Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: Redundancies and convergence

Journal of Bacteriology

Volumn 187, Issue 12, 2005, Pages 4050-4063

  Patrauchan, Marianna A ^a   Florizone, Christine ^a   Dosanjh, Manisha ^a   Mohn, William W ^a   Davies, Julian ^a   Eltis, Lindsay D ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADIPIC ACID; BENZOIC ACID; CYTOCHROME P450; GENE PRODUCT; PHTHALIC ACID;

ACTINOBACTERIA; ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIAL STRAIN; CATABOLISM; CELL GROWTH; ENZYME ACTIVITY; ENZYME ASSAY; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; RHODOCOCCUS; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; WILD TYPE;

BACTERIAL PROTEINS; BENZOATES; CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; GENES, BACTERIAL; PHTHALIC ACIDS; RHODOCOCCUS;

PISUM SATIVUM; RHODOCOCCUS SP.;

EID: 20444506446     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.187.12.4050-4063.2005     Document Type: Article

References (85)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Apweiler, R., T. K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M. D. Croning, R. Durbin, L. Falquet, W. Fleischmann, J. Gouzy, H. Hermjakob, N. Hulo, I. Jonassen, D. Kahn, A. Kanapin, Y. Karavidopoulou, R. Lopez, B. Marx, N. J. Mulder, T. M. Oinn, M. Pagni, F. Servant, C. J. Sigrist, and E. M. Zdobnov. 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29:37-40.
3. Badger, J. H., and G. J. Olsen. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16:512-524.
4. Barnett, M. J., R. F. Fisher, T. Jones, C. Komp, A. P. Abola, F. Barloy-Hubler, L. Bowser, D. Capela, F. Galibert, J. Gouzy, M. Gurjal, A. Hong, L. Huizar, R. W. Hyman, D. Kahn, M. L. Kahn, S. Kalman, D. H. Keating, C. Palm, M. C. Peck, R. Surzycki, D. H. Wells, K. C. Yeh, R. W. Davis, N. A. Federspiel, and S. R. Long. 2001. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc. Natl. Acad. Sci. USA 98:9883-9888.
5. Batie, C. J., E. LaHaie, and D. P. Ballou. 1987. Purification and characterization of phthalate oxygenase and phthalate oxygenase reductase from Pseudomonas cepacia. J. Biol. Chem. 262:1510-1518.
6. Bell, K. S., J. C. Philp, D. W. Aw, and N. Christofi. 1998. The genus Rhodococcus. J. Appl. Microbiol. 85:195-210.
7. Bentley, S. D., K. F. Chater, A. M. Cerdeno-Tarraga, G. L. Challis, N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C. H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M. A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill, and D. A. Hopwood. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141-147.
8. Bjellqvist, B., G. J. Hughes, C. Pasquali, N. Paquet, F. Ravier, J. C. Sanchez, S. Frutiger, and D. Hochstrasser. 1993. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 14:1023-1031.
9. Bourhy, P., A. Martel, D. Margarita, I. Saint Girons, and J. Belfaiza. 1997. Homoserine O-acetyltransferase, involved in the Leptospira meyeri methionine biosynthetic pathway, is not feedback inhibited. J. Bacteriol. 179:4396-4398.
10. Boynton, Z. L., G. N. Bennet, and F. B. Rudolph. 1996. Cloning, sequencing, and expression of clustered genes encoding beta-hydroxybutyryl- coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 178:3015-3024.
11. Brzostowicz, P. C., A. B. Reams, T. J. Clark, and E. L. Neidle. 2003. Transcriptional cross-regulation of the catechol and protocatechuate branches of the beta-ketoadipate pathway contributes to carbon source-dependent expression of the Acinetobacter sp. strain ADP1 pobA gene. Appl. Environ. Microbiol. 69:1598-1606.
12. Brzostowicz, P. C., D. M. Walters, S. M. Thomas, V. Nagarajan, and P. E. Rouviere. 2003. mRNA differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species. Appl. Environ. Microbiol. 69:334-342.
13. Chang, H. K., and G. J. Zylstra. 1999. Characterization of the phthalate permease OphD from Burkholderia cepacia ATCC 17616. J. Bacteriol. 181: 6197-6199.
14. Chang, H. K., and G. J. Zylstra. 1998. Novel organization of the genes for phthalate degradation from Burkholderia cepacia DBO1. J. Bacteriol. 180: 6529-6537.
15. Chauvaux, S., F. Chevalier, C. Le Dantec, F. Fayolle, I. Miras, F. Kunst, and P. Beguin. 2001. Cloning of a genetically unstable cytochrome P-450 gene cluster involved in degradation of the pollutant ethyl tert-butyl ether by Rhodococcus ruber. J. Bacteriol. 183:6551-6557.
16. Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry, 3rd, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, B. G. Barrell, et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
17. Cowles, C. E., N. N. Nichols, and C. S. Harwood. 2000. BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. J. Bacteriol. 182:6339-6346.
18. Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97:6640-6645.
19. Dean, C. R., and J. B. Goldberg. 2000. The wbpM gene in Pseudomonas aeruginosa serogroup O17 resides on a cryptic copy of the serogroup O11 O antigen gene locus. FEMS Microbiol. Lett. 187:59-63.
20. Delcher, A. L., D. Harmon, S. Kasif, O. White, and S. L. Salzberg. 1999. Improved microbial gene identification with GLIMMER. Nucleic. Acids Res. 27:4636-4641.
21. De Mot, R., I. Nagy, G. Schoofs, and J. Vanderleyden. 1994. Sequences of the cobalamin biosynthetic genes cobK, cobL and cobM from Rhodococcus sp. NI86/21. Gene 143:91-93.
22. Dorn, E., and H. J. Knackmuss. 1978. Chemical structure and biodegradability of halogenated aromatic compounds. Substituent effects on 1,2-dioxygenation of catechol. Biochem. J. 174:85-94.
23. Doten, R. C., K. L. Ngai, D. J. Mitchell, and L. N. Ornston. 1987. Cloning and genetic organization of the pca gene cluster from Acinetobacter calcoaceticus. J. Bacteriol. 169:3168-3174.
24. Duffner, F. M., and R. Muller. 1998. A novel phenol hydroxylase and catechol 2,3-dioxygenase from the thermophilic Bacillus thermoleovorans strain A2: nucleotide sequence and analysis of the genes. FEMS Microbiol. Lett. 161:37-45.
25. Eaton, R. W. 2001. Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B. J. Bacteriol. 183:3689-3703.
26. Eaton, R. W., and D. W. Ribbons. 1982. Metabolism of dibutylphthalate and phthalate by Micrococcus sp. strain 12B. J. Bacteriol. 151:48-57.
27. Eltis, L. D., U. Karlson, and K. N. Timmis. 1993. Purification and characterization of cytochrome P450RR1 from Rhodococcus rhodochrous. Eur. J. Biochem. 213:211-216.
28. Eulberg, D., L. A. Golovleva, and M. Schlomann. 1997. Characterization of catechol catabolic genes from Rhodococcus erythropolis ICP. J. Bacteriol. 179:370-381.
29. Eulberg, D., S. Lakner, L. A. Golovleva, and M. Schlomann. 1998. Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: evidence for a merged enzyme with 4-carboxymuconolactone- decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity. J. Bacteriol. 180:1072-1081.
30. Furukawa, K., H. Suenaga, and M. Goto. 2004. Biphenyl dioxygenases: functional versatilities and directed evolution. J. Bacteriol. 186:5189-5196.
31. Gorg, A., C. Obermaier, G. Boguth, A. Harder, B. Scheibe, R. Wildgruber, and W. Weiss. 2000. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21:1037-1053.
32. Gorg, A., C. Obermaier, G. Boguth, and W. Weiss. 1999. Recent developments in two-dimensional gel electrophoresis with immobilized pH gradients: wide pH gradients up to pH 12, longer separation distances and simplified procedures. Electrophoresis 20:712-717.
33. Grogan, G., G. A. Roberts, D. Bougioukou, N. J. Turner, and S. L. Flitsch. 2001. The desymmetrization of bicyclic beta-diketones by an enzymatic retro-Claisen reaction. A new reaction of the crotonase superfamily. J. Biol. Chem. 276:12565-12572.
34. Gurtler, V., B. C. Mayall, and R. Seviour. 2004. Can whole genome analysis refine the taxonomy of the genus Rhodococcus? FEMS Microbiol. Rev. 28:377-403.
35. Gust, B., G. L. Challis, K. Fowler, T. Kieser, and K. F. Chater. 2003. PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc. Natl. Acad. Sci. USA 100:1541-1546.
36. Harwood, C. S., N. N. Nichols, M. K. Kim, J. L. Ditty, and R. E. Parales. 1994. Identification of the pca RKF gene cluster from Pseudomonas putida: involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate. J. Bacteriol. 176:6479-6488.
37. Harwood, C. S., and R. E. Parales. 1996. The beta-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 50:553-590.
38. Herrmann, H., C. Muller, I. Schmidt, J. Mahnke, L. Petruschka, and K. Hahnke. 1995. Localization and organization of phenol degradation genes of Pseudomonas putida strain H. Mol. Gen. Genet. 247:240-246.
39. Huston, W. M., M. P. Jennings, and A. G. McEwan. 2002. The multicopper oxidase of Pseudomonas aeruginosa is a ferroxidase with a central role in iron acquisition. Mol. Microbiol. 45:1741-1750.
40. Irvine, V. A., L. A. Kulakov, and M. J. Larkin. 2000. The diversity of extradiol dioxygenase (edo) genes in cresol degrading rhodococci from a creosote-contaminated site that express a wide range of degradative abilities. Antonie van Leeuwenhoek 78:341-352.
41. Iwagami, S. G., K. Yang, and J. Davies. 2000. Characterization of the protocatechuic acid catabolic gene cluster from Streptomyces sp. strain 2065. Appl. Environ. Microbiol. 66:1499-1508.
42. Jimenez, J. I., and J. L. Garcia. 2004. Genomic insights in the metabolism of aromatic compounds in Pseudomonas, p. 425-461. In J.-L. Ramos (ed.), Pseudomonas, vol. 3. Kluwer Academic/Plenum Publishers, New York, N.Y.
43. Jimenez, J. I., B. Minambres, J. L. Garcia, and E. Diaz. 2002. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol. 4:824-841.
44. Johnson, B. F., and R. Y. Stanier. 1971. Regulation of the-ketoadipate pathway in Alcaligenes eutrophus. J. Bacteriol. 107:476-485.
45. Kalinowski, J., B. Bathe, D. Bartels, N. Bischoff, M. Bott, A. Burkovski, N. Dusch, L. Eggeling, B. J. Eikmanns, L. Gaigalat, A. Goesmann, M. Hartmann, K. Huthmacher, R. Kramer, B. Linke, A. C. McHardy, F. Meyer, B. Mockel, W. Pfefferle, A. Puhler, D. A. Rey, C. Ruckert, O. Rupp, H. Sahm, V. F. Wendisch, I. Wiegrabe, and A. Tauch. 2003. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J. Biotechnol. 104:5-25.
46. Kaschabek, S. R., B. Kuhn, D. Muller, E. Schmidt, and W. Reineke. 2002. Degradation of aromatics and chloroaromatics by Pseudomonas sp. strain B13: purification and characterization of 3-oxoadipate:succinyl-coenzyme A (CoA) transferase and 3-oxoadipyl-CoA thiolase. J. Bacteriol. 184:207-215.
47. Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces genetics. The John Innes Foundation, Norwich, United Kingdom.
48. Kim, Y. R., S. E. Lee, C. M. Kim, S. Y. Kim, E. K. Shin, D. H. Shin, S. S. Chung, H. E. Choy, A. Progulske-Fox, J. D. Hillman, M. Handfield, and J. H. Rhee. 2003. Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients. Infect. Immun. 71: 5461-5471.
49. Kinter, M. T., and N. E. Sherman. 2000. Protein sequencing and identification using tandem mass spectrometry. John Wiley & Sons Inc., New York, N.Y.
50. Kitagawa, W., K. Miyauchi, E. Masai, and M. Fukuda. 2001. Cloning and characterization of benzoate catabolic genes in the gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. J. Bacteriol. 183: 6598-6606.
51. Kitagawa, W., A. Suzuki, T. Hoaki, E. Masai, and M. Fukuda. 2001. Multiplicity of aromatic ring hydroxylation dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHAI demonstrated by denaturing gradient gel electrophoresis. Biosci. Biotechnol. Biochem. 65:1907-1911.
52. Kornberg, H. L. 1966. The role and control of the glyoxylate cycle in Escherichia coli. Biochem. J. 99:1-11.
53. Kulakov, L. A., and M. J. Larkin. 2002. Genetic organization of Rhodococcus, p. 15-46. In A. Danchin (ed.), Genomics of GC-rich gram-positive bacteria. Caister Academic Press, Wymondham, United Kingdom.
54. Lessard, P. A., X. M. O'Brien, N. A. Ahlgren, S. A. Ribich, and A. J. Sinskey. 1999. Characterization of IS1676 from Rhodococcus erythropolis SQ1. Appl. Microbiol. Biotechnol. 52:811-819.
55. Maeda, M., S. Y. Chung, E. Song, and T. Kudo. 1995. Multiple genes encoding 2,3-dihydroxybiphenyl 1,2-dioxygenase in the gram-positive polychlorinated biphenyl-degrading bacterium Rhodococcus erythropolis TA421, isolated from a termite ecosystem. Appl. Environ. Microbiol. 61:549-555.
56. Mahenthiralingam, E., B. I. Marklund, L. A. Brooks, D. A. Smith, G. J. Bancroft, and R. W. Stokes. 1998. Site-directed mutagenesis of the 19-kilodalton lipoprotein antigen reveals No essential role for the protein in the growth and virulence of Mycobacterium intracellular. Infect. Immun. 66: 3626-3634.
57. Masai, E., A. Yamada, J. M. Healy, T. Hatta, K. Kimbara, M. Fukuda, and K. Yano. 1995. Characterization of biphenyl catabolic genes of gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 61:2079-2085.
58. Morii, S., S. Sawamoto, Y. Yamauchi, M. Miyamoto, M. Iwami, and E. Itagaki. 1999. Steroid monooxygenase of Rhodococcus rhodochrous: sequencing of the genomic DNA, and hyperexpression, purification, and characterization of the recombinant enzyme. J. Biochem. (Tokyo) 126:624-631.
59. Nagy, I., G. Schoofs, F. Compernolle, P. Proost, J. Vanderleyden, and R. de Mot. 1995. Degradation of the thiocarbamate herbicide EPTC (S-ethyl dipropylcarbamothioate) and biosafening by Rhodococcus sp. strain NI86/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase. J. Bacteriol. 177:676-687.
60. Navarro-Llorens, J. M., M. A. Patrauchan, G. R. Stewart, J. E. Davies, L. D. Eltis, and W. W. Mohn. Phenylacetate catabolism in Rhodococcus sp. strain RHA1: a central pathway for degradation of aromatic compounds. J. Bacteriol., in press.
61. Nichols, N. N., and C. S. Harwood. 1995. Repression of 4-hydroxybenzoate transport and degradation by benzoate: a new layer of regulatory control in the Pseudomonas putida beta-ketoadipate pathway. J. Bacteriol. 177:7033-7040.
62. Nierman, W. C., T. V. Feldblyum, M. T. Laub, I. T. Paulsen, K. E. Nelson, J. A. Eisen, J. F. Heidelberg, M. R. Alley, N. Ohta, J. R. Maddock, I. Potocka, W. C. Nelson, A. Newton, C. Stephens, N. D. Phadke, B. Ely, R. T. DeBoy, R. J. Dodson, A. S. Durkin, M. L. Gwinn, D. H. Haft, J. F. Kolonay, J. Smit, M. B. Craven, H. Khouri, J. Shetty, K. Berry, T. Utterback, K. Tran, A. Wolf, J. Vamathevan, M. Ermolaeva, O. White, S. L. Salzberg, J. C. Venter, L. Shapiro, C. M. Fraser, and J. Eisen. 2001. Complete genome sequence of Caulobacter crescentus. Proc. Natl. Acad. Sci. USA 98:4136-4141.
63. Omura, S., H. Ikeda, J. Ishikawa, A. Hanamoto, C. Takahashi, M. Shinose, Y. Takahashi, H. Horikawa, H. Nakazawa, T. Osonoe, H. Kikuchi, T. Shiba, Y. Sakaki, and M. Hattori. 2001. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc. Natl. Acad. Sci. USA 98:12215-12220.
64. Paget, M. S., L. Chamberlin, A. Atrih, S. J. Foster, and M. J. Buttner. 1999. Evidence that the extracytoplasmic function sigma factor sigmaE is required for normal cell wall structure in Streptomyces coelicolor A3(2). J. Bacteriol. 181:204-211.
65. Pinyakong, O., H. Habe, T. Yoshida, H. Nojiri, and T. Omori. 2003. Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2. Biochem. Biophys. Res. Commun. 301:350-357.
66. Roberts, G. A., G. Grogan, A. Greter, S. L. Flitsch, and N. J. Turner. 2002. Identification of a new class of cytochrome P450 from a Rhodococcus sp. J. Bacteriol. 184:3898-3908.
67. Sakai, M., E. Masai, H. Asami, K. Sugiyama, K. Kimbara, and M. Fukuda. 2002. Diversity of 2,3-dihydroxybiphenyl dioxygenase genes in a strong PCB degrader, Rhodococcus sp strain RHA1. J. Biosci. Bioeng. 93:421-427.
68. Sakai, M., K. Miyauchi, N. Kato, E. Masai, and M. Fukuda. 2003. 2-Hydroxypenta-2,4-dienoate metabolic pathway genes in a strong polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 69:427-433.
69. a. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual. 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
70. Seto, M., K. Kimbara, M. Shimura, T. Hatta, M. Fukuda, and K. Yano. 1995. A novel transformation of polychlorinated biphenyls by Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 61:3353-3358.
71. Shanley, M. S., A. Harrison, R. E. Papales, G. Kowalchuk, D. J. Mitchell, and L. N. Ornston. 1994. Unusual G + C content and codon usage in catlJF, a segment of the ben-cat supra-operonic cluster in the Acinetobacter calcoaceticus chromosome. Gene 138:59-65.
72. Shigematsu, T., K. Yumihara, Y. Ueda, S. Morimura, and K. Kida. 2003. Purification and gene cloning of the oxygenase component of the terephthalate 1.2-dioxygenase system from Delftia tsuruhatensis strain T7. FEMS Microbiol. Lett. 220:255-260.
73. Shimizu, S., H. Kobayashi, E. Masai, and M. Fukuda. 2001. Characterization of the 450-kb linear plasmid in a polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 67:2021-2028.
74. Skurnik, M., A. Pelppo, and E. Ervela. 2000. Characterization of the O-antigen gene clusters of Yersinia pseudotuberculosis and the cryptic O-antigen gene cluster of Yersinia pestis shows that the plague bacillus is most closely related to and has evolved from Y. pseudotuberculosis serotype O:1b. Mol. Microbiol. 37:316-330.
75. Steele, M. I., D. Lorenz, K. Hatter, A. Park, and J. R. Sokatch. 1992. Characterization of the mmsAB operon of Pseudomonas aeruginosa PAO encoding methylmalonate-semialdehyde dehydrogenase and 3-hydroxy-isobutyrate dehydrogenase. J. Biol. Chem. 267:13585-13592.
76. Stim-Herndon, K. P., D. J. Petersen, and G. N. Bennett. 1995. Characterization of an acetyl-CoA C-acetyltransferase (thiolase) gene from Clostridium acetobutylicum ATCC 824. Gene 154:81-85.
77. Streit, W. R., R. A. Schmitz, X. Perret, C. Staehelin, W. J. Deakin, C. Raasch, H. Liesegang, and W. J. Broughton. 2004. An evolutionary hot spot: the pNGR234b replicon of Rhizobium sp. strain NGR234. J. Bacteriol. 186:535-542.
78. Taguchi, K., M. Motoyama, and T. Kudo. 2004. Multiplicity of 2,3-dihydroxybiphenyl dioxygenase genes in the Gram-positive polychlorinated biphenyl degrading bacterium Rhodococcus rhodochrous K37. Biosci. Biotechnol. Biochem. 68:787-795.
79. Takeda, H., A. Yamada, K. Miyauchi, E. Masai, and M. Fukuda. 2004. Characterization of transcriptional regulatory genes for biphenyl degradation in Rhodococcus sp. strain RHA1. J. Bacteriol. 186:2134-2146.
80. 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.
81. Trott, S., S. Burger, C. Calaminus, and A. Stolz. 2002. Cloning and heterologous expression of an enantioselective amidase from Rhodococcus erythropolis strain MP50. Appl. Environ. Microbiol. 68:3279-3286.
82. van der Geize, R., and L. Dijkhuizen. 2004. Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr. Opin. Microbiol. 7:255-261.
83. van der Geize, R., G. I. Hessels, R. van Gerwen, P. van der Meijden, and L. Dijkhuizen. 2001. Unmarked gene deletion mutagenesis of kstD, encoding 3-ketosteroid Delta1-dehydrogenase, in Rhodococcus erythropolis SQ1 using sacB as counter-selectable marker. FEMS Microbiol. Lett. 205:197-202.
84. van Hylckama Vlieg, J. E., and D. B. Janssen. 2001. Formation and detoxification of reactive intermediates in the metabolism of chlorinated ethenes. J. Biotechnol. 85:81-102.
85. Warren, R., W. W. L. Hsiao, H. Kudo, M. Myhre, M. Dosanjh, A. Petrescu, H. Kobayashi, S. Shimizu, K. Miyauchi, E. Masai, G. Yang, J. M. Stott, J. E. Schein, H. Shin, J. Khattra, D. Smailus, Y. S. Butterfield, A. Siddiqui, R. A. Holt, M. A. Marra, S. J. M. Jones, W. W. Mohn, F. S. Brinkman, M. Fukuda, J. Davies, and L. D. Eltis. 2004. Functional characterization of a catabolic plasmid from polychlorinated biphenyl-degrading Rhodococcus sp. RHA1. J. Bacteriol. 186:7783-7795.