PDF(Pubmed)
Abstract：
On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of \"hybrid\" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell\'s information content.
摘要：
在圆形细菌染色体上，大多数基因都在前导链上编码。这种基因链偏倚（GSB）的范围从某些芽孢杆菌的85％到其他门的50％以上。决定链偏倚程度的因素仍有待发现。这里,我们报告说，Gemmaatimonadota门的物种具有独特的染色体结构，与邻近的门不同：在复制末端周围的保守的600kb区域中，几乎所有基因都位于前导链，而在染色体的剩余部分，链偏好更平衡。高链偏倚（HSB）区域包含rRNA簇，核心,和高度表达的基因。减少与DNA复制碰撞以最小化有害突变的选择性压力可以解释该区域中必需基因的保守性。重复性和流动性因素代表性不足，表明通过与染色体其他部分的结构分离来降低重组频率。我们建议HSB区形成不同的染色体结构域。Gemmaatimonadota染色体主要是通过水平基因转移和古代高链偏向区域之外的重复进行扩展而进化的。为了支持我们的假设，我们可以在相似的进化路径上进一步鉴定出两种螺旋体菌株。重要细菌染色体，基因在前导链上的优选位置已经进化以减少复制和转录之间的冲突。尽管进行了大量的研究，为什么细菌在基因链偏倚上表现出巨大差异的问题仍然没有解决。在不同的门中发现了“杂种”染色体，包括Gemmatimonadota,其中保守的高链偏倚仅在一个区域中发现，指向类核苷酸结构的作用，除了复制，在链偏好的演变中。对不断增加的可用细菌基因组数量的细粒度结构分析可以帮助更好地理解形成细胞信息内容的顺序和空间组织的力量。
