GSE106129
Inter-replicon gene flow contributes to transcriptional integration in the Sinorhizobium meliloti multipartite genome
Integration of newly acquired genes into existing regulatory networks is necessary for successful horizontal gene transfer (HGT). Ten percent of bacterial species contain at least two DNA replicons over 300 kilobases in size, with the secondary replicons derived predominately through HGT.  The Sinorhizobium meliloti genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid (termed pSymB) consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid (termed pSymA) consisting primarily of recently acquired genes.  Here, RNA-sequencing is used to examine the transcriptional consequences of massive, synthetic genome reduction produced through the removal of the megaplasmid and/or the chromid.  Removal of the megaplasmid influenced the transcription of only six genes. In contrast, removal of the chromid influenced expression of ~ 8% of chromosomal genes and ~ 4% of megaplasmid genes. This was mediated in part by the loss of the ETR DNA region whose presence on pSymB is due to a translocation from the chromosome.  No obvious functional bias among the up-regulated genes was detected, although genes with putative homologs on the chromid were enriched.  Down-regulated genes were enriched in motility and sensory transduction pathways.  Four transcripts were examined further, and in each case the transcriptional change could be traced to loss of specific pSymB regions.  In particularly, a chromosomal transporter was induced due to deletion of bdhA likely mediated through 3-hydroxybutyrate accumulation. These data provide new insights into the evolution of the multipartite bacterial genome, and more generally into the integration of horizontally acquired genes into the transcriptome. Overall design: There was a total of 10 samples for the RNA-sequencing analysis: five strains performed in biological duplicates.  Total RNA was isolated from S. meliloti RmP3496 (?pSymAB), RmP3497 (?pSymB), RmP3498 (?pSymA), RmP3499 (wild-type), and RmP3500 (?pSymB with the ETR region of S. fredii integrated into the chromosome), grown in minimal medium with 10 mM sucrose as the carbon source and ammonia as the nitrogen source.  Sequencing was performed using Illumina HiSeq 1500 with 75 nt single reads.