The extent and characteristics of DNA transfer between plasmids and chromosomes

Plasmids are extrachromosomal genetic elements that reside in prokaryotes. The acquisition of plasmids encoding beneficial traits can facilitate short-term survival in harsh environmental conditions or long-term adaptation of new ecological niches. Due to their ability to transfer between cells, plasmids are considered agents of gene transfer. Nonetheless, the frequency of DNA transfer between plasmids and chromosomes remains understudied. Using a novel approach for detection of homologous loci between genome-pairs we uncover gene sharing with the chromosome in 1,974 (66%) plasmids residing in 1,016 (78%) taxonomically diverse isolates. The majority of homologous loci correspond to mobile elements, which may be duplicated in the host chromosomes in tens of copies. Neighboring shared genes often encode similar functional categories, indicating the transfer multigene functional units. Rare transfer events of antibiotics resistance genes are observed mainly with mobile elements. The frequent erosion of sequence similarity in homologous regions indicates that the transferred DNA is often devoid of function. DNA transfer between plasmids and chromosomes thus generates genetic variation that is akin to workings of endosymbiotic gene transfer in eukaryote evolution. Our findings imply that plasmid contribution to gene transfer most often corresponds to transfer of the plasmid entity rather than transfer of protein-coding genes between plasmids and chromosomes.

质粒（plasmid）是一类存在于原核生物（prokaryote）中的染色体外遗传因子。获得编码有益性状的质粒，可帮助宿主在严苛环境条件下实现短期存活，或长期适应全新生态位。由于质粒能够在细胞间进行转移，因此被视为基因转移的载体。尽管如此，质粒与染色体之间的DNA转移频率仍未得到充分研究。本研究采用一种用于检测基因组对间同源基因座（homologous locus）的全新方法，对1016株（占比78%）分类学背景多样的分离株所携带的1974个质粒展开分析，结果显示其中66%的质粒存在与宿主染色体共享的基因。大多数同源基因座对应可移动遗传因子（mobile element），这类因子可在宿主染色体中以数十个拷贝的形式存在。相邻的共享基因往往编码功能类别相近的蛋白，这表明转移的是多基因功能单位。抗生素抗性基因（antibiotic resistance gene）的转移事件较为罕见，且主要与可移动遗传因子相关。同源区域间的序列相似性常会发生衰减，这表明转移而来的DNA往往丧失了功能。由此可见，质粒与染色体间的DNA转移所产生的遗传变异，与真核生物（eukaryote）演化过程中内共生基因转移（endosymbiotic gene transfer）的作用机制类似。本研究结果表明，质粒在基因转移中的作用，大多体现为质粒整体的转移，而非质粒与染色体间的蛋白质编码基因转移。