diCenzo George C, Wellappili Deelaka, Golding G Brian, Finan Turlough M
Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
G3 (Bethesda). 2018 May 4;8(5):1711-1720. doi: 10.1534/g3.117.300405.
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 genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid 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 pSymA 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 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.
新获得的基因整合到现有的调控网络中是水平基因转移（HGT）成功的必要条件。10%的细菌物种含有至少两个大小超过300千碱基的DNA复制子，其中次要复制子主要通过HGT衍生而来。该基因组分为一个3.7兆碱基的染色体、一个1.7兆碱基的染色体外基因，主要由通过古代HGT获得的基因组成，以及一个1.4兆碱基的大质粒，主要由最近获得的基因组成。在这里，RNA测序用于研究通过去除大质粒和/或染色体外基因产生的大规模合成基因组减少的转录后果。去除pSymA大质粒仅影响六个基因的转录。相比之下，去除染色体外基因影响了约8%的染色体基因和约4%的大质粒基因的表达。这部分是由ETR DNA区域的缺失介导的，其在pSymB上的存在是由于从染色体易位而来。上调基因中未检测到明显的功能偏向，尽管在染色体外基因上具有推定同源物的基因富集。下调基因在运动性和感觉转导途径中富集。进一步研究了四个转录本，在每种情况下，转录变化都可以追溯到特定pSymB区域的缺失。特别是，由于可能通过3-羟基丁酸积累介导的缺失，诱导了一种染色体转运蛋白。这些数据为多分体细菌基因组的进化提供了新的见解，更广泛地为水平获得的基因整合到转录组中提供了新的见解。
