takeuchiETAL_table-S2_ESM.xlsx from Prophages and plasmids can display opposite trends in the types of accessory genes they carry

Mobile genetic elements (MGEs), such as phages and plasmids, often possess accessory genes encoding bacterial functions, facilitating bacterial evolution. Are there rules governing the arsenal of accessory genes MGEs carry? If such rules exist, they might be reflected in the types of accessory genes different MGEs carry. To test this hypothesis, we compare prophages and plasmids with respect to the frequencies at which they carry antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the genomes of 21 pathogenic bacterial species using public databases. Our results indicate that prophages tend to carry VFGs more frequently than ARGs in three species, whereas plasmids tend to carry ARGs more frequently than VFGs in nine species, relative to genomic backgrounds. In Escherichia coli, where this prophage-plasmid disparity is detected, prophage-borne VFGs encode a much narrower range of functions than do plasmid-borne VFGs, typically involved in damaging host cells or modulating host immunity. In the species where the above disparity is not detected, ARGs and VFGs are barely found in prophages and plasmids. These results indicate that MGEs can differentiate in the types of accessory genes they carry depending on their infection strategies, suggesting a rule governing horizontal gene transfer mediated by MGEs.

可移动遗传元件（Mobile genetic elements, MGEs）如噬菌体与质粒，通常携带有编码细菌功能的附属基因，进而助力细菌演化。可移动遗传元件所携带的附属基因库是否存在特定的调控规律？若存在此类规律，则可能体现在不同可移动遗传元件所携带的附属基因类型差异之中。为验证这一假说，本研究依托公共数据库，针对21种病原细菌的基因组，对比前噬菌体与质粒各自携带抗生素抗性基因（ARGs）与毒力因子基因（VFGs）的频率差异。研究结果表明，相较于基因组背景，有3个物种的前噬菌体携带毒力因子基因的频率显著高于抗生素抗性基因，而9个物种的质粒携带抗生素抗性基因的频率显著高于毒力因子基因。在观察到上述前噬菌体-质粒差异的大肠杆菌（Escherichia coli）中，前噬菌体携带的毒力因子基因所编码的功能范围远窄于质粒携带的毒力因子基因，其功能通常涉及宿主细胞损伤或宿主免疫调控。在未观察到上述差异的物种中，前噬菌体与质粒几乎均未携带抗生素抗性基因与毒力因子基因。上述结果表明，可移动遗传元件可依据自身感染策略，在携带的附属基因类型上产生分化，这提示存在一条由可移动遗传元件介导的水平基因转移调控规律。