Bakkali M, Chen T-Y, Lee H C, Redfield R J
Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4.
Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4513-8. doi: 10.1073/pnas.0306366101. Epub 2004 Mar 19.
The DNA-uptake signal sequence (USS) of the bacterium Haemophilus influenzae is highly over-represented in its genome (1,471 copies of the core sequence AAGTGCGGT), and DNA fragments containing USS are preferentially taken up by competent cells. Because this bias favors uptake of conspecific DNA, USSs are often considered a kind of mate recognition system in bacteria, acting as species-specific barriers against uptake of unrelated DNA. However, the H. influenzae USS is highly over-represented in the genomes of three otherwise-divergent Pasteurellaceae species (Pasteurella multocida, Haemophilus somnus, and Actinobacillus actinomycetemcomitans, 927, 1,205, and 1,760 copies, respectively), suggesting that USSs do not always limit exchange. USSs in all these genomes are mainly in coding regions and show no orientation bias around the chromosome, weakening proposed USS functions in transcription termination and chromosome replication. Alignment of homologous genes was used to determine evolutionary relationships between individual USSs. Most H. influenzae USSs were found to have perfect or imperfect homologs (USS at the same location) in at least one other species, and most USSs in the other species had perfect or imperfect homologs in H. influenzae. These homologies suggest that the use of a common USS is due to inheritance of the USS-based uptake system from a common ancestor of the Pasteurellaceae, and it indicates that individual USSs can be evolutionarily stable elements of their genomes. The pattern is consistent with a molecular drive model of USS evolution, with new USSs arising by mutation and preferentially spread to new genomes by the biased DNA-uptake system.
流感嗜血杆菌的DNA摄取信号序列（USS）在其基因组中高度富集（核心序列AAGTGCGGT有1471个拷贝），含有USS的DNA片段会被感受态细胞优先摄取。由于这种偏向性有利于摄取同种DNA，USS通常被认为是细菌中的一种配偶识别系统，作为物种特异性屏障阻止无关DNA的摄取。然而，流感嗜血杆菌的USS在另外三种不同的巴斯德菌科物种（多杀巴斯德菌、睡眠嗜血杆菌和伴放线放线杆菌，分别有927、1205和1760个拷贝）的基因组中也高度富集，这表明USS并不总是限制基因交换。所有这些基因组中的USS主要位于编码区，且在染色体周围没有方向偏向性，这削弱了USS在转录终止和染色体复制中所提出的功能。通过同源基因比对来确定各个USS之间的进化关系。发现大多数流感嗜血杆菌的USS在至少一个其他物种中具有完美或不完美的同源物（位于相同位置的USS），并且其他物种中的大多数USS在流感嗜血杆菌中也有完美或不完美的同源物。这些同源性表明，使用共同的USS是由于基于USS的摄取系统从巴斯德菌科的共同祖先那里继承而来，这表明单个USS在其基因组中可以是进化上稳定的元件。这种模式与USS进化的分子驱动模型一致，新的USS通过突变产生，并通过有偏向性的DNA摄取系统优先传播到新的基因组中。
