Nov 22, 2018 // Divide and conquer: the contribution of the divided bacterial genome in conquering multiple niches
Dr. George diCenzo, Dept of Biology, University of Florence, Italy
Approximately 10% of bacterial species contain a genome divided between two or more large (> 300 kb) DNA replicons. One such organism is Sinorhizobium meliloti, a soil-dwelling a-proteobacterium that can enter into N2-fixing endosymbiotic interactions with leguminous plants. A synthetic genome reduction approach was used to construct a S. meliloti derivative lacking both of its secondary replicons, which together encode 2900 genes. High-throughput growth assays and soil mesocosm experiments demonstrated that the secondary replicons likely have small contributions to growth in bulk soil despite encoding a broad range of metabolic capabilities. Instead, in silico modelling of S. meliloti metabolism suggested that the metabolic properties of the secondary replicons are associated with specific environments, such as the rhizosphere. Consistent with this being a generalizable property, comparative genomics of ~300 strains from the family Burkholderiaceae suggested that their secondary replicons are enriched in environmental adaptation genes. Nevertheless, massively-parallel transposon-sequencing uncovered extensive genetic interactions between the S. meliloti replicons. Similarly, transcriptomics (RNA-seq) and non-targeted metabolomics illustrated that the more conserved secondary replicon of S. meliloti has become integrated into the general metabolic and transcriptomic networks of the cell. This integration is due, at least in part, to the transfer of core genes from the chromosome to the secondary replicon. Overall, these systems-level data support a model in which large secondary replicon(s) provide increased genome flexibility, facilitating more rapid adaptation to novel environments. These results can have implications in elucidating the genomics of host-adaptation, which is applicable to the many human pathogens and plant symbionts that harbour divided genomes.