Advertisement

Genomes and Plasmids in Rhodococcus

  • Michael J. LarkinEmail author
  • Leonid A. Kulakov
  • Christopher C. R. Allen
Chapter
Part of the Microbiology Monographs book series (MICROMONO, volume 16)

Abstract

Members of the genus Rhodococcus are a very diverse group of bacteria that are found in many different niches. They are commonly found in the wider environment, but are also associated with pathogenesis in plants and mammals, including humans. They possess the ability to degrade a large number of organic compounds including some of the most difficult compounds with regard to recalcitrance and toxicity. This ability appears to be based upon the acquisition of a wide and diverse range of catabolic genes by cells that can withstand stressful conditions. Recent completion of genome sequences and analysis has revealed that they have very large genomes (up to 9.7 Mbp) and many possess genes that encode multiple catabolic enzymes and pathways. In addition to smaller circular plasmids, they also harbour many large linear plasmids that contribute to their substrate diversity, and these appear to be vehicles for the “mass storage” of numerous catabolic genes. The presence of multiple catabolic pathways and gene homologues seems to be the basis of their catabolic versatility. However, many of the genes associated with the pathways are dispersed around the genome, and it is becoming clear that their co-regulation of gene expression is a feature of how the rhodococci adapt to utilise many substrates.

Keywords

Mobile Genetic Element Catabolic Gene Linear Plasmid Circular Plasmid Rhodococcus Erythropolis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Adams JN (1964) Recombination between Nocardia erythropolis and canicruria. J Bacteriol 88:865–876PubMedGoogle Scholar
  2. Adams JN, Bradley SG (1963) Recombination events in the bacterial genus Nocardia. Science 140:1392–1394PubMedCrossRefGoogle Scholar
  3. 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 179:6145–6153PubMedGoogle Scholar
  4. Bell KS, Philp JC, Aw DW, Christofi N (1998) The genus Rhodococcus. J Appl Microbiol 85:195–210PubMedCrossRefGoogle Scholar
  5. Brownell GH, Adams JN (1968) Linkage and segregation of a mating type specific phage and resistance chararacters innocardial recombinants. Genetics 60:437–448PubMedGoogle Scholar
  6. Brownell GH, Denniston K (1984) Genetics of the nocardioform bacteria. In: Goodfellow M, Mordarski M, Williams ST (eds) The biology of the Actinomycetes. Academic Press, New York, pp 201–208Google Scholar
  7. Brownell GH, Kelly KL (1969) Inheritance of mating type factors in nocardial recombinants. J Bacteriol 99:25–36PubMedGoogle Scholar
  8. Clark JE, Brownell GH (1972) Genophore homologies among compatible nocardiae. J Bacteriol 109:720–729PubMedGoogle Scholar
  9. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544PubMedCrossRefGoogle Scholar
  10. Crespi M, Messens E, Caplan AB, van Montagu M, Desomer J (1992) Fasciation induction by the phytopathogen Rhodococcus fascians depends upon a linear plasmid encoding a cytokinin synthase gene. EMBO J 11:795–804PubMedGoogle Scholar
  11. 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 60:853–860PubMedGoogle Scholar
  12. 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(Pt 10):3137–3147PubMedCrossRefGoogle Scholar
  13. de Vries J, Wackernagel W (2002) Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proc Natl Acad Sci U S A 99:2094–2099PubMedCrossRefGoogle Scholar
  14. Denger K, Ruff J, Schleheck D, Cook AM (2004) Rhodococcus opacus expresses the xsc gene to utilize taurine as a carbon source or as a nitrogen source but not as a sulfur source. Microbiology 150:1859–1867PubMedCrossRefGoogle Scholar
  15. Denis-Larose C, Labbe D, Bergeron H, Jones AM, Greer CW, Al-Hawari J, Grossman MJ, Sankey BM, Lau PC (1997) Conservation of plasmid-encoded dibenzothiophene desulfurization genes in several rhodococci. Appl Environ Microbiol 63:2915–2919PubMedGoogle Scholar
  16. Denome SA, Young KD (1995) Identification and activity of two insertion sequence elements in Rhodococcus sp. strain IGTS8. Gene 161:33–38PubMedCrossRefGoogle Scholar
  17. Desomer J, Crespi M, Van Montagu M (1991) Illegitimate integration of non-replicative vectors in the genome of Rhodococcus fascians upon electrotransformation as an insertional mutagenesis system. Mol Microbiol 5:2115–2124PubMedCrossRefGoogle Scholar
  18. Fernandes PJ, Powell JA, Archer JA (2001) Construction of Rhodococcus random mutagenesis libraries using Tn5 transposition complexes. Microbiology 147:2529–2536PubMedGoogle Scholar
  19. Finnerty WR (1992) The biology and genetics of the genus Rhodococcus. Annu Rev Microbiol 46:193–218PubMedCrossRefGoogle Scholar
  20. Gay P, Le Coq D, Steinmetz M, Berkelman T, Kado CI (1985) Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J Bacteriol 164:918–921PubMedGoogle Scholar
  21. Goncalves ER, Hara H, Miyazawa D, Davies JE, Eltis LD, Mohn WW (2006) Transcriptomic assessment of isozymes in the biphenyl pathway of Rhodococcus sp. strain RHA1. Appl Environ Microbiol 72:6183–6193PubMedCrossRefGoogle Scholar
  22. Goodfellow M (1989) Suprageneric classification of actinomycetes. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s Manual, vol 4. Williams and Wilkinsons, Baltimore, pp 2333–2339Google Scholar
  23. Gowan B, Dabbs ER (1994) Identification of DNA involved in Rhodococcus chromosomal conjugation and self-incompatibility. FEMS Microbiol Lett 115:45–50PubMedCrossRefGoogle Scholar
  24. Grund E, Denecke B, Eichenlaub R (1992) Naphthalene degradation via salicylate and gentisate by Rhodococcus sp. strain B4. Appl Environ Microbiol 58:1874–1877PubMedGoogle Scholar
  25. Grzeszik C, Lubbers M, Reh M, Schlegel HG (1997) Genes encoding the NAD-reducing hydrogenase of Rhodococcus opacus MR11. Microbiology 143(Pt 4):1271–1286PubMedCrossRefGoogle Scholar
  26. Gurtler V, Mayall BC, Seviour R (2004) Can whole genome analysis refine the taxonomy of the genus Rhodococcus? FEMS Microbiol Rev 28:377–403PubMedCrossRefGoogle Scholar
  27. Hara H, Eltis LD, Davies JE, Mohn WW (2007) Transcriptomic analysis reveals a bifurcated terephthalate degradation pathway in Rhodococcus sp. strain RHA1. J Bacteriol 189:1641–1647PubMedCrossRefGoogle Scholar
  28. Hinnebusch J, Tilly K (1993) Linear plasmids and chromosomes in bacteria. Mol Microbiol 10:917–922PubMedCrossRefGoogle Scholar
  29. Honda K, Yamashita S, Nakagawa H, Sameshima Y, Omasa T, Kato J, Ohtake H (2008) Stabilization of water-in-oil emulsion by Rhodococcus opacus B-4 and its application to biotransformation. Appl Microbiol Biotechnol 78:767–773PubMedCrossRefGoogle Scholar
  30. Ishikawa J, Yamashita A, Mikami Y, Hoshino Y, Kurita H, Hotta K, Shiba T, Hattori M (2004) The complete genomic sequence of Nocardia farcinica IFM 10152. Proc Natl Acad Sci U S A 101:14925–14930PubMedCrossRefGoogle Scholar
  31. Iwasaki T, Miyauchi K, Masai E, Fukuda M (2006) Multiple-subunit genes of the aromatic-ring-hydroxylating dioxygenase play an active role in biphenyl and polychlorinated biphenyl degradation in Rhodococcus sp. strain RHA1. Appl Environ Microbiol 72:5396–5402PubMedCrossRefGoogle Scholar
  32. Iwasaki T, Takeda H, Miyauchi K, Yamada T, Masai E, Fukuda M (2007) Characterization of two biphenyl dioxygenases for biphenyl/PCB degradation in A PCB degrader, Rhodococcus sp. strain RHA1. Biosci Biotechnol Biochem 71:993–1002PubMedCrossRefGoogle Scholar
  33. Jager W, Schafer A, Kalinowski J, Puhler 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 126:1–6PubMedCrossRefGoogle Scholar
  34. Kalkus J, Reh M, Schlegel HG (1990) Hydrogen autotrophy of Nocardia opaca strains is encoded by linear megaplasmids. J Gen Microbiol 136:1145–1151PubMedGoogle Scholar
  35. Kalkus J, Dorrie C, Fischer D, Reh M, Schlegel HG (1993) The giant linear plasmid pHG207 from Rhodococcus sp. encoding hydrogen autotrophy: characterization of the plasmid and its termini. J Gen Microbiol 139:2055–2065PubMedGoogle Scholar
  36. Kalkus J, Menne R, Reh M, Schlegel HG (1998) The terminal structures of linear plasmids from Rhodococcus opacus. Microbiology 144(Pt 5):1271–1279PubMedCrossRefGoogle Scholar
  37. Kim D, Kim YS, Kim SK, Kim SW, Zylstra GJ, Kim YM, Kim E (2002) Monocyclic aromatic hydrocarbon degradation by Rhodococcus sp. strain DK17. Appl Environ Microbiol 68:3270–3278PubMedCrossRefGoogle Scholar
  38. Kim D, Chae JC, Zylstra GJ, Sohn HY, Kwon GS, Kim E (2005) Identification of two-component regulatory genes involved in o-xylene degradation by Rhodococcus sp. strain DK17. J Microbiol 43:49–53PubMedGoogle Scholar
  39. Kitagawa W, Miyauchi K, Masai E, Fukuda M (2001) Cloning and characterization of benzoate catabolic genes in the gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. J Bacteriol 183:6598–6606PubMedCrossRefGoogle Scholar
  40. Knoppova M, Phensaijai M, Vesely M, Zemanova M, Nesvera J, Patek M (2007) Plasmid vectors for testing in vivo promoter activities in Corynebacterium glutamicum and Rhodococcus erythropolis. Curr Microbiol 55:234–239PubMedCrossRefGoogle Scholar
  41. Komeda H, Hori Y, Kobayashi M, Shimizu S (1996a) Transcriptional regulation of the Rhodococcus rhodochrous J1 nitA gene encoding a nitrilase. Proc Natl Acad Sci U S A 93:10572–10577PubMedCrossRefGoogle Scholar
  42. Komeda H, Kobayashi M, Shimizu S (1996b) Characterization of the gene cluster of high-molecular-mass nitrile hydratase (H-NHase) induced by its reaction product in Rhodococcus rhodochrous J1. Proc Natl Acad Sci U S A 93:4267–4272PubMedCrossRefGoogle Scholar
  43. Konig C, Eulberg D, Groning J, Lakner S, Seibert V, Kaschabek SR, Schlomann M (2004) A linear megaplasmid, p1CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP. Microbiology 150:3075–3087PubMedCrossRefGoogle Scholar
  44. Kostichka K, Tao L, Bramucci M, Tomb JF, Nagarajan V, Cheng Q (2003) A small cryptic plasmid from Rhodococcus erythropolis: characterization and utility for gene expression. Appl Microbiol Biotechnol 62:61–68PubMedCrossRefGoogle Scholar
  45. Kulakov LA, Larkin MJ (2002) Genomic organization of Rhodococcus. In: Danchin A (ed) Genomics of GC-rich gram-positive bacteria. Caister Academic Press, Norfolk, UK, pp 15–46Google Scholar
  46. Kulakov LA, Larkin MJ, Kulakova AN (1997) Cryptic plasmid pKA22 isolated from the naphthalene degrading derivative of Rhodococcus rhodochrous NCIMB13064. Plasmid 38:61–69PubMedCrossRefGoogle Scholar
  47. Kulakov LA, Poelarends GJ, Janssen DB, Larkin MJ (1999) Characterization of IS2112, a new insertion sequence from Rhodococcus, and its relationship with mobile elements belonging to the IS110 family. Microbiology 145(Pt 3):561–568PubMedCrossRefGoogle Scholar
  48. Kulakov LA, Chen S, Allen CC, Larkin MJ (2005) Web-type evolution of Rhodococcus gene clusters associated with utilization of naphthalene. Appl Environ Microbiol 71:1754–1764PubMedCrossRefGoogle Scholar
  49. Kulakova AN, Stafford TM, Larkin MJ, Kulakov LA (1995) Plasmid pRTL1 controlling 1-chloroalkane degradation by Rhodococcus rhodochrous NCIMB13064. Plasmid 33:208–217PubMedCrossRefGoogle Scholar
  50. Labbe D, Garnon J, Lau PC (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 179:2772–2776PubMedGoogle Scholar
  51. Larkin MJ, De Mot R, Kulakov LA, Nagy I (1998) Applied aspects of Rhodococcus genetics. Antonie Van Leeuwenhoek 74:133–153PubMedCrossRefGoogle Scholar
  52. Larkin MJ, Kulakov LA, Allen CCR (2005) Biogegradation and Rhodococcus – masters of catabolic versatility. Curr Opin Biotechnol 16:282–290PubMedCrossRefGoogle Scholar
  53. Larkin MJ, Allen CCR, Kulakov LA (2006) Biodegradation by members of the genus Rhodococcus: biochemistry, physiology, and genetic adaptation. Adv Appl Microbiol 59:1–28PubMedCrossRefGoogle Scholar
  54. Leahy JG, Batchelor PJ, Morcomb SM (2003) Evolution of the soluble diiron monooxygenases. FEMS Microbiol Rev 27:449–479PubMedCrossRefGoogle Scholar
  55. LeBlanc JC, Goncalves ER, Mohn WW (2008) Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol 74:2627–2636PubMedCrossRefGoogle Scholar
  56. Lessard PA, O'Brien XM, Ahlgren NA, Ribich SA, Sinskey AJ (1999) Characterization of IS1676 from Rhodococcus erythropolis SQ1. Appl Microbiol Biotechnol 52:811–819PubMedCrossRefGoogle Scholar
  57. Letek M, Ocampo-Sosa AA, Sanders M, Fogarty U, Buckley T, Leadon DP, Gonzalez P, Scortti M, Meijer WG, Parkhill J, Bentley S, Vazquez-Boland JA (2008) Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids. J Bacteriol 190:5797–5805PubMedCrossRefGoogle Scholar
  58. Locci R, Sharples GP (1984) Morphology. In: Goodfellow M, Mordarski M, Williams ST (eds) The biology of the Actinomycetes. Academic Press, New York, pp 165–199Google Scholar
  59. Mahillon J, Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62:725–774PubMedGoogle Scholar
  60. Masai E, Yamada A, Healy JM, Hatta T, Kimbara K, Fukuda M, Yano K (1995) Characterization of biphenyl catabolic genes of gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. Appl Environ Microbiol 61:2079–2085PubMedGoogle Scholar
  61. Matsui T, Saeki H, Shinzato N, Matsuda H (2007) Analysis of the 7.6-kb cryptic plasmid pNC500 from Rhodococcus rhodochrous B-276 and construction of Rhodococcus-E. coli shuttle vector. Appl Microbiol Biotechnol 74:169–175PubMedCrossRefGoogle Scholar
  62. McLeod MP, Eltis LD (2008) Genomic insights into the aerobic pathways for degradation of organic pollutants. In: Anonymous (ed) Microbial biodegradation: genomics and molecular biology, 1st edn. Caister Academic Press, UKGoogle Scholar
  63. McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD (2006) The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A 103:15582–15587PubMedCrossRefGoogle Scholar
  64. Na KS, Kuroda A, Takiguchi N, Ikeda T, Ohtake H, Kato J (2005) Isolation and characterization of benzene-tolerant Rhodococcus opacus strains. J Biosci Bioeng 99:378–382PubMedCrossRefGoogle Scholar
  65. Nagy I, Schoofs G, Vanderleyden J, De Mot R (1997) Transposition of the IS21-related element IS1415 in Rhodococcus erythropolis. J Bacteriol 179:4635–4638PubMedGoogle Scholar
  66. Navarro-Llorens JM, Patrauchan MA, Stewart GR, Davies JE, Eltis LD, Mohn WW (2005) Phenylacetate Catabolism in Rhodococcus sp. Strain RHA1: a Central Pathway for Degradation of Aromatic Compounds. J Bacteriol 187:4497–4504PubMedCrossRefGoogle Scholar
  67. Nga DP, Altenbuchner J, Heiss GS (2004) NpdR, a repressor involved in 2, 4, 6-trinitrophenol degradation in Rhodococcus opacus HL PM-1. J Bacteriol 186:98–103PubMedCrossRefGoogle Scholar
  68. O'Brien XM, Parker JA, Lessard PA, Sinskey AJ (2002) Engineering an indene bioconversion process for the production of cis-aminoindanol: a model system for the production of chiral synthons. Appl Microbiol Biotechnol 59:389–399PubMedCrossRefGoogle Scholar
  69. Okamoto S, Eltis LD (2007) Purification and characterization of a novel nitrile hydratase from Rhodococcus sp. RHA1. Mol Microbiol 65:828–838PubMedCrossRefGoogle Scholar
  70. Patrauchan MA, Florizone C, Dosanjh M, Mohn WW, Davies J, Eltis LD (2005) Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: redundancies and convergence. J Bacteriol 187:4050–4063PubMedCrossRefGoogle Scholar
  71. Patrauchan MA, Florizone C, Eapen S, Gomez-Gil L, Sethuraman B, Fukuda M, Davies J, Mohn WW, Eltis LD (2008) Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1. J Bacteriol 190:37–47PubMedCrossRefGoogle Scholar
  72. Peng X, Taki H, Komukai S, Sekine M, Kanoh K, Kasai H, Choi SK, Omata S, Tanikawa S, Harayama S, Misawa N (2006) Characterization of four Rhodococcus alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols. Appl Microbiol Biotechnol 71:824–832PubMedCrossRefGoogle Scholar
  73. Pisabarro A, Correia A, Martin JF (1998) Pulsed-field gel electrophoresis analysis of the genome of Rhodococcus fascians: genome size and linear and circular replicon composition in virulent and avirulent strains. Curr Microbiol 36:302–308PubMedCrossRefGoogle Scholar
  74. Poelarends GJ, Kulakov LA, Larkin MJ, van Hylckama Vlieg JE, Janssen DB (2000a) Roles of horizontal gene transfer and gene integration in evolution of 1, 3-dichloropropene- and 1, 2-dibromoethane-degradative pathways. J Bacteriol 182:2191–2199PubMedCrossRefGoogle Scholar
  75. Poelarends GJ, Zandstra M, Bosma T, Kulakov LA, Larkin MJ, Marchesi JR, Weightman AJ, Janssen DB (2000b) Haloalkane-utilizing Rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism. J Bacteriol 182:2725–2731PubMedCrossRefGoogle Scholar
  76. Prescott JF (1991) Rhodococcus equi: an animal and human pathogen. Clin Microbiol Rev 4:20–34PubMedGoogle Scholar
  77. Priefert H, O'Brien XM, Lessard PA, Dexter AF, Choi EE, Tomic S, Nagpal G, Cho JJ, Agosto M, Yang L, Treadway SL, Tamashiro L, Wallace M, Sinskey AJ (2004) Indene bioconversion by a toluene inducible dioxygenase of Rhodococcus sp. I24. Appl Microbiol Biotechnol 65:168–176PubMedCrossRefGoogle Scholar
  78. Rainey FA, Klatte S, Kroppenstedt RM, Stackebrandt E (1995) Dietzia, a new genus including Dietzia maris comb. nov., formerly Rhodococcus maris. Int J Syst Bacteriol 45:32–36PubMedCrossRefGoogle Scholar
  79. Saeki H, Akira M, Furuhashi K, Averhoff B, Gottschalk G (1999) Degradation of trichloroethene by a linear-plasmid-encoded alkene monooxygenase in Rhodococcus corallinus (Nocardia corallina) B-276. Microbiology 145(Pt 7):1721–1730PubMedCrossRefGoogle Scholar
  80. Sallam KI, Mitani Y, Tamura T (2006) Construction of random transposition mutagenesis system in Rhodococcus erythropolis using IS1415. J Biotechnol 121:13–22PubMedCrossRefGoogle Scholar
  81. Sallam KI, Tamura N, Tamura T (2007) A multipurpose transposon-based vector system mediates protein expression in Rhodococcus erythropolis. Gene 386:173–182PubMedCrossRefGoogle Scholar
  82. Sekine M, Tanikawa S, Omata S, Saito M, Fujisawa T, Tsukatani N, Tajima T, Sekigawa T, Kosugi H, Matsuo Y, Nishiko R, Imamura K, Ito M, Narita H, Tago S, Fujita N, Harayama S (2006) Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4. Environ Microbiol 8:334–346PubMedCrossRefGoogle Scholar
  83. Seth-Smith HM, Edwards J, Rosser SJ, Rathbone DA, Bruce NC (2008) The explosive-degrading cytochrome P450 system is highly conserved among strains of Rhodococcus spp. Appl Environ Microbiol 74:4550–4552PubMedCrossRefGoogle Scholar
  84. Seto M, Masai E, Ida M, Hatta T, Kimbara K, Fukuda M, Yano K (1995) Multiple polychlorinated biphenyl transformation systems in the gram-positive bacterium Rhodococcus sp. strain RHA1. Appl Environ Microbiol 61:4510–4513PubMedGoogle Scholar
  85. Sharp JO, Sales CM, LeBlanc JC, Liu J, Wood TK, Eltis LD, Mohn WW, Alvarez-Cohen L (2007) An inducible propane monooxygenase is responsible for N-nitrosodimethylamine degradation by Rhodococcus sp. strain RHA1. Appl Environ Microbiol 73:6930–6938PubMedCrossRefGoogle Scholar
  86. Shimizu S, Kobayashi H, Masai E, Fukuda M (2001) Characterization of the 450-kb linear plasmid in a polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl Environ Microbiol 67:2021–2028PubMedCrossRefGoogle Scholar
  87. Stackebrandt E, Rainey FA, WardRainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491CrossRefGoogle Scholar
  88. Stecker C, Johann A, Herzberg C, Averhoff B, Gottschalk G (2003) Complete nucleotide sequence and genetic organization of the 210-kilobase linear plasmid of Rhodococcus erythropolis BD2. J Bacteriol 185:5269–5274PubMedCrossRefGoogle Scholar
  89. Steinmetz M, Le Coq D, Aymerich S, Gonzy-Treboul G, Gay P (1985) The DNA sequence of the gene for the secreted Bacillus subtilis enzyme levansucrase and its genetic control sites. Mol Gen Genet 200:220–228PubMedCrossRefGoogle Scholar
  90. Taguchi K, Motoyama M, Kudo T (2004) Multiplicity of 2, 3-dihydroxybiphenyl dioxygenase genes in the Gram-positive polychlorinated biphenyl degrading bacterium Rhodococcus rhodochrous K37. Biosci Biotechnol Biochem 68:787–795PubMedCrossRefGoogle Scholar
  91. Taguchi K, Motoyama M, Iida T, Kudo T (2007) Polychlorinated biphenyl/biphenyl degrading gene clusters in Rhodococcus sp. K37, HA99, and TA431 are different from well-known bph gene clusters of rhodococci. Biosci Biotechnol Biochem 71:1136–1144PubMedCrossRefGoogle Scholar
  92. Takai S, Sekizaki T, Ozawa T, Sugawara T, Watanabe Y, Tsubaki S (1991) Association between a large plasmid and 15- to 17-kilodalton antigens in virulent Rhodococcus equi. Infect Immun 59:4056–4060PubMedGoogle Scholar
  93. Takeda H, Hara N, Sakai M, Yamada A, Miyauchi K, Masai E, Fukuda M (2004a) Biphenyl-inducible promoters in a polychlorinated biphenyl-degrading bacterium, Rhodococcus sp. RHA1. Biosci Biotechnol Biochem 68:1249–1258PubMedCrossRefGoogle Scholar
  94. Takeda H, Yamada A, Miyauchi K, Masai E, Fukuda M (2004b) Characterization of transcriptional regulatory genes for biphenyl degradation in Rhodococcus sp. strain RHA1. J Bacteriol 186:2134–2146PubMedCrossRefGoogle Scholar
  95. Tkachuk-Saad O, Prescott J (1991) Rhodococcus equi plasmids: isolation and partial characterization. J Clin Microbiol 29:2696–2700PubMedGoogle Scholar
  96. Treadway SL, Yanagimachi KS, Lankenau E, Lessard PA, Stephanopoulos G, Sinskey AJ (1999) Isolation and characterization of indene bioconversion genes from Rhodococcus strain I24. Appl Microbiol Biotechnol 51:786–793PubMedCrossRefGoogle Scholar
  97. Uz I, Duan YP, Ogram A (2000) Characterization of the naphthalene-degrading bacterium, Rhodococcus opacus M213. FEMS Microbiol Lett 185:231–238PubMedCrossRefGoogle Scholar
  98. van der Geize R, Dijkhuizen L (2004) Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr Opin Microbiol 7:255–261PubMedCrossRefGoogle Scholar
  99. Van der Geize R, Yam K, Heuser T, Wilbrink MH, Hara H, Anderton MC, Sim E, Dijkhuizen L, Davies JE, Mohn WW, Eltis LD (2007) A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc Natl Acad Sci U S A 104:1947–1952PubMedCrossRefGoogle Scholar
  100. Waksman SA (1950) The actinomycetes. Chimica Botanica, Waltham, MA, USAGoogle Scholar
  101. Wang Y, Shimodaira J, Miyasaka T, Morimoto S, Oomori T, Ogawa N, Fukuda M, Fujii T (2008) Detection of bphAa gene expression of Rhodococcus sp. strain RHA1 in soil using a new method of RNA preparation from soil. Biosci Biotechnol Biochem 72:694–701PubMedCrossRefGoogle Scholar
  102. Warhurst AM, Fewson CA (1994) Biotransformations catalyzed by the genus Rhodococcus. Crit Rev Biotechnol 14:29–73PubMedCrossRefGoogle Scholar
  103. Warren R, Hsiao WW, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt R, Marra MA, Jones SJ, Mohn WW, Brinkman FS, Fukuda M, Davies J, Eltis LD (2004) Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol 186:7783–7795PubMedCrossRefGoogle Scholar
  104. Williams S, 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. Academic Press, London, pp 103–140Google Scholar
  105. Wu G, Nie L, Zhang W (2006) Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence. Antonie Van Leeuwenhoek 89:135–146PubMedCrossRefGoogle Scholar
  106. Yamada A, Kishi H, Sugiyama K, Hatta T, Nakamura K, Masai E, Fukuda M (1998) Two nearly identical aromatic compound hydrolase genes in a strong polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl Environ Microbiol 64:2006–2012PubMedGoogle Scholar
  107. Yang JC, Lessard PA, Sengupta N, Windsor SD, O'Brien XM, Bramucci M, Tomb JF, Nagarajan V, Sinskey AJ (2007a) TraA is required for megaplasmid conjugation in Rhodococcus erythropolis AN12. Plasmid 57:55–70PubMedCrossRefGoogle Scholar
  108. Yang JC, Lessard PA, Sinskey AJ (2007b) Characterization of the mobilization determinants of pAN12, a small replicon from Rhodococcus erythropolis AN12. Plasmid 57:71–81PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Michael J. Larkin
    • 1
    Email author
  • Leonid A. Kulakov
    • 1
  • Christopher C. R. Allen
    • 1
  1. 1.School of Biological Sciences and The QUESTOR CentreThe Queen’s University of BelfastBelfastUK

Personalised recommendations