Skip to main content
SpringerLink
Log in

Rhodococcus: Genetics and Functional Genomics

  • Reference work entry
Handbook of Hydrocarbon and Lipid Microbiology

Abstract:

Members of the genus Rhodococcus (See also Chapter 17, Vol. 3, Part 1) are a very diverse group of bacteria that 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 is based upon the acquisition of a wide and diverse range of catabolic genes housed in a robust cellular environment. They have very large genomes (up to 9.7 Mbps) and multiple catabolic enzymes. They also harbor many large linear plasmids that contribute to their substrate diversity by acting as a “mass storage” for a numerous catabolic genes. The presence of multiple catabolic pathways and gene homologs 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 is a feature of how the rhodoccci adapt to utilize many substrates.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 1,499.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 549.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • 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.

    PubMed  CAS  Google Scholar 

  • Bell KS, Philp JC, Aw DW, Christofi N (1998) The genus Rhodococcus. J Appl Microbiol 85: 195–210.

    Article  PubMed  CAS  Google Scholar 

  • 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 USA 99: 2094–2099.

    Article  PubMed  Google Scholar 

  • 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: 1859–1867.

    Article  PubMed  CAS  Google Scholar 

  • 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: 2915–2919.

    PubMed  CAS  Google Scholar 

  • 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: 2115–2124.

    Article  PubMed  CAS  Google Scholar 

  • 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: 6183–6193.

    Article  PubMed  CAS  Google Scholar 

  • Gurtler V, Mayall BC, Seviour R (2004) Can whole genome analysis refine the taxonomy of the genus Rhodococcus? FEMS Microbiol Rev 28: 377–403.

    Article  PubMed  CAS  Google Scholar 

  • 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: 1641–1647.

    Article  PubMed  CAS  Google Scholar 

  • 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: 5396–5402.

    Article  PubMed  CAS  Google Scholar 

  • 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: 993–1002.

    Article  PubMed  CAS  Google Scholar 

  • 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: 2055–2065.

    PubMed  CAS  Google Scholar 

  • Kalkus J, Menne R, Reh M, Schlegel HG (1998) The terminal structures of linear plasmids from Rhodococcus opacus. Microbiology 144(Pt 5): 1271–1279.

    Article  PubMed  CAS  Google Scholar 

  • Kalkus J, Reh M, Schlegel HG (1990) Hydrogen autotrophy of Nocardia opaca strains is encoded by linear megaplasmids. J Gen Microbiol 136: 1145–1151.

    PubMed  CAS  Google Scholar 

  • 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: 49–53.

    PubMed  CAS  Google Scholar 

  • 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: 3270–3278.

    Article  PubMed  CAS  Google Scholar 

  • 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: 6598–6606.

    Article  PubMed  CAS  Google Scholar 

  • Komeda H, Hori Y, Kobayashi M, Shimizu S (1996) Transcriptional regulation of the Rhodococcus rhodochrous J1 nitA gene encoding a nitrilase. Proc Natl Acad Sci USA 93: 10572–10577.

    Article  PubMed  CAS  Google Scholar 

  • 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: 3075–3087.

    Article  PubMed  Google Scholar 

  • 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: 1754–1764.

    Article  PubMed  CAS  Google Scholar 

  • Kulakov LA, Larkin MJ (2002) Genomic organization of Rhodococcus. In A Danchin (ed.). Genomics of GC-Rich gram-positive bacteria. Norfolk UK: Caister Academic Press, pp. 15–46.

    Google Scholar 

  • 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): 561–568.

    Article  PubMed  CAS  Google Scholar 

  • Kulakova AN, Stafford TM, Larkin MJ, Kulakov LA (1995) Plasmid pRTL1 controlling 1-chloroalkane degradation by Rhodococcus rhodochrous NCIMB13064. Plasmid 33: 208–217.

    Article  PubMed  CAS  Google Scholar 

  • 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: 2772–2776.

    PubMed  CAS  Google Scholar 

  • Larkin MJ, Allen CCR, Kulakov LA (2006) Biodegradation by Members of the Genus Rhodococcus: Biochemistry, Physiology,and Genetic Adaptation. Adv Appl Microbiol 59: 1–28.

    Article  PubMed  CAS  Google Scholar 

  • Larkin MJ, Kulakov LA, Allen CCR (2005) Biodegradation and Rhodococcus - masters of catabolic versatility. Curr Opin Biotechnol 16(3): 282–290.

    Article  PubMed  CAS  Google Scholar 

  • Leahy JG, Batchelor PJ, Morcomb SM (2003) Evolution of the soluble diiron monooxygenases. FEMS Microbiol Rev 27: 449–479.

    Article  PubMed  CAS  Google Scholar 

  • LeBlanc JC, Goncalves ER, Mohn WW (2008) Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol 74: 2627–2636.

    Article  PubMed  CAS  Google Scholar 

  • Lessard PA, O’Brien XM, Ahlgren NA, Ribich SA, Sinskey AJ (1999) Characterization of IS1676 from Rhodococcus erythropolis SQ1. Appl Microbiol Biotechnol 52: 811–819.

    Article  PubMed  CAS  Google Scholar 

  • Locci R (1984) Morphology. In: The Biology of the Actinomycetes. M Goodfellow (ed.). New York: Academic press, pp. 165–199.

    Google Scholar 

  • McLeod MP, Eltis LD (2008) Genomic insights into the aerobic pathways for degradation of organic pollutants. In E Diaz (ed.). Microbial Biodegradation: Genomics and Molecular Biology, 1st edn. UK: Caister Academic Press.

    Google Scholar 

  • 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 USA 103: 15582–15587.

    Article  PubMed  Google Scholar 

  • Nagy I, Schoofs G, Vanderleyden J, De Mot R (1997) Transposition of the IS21-related element IS1415 in Rhodococcus erythropolis. J Bacteriol 179: 4635–4638.

    PubMed  CAS  Google Scholar 

  • 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: 4497–4504.

    Google Scholar 

  • 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: 98–103.

    Article  PubMed  CAS  Google Scholar 

  • 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: 389–399.

    Article  PubMed  Google Scholar 

  • Okamoto S, Eltis LD (2007) Purification and characterization of a novel nitrile hydratase from Rhodococcus sp. RHA1. Mol Microbiol 65: 828–838.

    Article  PubMed  CAS  Google Scholar 

  • 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: 4050–4063.

    Article  PubMed  CAS  Google Scholar 

  • 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: 37–47.

    Article  PubMed  CAS  Google Scholar 

  • 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: 2191–2199.

    Article  PubMed  CAS  Google Scholar 

  • 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: 2725–2731.

    Article  PubMed  CAS  Google Scholar 

  • 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: 168–176.

    Article  PubMed  CAS  Google Scholar 

  • 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): 1721–1730.

    Article  PubMed  CAS  Google Scholar 

  • 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: 4550–4552.

    Article  PubMed  CAS  Google Scholar 

  • 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: 4510–4513.

    PubMed  CAS  Google Scholar 

  • 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: 6930–6938.

    Article  PubMed  CAS  Google Scholar 

  • 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: 2021–2028.

    Article  PubMed  CAS  Google Scholar 

  • 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: 5269–5274.

    Article  PubMed  CAS  Google Scholar 

  • 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: 1136–1144.

    Article  PubMed  CAS  Google Scholar 

  • 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: 787–795.

    Article  PubMed  CAS  Google Scholar 

  • 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: 1249–1258.

    Article  PubMed  CAS  Google Scholar 

  • 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: 2134–2146.

    Article  PubMed  CAS  Google Scholar 

  • Uz I, Duan YP, Ogram A (2000) Characterization of the naphthalene-degrading bacterium, Rhodococcus opacus M213. FEMS Microbiol Lett 185: 231–238.

    Article  PubMed  CAS  Google Scholar 

  • van der Geize R, Dijkhuizen L (2004) Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr Opin Microbiol 7: 255–261.

    Article  PubMed  Google Scholar 

  • 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 USA 104: 1947–1952.

    Article  PubMed  Google Scholar 

  • 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: 694–701.

    Article  PubMed  CAS  Google Scholar 

  • Warhurst AM, Fewson CA (1994) Biotransformations catalyzed by the genus Rhodococcus. Crit Rev Biotechnol 14: 29–73.

    Article  PubMed  CAS  Google Scholar 

  • 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: 7783–7795.

    Article  PubMed  CAS  Google Scholar 

  • Williams ST (1976) The micromorpholpgy and fine structure of nocardioformorganisms. In: The Biology of the Nocardiae. M Goodfellow, GH Brownell, JA Serrano (eds.). New York: Academic Press pp. 103–140.

    Google Scholar 

  • 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: 2006–2012.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Biological Sciences and The QUESTOR Centre, The Queen’s University of Belfast, Belfast, Northern Ireland, UK

    M. J. Larkin, L. A. Kulakov & C. C. R. Allen

Authors
  1. M. J. Larkin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. L. A. Kulakov
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. C. C. R. Allen
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Environmental Microbiology Laboratory, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany

    Kenneth N. Timmis (Professor) (Professor)

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this entry

Cite this entry

Larkin, M.J., Kulakov, L.A., Allen, C.C.R. (2010). Rhodococcus: Genetics and Functional Genomics. In: Timmis, K.N. (eds) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77587-4_94

Download citation

Publish with us

Policies and ethics

Search

Navigation