Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America ; Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.
PLoS One. 2013 Nov 29;8(11):e81016. doi: 10.1371/journal.pone.0081016. eCollection 2013.
Presence of overlapping genes (OGs) is a common phenomenon in bacterial genomes. Most frequently, overlapping genes share coding regions with as few as one nucleotide to as many as thousands of nucleotides. Overlapping genes are often co-regulated, transcriptionally and translationally. Overlapping genes are also subject to the whims of evolution, as the gene overlap is known to be disrupted in some species/strains and participating genes are sometimes lost in independent lineages. Therefore, a better understanding of evolutionary patterns and rates of the disruption of overlapping genes is an important component of genome structure and evolution of gene function. In this study, we investigate the fate of ancestrally overlapping genes in complete genomes from 15 contemporary strains of Salmonella species. We find that the fates of overlapping genes inside and outside operons are distinctly different. A larger fraction of overlapping genes inside operons conserves their overlap as compared to gene pairs outside of the operons (average 0.89 vs. 0.83 per genome). However, when overlapping genes in the operons separate, one partner is lost more frequently than in those separated genes outside of operons (average 0.02 vs. 0.01 per genome). We also investigate the fate of a pan set of overlapping genes at the present and ancestral nodes over a phylogenetic tree based on genome sequence data, respectively. We propose that co-regulation plays important roles on the fates of genes. Furthermore, a vast majority of disruptions occurred prior to the common ancestor of all 15 Salmonella strains, which enables us to obtain an estimate of disruptions between Salmonella and E. coli.
重叠基因 (OGs) 的存在是细菌基因组中的常见现象。最常见的是，重叠基因的编码区只有一个核苷酸到数千个核苷酸的重叠。重叠基因通常在转录和翻译上是共调控的。重叠基因也受到进化的影响，因为基因重叠在某些物种/菌株中被破坏，参与的基因在独立的谱系中有时会丢失。因此，更好地了解重叠基因的进化模式和破坏率是基因组结构和基因功能进化的重要组成部分。在这项研究中，我们调查了 15 个当代沙门氏菌种完整基因组中祖先重叠基因的命运。我们发现操纵子内和外重叠基因的命运明显不同。与操纵子外的基因对相比，操纵子内重叠基因保留其重叠的比例更大（每个基因组的平均值分别为 0.89 和 0.83）。然而，当操纵子内的重叠基因分离时，一个伙伴比操纵子外的分离基因更频繁地丢失（每个基因组的平均值分别为 0.02 和 0.01）。我们还分别基于基因组序列数据，在系统发育树上调查了重叠基因在当前和祖先节点处的命运。我们提出共调控在基因命运中起着重要作用。此外，绝大多数破坏发生在所有 15 株沙门氏菌的共同祖先之前，这使我们能够获得沙门氏菌和大肠杆菌之间的破坏估计值。
