Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

Abstract

Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven ''central aromatic'' and twenty ''peripheral aromatic'' pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.genomics ͉ niche adaptation ͉ evolution ͉ biodegradation ͉ redundancy

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

“…In Burkholderia, Chain et al (2006) also showed that the different replication units are evolving under independent evolutionary dynamics. Even though no significant fitness effect has been detected in S. meliloti strains characterized by atypical genome architectures (Guo et al, 2003), the organisation and the polymorphism of the S. medicae genome raise questions about the mechanisms leading to the differing gene content of its replicons and the possible adaptive nature of this organisation.…”

Genome-wide transcriptome analyses of the ‘Knallgas’ bacterium Ralstonia eutropha H16 with regard to polyhydroxyalkanoate metabolism

“…Analysis of several bacterial genome sequences revealed the presence of more than one PHA synthase in many species. In strains of the genus Burkholderia, the presence of multiple PHA synthase genes is common, all sharing similar neighbouring genes (Chain et al, 2006;Holden et al, 2004;Nierman et al, 2004). In R. eutropha strain JMP222, a phaC2 gene has been identified (sequence available online http://www.jgi.doe.gov) that is neither a homologue of the phaC1 family of PHA synthase genes nor similar to phaC2 from strain H16.…”

Expression of the six chromate ion transporter homologues of Burkholderia xenovorans LB400

“…In agreement with the promoter distribution of the chr genes, the B. xenovorans LB400 genome encodes four rpoD genes (encoding s 70 ) and two rpoN genes (encoding s 54 ) as its main transcriptional factors (Chain et al, 2006).…”

“…For example, the B. xenovorans LB400 9.7 Mb genome displays 17.6 % of redundant genes, a relatively large value when compared with other bacterial genomes, which average 7.6 % (±4.0 %); possession of multiple paralogues, as a result of gene duplication, has been related to the high level of metabolic versatility displayed by B. xenovorans LB400 (Chain et al, 2006). The largest number of redundant genes in B. xenovorans pertains to transport proteins (230 paralogues), including 180 efflux systems, which comprise 21 heavy metal efflux pumps (Chain et al, 2006). Among these transporters are the six homologues of the CHR superfamily: four proteins from the monodomain LCHR family and two protein pairs from the bidomain SCHR family (Díaz-Pérez et al, 2007).…”

“…The genomes of species of the betaproteobacteria genus Burkholderia commonly encode multiple CHR homologues of different subfamilies (Chain et al, 2006;Díaz-Pérez et al, 2007). We reported previously that Burkholderia vietnamiensis TVV75 and Burkholderia xenovorans LB400 possess seven and six CHR homologues, respectively (Díaz-Pérez et al, 2007).…”