Applied aspects of Rhodococcus genetics

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 74, Issue 1-3, 1998, Pages 133-153

  Larkin, Michael J ^a   De Mot, René ^b   Kulakov, Leonid A ^a   Nagy, István ^b  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^b UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

Cloning vectors; Genetics; Plasmids; Rhodococcus

Indexed keywords

BACTERIAL GENETICS; BACTERIOPHAGE; BIOTECHNOLOGY; CLONING VECTOR; GENE CONTROL; GENE EXPRESSION; GENE INSERTION SEQUENCE; GENE TRANSFER; GENETIC PROCEDURES; GENETIC RECOMBINATION; NONHUMAN; PRIORITY JOURNAL; RECOMBINANT PLASMID; REPORTER GENE; REVIEW; RHODOCOCCUS;

BIOTECHNOLOGY; GENE EXPRESSION REGULATION, BACTERIAL; GENE TRANSFER TECHNIQUES; GENES, REPORTER; GENETIC VECTORS; PLASMIDS; RECOMBINATION, GENETIC; RHODOCOCCUS;

EID: 0032460397     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1001776500413     Document Type: Review

References (188)

1. Adams JN (1964) Recombination between Nocardia erythropolis and canicruria. J. Bacteriol. 88: 865-876
2. Adams JN & Bradley SG (1963) Recombination events in the bacterial genus Nocardia. Science 140: 1392-1394
3. Adams JN & Brownell GH (1976) Genetic studies in Nocardia erythropolis. In: Goodfellow M, Brownell GH & Serrano JA (Eds) The Biology of the Nocardiae (pp 285-309). Academic Press, London
4. Allen CCR, Boyd DR, Larkin MJ, Reid KA, Sharma ND & Wilson K (1997) Metabolism of naphthalene, 1-naphthol, indene, and indole by Rhodococcus sp strain N CIMB 12038. Appl. Environ. Microbiol. 63: 151-155
5. Andersen SJ, Quan S, Gowan B & Dabbs ER (1997) Monooxygenase-like sequence of a Rhodococcus equi gene conferring increased resistance to rifampin by inactivating this antibiotic. Antimicrob. Agents Chemother. 41: 218-221
6. Archer JAC & Griffiths H (1995) Linear plasmids in Rhodococcus corallina V49. J. Cell. Biochem. NoS21A p45 abstract
7. Assaf NA & Dick WA (1993) Spheroplast formation and plasmid isolation from Rhodococcus spp. Biotechniques 15: 1010-1015
8. Asturias JA & Timmis KN (1993) Three different 2,3-dihydroxybiphenyl-1,2-dioxygenase genes in the Gram-positive polychlorobiphenyl-degrading bacterium Rhodococcus globerulus P6. J. Bacteriol. 175: 4631-4640
9. Asturias JA, Eltis LD, Prucha M & Timmis KN (1994a) Analysis of 3,2,3-dihydroxybiphenyl 1,2-dioxygenases found in Rhodococcus globerulus P6 - identification of a new family of extradiol dioxygenases. J. Biol. Chem. 269: 7807-7815
10. Asturias JA, Moore E, Yakimov MM, Klatte S & Timmis KN (1994b) Reclassification of the polychlorinated biphenyldegraders Acinetobacter sp. strain P6 and Corynebacterium sp. strain MB1 as Rhodococcus globerulus. Syst. Appl. Microbiol. 17: 226-231
11. Asturias JA, Díaz E & Timmis KN (1995) The evolutionary relationship of biphenyl dioxygenase from Gram-positive Rhodococcus globerulus P6 to multicomponent dioxygenases from Gramnegative bacteria. Gene 156: 11-18
12. Baltz RH & Hosted TH (1996) Molecular genetic methods for improving secondary-metabolite production in actinomycetes. Trends Biotechnol. 14: 245-250
13. Bardarov S, Kriakov J, Carrierre C, Yu S, Vaamonde C, McAdam RA, Bloom BR, Hatfull GF & Jacobs Jr WR (1997) Conditionally replicating mycobacteriophages: a system for transposon delivery to Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 94: 10961-10966
14. Baril C, Richaud C, Baranton g & Saint Girons IS (1989) Linear chromosome of Borrelia burgdorferi. Res. Microbiol. 140: 507-516
15. Barnes MR, Duetz WA & Williams PA (1997) A 3-(3-hydroxyphenyl)propionic acid catabolic pathway in Rhodococcus globerulus PWD1: cloning and characterization of the hpp operon. J. Bacteriol. 179: 6145-6153
16. Bashyam MD, Kaushal D, Dasgupta SK & Tyagi AK (1996) A study of the mycobacterial transcriptional apparatus: identification of novel features in promoter elements. J. Bacteriol. 178: 4847-4853
17. Behki RM (1991) Di-allate degradation by an EPTC-degrading Rhodococcus, and in eptc- treated soil. Soil Biol. Biochem. 23: 789-793
18. Behki R, Topp E, Dick W & Germon P (1993) Metabolism of the herbicide atrazine by Rhodococcus strains. Appl. Environ. Microbiol. 59: 1955-1959
19. Behki RM, Topp EE & Blackwell BA (1994) Ring hydroxylation of N-methylcarbamate insecticides by Rhodococcus TE1. J. Agric. Fd. Chem. 42: 1375-1378
20. Bigey F, Grossiord B, Chan Kwo Chion CKN, Arnaud A & Galzy P (1995) Brevibacterium linens pBL33 and Rhodococcus rhodochrous pRC1 cryptic plasmids replicate in Rhodococcus sp. R312 (formerly Brevibacterium sp. R312) Gene 154: 77-79
21. Blake JA, Ganguly N & Sherratt DJ (1997) DNA sequence of recombinase-binding sites can determine Xer site-specific recombination outcome. Mol. Microbiol. 23: 387-398
22. Blakely GW, Davidson AO & Sherratt DJ (1997) Binding and cleaving of nicked substrates by site-specific recombinases XerC and XerD. J. Mol. Biol. 265: 30-39
23. Bourn WR & Babb B (1995) Computer assisted identification and classification of streptomycete promoters. Nucleic Acids Res. 23: 3696-3703
24. T to the genus Mycobacterium. Int. J. Syst. Bacteriol. 44: 494-498
25. Brownell GH (1974) A new nocardial mating strain. Am. Soc. Microbiol. Abstract p 41
26. Brownell GH & Adams JN (1968) Linkage and segregation of a mating type specific phage and resistance chararacters in nocardial recombinants. Genetics 60: 437-448
27. Brownell GH & Denniston K (1984) Genetics of the nocardioform bacteria. In: Goodfellow M, Mordarski M & Williams ST (Eds) The Biology of the Actinomycetes, (pp 201-208). Academic Press, New York
28. Brownell GH & Kelly KL (1969) Inheritance of mating type factors in nocardial recombinants. J. Bacteriol. 99: 25-36
29. Brownell GH, Adams JN & Bradley SG (1967) Growth and characterisation of nocardiophages for Nocardia canicruria and Nocardia erythropolis mating types. J. Gen. Microbiol. 47: 247-256
30. Brownell GH, Enquist LW & Denniston-Thompson K (1980) An analysis of the genome of the actinophage ØEC. Gene 12: 311-314
31. Brownell GH, Saba JA, Denniston-Thompson K & Enquist LW (1982) The development of a Rhodococcus-actinophage cloning system. Dev. Ind. Microbiol. 23: 287-298
32. Brunhuber NM, Banerjee A, Jacobs WR Jr. & Blanchard JS (1994) Cloning, sequencing, and expression of Rhodococcus 1-phenylalanine dehydrogenase. Sequence comparisons to aminoacid dehydrogenases. J. Biol. Chem. 269: 16203-16211
33. Candidus S, VanPee KH & Lingens F (1994) The catechol 2,3-dioxygenase gene of Rhodococcus rhodochrous CTM - nucleotide sequence, comparison with isofunctional dioxygenases and evidence for an active-site histidine. Microbiology 140: 321-330
34. Chan Kwo Chion CKN, Duran R, Arnaud A & Galzy P (1991a) Cloning vectors and antibiotic-resistance markers for Brevibacterium sp. R312. Gene 105: 119-124
35. Chan Kwo Chion CKN, Duran R, Arnaud A & Galzy P (1991b) Electrotransformation of whole cells of Brevibacterium sp. R312, a nitrile hydratase producing strain: construction of a cloning vector. FEMS Microbiol. Lett. 81: 177-187
36. Chen CW (1996) Complications and implications of linear bacterial chromosomes. Trends Genet. 12: 192-196
37. Clark JE & Brownell GH (1972) Genophore homologies among compatible nocardiae. J. Bacteriol. 109: 720-729
38. Crespi M, Messens E, Caplan AB, Vanmontagu M & Desomer J (1992) Fasciation induction by the phytopathogen Rhodococcus fascians depends upon a linear plasmid encoding a cytokinin synthase gene. EMBO Journal 11: 795-804
39. Crespi M, Vereecke D, Temmerman W, Vanmontagu M & Desomer J (1994) The fas operon of Rhodococcus fascians encodes new genes required for efficient fasciation of host plants. J. Bacteriol. 176: 2492-2501
40. Crockett JK & Brownell GH (1972) Isolation and characterisation of a lysogenic strain of Nocardia erythropolis. J. Gen. Virol. 10: 737-742
41. Curragh H, Flynn O, Larkin MJ, Stafford TM, Hamilton JTG & Harper DB (1994) Haloalkane degradation and assimilation by Rhodococcus rhodochrous NCIMB13064. Microbiology 140: 1433-1442
42. Dabbs ER (1987) A generalized transducing bacteriophage for Rhodococcus erythropolis. Mol. Gen Genet. 206: 116-120
43. Dabbs ER (1998) Cloning of genes that have environmental and clinical importance from rhodococci and related bacteria. Antonie van Leeuwenhoek 74: 155-168
44. Dabbs ER & Sole GJ (1988) Plasmid-borne resistance to arsenate, arsenite, cadmium and chloramphenicol in a Rhodococcus species. Mol. Gen. Genet. 211: 148-154
45. Dabbs ER, Gowan B & Andersen SJ (1990) Nocardioform arsenic resistance plasmids and construction of Rhodococcus cloning vectors. Plasmid 23: 242-247
46. Dabbs ER, Gowan B, Quan S & Andersen SJ (1995) Development of improved Rhodococcus plasmid vectors and their use in cloning genes of potential commercial and medical importance. Biotechnologia 7-8: 129-135
47. Dabrock B, Kessel er M, Averhoff B & Gottschalk G (1994) Identification and characterization of a transmissible linear plasmid from Rhodococcus erythropolis BD2 that encodes isopropylbenzene and trichloroethene catabolism. Appl. Environ. Microbiol. 60: 853-860
48. de la Pena-Moctezuma A & Prescott JF (1995) A physical map of the 85 kb virulence plasmid of Rhodococcus equi 103. Can. J. Vet. Res. 59: 229-231
49. De Mot R, Nagy I, Schoofs G & Vanderleyden J (1994a) Sequences of the cobalamin biosynthetic genes cobK, cobL, and cobM from Rhodococcus sp. NI86/21. Gene 143: 91-93
50. De Mot R, Nagy I, Schoofs G & Vanderleyden J (1994b) Sequence of a Rhodococcus gene cluster encoding the subunits of ethanolamine ammonia-lyase and an APC-like permease. Can. J. Microbiol. 40: 403-407
51. De Mot R, Nagy I, De Schrijver A, Pattanapipitpaisal P, Schoofs G & Vanderleyden J (1997). Structural analysis of the 6 kb cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 and construction of Escherichia coli-Rhodococcus shuttle vectors. Microbiology 143: 3137-3147
52. Denis-Larose C, Labbe D, Bergeron H, Jones AM, Greer CW, Alhawari J, Grossman MJ, Sankey BM & Lau PCK (1997) Conservation of plasmid-encoded dibenzothiophene desulfurisation genes in several rhodococci. Appl. Environ. Microbiol. 63: 2915-2919
53. Denome SA & Young KD (1995) Identification and activity of two insertion-sequence elements in Rhodococcus sp strain IGTS8. Gene 161:33-38
54. Denome SA, Olson ES & Young KD (1993) Identification and cloning of genes involved in specific desulfurization of dibenzothiophene by Rhodococcus sp strain IGTS8. Appl. Environ. Microbiol. 59: 2837-2843
55. Denome SA, Oldfield C, Nash LJ & Young KD (1994) Characterization of the desulfurization genes from Rhodococcus sp. strain IGTS8. J. Bacteriol. 176: 6707-6716
56. De Schrijver A, Nagy I, Schoofs G, Proost P, Vanderleyden J, van Pée K-H & De Mot R (1997) The thiocarbamate herbicide-inducible nonheme chloroperoxidase of Rhodococcus erythropolis NI86/21. Appl. Environ. Microbiol. 634: 1911-1916
57. Desomer J, Dhaese P & Van Montagu M (1988) Conjugative transfer of cadmium resistance plasmids in Rhodococcus fascians strains. J. Bacteriol. 170: 2401-2405
58. Desomer J, Dhaese P & Van Montagu M (1990) Transformation of Rhodococcus fascians by high-voltage electroporation and development of R. fascians cloning vectors. Appl. Environ. Microbiol. 56: 2818-2825
59. Desomer J, Crespi M & Vanmontagu M (1991) Illegitimate integration of non-replicative vectors in the genome of Rhodococcus fascians upon electrotransformation as an insertional mutagenesis system. Mol. Microbiol. 5: 2115-2124
60. Desomer J, Vereecke D, Crespi M & Van Montagu M (1992) The plasmid-encoded chloramphenicol-resistance protein of Rhodococcus fascians is homologous to the transmembrane efflux proteins. Mol. Microbiol. 6: 2377-2385
61. Dhandayuthapani S, Via LE, Thomas CA, Horowitz PM & Deretic D (1995). Green fluorescent protein as a marker for gene expression and cell biology of mycobacterial interactions with macrophages. Mol. Microbiol. 17: 901-912
62. Eltis LD & Bolin JT (1996) Evolutionary relationship among extradiol dioxygenases. J. Bacteriol. 178: 5930-5937
63. Eulberg D, Golovleva LA & Schlomann M (1997) Characterisation of catechol catabolic genes from Rhodococcus erythropolis 1CP. J. Bacteriol. 179: 370-381
64. Ferdows MS & Barbour AG (1989) Megabase-sized linear DNA in the bacterium Borrelia burgdorferi, the Lyme disease agent. Proc. Natl. Acad. Sci. USA 86: 5969-5973
65. Finnerty WR (1992) The biology and genetics of the genus Rhodococcus. Ann. Rev. Microbiol. 46: 193-218
66. Gallardo ME, Ferrández A, de Lorenzo V, García JL & Díaz E (1997) Designing recombinant Pseudomonas strains to enhance biodesulfurization. J. Bacteriol. 179:7156-7160
67. Gallegos M-T, Schleif R, Bairoch A, Hofmann K & Ramos J (1997) AraC/XylS family of transcriptional regulators. Microbiol. Mol. Biol. Rev. 61: 393-410
68. Gonzalez-y-Merchand JA, Colston MJ & Cox RA (1996) The rRNA operons of Mycobacterium smegmatis and Mycobacterium tuberculosis: comparison of promoter elements and of neighbouring upstream genes. Microbiology 142: 667-674
69. Goodfellow M, Alderson G & Chun I (1998) Rhodococcal systematics: problems and developments. Antonie van Leeuwenhoek 74: 3-20
70. Goodfellow M (1989) Suprageneric classification of actinomycetes. In: Williams ST, Sharpe ME & Holt JG (Eds) Bergey's Manual of Systematic Bacteriology, Vol 4 (pp 2333-2339). Williams and Wilkins, Baltimore
71. Gowan B & Dabbs ER (1994) Identification of DNA involved in Rhodococcus chromosomal conjugation and self-incompatibility. FEMS Microbiol. Lett. 115: 45-50
72. Green EP, Tizard ML, Moss MT, Thompson J, Winterbourne DJ, McFadden JJ & Hermon-Taylor J (1989) Sequence and characteristics of IS900, an insertion element identified in human Crohn's disease isolate of Mycobacterium paratuberculosis. Nucleic Acids Res. 17: 9063-9073
73. Grzeszik C, Lubbers M, Reh M & Schlegel HG (1997) Genes encoding the NAD-reducing hydrogenase of Rhodococcus opacus MR11. Microbiology 143: 1271-1286
74. Guilhot C, Otal I, Van Rompaey I, Martìn C & Gicquel B (1994) Efficient transposition in mycobacteria: construction of Mycobacterium smegmatis insertional mutant libraries. J. Bacteriol. 176: 535-539
75. Haas D, Berger B, Schmid S, Seitz T & Reimmann C (1996) Insertion sequence IS21: related insertion sequence elements, transpositional mechanisms, and application to linker insertion mutagenesis. In Nakazawa T, Furukawa K, Haas D & Silver S (Eds) Molecular Biology of Pseudomonads (pp 238-249). ASM Press, Washington DC.
76. Häggblom Mm, Nohynek LJ, Palleroni NJ, Kronqvist K, Nurmiaho-Lassila E-L, Salkinoja-Salonen MS, Klatte S & Kroppenstedt RM (1994) Transfer of polychlorophenol-degrading Rhodococcus chlorophenolicus (Apajalahti et al. 1986) to the genus Mycobacterium as Mycobacterium chlorophenolicum comb. nov. Int. J. Syst. Bacteriol. 44: 485-493
77. Hall RM 1997. Mobile gene cassettes and integrons: moving antibiotic resistance genes in gram-negative bacteria. Ciba Found. Symp. 207: 192-202
78. Hall RM, Brown HJ, Brookes DE & Stokes HW (1994) Integrons found in different locations have identical 5′-ends but variable 3′ ends. J. Bacteriol. 176: 6286-6294
79. Hashimoto Y, Nishiyama M, Ikehata O, Horinouchi S & Beppu T (1991) Cloning and characterization of an amidase gene from Rhodococcus species N-774 and its expression in Escherichia coli. Biochim. Biophys. Acta 1088: 225-233
80. Hashimoto Y, Nishiyama M, Yu F, Watanabe I, Horinouchi S & Beppu T (1992) Development of a host-vector system in a Rhodococcus strain and its use for expression of the cloned nitrile hydratase gene cluster. J. Gen. Microbiol. 138: 1003-1010
81. Hayakawa T, Tanaka, T, Sakaguchi K, Otake N & Yonehara H (1979) A linear plasmid-like DNA in Streptomyces sp. producing lankacidin group antibiotics. J. Gen. Appl. Microbiol. 25: 255-260
82. Heiss GS, Gowan B & Dabbs ER (1992) Cloning of DNA from a Rhodococcus strain conferring the ability to decolorize sulfonated azo dyes. FEMS Microbiol. Lett. 99: 221-226
83. Hinnebusch J & Tilly K (1993) Linear plasmids and chromosomes in bacteria. Mol. Microbiol. 10: 917-922
84. Hiraga S-I, Sugiyama T & Itoh T (1994) Comparative analysis of the replicon region of eleven ColE2-related plasmids. J. Bacteriol. 176: 7233-7243
85. Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ, Kieser HM, Lydiate DJ, Smith CP, Ward JM & Schrempf H (1985) Genetic Manipulation of Streptomyces: A Laboratory Manual. John Innes, Norwich, UK
86. Hopwood DA, Bibb MJ, Chater KF, Janssen GR, Malpartida F & Smith P (1986) In Booth JR & Higgins CF (Eds) Regulation of Gene Expression. 25 Years on (pp 251-276). Symp. Soc. Gen. Microbiol., University of Cambridge Press, Cambridge, UK
87. Izsvak Z, Jobbagy Z, Takacs I & Duda E (1997) Cloning and characterization of the genes of the CeqI restriction-modification system. Int. J. Biochem. Cell Biol. 29: 895-900
88. Izu H, Izumi Y, Kurome Y, Sano M, Kondo A, Kato I & Ito M (1997) Molecular cloning, expression, and sequence analysis of the endoglycoceramidase II gene from Rhodococcus species strain M777. J. Biol. Chem. 72: 19846-19850
89. Jäger W, Schäfer A, Pühler A, Labes g & Wohlleben W (1992) Expression of the Bacillus subtilis sacB gene leads to sucrose sensitivity in the gram-positive bacterium Corynebacterium glutamicum but not in Streptomyces lividans. J. Bacteriol. 174: 5462-5465
90. Jäger W, Schäfer A, Kalinowski J & Pühler A (1995) Isolation of insertion elements from Gram-positive Brevibacterium, Corynebacterium and RhoJococcus strains using the Bacillus subtilis sacB gene as a positive selection marker. FEMS Microbiol. Lett. 126: 1-6
91. Kalkus J, Dorrie C, Fischer D, Reh M & Schlegel H G (1993) The giant linear plasmid pHG207 from Rhodococcus sp. encoding hydrogen autotrophy - characterization of the plasmid and its termini. J. Gen. Microbiol. 139: 2055-2065
92. Kasweck KL & Little ML (1982) Genetic recombination in Nocardia asteroides. J. Bacteriol. 149: 403-406
93. Kesseler M, Dabbs E R, Averhoff B & Gottschalk G (1996) Studies on the isopropylbenzene 2,3-dioxygenase and the 3-isopropylcatechol 2,3-dioxygenase genes encoded by the linear plasmid of Rhodococcus erythropolis BD2. Microbiology 142: 3241-3251
94. Kholodii GY, Mindlin SZ, Bass IA, Yurieva OV, Minakhina SV & Nikiforov VG (1995) Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron. Mol. Microbiol. 17: 1189-1200
95. Kobayashi M, Nishiyama M, Nagasawa T, Horinouchi S, Beppu T & Yamada H (1991) Cloning, nucleotide sequence and expression in Escherichia coli of two cobalt-containing nitrile hydratase genes from Rhodococcus rhodochrous J1. Biochim. Biophys. Acta 1129: 23-33
96. Kobayashi M, Komeda M, Yanaka N, Nagasawa T & Yamada H (1992a) Nitrilase from Rhodococcus rhodochrous J1. Sequencing and overexpression of the gene and identification of an essential cysteine residue. J. Biol. Chem. 267: 20746-20751
97. Kobayashi M, Yanaka N, Nagasawa T & Yamada H (1992b) Primary structure of an aliphatic nitrile-degrading enzyme, aliphatic nitrilase, from Rhodococcus rhodochrous K22 and expression of its gene and identification of its active site residue. Biochemistry 31: 9000-9007
98. Kobayashi M, Komeda H, Nagasawa T, Nishiyama M, Horinouchi S, Beppu T, Yamada H & Shimizu S (1993) Amidase coupled with low-molecular-mass nitrile hydratase from Rhodococcus rhodochrous J1. Sequencing and expression of the gene and purification and characterization of the gene product. Eur. J. Biochem. 217: 327-336
99. Kobayashi M, Komeda H, Shimizu S, Yamada H & Beppu T (1997) Characterization and distribution of IS1164 that exists in the high molecular mass nitrile hydratase gene cluster of the industrial microbe Rhodococcus rhodochrous J1. Proc. Jpn. Acad. 73B: 104-108
100. Kolstø AB (1997) Dynamic bacterial genome organization. Mol. Microbiol. 24: 241-248
101. Komeda H, Kobayashi M & Shimizu S (1996a) A novel gene-cluster including the Rhodococcus rhodochrous J1 nhlBA genes encoding a low-molecular-mass nitrile hydratase (1- nhase) induced by its reaction product. J. Biol. Chem. 271: 15796-15802
102. Komeda H, Kobayashi M & Shimizu S (1996b) Characterization of the gene cluster of high molecular mass nitrile hydratase (L-NHase) induced by its reaction product in Rhodococcus rhodochrous J1. Proc. Natl. Acad. Sci. USA 93: 4267-4272
103. Komeda H, Hori Y, Kobayashi M & Shimizu S (1996c) Transcriptional regulation of the Rhodococcus rhodochrous J1 nitA gene encoding a nitrilase. Proc. Natl. Acad. Sci. USA 93: 10572-10577
104. Komeda H, Kobayashi M & Shimizu S (1997) A novel transporter involved in cobalt uptake. Proc. Natl. Acad. Sci. USA 94: 36-41
105. Kosono S, Maeda M, Fuji F, Arai H & Kudo T (1997) Three of the seven bphC genes of Rhodococcus erythropolis TA421, isolated from a termite ecosystem, are located on an indigenous plasmid associated with biphenyl degradation. Appl. Environ. Microbiol. 63: 3282-3285
106. Kremer L, Baulard A, Estaquier J, Poulain-Godefroy O & Locht C (1995) Green fluorescent protein as a new expression marker in mycobacteria. Mol. Microbiol. 17: 913-922
107. Kulakova AN, Stafford TM, Larkin MJ & Kulakov LA (1995) Plasmid pRTL1 controlling 1-chloroalkane degradation by Rhodococcus rhodochrous NCIMB 13064. Plasmid 33: 208-217
108. Kulakova AN, Reid KA, Larkin MJ, Allen CCR & Kulakov LA (1996) Isolation of Rhodococcus rhodochrous NCIMB13064 derivatives with new biodegradative abilities. FEMS Microbiol. Lett. 145: 227-231
109. Kulakova AN, Larkin MJ & Kulakov LA (1997) The plasmid-located haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB 13064. Microbiology 143: 109-115
110. Kulakov LA, Larkin MJ & Kulakova AN (1997) Cryptic plasmid pKA22 isolated from the naphthalene degrading derivative of Rhodococcus rhodochrous NCIMB13064. Plasmid 38: 61-69
111. Kulakov LA, Delcroix VA, Larkin MJ, Ksenzenko VN & Kulakova AN (1998) Cloning of new Rhodococcus extradiol dioxygenase genes and study of their distribution in different Rhodococcus strains. Microbiology 144: 955-963
112. Labbé D, Garnon J & Lau PCK (1997) Characterization of the genes encoding a receptor-like histidine kinase and a cognate response regulator from a biphenyl/polychlorobiphenyl-degrading bacterium, Rhodococcus sp. strain M5. J. Bacteriol. 179: 2772-2776
113. Lefebvre G, Martin N, Kilbertus G & Gay R (1978) Studies on the morphogenesis of nocardioform organisms related to the 'rhodochrous' taxon in synchronous cultures. J. Gen. Microbiol. 108: 125-131
114. Lei B & Tu S-C (1996) Gene expression, purification, and identification of a desulfurization enzyme from Rhodococcus sp. strain IGTS8 as a sulfide/sulfoxide monooxygenase. J. Bacteriol. 178: 5699-5705
115. Leskiw BK, Mevarech M, Barritt LS, Jensen SE, Henderson DJ, Hopwood DA, Bruton CJ & Chater KF (1990) Discovery of an insertion sequence, IS116, from Streptomyces clavuligerus and its relatedness to other transposable elements from actinomycetes. J. Gen. Microbiol. 136: 1251-1258
116. Li MZ, Squires CH, Monticello DJ & Childs JD (1996) Genetic analysis of the dsz promoter and associated regulatory regions of Rhodococcus erythropolis IGTS8. J. Bacteriol. 178: 6409-6418
117. Locci R & Sharples GP (1984) Morphology. In: Goodfellow M, Mordarski M & Williams ST (Eds) The Biology of the Actinomycetes (pp 165-199) Academic Press, New York
118. Lupas A, Zühl F, Tamura T, Wolf S, Nagy I, De Mot R & Baumeister W (1997) Eubacterial proteasomes. Mol. Biol. Rep. 24: 125-131
119. Masai E, Yamada A, Healey JM, Hatta T, Kimbara K, Fukuda M & Yano K (1995) Characterisation of biphenyl catabolic genes of Gram-positive polychlorinated biphenyl degrader Rhodococcus sp strain RHA1. Appl. Environ. Microbiol. 61: 2079-2085
120. Masai E, Sugiyama K, Iwashita N, Shimizu S, Hauschild J E, Hatta T, Kimbara K, Yano K & Fukuda M (1997) The bphDEF metacleavage pathway genes involved in biphenyl/polychlorinated biphenyl degradation are located on a linear plasmid and separated from the initial bphABC genes in Rhodococcus sp. strain RHA1. Gene 187: 141-149
121. Mayaux JF, Cerbelaud E, Soubrier F, Yeh P, Blanche F & Petre D (1991) Purification, cloning, and primary structure of a new enantiomer-selective amidase from a Rhodococcus strain - structural evidence for a conserved genetic coupling with nitrile hydratase. J. Bacteriol. 173: 6694-6704
122. McKay DB, Seeger M, Zielinski M, Hofer B & Timmis KN (1997) Heterologous expression of biphenyl dioxygenase-encoding genes from a gram-positive broad-spectrum polychlorinated biphenyl degrader and characterization of chlorobiphenyl oxidation by the gene products. J. Bacteriol. 179: 1924-1930
123. Meinhardt F, Schaffrath R & Larsen M (1997) Microbial linear plasmids. Appl. Microbiol. Biotech. 47: 329-336
124. Motallebi-Veshareh M, Rouch DA & Thomas CM (1990) A family of ATPases involved in active partitioning of diverse bacterial plasmids. Mol. Microbiol. 4: 1455-1463
125. Nagy I, Compernolle F, Ghys K, Vanderleyden J & De Mot R (1995a) A single cytochrome P-450 system is involved in degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine by Rhodococcus sp. NI86/21. Appl. Environ. Microbiol. 61: 2056-2060
126. Nagy I, Schoofs G, Compernolle F, Proost P, Vanderleyden J & De Mot R (1995b) Degradation of the thiocarbamate herbicide EPTC (S-ethyl dipropylcarbamothioate) and biosafening by Rhodococcus sp. NI86/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase. J. Bacteriol. 177: 676-687
127. Nagy I, Schoofs G, De Schrijver A, Vanderleyden J & De Mot R (1997a) New method for RNA isolation from actinomycetes: application to the transcriptional analysis of the alcohol oxidoreductase gene thcE in Rhodococcus and Mycobacterium. Lett. Appl. Microbiol. 25: 75-79
128. Nagy I, Schoofs G, Vanderleyden J & De Mot R (1997b) Transposition of the IS21-related element IS1415 in Rhodococcus erythropolis. J. Bacteriol. 179: 4635-4638
129. Nagy I, Schoofs G, Vanderleyden J & De Mot R (1997c). Further sequence analysis of the DNA regions with the Rhodococcus 20S proteasome structural genes reveals extensive homology with Mycobacterium leprae. DNA Seq. 7: 225-228
130. Nicholson VM & Prescott JF (1997) Restriction enzyme analysis of the virulence plasmids of VapA-positive Rhodococcus equi strains isolated from humans and horses. J. Clin. Microbiol. 35: 738-740
131. Nordmann P, Keller M, Espinasse F & Ronco E (1994) Correlation between antibiotic-resistance, phage-like particle presence, and virulence in Rhodococcus-equi human isolates. J. Clin. Microbiol. 32: 377-382
132. Oh S-H & Chater KF (1997) Denaturation of circular or linear DNA facilitates targeted integrative transformation of Streptomyces coelicolor A3(2): possible relevance to other organisms. J. Bacteriol. 179: 122-127
133. Okanishi M, Suzuki K & Umezawa H (1974) Formation and reversion of streptomycete protoplasts: cultural conditions and morphological study. J. Gen. Microbiol. 80: 389-400
134. Pelicic V, Reyrat J-M & Gicquel B (1996) Generation of unmarked directed mutations in mycobacteria, using sucrose counter-selectable vectors. Mol. Microbiol. 20: 919-925
135. Pelicic V, Jackson M, Reyrat J-M, Jacobs WR Jr, Gicquel B & Guilhot C (1997) Efficient allelic exchange and transposons mutagenesis in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 94: 10955-10960
136. Picardeau M, Varnerot A, Rauzier J, Gicquel B & Vincent V (1996) Mycobacterium xenopi IS1395, a novel insertion sequence expanding the IS256 family. Microbiology 142: 2453-2461
137. Picardeau M, Bull T J & Vincent V (1997) Identification and characterization of IS-like elements in Mycobacterium gordonae. FEMS Microbiol. Lett. 154: 95-102
138. Piddington CS, Kovacevich BR & Rambosek J (1995) Sequence and molecular characterization of a DNA region encoding the dibenzothiophene desulfurization operon of Rhodococcus sp. strain IGTS8. Appl. Environ. Microbiol. 61: 468-475
139. Pisabarro A, Correia A & Martin JF (1998) Pulsed-field gel electrophoresis analysis of the genome of Rhodococcus fuscians: genome size and linear and circular replicon composition in virulent and avirulent strains. J. Biol. Chem. 47, 29454-29459
140. Pogorelova TE, Ryabchenko LE, Sunzov NI & Yanenko AS (1996) Cobalt-dependent transcription of the nitrile hydratase gene in Rhodococcus rhodochrous M8. FEMS Microbiol. Lett. 144: 191-195
141. Prauser H (1976) Host-phage relationships in nocardioform organisms. In: Goodfellow M, Brownell GH & Serrano JA (Eds) The Biology of the Nocardiae (pp 206-284). Academic Press, London
142. Prescott JF (1991) Rhodococcus equi: an animal and human pathogen. Clin. Microbiol. Rev. 4: 20-34.
143. Quan S & Dabbs ER (1993) Nocardioform arsenic resistance plasmid characterization and improved Rhodococcus cloning vectors. Plasmid 29: 74-79
144. Radstrom P, Sköld O, Swedberg G, Flensburg J, Roy PH & Sundström L (1994) Transposon Tn5090 of plasmid R751, which carries an integron, is related to Tn7, Mu, and the retroelements. J. Bacteriol. 176: 3257-3268
145. Rainey FA, Burghardt J, Kroppenstedt RM, Klatte S & Stackebrandt E (1995) Phylogenetic analysis of the genera Rhodococcus and Nocardia and evidence for the evolutionary origin of the genus Nocardia from within the radiation of Rhodococcus species. Microbiology 141: 523-528
146. Ramakrishnan L, Tran HT, Federspiel NA & Falkow S (1997) A crtB homolog essential for photochromogenicity in Mycobacterium marinum: isolation, characterization, and gene disruption via homologous recombination. J. Bacteriol. 179: 5862-5868
147. Rathbone DA, Holt PJ, Lowe CR & Bruce NC (1997) Molecular analysis of the Rhodococcus sp. strain H1 her gene and characterization of its product, a heroin esterase, expressed in Escherichia coli. Appl. Environ. Microbiol. 63: 2062-2066
148. Roberts RJ & Macelis D (1997) REBASE-restriction enzymes and methylases. Nucleic Acids Res. 25: 248-262.
149. +: a dominant selectable marker for gene replacement in mycobacteria. Mol. Microbiol. 16: 991-1000
150. Schreiner A, Fuchs K, Lottspeich F, Poth H & Lingens F (1991) Degradation of 2-methylaniline in Rhodococcus-rhodochrous - cloning and expression of 2 clustered catechol 2,3-dioxygenase genes from strain CTM. J. Gen. Microbiol. 137: 2041-2048
151. Schupp R, Hütter R & Hopwood DA (1975) Genetic recombination in Nocardia mediterranei. J. Bacteriol. 121: 128-136
152. Scott MA, Graham BS, Verall R, Dixon R, Schaffner W & Tham KY (1995) Rhodococcus equi - an increasingly recognised opportunist pathogen. Am. J. Clin. Pathol. 103: 649-655
153. Sensfuss C, Reh M & Schlegel HG (1986) No correlation exists between the conjugative transfer of the autotrophic character and that of plasmids in Nocardia opaca strains. J. Gen. Microbiol. 132: 779-1007
154. Shao ZQ & Behki R (1995) Cloning of the genes for degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine from Rhodococcus sp. strain TE1. Appl. Environ. Microbiol. 61: 2061-2065
155. Shao ZQ & Behki R (1996) Characterization of the expression of the thcB gene, coding for a pesticide-degrading cytochrome P-450 in Rhodococcus strains. Appl. Environ. Microbiol. 62: 403-407
156. Shao ZQ, Dick W A & Behki R M (1995a) An improved Escherichia coli-Rhodococcus shuttle vector and plasmid transformation in Rhodococcus spp. using electroporation. Lett. Appl. Microbiol. 21: 261-266
157. Shao ZQ, Seffens W, Mulbry W & Behki R M (1995b) Cloning and expression of the s-triazine hydrolase gene (frzA) from Rhodococcus corallinus and development of Rhodococcus recombinant strains capable of dealkylating and dechlorinating the herbicide atrazine. J. Bacteriol. 177: 5748-5755
158. Shinohara M & Itoh T (1996) Specificity determinants in interaction of the initiator (Rep) proteins with the origins in the plasmids ColE2-P9 and ColE3-CA38 identified by chimera analysis. J. Mol. Biol. 257: 290-300
159. Singer MEV & Finnerty WR (1988) Construction of an Escherichia coli-Rhodococcus shuttle vector and plasmid transformation in Rhodococcus species. J. Bacteriol. 170: 638-645
160. Stark WM, Boocock MR & Sherratt DJ (1992) Catalysis by site-specific recombinases. Trends Genet. 8: 432-439
161. Stolt P & Stoker NG (1996a) Functional definition of regions necessary for replication and incompatibility in the Mycobacterium fortuitum plasmid pAL5000. Microbiology 142: 2795-2802
162. Stolt P & Stoker NG (1996b) Protein - DNA interactions in the ori region of the Mycobacterium fortuitum plasmid pAL5000. J. Bacteriol. 178: 6693-6700
163. Stolt P & Stoker NG (1997) Mutational analysis of the regulatory region of the Mycobacterium plasmid pAL5000. Nucleic Acids Res. 25: 3840-3846
164. Strohl W. R. (1992) Compilation and analysis of DNA sequences associated with apparent streptomycete promoters. Nucleic Acids Res. 20: 961-974
165. Sunairi M, Watanabe T, Oda H, Murooka H & Nakajima M (1993) Characterization of the genome of the Rhodococcus rhodochrous bacteriophage NJL. Appl. Environ. Microbiol. 59: 97-100
166. Takai S (1997) Epidemiology of Rhodococcus equi infections: a review. Vet. Microbiol. 56: 167-176
167. Takai S, Sekizaki T, Ozawa T, Sugawara T, Watanabe Y & Tsubaki S (1991) Association between a large plasmid and 15-kilodalton to 17- kilodalton antigens in virulent Rhodococcus equi. Infect. Immun. 59: 4056-4060
168. Takai S, Watanabe Y, Ikeda T, Ozawa T, Matsukura S, Tamada Y, Tsubaki S & Sekizaki T (1993) Virulence-associated plasmids in Rhodococcus equi. J. Clin. Microbiol. 31: 1726
169. Takai S, Sasaki Y, Ikeda T, Uchida Y, Tsubaki S & Sekizaki T (1994) Virulence of Rhodococcus equi isolates from patients with and without aids. J. Clin. Microbiol. 32: 457-462
170. Takai S, Madarame H, Matsumoto C, Inoue M, Sasaki Y, Hasegawa Y, Tsubaki S & Nakane A (1995a) Pathogenesis of Rhodococcus equi infection in mice - roles of virulence plasmids and granulomagenic activity of bacteria. FEMS Immunol. Med. Microbiol. 11: 181-190
171. Takai S, Imai Y, Fukunaga N, Uchida Y, Kamisawa K, Sasaki Y, Tsubaki S & Sekizaki T (1995b) Identification of virulence-associated antigens and plasmids in Rhodococcus-equi from patients with AIDS. J. Infect. Dis. 172: 1306-1310
172. Takechi S. & Itoh T (1995) Initiation of unidirectional ColE2 DNA replication by a unique priming mechanism. Nucleic Acids Res. 23: 4196-4201
173. Takechi S, Matsui H & Itoh T (1995) Primer RNA synthesis by plasmid-specified Rep protein for initiation of ColE2 DNA replication. EMBO. 14: 5141-5147
174. Tam AC, Behki RM & Kahn SU (1987) Isolation and characterisation of an EPTC-degrading Arthrobacter strain and evidence for plasmid-associated EPTC degradation. Appl. Environ. Microbiol. 53: 1088-1093
175. Tamura T, Nagy I, Lupas A, Lottspeich F, Cejka Z, Schoofs G, Tanaka K, De Mot R & Baumeister W (1995) The first characterization of a eubacterial proteasome: the 20S complex of Rhodococcus. Curr. Biol. 5: 766-774
176. Vereecke D (1997) Leafy gall induction by Rhodococcus fascians. PhD Thesis, University of Ghent, Belgium, 196 pp.
177. Vereecke D, Villarroel R, Vanmontagu M & Desomer J, (1994) Cloning and sequence-analysis of the gene encoding isocitrate lyase from Rhodococcus fascians. Gene: 145, 109-114
178. Vieira J & Messing J (1982) The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19: 159-268
179. Voeykova T, Tabakov V, Mkrtumyan N, Yanenko A & Ryabchenko L (1994) Conjugative transfer of plasmid pTO1 from Escherichia coli to Rhodococcus spp. Biotechnol. Lett. 16: 555-560
180. Waksman SA (1950) The Actinomycetes. Chimica Botanica Company Waltham, Massachusetts, USA
181. Wang Y, Garnon J, Labbé D, Bergeron H & Lau PCK (1995) Sequence and expression of the bpdC1C2BADE genes involved in the initial steps of biphenyl/chlorobiphenyl degradation by Rhodococcus sp. M5. Gene 164: 117-122
182. Warhurst AM & Fewson CA (1994) Biotransformations catalyzed by the genus Rhodococcus. Crit. Rev. Biotechnol. 14: 29-73
183. Williams DR & Thomas CM (1992) Active partitioning of bacterial plasmids. J. Gen. Microbiol. 138: 1-6
184. Williams ST, Sharples GP, Serrano JA, Serrano AA & Lacey J (1976) The micromorpholpgy and fine structure of nocardioform organisms. In: Goodfellow M, Brownell GH & Serrano JA (Eds) The Biology of the Nocardiae (pp 103-140). Academic Press, London
185. Wolf S, Nagy I, Lupas A, Pfeifer G, Cejka Z, Müller S, Engel A, De Mot R & Baumeister W (1998) Characterization of ARC, a divergent member of the AAA ATPase family from Rhodococcus erythropolis. J. Mol. Biol. 277: 13-25
186. Yoon JH, Lee JS, Shin YK, Park YH & Lee ST (1997) Reclassification of Nocaridioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis. Int. J. Syst. Bacteriol. 47: 904-907
187. Zheng H, Thachuk-Saad O & Prescott JF (1997) Development of a Rhodococcus equi-Escherichia coli plasmid shuttle vector. Plasmid 38: 180-187
188. Zühl F, Tamura T, Dolenc I, Cejka Z, Nagy I, De Mot R & Baumeister W (1997) Subunit topology of the Rhodococcus proteasome. FEBS. Lett. 400: 83-90