Most bacterial gene families are biased toward specific chromosomal positions

The arrangement of genes along bacterial chromosomes influences their expression through growth rate-dependent gene copy number changes during DNA replication. While translation and transcription genes often cluster near the origin of replication, the extent of positional biases across gene families remains unclear. We hypothesized that natural selection broadly favors specific chromosomal positions to optimize growth rate-dependent expression. Analyzing 910 bacterial species and proteomics data from Escherichia coli and Bacillus subtilis, we find that about two-thirds of bacterial gene families are positionally biased, mainly near the origin or terminus of replication, with the strongest natural selection in fast-growing species. Our findings reveal chromosomal positioning as a fundamental mechanism for coordinating gene expression with growth rate, highlighting evolutionary constraints on bacterial genome architecture.

细菌染色体上的基因排布会通过DNA复制过程中依赖于生长速率的基因拷贝数变化，影响基因的表达水平。尽管与翻译、转录相关的基因通常聚集在复制起点（origin of replication）附近，但不同基因家族间的位置偏好程度仍不明确。我们提出假说：自然选择整体上偏好特定的染色体位置，以优化依赖于生长速率的基因表达。通过分析910种细菌的基因组数据以及大肠杆菌（Escherichia coli）、枯草芽孢杆菌（Bacillus subtilis）的蛋白质组数据，我们发现约三分之二的细菌基因家族存在位置偏好性，主要集中在复制起点或复制终点（terminus of replication）附近，且在快速生长的物种中自然选择作用最强。本研究结果表明，染色体排布是协调基因表达与生长速率的核心机制之一，同时也凸显了细菌基因组结构所受的进化约束。