And Other Genetic Determinants of Their Catabolic Versatility

Rhodococci are aerobic, nocardioform actinomycetes with the ability to assimilate a wide variety of organic compounds, including hydrophobic xeno-biotics like polychlorinated biphenyls (PCBs) or dibenzo-p-dioxins. Their general tolerance to toxic substrates, solvents, desiccation, and other (environmental) stress factors, as well as their ability to produce mycolic acid surfactants which may facilitate uptake of hydrophobic compounds, are thought to contribute to the success of members of this genus in biodegradation and bioremediation (Patrauchan et al. 2005; Larkin et al. 2005).

A large number of plasmids have been identified in different Rhodococcus spp., which range from small circular to large linear DNA molecules. Many linear plasmids of rhodococci code for catabolic functions. In contrast, the linear conjugative plasmid pFiD188 of the phytopathogenic R. fascians strain D188 carries different pathogenicity loci involved in induction of leafy gall formation (reviewed by Goethals et al. 2001; Francis et al. 2007, in this volume).

The termini of rhodococcal linear plasmids, in contrast to those of many Streptomyces replicons (Chen 2007, in this volume), generally do not contain long inverted repeats; however, alignments of terminal sequences of linear plasmids from rhodococci and other actinobacteria revealed the presence of palindromes with the common central motif GCTXCGC (Stecker et al. 2003; Warren et al. 2004; König et al. 2004). This highly conserved motif was originally identified by Kalkus et al. (1998) in pHG201 of R. opacus MR11. In palindromic sequences of single-stranded terminal 3' overhangs, it has the potential to form a stable single-residue hairpin loop closed by sheared purine:purine pairing, which may have a role in replication at the telom-eres (Huang et al. 1998). Remarkably, the two binding sites of single-stranded DNA on telomeric 3' overhangs of the Streptomyces plasmid pSLA2, which are recognized by the telomere-associated protein (Tap) involved in telomere patching, comprise this conserved GCTXCGC sequence as a core motif (Bao and Cohen 2003).

The ability of rhodococci to attack a wide range of aromatic compounds is in part due to the abundant presence of several types of oxygenases (Larkin et al. 2005); for example, 122 oxygenase genes were annotated to the genome of Rhodoccoccus sp. strain RHA1 ( Moreover, their genomes often contain multiple copies of homologous genes and degradative gene clusters (contributing to their large genome sizes), resulting in genetic redundancy which is believed to be an important factor for their catabolic efficiency and versatility (van der Geize and Dijkhuizen 2004; Larkin et al. 2005). Well-studied examples are the presence of multiple alkane monooxy-genase genes (alkB) (Whyte et al. 2002; van Beilen et al. 2002) and extradiol dioxygenase genes (Irvine et al. 2000; Vaillancourt et al. 2003; McKay et al. 2003; Iida et al. 2002b; Taguchi et al. 2004). Multiple copies of biodegradative genes appear to be "stored" on large linear plasmids (Table 1), but circular plasmids encoding catabolic traits likewise exist in rhodococci, such as pRTLl (chloroalkane degradation), pTE1 (atrazine degradation), or pTC1 (2-methylaniline metabolism) (for reviews, see Larkin et al. 1998; Nojiri et al. 2004).

As exemplified in Sects. 3.2 and 3.3, some catabolic gene clusters found on linear plasmids of different Rhodococcus strains share an extremely high degree of similarity in gene organization and sequence, suggesting that they may have been distributed via horizontal gene transfer. Moreover, rhodococ-cal plasmids may have undergone rearrangements, since catabolic genes were often found to be flanked by transposon-related ORFs and putative insertion sequences (ISs). Genome analyses, and the observation of frequent nonhomologous illegitimate recombination, led to the hypothesis that rhodococci have adopted an evolutionary strategy of gene storage and hyper-recombination, i.e., acquisition and accumulation of many—even multiple— catabolic genes in large genomes, and genomic rearrangements to promote adaptation to organic substrates (Larkin et al. 1998, 2005).

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