PDF(Pubmed)
Abstract：
Despite the critical role of bacterial cell walls in maintaining cell shapes, certain environmental stressors can induce the transition of many bacterial species into a wall-deficient state called L-form. Long-term induced Escherichia coli L-forms lose their rod shape and usually hold significant mutations that affect cell division and growth. Besides this, the genetic background of L-form bacteria is still poorly understood. In the present study, the genomes of two stable L-form strains of E. coli (NC-7 and LWF+) were sequenced and their gene mutation status was determined and compared with their parental strains. Comparative genomic analysis between two L-forms reveals both unique adaptions and common mutated genes, many of which belong to essential gene categories not involved in cell wall biosynthesis, indicating that L-form genetic adaptation impacts crucial metabolic pathways. Missense variants from L-forms and Lenski\'s long-term evolution experiment (LTEE) were analyzed in parallel using an optimized DeepSequence pipeline to investigate predicted mutation effects (α) on protein functions. We report that the two L-form strains analyzed display a frequency of 6-10% (0% for LTEE) in mutated essential genes where the missense variants have substantial impact on protein functions (α<0.5). This indicates the emergence of different survival strategies in L-forms through changes in essential genes during adaptions to cell wall deficiency. Collectively, our results shed light on the detailed genetic background of two E. coli L-forms and pave the way for further investigations of the gene functions in L-form bacterial models.
摘要：
尽管细菌细胞壁在维持细胞形状中起着关键作用，某些环境压力可以诱导许多细菌物种转变为称为L型的壁缺陷状态。长期诱导的大肠杆菌L型失去其杆状，通常具有影响细胞分裂和生长的重要突变。除此之外,L型细菌的遗传背景仍然知之甚少。在这项研究中,对两种稳定的大肠杆菌L型菌株(NC-7和LWF+)的基因组进行测序,确定其基因突变状态,并与其亲本菌株进行比较.两种L型之间的比较基因组分析揭示了独特的适应和常见的突变基因，其中许多属于不参与细胞壁生物合成的必需基因类别，表明L型遗传适应影响关键的代谢途径。使用优化的DeepSequence管道平行分析了L型和Lenski长期进化实验（LTEE）的错义变体，以研究预测的突变对蛋白质功能的影响（α）。我们报告，分析的两个L型菌株在突变的必需基因中显示出6％-10％（LTEE为0％）的频率，其中错义变体对蛋白质功能具有实质性影响（α<0.5）。这表明在适应细胞壁缺陷期间，通过必需基因的变化，L型中出现了不同的生存策略。总的来说，我们的研究结果揭示了两种大肠杆菌L型的详细遗传背景,并为进一步研究L型细菌模型中的基因功能铺平了道路.
