Rhodococcus: Genetics and Functional Genomics
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 recalcitran
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K. N. Timmis (ed.), Handbook of Hydrocarbon and Lipid Microbiology, DOI 10.1007/978-3-540-77587-4_94, # Springer-Verlag Berlin Heidelberg, 2010
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Rhodococcus: Genetics and Functional Genomics
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.
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Introduction
Members of the genus Rhodococcus are aerobic bacteria that possess the ability to degrade many recalcitrant and toxic pollutants in the environment and they have been discovered in many niches. Aspects of their phylogeny, physiology and biochemistry are reported elsewhere in the manual (cross reference: Volume 2(10) the Microbes) and will not be covered here. Instead this section will concentrate on the genetic basis of their catabolic abilities and developments regarding gene regulation and genomics; particularly related to catabolism and biodegradation. All of the rhodococci investigated to date appear to have large and complex genomes that may have acquired many genes by recombination in the distant past. There is increasing evidence that multiple pathways and gene homologs are present that further increases Rhodococcus catabolic versatility. Many also possess both large linear plasmids and circular plasmids that contribute greatly to the repertoire of catabolic genes. There appears to be an ability to adapt to degrade many new substrates, however the mechanisms underlying the flexibility of the Rhodococcus genome are not well understood. One striking feature is the presence of large linear plasmids in many of the strains isolated. Other characteristics are a system that promotes high frequency illegitimate recombination and the presence of relatively few transposons (although a small number of insertion sequences have been identified). Other, as yet unknown events of illegitimate recombination may serve to promote the introgression of DNA in their genomes without the help of mobile genetic elements (de Vries and Wackernagel, 2002). Aspects of their overall metabolic diversity and genetics have been covered previously in reviews (Bell et al., 1998; Gurtler et al., 2004; Kulakov and Larkin, 2002; Larkin et al., 2005; Larkin et al., 2006; McLeod and Eltis, 200
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