Rhodococcus

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Rhodococcus
Rhodococcus species.jpg
Rhodococcus sp.
Scientific classification
Kingdom: Bacteria
Phylum: Actinobacteria
Order: Actinomycetales
Suborder: Corynebacterineae
Family: Nocardiaceae
Genus: Rhodococcus
Zopf 1891

Rhodococcus is a genus of aerobic, nonsporulating, nonmotile Gram-positive bacteria closely related to Mycobacterium and Corynebacterium.[1][2] While a few species are pathogenic, most are benign, and have been found to thrive in a broad range of environments, including soil, water, and eukaryotic cells. Some species have large genomes, including the 9.7 megabasepair genome (67% G/C) of Rhodococcus sp. RHA1.[3]

Strains of Rhodococcus are important owing to their ability to catabolize a wide range of compounds and produce bioactive steroids, acrylamide, and acrylic acid, and their involvement in fossil fuel biodesulfurization.[3] This genetic and catabolic diversity is not only due to the large bacterial chromosome, but also to the presence of three large linear plasmids.[1] Rhodococcus is also an experimentally advantageous system owing to a relatively fast growth rate and simple developmental cycle, but is not well characterized.[3]

Another important application of Rhodococcus comes from bioconversion, using biological systems to convert cheap starting material into more valuable compounds, such as its ability to metabolize harmful environmental pollutants, including toluene, naphthalene, herbicides, and PCBs. Rhodococcus species typically metabolize aromatic substrates by first oxygenating the aromatic ring to form a diol (two alcohol groups). Then, the ring is cleaved with intra/extradiol mechanisms, opening the ring and exposing the substrate to further metabolism. Since the chemistry is very stereospecific, the diols are created with predictable chirality. While controlling the chirality of chemical reaction presents a significant challenge for synthetic chemists, biological processes can be used instead to faithfully produce chiral molecules in cases where direct chemical synthesis is not feasible or efficient. An example of this is the use of Rhodococcus to produce indene, a precursor to the AIDS drug indinavir, a protease inhibitor, and containing two of the five chiral centers needed in the complex.[4]

Indinavir, indene shown in green[4]

Biodegradation of organic pollutants[edit]

Rhodococcus has been greatly researched as a potential agent for the bioremediation of pollutants as it is commonly found in the natural environment, and they possess certain characteristics that allow them to thrive under a variety of conditions, and they have the capability to metabolize many hydrocarbons.[5]

Rhodococci possess many properties that makes them suitable for bioremediation under a range of environments. Their ability to undergo microaerophilic respiration allows them to survive in environments containing low oxygen concentrations, and their ability to undergo aerobic respiration also allows them to survive in oxygenated environments.[6] They also undergo nitrogen fixation, which allows them to generate their own nutrients in environments with low nutrients.[7]

Rhodococci also contain characteristics that enhances their ability to degrade organic pollutants. Their hydrophobic surface allows for adhesion to hydrocarbons, which enhances its ability to degrade these pollutants.[8] They have a wide variety of catabolic pathways and many unique enzyme functions.[9] This gives them the ability to degrade many recalcitrant, toxic hydrocarbons. For example, Rhodococci expresses dioxygenases, which can be used to degrade benzotrifluoride, a recalcitrant pollutant.[10] Rhodococcus sp. strain Q1, a strain naturally found in soil and paper mill sludge, contains the ability to degrade quinoline, various pyridine derivatives, catechol, benzoate, and protocatechuic acid.[11] Rhodococci are also capable of accumulating heavy metal ions, such as radioactive caesium, allowing for easier removal from the environment.[12] Other pollutants, such as azo dyes,[13] pesticides[14] and polychlorinated biphenyls[15] can also be degraded by Rhodococci.

Scanning electron micrograph of Rhodococcus sp. strain Q1 grown on quinoline - the organism can use quinoline as a sole source of carbon, nitrogen, and energy, tolerating concentrations up to 3.88 millimoles per liter.

Pathogenic Rhodococcus[edit]

The genus Rhodococcus has two pathogenic species: R. fascians and R. equi. The former, a plant pathogen, causes leafy gall disease in both angiosperm and gymnosperm plants.[16] R. equi is the causative agent of foal pneumonia (rattles) and mainly infects foals up to three months in age. However, it has a wide host range, sporadically infecting pigs, cattle, and immunocompromised humans, in particular AIDS patients and those undergoing immunosuppressive therapy.[17] Interestingly, both pathogens rely on a conjugative virulence plasmid to cause disease. In case of R. fascians, this is a linear plasmid, whereas R. equi harbors a circular plasmid. Both pathogens are economically significant. R. fascians is a major pathogen of tobacco plants. R. equi, one of the most important foal pathogens, is endemic on many stud farms around the world.

In molecular biology[edit]

Rhodococcus has also been identified as a contaminant of DNA extraction kit reagents and ultrapure water systems, which may lead to its erroneous appearance in microbiota or metagenomic datasets.[18]

Species[edit]

References[edit]

  1. ^ a b van der Geize R. & L. Dijkhuizen (2004). "Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications". Microbiology. 7 (3): 255–261. doi:10.1016/j.mib.2004.04.001. PMID 15196492. 
  2. ^ Burkovski A (editor). (2008). Corynebacteria: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-30-1. [1]. 
  3. ^ a b c McLeod MP, Warren RL, Hsiao WW, Araki N, Mihre 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 (October 17, 2006). "The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse". PNAS. 103 (42): 15582–15587. doi:10.1073/pnas.0607048103. PMC 1622865Freely accessible. PMID 17030794. 
  4. ^ a b Treadway, S.L., K.S. Yanagimachi, E. Lankenau, P.A. Lessard, G. Stephanopoulos and A.J. Sinskey (1999). "Isolation and characterization of indene bioconversion genes from Rhodococcus strain I24". Appl. Microbiol. Biotechnol. 51 (6): 786–793. doi:10.1007/s002530051463. PMID 10422226. 
  5. ^ Alvarez, Héctor (2010). Biology of Rhodococcus. Springer Science & Business Media. pp. 231–256. ISBN 9783642129377. 
  6. ^ Fuller, M.E.; Perreault, N. (July 8, 2010). "Microaerophilic degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by three Rhodococcus strains". Letters in Applied Microbiology. 51: 313–318. doi:10.1111/j.1472-765x.2010.02897.x. PMID 20666987 – via Wiley. 
  7. ^ Blasco, Rafael (2001). "Rhodococcus sp. RB1 grows in the presence of high nitrate and nitrite concentrations and assimilates nitrate in moderately saline environments". Archives of Microbiology. 175: 435–440. doi:10.1007/s002030100285 – via Springer. 
  8. ^ Mendez-Volas, A. (2012). Microbes in applied research; current advances and challenges; proceedings. World Scientific. pp. 197–200. ISBN 9789814405034. 
  9. ^ Laczi, Krisztián; Kis, Ágnes; Horváth, Balázs; Maróti, Gergely; Hegedüs, Botond (November 2015). "Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons". Applied Microbiology and Biotechnology. 99 (22): 9745–9759. doi:10.1007/s00253-015-6936-z. 
  10. ^ Yano, Kenichi; Wachi, Masaaki; Tsuchida, Sakiko; Kitazume, Tomoya; Iwai, Noritaka (2015). "Degradation of benzotrifluoride via the dioxygenase pathway in Rhodococcus sp. 065240". Bioscience, Biotechnology, and Biochemistry. 79 (3): 496–504. doi:10.1080/09168451.2014.982502. ISSN 1347-6947. PMID 25412819. 
  11. ^ O'Loughlin, E.J.; Kehrmeyer, S.R.; Sims, G.K. (1996). "Isolation, characterization, and substrate utilization of a quinoline degrading bacterium". International Biodeterioration and Biodegradation. 38 (2): 107–118. doi:10.1016/S0964-8305(96)00032-7. 
  12. ^ Takei, Takayuki; Yamasaki, Mika; Yoshida, Masahiro (2014-04-01). "Cesium accumulation of Rhodococcus erythropolis CS98 strain immobilized in hydrogel matrices". Journal of Bioscience and Bioengineering. 117 (4): 497–500. doi:10.1016/j.jbiosc.2013.09.013. 
  13. ^ Heiss, G. S.; Gowan, B.; Dabbs, E. R. (1992-12-01). "Cloning of DNA from a Rhodococcus strain conferring the ability to decolorize sulfonated azo dyes". FEMS Microbiology Letters. 78 (2–3): 221–226. doi:10.1016/0378-1097(92)90030-r. ISSN 0378-1097. PMID 1490602. 
  14. ^ Parekh, N. R.; Walker, A.; Roberts, S. J.; Welch, S. J. (November 1994). "Rapid degradation of the triazinone herbicide metamitron by a Rhodococcus sp. isolated from treated soil". The Journal of Applied Bacteriology. 77 (5): 467–475. doi:10.1111/j.1365-2672.1994.tb04389.x. ISSN 0021-8847. PMID 8002472. 
  15. ^ Boyle, Alfred W.; Silvin, Christopher J.; Hassett, John P.; Nakas, James P.; Tanenbaum, S. W. (1992-06-01). "Bacterial PCB biodegradation". Biodegradation. 3 (2–3): 285–298. doi:10.1007/BF00129089. ISSN 0923-9820. 
  16. ^ Goethals, K.; Vereecke, D.; Jaziri, M.; Van, Montagu M.; Holsters, M. (2001). "Leafy gall formation by Rhodococcus fascians". Annu. Rev. Phytopathol. 39: 27–52. doi:10.1146/annurev.phyto.39.1.27. PMID 11701858. 
  17. ^ Muscatello, G.; Leadon, D. P.; Klay, M.; Ocampo-Sosa, A.; Lewis, D. A.; Fogarty, U.; Buckley, T.; Gilkerson, J. R.; Meijer, W. G.; et al. (2007). "Rhodococcus equi infection in foals: the science of 'rattles'". Equine Vet. J. 39 (5): 470–478. doi:10.2746/042516407x209217. PMID 17910275. 
  18. ^ Salter, S; Cox, M; Turek, E; Calus, S; Cookson, W; Moffatt, M; Turner, P; Parkhill, J; Loman, N; Walker, A (2014). "Reagent contamination can critically impact sequence-based microbiome analyses". bioRxiv 007187Freely accessible. 
  19. ^ a b c d e f g h i j k l m n o p q r s Parte, A.C. "Rhodococcus". www.bacterio.net. 
  20. ^ Klatte, S.; et al. (1994). "Rhodococcus luteus is a later subjective synonym of Rhodococcus fascians". Int. J. Syst. Bacteriol. 44 (4): 627–630. doi:10.1099/00207713-44-4-627. 
  21. ^ http://www.physorg.com/news/2011-06-wood-digesting-enzyme-bacteria-boost-biofuel.html
  22. ^ Takeuchi, M; Hatano, K; Sedlácek, I; Pácová, Z (2002). "Rhodococcus jostii sp. nov., isolated from a medieval grave". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 2): 409–13. doi:10.1099/00207713-52-2-409. PMID 11931149. 

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