Applied aspects of Rhodococcus genetics

Adams JN (1964) Recombination between Nocardia erythropolis and canicruria. J. Bacteriol. 88: 865–876 Adams JN & Bradley SG (1963) Recombination events in the bacterial genus Nocardia. Science 140: 1392–1394 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 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 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 Archer JAC & Griffiths H (1995) Linear plasmids in Rhodococcus corallina V49. J. Cell. Biochem. NoS21A p45 abstract Assaf NA & Dick WA (1993) Spheroplast formation and plasmid isolation from Rhodococcus spp. Biotechniques 15: 1010–1015 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 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 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 Asturias JA, D & #x00ED;az E & Timmis KN (1995) The evolutionary relationship of biphenyl dioxygenase from Gram-positive Rhodococcus globerulus P6 to multicomponent dioxygenases from Gram-negative bacteria. Gene 156: 11–18 Baltz RH & Hosted TH (1996) Molecular genetic methods for improving secondary-metabolite production in actinomycetes. Trends Biotechnol. 14: 245–250 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 Baril C, Richaud C, Baranton g & Saint Girons IS (1989) Linear chromosome of Borrelia burgdorferi. Res. Microbiol. 140: 507–516 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 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 Behki RM (1991) Di-allate degradation by an EPTC-degrading Rhodococcus, and in eptc-treated soil. Soil Biol. Biochem. 23: 789–793 Behki R, Topp E, Dick W & Germon P (1993) Metabolism of the herbicide atrazine by Rhodococcus strains. Appl. Environ. Microbiol. 59: 1955–1959 Behki RM, Topp EE & Blackwell BA (1994) Ring hydroxylation of N-methylcarbamate insecticides by Rhodococcus TE1. J. Agric. Fd. Chem. 42: 1375–1378 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 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 Blakey 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 Bourn WR & Babb B (1995) Computer assisted identification and classification of streptomycete promoters. Nucleic Acids Res. 23: 3696–3703 Briglia M, Eggen RIL, van Elsas D & de Vos WM (1994) Phylogenetic evidence for transfer of pentachlorophenol-mineralizing Rhodococcus chlorophenolicus PCP-IT to the genus Mycobacterium. Int. J. Syst. Bacteriol. 44: 494–498 Brownell GH (1974) A new nocardial mating strain. Am. Soc. Microbiol. Abstract p 41 Brownell GH & Adams JN (1968) Linkage and segregation of a mating type specific phage and resistance chararacters in nocardial recombinants. Genetics 60: 437–448 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 Brownell GH & Kelly KL (1969) Inheritance of mating type factors in nocardial recombinants. J. Bacteriol. 99: 25–36 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 Brownell GH, Enquist LW & Denniston-Thompson K (1980) An analysis of the genome of the actinophage ?EC. Gene 12: 311–314 Brownell GH, Saba JA, Denniston-Thompson K & Enquist LW (1982) The development of a Rhodococcus-actinophage cloning system. Dev. Ind. Microbiol. 23: 287–298 Brunhuber NM, Banerjee A, Jacobs WR Jr. & Blanchard JS (1994) Cloning, sequencing, and expression of Rhodococcus l-phenylalanine dehydrogenase. Sequence comparisons to amino acid dehydrogenases. J. Biol. Chem. 269: 16203–16211 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 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 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 Chen CW (1996) Complications and implications of linear bacterial chromosomes. Trends Genet. 12: 192–196 Clark JE & Brownell GH (1972) Genophore homologies among compatible nocardiae. J. Bacteriol. 109: 720–729 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 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 Crockett JK & Brownell GH (1972) Isolation and characterisation of a lysogenic strain of Nocardia erythropolis. J. Gen. Virol. 10: 737–742 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 Dabbs ER (1987) A generalized transducing bacteriophage for Rhodococcus erythropolis. Mol. Gen Genet. 206: 116–120 Dabbs ER (1998) Cloning of genes that have environmental and clinical importance from rhodococci and related bacteria. Antonie van Leeuwenhoek 74: 155–168 Dabbs ER & Sole GJ (1988) Plasmid-borne resistance to arsenate, arsenite, cadmium and chloramphenicol in a Rhodococcus species. Mol. Gen. Genet. 211: 148–154 Dabbs ER, Gowan B & Andersen SJ (1990) Nocardioform arsenic resistance plasmids and construction of Rhodococcus cloning vectors. Plasmid 23: 242–247 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 Dabrock B, Kesseler 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 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 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 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 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 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 Denome SA & Young KD (1995) Identification and activity of two insertion-sequence elements in Rhodococcus sp strain IGTS8. Gene 161: 33–38 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 Denome SA, Oldfield C, Nash LJ & Young KD (1994) Characterization of the desulfurization genes from Rhodococcus sp. strain IGTS8. J. Bacteriol. 176: 6707–6716 De Schrijver A, Nagy I, Schoofs G, Proost P, Vanderleyden J, van P & #x00E9;e K-H & De Mot R (1997) The thiocarbamate herbicide-inducible nonheme chloroperoxidase of Rhodococcus erythropolis NI86/21. Appl. Environ. Microbiol. 634: 1911–1916 Desomer J, Dhaese P & Van Montagu M (1988) Conjugative transfer of cadmium resistance plasmids in Rhodococcus fascians strains. J. Bacteriol. 170: 2401–2405 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 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 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 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 Eltis LD & Bolin JT (1996) Evolutionary relationship among extradiol dioxygenases. J. Bacteriol. 178: 5930–5937 Eulberg D, Golovleva LA & Schlomann M (1997) Characterisation of catechol catabolic genes from Rhodococcus erythropolis 1CP. J. Bacteriol. 179: 370–381 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 Finnerty WR (1992) The biology and genetics of the genus Rhodococcus. Ann. Rev. Microbiol. 46: 193–218 Gallardo ME, Ferr & #x00E1;ndez A, de Lorenzo V, Garc & #x00ED;a JL & D & #x00ED;az E (1997) Designing recombinant Pseudomonas strains to enhance biodesulfurization. J. Bacteriol. 179: 7156–7160 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 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 Goodfellow M, Alderson G & Chun I (1998) Rhodococcal systematics: problems and developments. Antonie van Leeuwenhoek 74: 3–20 Goodfellow M (1989) Suprageneric classification of actinomycetes. In: Williams ST, Sharpe ME & Holt JG (Eds) Bergey & #x2019;s Manual of Systematic Bacteriology, Vol 4 (pp 2333–2339). Williams and Wilkins, Baltimore Gowan B & Dabbs ER (1994) Identification of DNA involved in Rhodococcus chromosomal conjugation and self-incompatibility. FEMS Microbiol. Lett. 115: 45–50 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 & #x2019;s disease isolate of Mycobacterium paratuberculosis. Nucleic Acids Res. 17: 9063–9073 Grzeszik C, L & #x00FC;bbers M, Reh M & Schlegel HG (1997) Genes encoding the NAD-reducing hydrogenase of Rhodococcus opacus MR11. Microbiology 143: 1271–1286 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 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. H & #x00E4;ggblom 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 Hall RM 1997. Mobile gene cassettes and integrons: moving antibiotic resistance genes in gram-negative bacteria. Ciba Found. Symp. 207: 192–202 Hall RM, Brown HJ, Brookes DE & Stokes HW (1994) Integrons found in different locations have identical 50-ends but variable 30 ends. J. Bacteriol. 176: 6286–6294 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 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 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 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 Hinnebusch J & Tilly K (1993) Linear plasmids and chromosomes in bacteria. Mol. Microbiol. 10: 917–922 Hiraga S-I, Sugiyama T & Itoh T (1994) Comparative analysis of the replicon region of eleven ColE2-related plasmids. J. Bacteriol. 176: 7233–7243 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 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 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 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 J & #x00E4;ger W, Sch & #x00E4;fer A, P & #x00FC;hler 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 J & #x00E4;ger W, Sch & #x00E4;fer A, Kalinowski J & P & #x00FC;hler A (1995) Isolation of insertion elements from Gram-positive Brevibacterium, Corynebacterium and Rhodococcus strains using the Bacillus subtilis sacB gene as a positive selection marker. FEMS Microbiol. Lett. 126: 1–6 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 Kasweck KL & Little ML (1982) Genetic recombination in Nocardia asteroides. J. Bacteriol. 149: 403–406 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 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 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 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 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 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 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 Kolst & #x00F8; AB (1997) Dynamic bacterial genome organization. Mol. Microbiol. 24: 241–248 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 (l-nhase) induced by its reaction product. J. Biol. Chem. 271: 15796–15802 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 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 Komeda H, Kobayashi M & Shimizu S (1997) A novel transporter involved in cobalt uptake. Proc. Natl. Acad. Sci. USA 94: 36–41 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 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 Kulakova AN, Stafford TM, Larkin MJ & Kulakov LA (1995) Plasmid pRTL1 controlling 1-chloroalkane degradation by Rhodococcus rhodochrous NCIMB 13064. Plasmid 33: 208–217 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 Kulakova AN, Larkin MJ & Kulakov LA (1997) The plasmidlocated haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB 13064. Microbiology 143: 109–115 Kulakov LA, Larkin MJ & Kulakova AN (1997) Cryptic plasmid pKA22 isolated from the naphthalene degrading derivative of Rhodococcus rhodochrous NCIMB13064. Plasmid 38: 61–69 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 Labb & #x00E9; 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 Lefebvre G, Martin N, Kilbertus G & Gay R (1978) Studies on the morphogenesis of nocardioform organisms related to the & #x2018;rhodochrous & #x2019; taxon in synchronous cultures. J. Gen. Microbiol. 108: 125–131 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 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 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 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 Lupas A, Z & #x00FC;hl F, Tamura T, Wolf S, Nagy I, De Mot R & Baumeister W (1997) Eubacterial proteasomes. Mol. Biol. Rep. 24: 125–131 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 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 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 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 Meinhardt F, Schaffrath R & Larsen M (1997) Microbial linear plasmids. Appl. Microbiol. Biotech. 47: 329–336 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 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 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 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 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 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 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 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 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 Okanishi M, Suzuki K & Umezawa H (1974) Formation and reversion of streptomycete protoplasts: cultural conditions and morphological study. J. Gen. Microbiol. 80: 389–400 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 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 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 Picardeau M, Bull T J & Vincent V (1997) Identification and characterization of IS-like elements in Mycobacterium gordonae. FEMS Microbiol. Lett. 154: 95–102 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 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 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 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 Prescott JF (1991) Rhodococcus equi: an animal and human pathogen. Clin. Microbiol. Rev. 4: 20–34. Quan S & Dabbs ER (1993) Nocardioform arsenic resistance plasmid characterization and improved Rhodococcus cloning vectors. Plasmid 29: 74–79 Rådstr & #x00F6;m P, Sk & #x00F6;ld O, Swedberg G, Flensburg J, Roy PH & Sundstr & #x00F6;m L (1994) Transposon Tn5090 of plasmid R751, which carries an integron, is related to Tn 7, Mu, and the retroelements. J. Bacteriol. 176: 3257–3268 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 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: 5862–868 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 Roberts RJ & Macelis D (1997) REBASE-restriction enzymes and methylases. Nucleic Acids Res. 25: 248–262. Sander P, Meier A & B & #x00F6;ttger EC (1995) rpsL +: a dominant selectable marker for gene replacement in mycobacteria. Mol. Microbiol. 16: 991–1000 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 Schupp R, H & #x00FC;tter R & Hopwood DA (1975) Genetic recombination in Nocardia mediterranei. J. Bacteriol. 121: 128–136 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 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 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 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 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 Shao ZQ, Seffens W, Mulbry W & Behki R M (1995b) Cloning and expression of the s-triazine hydrolase gene (trzA) from Rhodococcus corallinus and development of Rhodococcus re-combinant strains capable of dealkylating and dechlorinating the herbicide atrazine. J. Bacteriol. 177: 5748–5755 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 Singer MEV & Finnerty WR (1988) Construction of an Escherichia coli-Rhodococcus shuttle vector and plasmid transformation in Rhodococcus species. J. Bacteriol. 170: 638–645 Stark WM, Boocock MR & Sherratt DJ (1992) Catalysis by site-specific recombinases. Trends Genet. 8: 432–439 Stolt P & Stoker NG (1996a) Functional definition of regions necessary for replication and incompatibility in the Mycobacterium fortuitum plasmid pAL5000. Microbiology 142: 2795–2802 Stolt P & Stoker NG (1996b) Protein—DNA interactions in the ori region of the Mycobacterium fortuitum plasmid pAL5000. J. Bacteriol. 178: 6693–6700 Stolt P & Stoker NG (1997) Mutational analysis of the regulatory region of the Mycobacterium plasmid pAL5000. Nucleic Acids Res. 25: 3840–3846 Strohl W. R. (1992) Compilation and analysis of DNA sequences associated with apparent streptomycete promoters. Nucleic Acids Res. 20: 961–974 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 Takai S (1997) Epidemiology of Rhodococcus equi infections: a review. Vet. Microbiol. 56: 167–176 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 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 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 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 Takai S, Imai Y, Fukunaga N, Uchida Y, Kamisawa K, Sasaki Y, Tsubaki S & Sekizaki T (1995b) Identification of virulenceassociated antigens and plasmids in Rhodococcus-equi from patients with AIDS. J. Infect. Dis. 172: 1306–1310 Takechi S. & Itoh T (1995) Initiation of unidirectional ColE2 DNA replication by a unique priming mechanism. Nucleic Acids Res. 23: 4196–4201 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 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 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 Vereecke D (1997) Leafy gall induction by Rhodococcus fascians. PhD Thesis, University of Ghent, Belgium, 196 pp. 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 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 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 Waksman SA (1950) The Actinomycetes. Chimica Botanica Company Waltham, Massachusetts, USA Wang Y, Garnon J, Labb & #x00E9; 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 Warhurst AM & Fewson CA (1994) Biotransformations catalyzed by the genus Rhodococcus. Crit. Rev. Biotechnol. 14: 29–73 Williams DR & Thomas CM (1992) Active partitioning of bacterial plasmids. J. Gen. Microbiol. 138: 1–6 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 Wolf S, Nagy I, Lupas A, Pfeifer G, Cejka Z, M & #x00FC;ller 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 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 Zheng H, Thachuk-Saad O & Prescott JF (1997) Development of a Rhodococcus equi–Escherichia coli plasmid shuttle vector. Plasmid 38: 180–187 Z & #x00FC;hl 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