involved in the degradation of hydroxyhydroquinone
300. (1,2,4-trihydroxybenzene) by Desulfovibrio inopinatus. Arch. Microbiol. 173:206-212.
301. Reusser, D. E., J. D. Istok, H. R. Beller, and J. A. Field. 2002. In situ transformation of deuterated toluene and xylene to benzylsuccinic acid analogues in BTEX-contaminated aquifers. Environ. Sci. Technol. 36:4127-4134.
302. Rhee, S. K., and G. Fuchs. 1999. Phenylacetyl-CoA:acceptor oxidoreduc-tase, a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 262:507-515.
303. Rhee, S. K., G. M. Lee, J. H. Yoon, Y. H. Park, H. S. Bae, and S. T. Lee. 1997. Anaerobic and aerobic degradation of pyridine by a newly isolated denitrifying bacterium. Appl. Environ. Microbiol. 63:2578-2585.
304. Rhee, S. K., X. Liu, L. Wu. S. C. Chong, X. Wan, and J. Zhou. 2004. Detection of genes involved in biodegradation and biotransformations in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:4303-4317.
305. Rhodius, V. A., and S. J. W. Busby. 1998. Positive activation of gene expression. Curr. Opin. Microbiol. 1:151-159.
306. Rieger, P. G., H. M. Meier, M. Gerle, U. Vogt, T. Groth, and H. J. Knack-muss. 2002. Xenobiotics in the environment: present and future strategies to obviate the problem of biological persistence. J. Biotechnol. 94:101-123.
307. Rojo, F., and A. Dinamarca. 2004. Catabolite repression and physiological control, p. 365-387. In J. L. Ramos (ed.), Pseudomonas, vol. 2. Virulence and gene regulation. Kluwer Academic Press, New York, NY.
308. Romanowski, M. J., and S. K. Burley. 2002. Crystal structure of the Esch-erichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam. Proteins 47:558-562.
309. Rudolphi, A., A. Tschech, and G. Fuchs. 1991. Anaerobic degradation of cresols by denitrifying bacteria. Arch. Microbiol. 155:238-248.
310. Ruíz, R., M. I. Aranda-Olmedo, P. Dominguez-Cuevas, M. I. Ramos-González, and S. Marquéas. 2004. Transcriptional regulation of the toluene catabolic parthways, p. 509-537. In J. L. Ramos (ed.), Pseudomonas, vol. 2. Virulence and gene regulation. Kluwer Academic Press, New York, NY.
311. Safinowski, M., C. Griebler, and R. U. Meckenstock. 2006. Anaerobic cometabolic transformation of polycyclic and heterocyclic aromatic hydrocarbons: evidence from laboratory and field studies. Environ. Sci. Technol. 40:4165-4173.
312. Safinowski, M., and R. U. Meckenstock. 2006. Methylation is the initial reaction in anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Environ. Microbiol. 8:347-352.
313. Saier, M. H., Jr. 2000. A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev. 64:354-411.
314. Samanta, S. K., and C. S. Harwood. 2005. Use of the Rhodopseudomonas palustris genome sequence to identify a single amino acid that contributes to the activity of coenzyme A ligase with chlorinated substrates. Mol. Microbiol. 55:1151-1159.
315. Sánchez-Paérez, G., A. Mira, G. Nyiro, L. Pasić, and F. Rodríguez-Valera. 2008. Adapting to environmental changes using specialized paralogs. Trends Genet. 24:154-158.
316. Saraste, M., P. R. Sibbald, and A. Wittinghofer. 1990. The P-loop-a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15:43-44.
317. Sauer, R. T., R. R. Yocum, R. F. Doolittle, M. Lewis, and C. O. Pabo. 1982. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 298:447-451.
318. Schaefer, A. L., E. P. Greenberg, C. M. Oliver, Y. Oda, J. J. Huang, G. Bittan-Banin, C. M. Peres, S. Schmidt, K. Juhaszova, J. R. Sufrin, and C. S. Harwood. 2008. A new class of homoserine lactone quorum-sensing signals. Nature 454:595-599.
319. Schell, M. A. 1993. Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47:597-626.
320. Schennen, U., K. Braun, and H. J. Knasckmuss. 1985. Anaerobic degradation of 2-fluorobenzoate by benzoate-degrading denitrifying bacteria. J. Bacteriol. 161:321-325.
321. Schink, B., B. Phillips, and J. Müaller. 2000. Anaerobic degradation of phenolic compounds. Naturwissenschaften 87:12-23.
322. Schleissner, C., E. R. Olivera, M. Fernández-Valverde, and J. M. Luengo. 1994. Aerobic catabolism of phenylacetic acid in Pseudomonas putida U: biochemical characterization of a specific phenylacetic acid transport system and formal demonstration that phenylacetyl-coenzyme A is a catabolic intermediate. J. Bacteriol. 176:7667-7676.
323. Schmeling, S., A. Narmandakh, O. Schmitt, N. Gad'on, K. Schüahle, and G. Fuchs. 2004. Phenylphosphate synthase: a new phosphotransferase catalyzing the first step in aerobic phenol metabolism in Thauera awmatica.J. Bacteriol. 186:8044-8057.
324. Schneider, S., and G. Fuchs. 1998. Phenylacetyl-CoA:acceptor oxidoreduc-tase, a new alpha-oxidizing enzyme that produces phenylglyoxylate. Assay, membrane localization, and differential production in Thauera aromatica. Arch. Microbiol. 169:509-516.
325. Schneider, S., M. E. S. Mohamed, and G. Fuchs. 1997. Anaerobic metabolism of L-phenylalanine via benzoyl-CoA in the denitrifying bacterium Thauera aromatica. Arch. Microbiol. 168:310-320.
326. Schnell, S., F. Bak, and N. Pfennig. 1989. Anaerobic degradation of aniline and dihydroxybenzenes by newly isolated sulfate-reducing bacteria and description of Desulfobacterium anilini. Arch. Microbiol. 152:556-563.
327. Schnell, S., and B. Schink. 1991. Anaerobic aniline degradation via reduc-tive deamination of 4-aminobenzoyl-CoA in Desulfobacterium anilini. Arch. Microbiol. 155:183-190.
328. Schöcke, L., and B. Schink. 1998. Membrane-bound proton-translocating pyrophosphatase of Syntrophus gentianae, a syntrophically benzoate-de-grading fermenting bacterium. Eur. J. Biochem. 15:589-594.
329. Schöcke, L., and B. Schink. 1999. Energetics and biochemistry of fermentative benzoate degradation by Syntrophus gentianae. Arch. Microbiol. 171:331-337.
330. Schüohle, K., and G. Fuchs. 2004. Phenylphosphate carboxylase: a new C-C lyase involved in anaerobic phenol metabolism in Thauera aromatica.J. Bacteriol. 186:4556-4567.
331. Schüohle, K., J. Gescher, U. Feil, M. Paul, M. Jahn, H. Schäogger, and G. Fuchs. 2003. Benzoate-coenzyme A ligase from Thauera aromatica:an enzyme acting in anaerobic and aerobic pathways. J. Bacteriol. 185:4920-4929.
332. Schüohle, K., M. Jahn, S. Ghisla, and G. Fuchs. 2001. Two similar gene clusters coding for enzymes of a new type of aerobic 2-aminobenzoate (anthranilate) metabolism in the bacterium Azoarcus evansii. J. Bacteriol. 183:5268-5278.
333. Selmer, T., A. J. Pierik, and J. Heider. 2005. New glycyl radical enzymes catalysing key metabolic steps in anaerobic bacteria. Biol. Chem. 386:981-988.
334. Seyfried, B., A. Tschech, and G. Fuchs. 1991. Anaerobic degradation of phenylacetate and 4-hydroxyphenylacetate by denitrifying bacteria. Arch. Microbiol. 155:249-255.
335. Shingler, V. 2003. Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour. Environ. Microbiol. 5:1226-1241.
336. Shinoda, Y., J. Akagi, Y. Uchihashi, A. Hiraishi, H. Yukawa, H. Yurimoto, Y. Sakai, and N. Kato. 2005. Anaerobic degradation of aromatic compounds by Magnetospirillum strains: isolation and degradation genes. Biosci. Biotechnol. Biochem. 69:1483-1491.
337. Shinoda, Y., Y. Sakai, H. Uenishi, Y. Uchihashi, A. Hiraishi, H. Yukawa, H. Yurimoto, and N. Kato. 2004. Aerobic and anaerobic toluene degradation by a new isolated denitrifying bacterium, Thauera sp. strain DNT-1. Appl. Environ. Microbiol. 70:1385-1392.
338. Sikkema, J., J. A. de Bont, and B. Poolman. 1995. Mechanisms of membrane toxicity of hydrocarbons. Microbiol. Rev. 59:201-222.
339. Smidt, H., and W. M. de Vos. 2004. Anaerobic microbial dehalogenation. Annu. Rev. Microbiol. 58:43-73.
340. Song, B., L. J. Kerkhof, and M. M. Häggblom. 2002. Characterization of bacterial consortia capable of degrading 4-chlorobenzoate and 4-bromo-benzoate under denitrifying conditions. FEMS Microbiol. Lett. 213:183-188.
341. Song, B., N. J. Palleroni, and M. M. Haoggblom. 2000. Isolation and characterization of diverse halobenzoate-degrading denitrifying bacteria from soils and sediments. Appl. Environ. Microbiol. 66:3446-3453.
342. Song, B., N. J. Palleroni, L. J. Kerkhof, and M. M. Hoaggblom. 2001. Characterization of halobenzoate-degrading, denitrifying Azoarcus and Thauera isolates and description of Thauera chlorobenzoica sp. nov. Int. J. Syst. Evol. Microbiol. 51:589-602.
343. Song, B., and B. B. Ward. 2003. Nitrate reductase genes in halobenzoate degrading denitrifying bacteria. FEMS Microbiol. Ecol. 43:349-357.
344. Song, B., and B. B. Ward. 2005. Genetic diversity of benzoyl coenzyme A reductase genes detected in denitrifying isolates and estuarine sediment communities. Appl. Environ. Microbiol. 71:2036-2045.
345. Song, F., Z. Zhuang, L. Finci, D. Dunaway-Mariano, R. Kniewel, J. A. Buglino, V. Solorzano, J. Wu, and C. D. Lima. 2006. Structure, function, and mechanism of the phenylacetate pathway hot dog-fold thioesterase PaaI. J. Biol. Chem. 281:11028-11038.
346. Spormann, A. M., and F. Widdel. 2000. Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria. Biodegradation 11:85-105.
347. Springer, N., W. Ludwig, B. Philipp, and B. Schink. 1998. Azoarcus anaero-bius sp. nov., a resorcinol-degrading, strictly anaerobic, denitrifying bacterium. Int. J. Syst. Bacteriol. 48:953-956.
348. Stadtman, E. R., T. C. Stadtman, I. Pastan, and L. D. Smith. 1972. Clos-tridium barkeri sp. n. J. Bacteriol. 110:758-760.
349. Suh, S. J., L. J. Runyen-Janecky, T. C. Maleniak, P. Hager, C. H. MacGre-gor, N. A. Zielinski-Mozny, P. V. Phibbs, Jr., and S. E. West. 2002. Effect of vfr mutation on global gene expression and catabolite repression control of Pseudomonas aeruginosa. Microbiology 148:1561-1569.
350. Thiele, B., O. Rieder, N. Jehmlich, M. von Bergen, M. Muller, and M. Boll. 2008. Aromatizing cyclohexa-1,5-diene-1-carbonyl-coenzyme A oxidase: characterization and its role in anaerobic aromatic metabolism. J. Biol. Chem. 283:20713-20721.
351. Touati, D. 2000. Sensing and protecting against superoxide stress in Esch-erichia coli-how many ways are there to trigger soxRS response? Redox Res. 5:287-293.
352. Trautwein, K., S. Kühner, L. Woohlbrand, T. Halder, K. Kuchta, A. Stein-buochel, and R. Rabus. 2008. Solvent stress response of the denitrifying bacterium "Aromatoleum aromaticum" strain EbN1. Appl. Environ. Micro-biol. 74:2267-2274.
353. Tropel, D., and J. R. van der Meer. 2004. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol. Mol. Biol. Rev. 68:474-500.
354. Tschech, A., and B. Schink. 1985. Fermentative degradation of resorcinol and resorcylic acids. Arch. Microbiol. 143:52-59.
355. Unciuleac, M., E. Warkentin, C. C. Page, M. Boll, and U. Ermler. 2004. Structure of a xanthine oxidase-related 4-hydroxybenzoyl-CoA reductase with an additional [4Fe-4S] cluster and an inverted electron flow. Structure 12:2249-2256.
356. 2-dependent gene regulation in facultatively anaerobic bacteria. Arch. Microbiol. 164:81-90.
357. Vaillancourt, F. H., J. T. Bolin, and L. D. Eltis. 2006. The ins and outs of ring-cleaving dioxygenases. Crit. Rev. Biochem. Mol. Biol. 41:241-267.
358. Vallenet, D., P. Nordmann, V. Barbe, L. Poirel, S. Mangenot, E. Bataille, C. Dossat, S. Gas, A. Kreimeyer, P. Lenoble, S. Oztas, J. Poulain, B. Segurens, C. Robert, C. Abergel, J. M. Claverie, D. Raoult, C. Maédigue, J. Weissen-bach, and S. Cruveiller. 2008. Comparative analysis ofacinetobacters: three genomes for three lifestyles. PLoS ONE 3:e1805.
359. van der Meer, J. R. 2008. A genomic view on the evolution of catabolic pathways and bacterial adaptations to xenobiotics compounds, p. 219-267. In E. Díz (ed.), Microbial biodegradation: genomics and molecular biology. Caister Academic Press, Norfolk, United Kingdom.
360. van Hamme, J. D., A. Singh, and O. P. Ward. 2003. Recent advances in petroleum microbiology. Microbiol. Mol. Biol. Rev. 67:503-549.
361. Velasco, A., S. Alonso, J. L. García, J. Perera, and E. Díaz. 1998. Genetic and functional analysis of the styrene catabolic cluster of Pseudomonas sp. strain Y2. J. Bacteriol. 180:1063-1071.
362. Velázquez, F., V. de Lorenzo, and M. Valls. 2006. The m-xylene biodegra-dation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes. Environ. Microbiol. 8:591-602.
363. verBerkmoes, N. C., M. B. Shah, P. K. Lankford, D. A. Pelletier, M. B. Strader, D. L. Tabb, W. H. McDonald, J. W. Barton, G. B. Hurst, L. Hauser, B. H. Davison, J. T. Beatty, C. S. Harwood, F. R. Tabita, R. L. Hettich, and F. W. Larimer. 2006. Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J. Proteome Res. 5:287-298.
364. Verfu6rth, K., A. J. Pierik, C. Leutwein, S. Zorn, and J. Heider. 2004. Substrate specificities and electron paramagnetic resonance properties of benzylsuccinate synthases in anaerobic toluene and m-xylene metabolism. Arch. Microbiol. 181:155-162.
365. Villemur, R. 1995. Coenzyme A ligases involved in anaerobic biodegrada-tion of aromatic compounds. Can. J. Microbiol. 41:855-861.
366. Vogel, T. M., and D. Grbìc-Galìc. 1986. Incorporation of oxygen from water into toluene and benzene during anaerobic fermentative transformation. Appl. Environ. Microbiol. 52:200-202.
367. Vogels, G. D., and C. van der Drift. 1976. Degradation of purines and pyrimidines by microorganisms. Bacteriol. Rev. 40:403-468.
368. Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. 1982. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
369. Wang, Y., M. Rawlings, D. T. Gibson, D. Labbé, H. Bergeron, R. Brousseau, and P. C. Lau. 1995. Identification of a membrane protein and a truncated LysR-type regulator associated with the toluene degradation pathway in Pseudomonas putida F1. Mol. Gen. Genet. 246:570-579.
370. Washer, C. E., and E. A. Edwards. 2007. Identification and expression of benzylsuccinate synthase genes in a toluene-degrading methanogenic consortium. Appl. Environ. Microbiol. 73:1367-1369.
371. Weber, F. J., and J. A. de Bont. 1996. Adaptation mechanisms of microorganisms to the toxic effects of organic solvents on membranes. Biochim. Biophys. Acta 1286:225-245.
372. Weber, K. D., O. D. Vincent, and P. J. Kiley. 2005. Additionaldeterminants within Escherichia coli FNR activating region 1 and RNA polymerase αsubunit required for transcription activation. J. Bacteriol. 187:1724-1731.
373. Weickert, M. J., and S. Adhya. 1992. A family of bacterial regulators homologous to Gal and Lac repressors. J. Biol. Chem. 267:15869-15874.
374. Whipp, M. J., and A. J. Pittard. 1995. A reassessment of the relationship between aroK- and aroL-encoded shikimate kinase enzymes of Escherichia coli. J. Bacteriol. 177:1627-1629.
375. Widdel, F., and R. Rabus. 2001. Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr. Opin. Biotechnol. 12:259-276.
376. Winderl, C., S. Schaefer, and T. Lueders. 2007. Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzyl-succinate synthase (bssA) genes as a functional marker. Environ. Microbiol. 9:1035-1046.
377. Wing, H. J., J. Green, J. R. Guest, and S. J. Busby. 2000. Role of activating region 1 of Escherichia coli FNR protein in transcription activation at class II promoters. J. Biol. Chem. 275:29061-29065.
378. Wischgoll, S., D. Heintz, F. Peters, A. Erxleben, E. Sarnighausen, R. Reski, A. V. Dorssalaer, and M. Boll. 2005. Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens. Mol. Microbiol. 58:1238-1252.
379. Wo6hlbrand, L., B. Kallerhoff, D. Lange, P. Hufnagel, J. Thiermann, R. Reinhardt, and R. Rabus. 2007. Functional proteomic view of metabolic regulation in "Aromatoleum aromaticum" strain EbN1. Proteomics 7:2222-2239.
380. Wöhlbrand, L., H. Wilkes, T. Halder, and R. Rabus. 2008. Anaerobic degradation of p-ethylphenol by "Aromatoleum aromaticum" strain EbN1: pathway, regulation, and involved proteins. J. Bacteriol. 190:5699-5709.
381. Xiang, L., and B. S. Moore. 2003. Characterization of benzoyl coenzyme A biosynthesis genes in the enterocin-producing bacterium "Streptomyces maritimus." J. Bacteriol. 185:399-404.
382. Yoshida, T., and T. Nagasawa. 2000. Enzymatic functionalization of aromatic N-heterocycles: hydroxylation and carboxylation. J. Biosci. Bioeng. 89:111-118.
383. Young, D. M., D. Parke, and L. N. Ornston. 2005. Opportunities for genetic investigation afforded by Acinetobacter baylyi, a nutritionally versatile bacterial species that is highly competent for natural transformation. Annu. Rev. Microbiol. 59:519-551.
384. Young, L. Y., and C. D. Phelps. 2005. Metabolic biomarkers for monitoring in situ anaerobic hydrocarbon degradation. Environ. Health Perspect. 113:62-67.
385. Yu, L., M. Blaser, P. I. Andrei, A. J. Pierik, and T. Selmer. 2006. 4-Hy-droxyphenylacetate decarboxylases: properties of a novel subclass of glycyl radical enzyme systems. Biochemistry 45:9584-9592.
386. Zengler, K., J. Heider, R. Rossello-Mora, and F. Widdel. 1999. Phototro-phic utilization of toluene under anoxic conditions by a new strain of Blastochloris sulfoviridis. Arch. Microbiol. 172:204-212.
387. Zhang, C., and G. N. Bennett. 2005. Biodegradation of xenobiotics by anaerobic bacteria. Appl. Microbiol. Biotechnol. 67:600-618.
388. Zhang, X., and L. Y. Young. 1997. Carboxylationas aninitial reaction in the anaerobic metabolism of naphthalene and phenanthrene by sulfidogenic consortia. Appl. Environ. Microbiol. 63:4759-4764.
389. Ziegelhoffer, E. C., and P. J. Kiley. 1995. In vitro analysis of a constitutively active mutant form of the Escherichia coli global transcription factor FNR. J. Mol. Biol. 245:351-361.