Rhodococcus
Classification
Bacteria; Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Nocardiaceae; Rhodococcus
Species
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NCBI: Taxonomy |
Genus species
Description and Significance
Rhodococcus is a genus of non-motile, non-sporulating, aerobic gram-positive filamentous rods of the phylum Actinobacteria (1). These organisms reside in soil and water environments and are classified as one of the most industrial important organisms. Studies have shown these organisms to grow in both mesophilic (4) and psychrophilic (5) conditions. Strains of Rhodococcus contain enzymes that carry out biologically relevant reactions such as biodesulfurization of fossil fuels, degradation of polychlorinated biphenyls (PCBs), and utilization of a wide variety of other organic compounds as energy sources (4). Therefore, Rhodococcus plays an important role in the global recycling of carbon. Additionally, Rhododcoccus is used commercially as a biocatalyst in the production of fossil fuels, bioactive steroids, and acrylamide (1). The production of dioxygenases by Rhodococcus for the degradation of PCBs has become increasingly important to researchers, as they search for a method to degrade the biologically toxic compounds. Additionally, the ability of Rhodococcus to be used in bioremediaion may be essential in decontaminating polluted land and waterways throughout the United States.
Genome Structure
The genome of Rhodococcus sp. RHA1, a biphenyl degrading strain, is one of the largest geonomes to date that has been sequenced. It contains a linear chromosome and three linear plasmids totaling 9.7 kb and is 67% G-C base pairs. Within the genome, there are a predicted 9,145 genes. These genes encode 1,578 proteins belonging to known protein families, 2,538 hypothetical proteins, and 3,511 proteins of unknown function (1).
It is believed the linear conformation of the plasmid within Rhodococcus was acquired via bacteriophages (4). The three plasmids contain 11 genes which produce proteins necessary for the catabolism of aromatic molecules (1). The linear nature of the chromosome is hypothesized to have formed following recombination between a circular chromosome and linear plasmids (4).
Rhodococcus sp. RHA1 encodes for a total of 1,085 oxidoreductases and 192 ligases, which is abundant when compared to other Actinomycetes. The catabolic nature of oxygenases are utilized in hydroxylation of aromatic compounds, necessary for degradation (4). Of the oxidases encoded in the genome of Rhodococcus, 77% reside within the chromosome. Horizontal gene transfer is thought to comprise 7% of the oxygenases of Rhodococcus. Therefore, it is believed RHA1 has a fundamental aspect which requires it to carry out PCB degradation (1).
The diverse ability of Rhodococcus to carry out catabolic activities of aromatic compounds is believed to have been acquired through ancient horizontal gene transfer acquisitions. Following duplications within the genome the organism acquired the vast numeral abundance presented in genomic studies. However, due to few transposases, one psuedogene, and only to insertion sequences (IS), it is hypothesized Rhodococcus is a relatively stable genome and has experienced little genetic change recently (1).
Cell Structure, Metabolism and Life Cycle
The genus Rhodococcus has not been well characterized. Therefore, many strains recognized as rhodococcoci might not belong to this genus which is undergoing serious studies and reorganization. The rhodococci are included in a broad group of high G+C actinomycetes which is known as Mycolata because they have a cell envelope of mycolic acids connected to aribinogalactan wall polysaccharides on the inside and to glycolypids on the outside (2,4). Lipoarabinomannan (LAM) is another component of the cell wall of rhodoccoci that is shorter in this group than in mycobacteria, but also contains terminal mannose-containing side chains. In addition to the mycolic acids, the Rhodococcus cell wall includes free lipids like threhalose dimycolates, glycosyl monomycolates, and peptidolipids. The mycolic acid layer facilitates the intake of hydrophobic compounds in representatives of the Rhodococcus genus and helps them survive on harsh environmental conditions such as low pH and oxidative stress (1,2 and 4). Cell wall porins similar to those present in other mycolata like nocardia and mycobacterium have been found in Rhodococcus sp. These porins participate in the uptake of cations from the environment (4).
Rhodococci metabolize an exceptionally large variety of organic compounds, particularly hydrophobic xenobiotics, so they have an important role in the global carbon cycle. Their assimilatory capacities have been accredited to their diversity of enzymatic activities as well as their mycolic acid surfactants (3). For example, Rhodococcus sp. strain RHA1 has the ability to aerobically degrade polychlorinated biphenyls (PCBs) through cometabolization by the bph pathway, which is responsible for the aerobic degradation of biphenyl. The bph pathway consists of four enzymatic activities which act sequentially to transform biphenyl to benzoate and 2-hydroxypenta-2,4-dienoate. For each of these four steps, RHA1 appears to possess multiple isozymes, including at least three bph-type ring-hydroxylating dioxygenases and at least seven different bph-type ring cleavage enzymes. While most of the genes of the upper bph pathway are placed on two of three large linear plasmids, pRHL1 (1,100 kb) and pRHL2 (450 kb), genes encoding related isozymes are distributed hroughout the 9.7-Mb genome. This strain utilizes benzoate and phthalate as sole sources of carbon and energy. The catabolism of benzoate and phthalate occurs by a branched ketoadipate pathway in Rhodococcus sp. strain RHA1. The catechol and protocatechuate branches of the ketoadipate pathway in RHA1 converge at ketoadipate enol-lactone. Then, that metabolite is transformed by PcaL, a bifunctional enzyme that comprises a-carboxy-muconolactone decarboxylase and an enol-lactone hydrolase in separate domains (3). New data suggest that the catabolism of aromatic compounds in rhodococci is organized in a fashion similar to that found in the better-studied pseudomonads: a large number of “peripheral”pathways funnel a range of natural and xenobiotic compounds into a restricted number of “central” pathways that complete the transformation of these compounds to TCA cycle intermediates(3). There is also conclusive evidence that there is a phenylacetate (PAA) catabolic pathway in strain RHA1 which is encoded by the paa genes and proceeds via phenylacetyl-coenzyme A (CoA) where hydrolytic ring fission plays a central role in the degradation of a range of aromatic compounds (5).
References
1. McLeod, M. et. al. "The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse". Preceeding of the National Academy of Sciences. 2006. Volume 103. p. 15582-15587.
2. Meijer, W.G. and John F. Prescott "Rhodococcus equi". Veterinary Research-A Journal on Animal Infection and Epidemiology. 2004. Volume 35. p. 383-396.
3. Navarro-Llorens, J.M. et. al. "Phenylacetate Catabolism in Rhodococcus sp. Strain RHA1: a Central Pathway for Degradation of Aromatic Compounds". Journal of Bacteriology. 2005. Volume 187. p 4497-4504.
4. Lichtinger, T. et. al. "Biochemical Identification and Biophysical Characterization of a Channel-Forming Protein from Rhodococcus erythropolis". Journal of Bacteriology. 2000. Volume 182. p. 764-770.
5. Patrauchan, M. A. et. al. "Catabolism of Benzoate and Phthalate in Rhodococcus sp. Strain RHA1: Redundancies and Convergence". Journal of Bacteriology. 2005. Volume 187. p.4050-4063.
6. Warren, R. et. al. "Functional Characterization of a Catabolic Plasmid from Polychlorinated Biphenyl Degrading Rhodococcus sp. Strain RHA1". Journal of Bacteriology. 2004. Volume 186. p. 7783-7795.
7. Whyte, L. et. al. "Biodegradation of Variable-Chain-Length Alkanes at Low Temperatures by a Psychrotrophic Rhodococcus sp.". Applied and Environmental Microbiology. 1998. Volume 64. p. 2578-2584.
Author
Page authored by Bruce Fraser & Hermes Fernandez, students of Prof. Jay Lennon at Michigan State University.
