Data_Sheet_1_Evolution of the Natural Transformation Protein, ComEC, in Bacteria.pdf

Natural transformation enables the incorporation of exogenous DNA into host genomes and plays a fundamental role in the evolution of microbial populations. At the center of the natural transformation machinery, the ComEC protein mediates DNA import and serves potential functions in DNA recognition and single strand degradation. Despite its importance, the evolution of ComEC is not fully understood. Here, we aim to fill this knowledge gap by surveying putative ComEC proteins across 5,574 bacteria that span diverse phyla. We first derived the presence of a universal, core Competence domain through the analysis of ComEC proteins from known naturally competent species. Then, we followed this observation to identify Competence domain containing proteins (CDCPs) from all bacteria and used CDCPs as putative ComEC proteins for evolutionary analysis. A near universal presence of CDCPs was revealed, with 89% of the proteomes and 96% of the genomes encoding a single CDCP or a CDCP-like fragment. Two domains, DUF4131 and Lactamase_B, were found to commonly co-occur with the Competence domain. Ancestral state reconstruction of CDCPs over the bacterial species phylogeny suggested an origin of a Competence-only domain profile, while multiple gains and losses of the DUF4131 and Lactamase_B domains were observed among diverse bacterial lineages.

自然转化机制允许外源DNA整合至宿主基因组中，并在微生物群体的进化过程中发挥着至关重要的作用。自然转化机制的核心，ComEC蛋白介导DNA的导入，并在DNA识别和单链降解中发挥潜在功能。尽管其重要性不言而喻，ComEC的进化过程尚不完全明了。本研究旨在填补这一知识空白，通过对跨越不同门类的5,574种细菌中假定的ComEC蛋白进行调研。首先，我们通过分析已知自然转化物种的ComEC蛋白，推导出普遍存在的、核心的转化能力结构域。随后，我们基于这一观察结果，从所有细菌中识别出包含转化能力结构域的蛋白（CDCPs），并将其作为假定的ComEC蛋白用于进化分析。研究揭示，CDCPs的近普遍存在，其中89%的蛋白质组和96%的基因组编码单个CDCP或类似片段。研究发现，DUF4131和β-内酰胺酶结构域通常与转化能力结构域共同出现。通过对细菌物种系统发育树中CDCPs的祖先状态重建，推测了仅包含转化能力结构域的起源，同时在不同的细菌谱系中观察到DUF4131和β-内酰胺酶结构域的多次获得和丢失。