Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner

The binding of proteins can shield DNA from mutagenic processes but also interfere with efficient repair. How the presence of DNA-binding proteins shapes intra-genomic differences in mutability and, ultimately, sequence variation in natural populations, however, remains poorly understood. In this study, we examine sequence evolution in Escherichia coli in relation to the binding of four abundant nucleoid-associated proteins: Fis, H-NS, IhfA, and IhfB. We find that, for a subset of mutations, protein occupancy is associated with both increased and decreased mutability in the underlying sequence depending on when the protein is bound during the bacterial growth cycle. On average, protein-bound DNA exhibits reduced mutability compared to protein-free DNA. However, this net protective effect is weak and can be abolished or even reversed during stages of colony growth where binding coincides – and hence likely interferes with – DNA repair activity. We suggest that the four nucleoid-associated proteins analyzed here have played a minor but significant role in patterning extant sequence variation in E. coli.

蛋白质结合既可保护DNA免受诱变过程的侵害，同时也会干扰DNA的高效修复。然而，DNA结合蛋白的存在如何塑造基因组内的突变率差异，并最终影响自然种群中的序列变异，这一问题迄今仍未得到充分阐释。本研究针对四种丰度较高的类核关联蛋白（nucleoid-associated proteins）：Fis、H-NS、IhfA与IhfB的结合情况，分析了大肠杆菌（Escherichia coli）的序列演化特征。研究发现，针对部分突变子集而言，蛋白结合位点与靶序列的突变率升降存在关联，具体关联模式取决于细菌生长周期中蛋白结合的时机。整体而言，结合了蛋白的DNA相较于未结合蛋白的DNA，其突变率更低。但这种整体保护效应较为微弱，在菌落生长的特定阶段，若蛋白结合与DNA修复活动同时发生（并因此可能干扰修复过程），该保护效应会被消除，甚至出现逆转。我们认为，本研究分析的四种类核关联蛋白，在塑造大肠杆菌现存序列变异模式的过程中，发挥了微弱却显著的作用。