Canchaya Carlos, Fournous Ghislain, Brüssow Harald
Nestlé Research Centre, Nutrition and Health Department/Functional Microbiology Group, CH-1000 Lausanne 26 Vers-chez-les-Blanc, Switzerland.
Mol Microbiol. 2004 Jul;53(1):9-18. doi: 10.1111/j.1365-2958.2004.04113.x.
Prophages were automatically localized in sequenced bacterial genomes by a simple semantic script leading to the identification of 190 prophages in 115 investigated genomes. The distribution of prophages with respect to presence or absence in a given bacterial species, the location and orientation of the prophages on the replichore was not homogeneous. In bacterial pathogens, prophages are particularly prominent. They frequently encoded virulence genes and were major contributors to the genetic individuality of the strains. However, some commensal and free-living bacteria also showed prominent prophage contributions to the bacterial genomes. Lysogens containing multiple sequence-related prophages can experience rearrangements of the bacterial genome across prophages, leading to prophages with new gene constellations. Transfer RNA genes are the preferred chromosomal integration sites, and a number of prophages also carry tRNA genes. Prophage integration into protein coding sequences can lead to either gene disruption or new proteins. The phage repressor, immunity and lysogenic conversion genes are frequently transcribed from the prophage. The expression of the latter is sometimes integrated into control circuits linking prophages, the lysogenic bacterium and its animal host. Prophages are apparently as easily acquired as they are lost from the bacterial chromosome. Fixation of prophage genes seems to be restricted to those with functions that have been co-opted by the bacterial host.
通过一个简单的语义脚本，原噬菌体在已测序的细菌基因组中被自动定位，从而在115个被研究的基因组中鉴定出190个原噬菌体。原噬菌体在特定细菌物种中存在与否的分布、原噬菌体在复制子上的位置和方向并不均匀。在细菌病原体中，原噬菌体尤为突出。它们经常编码毒力基因，是菌株遗传个体性的主要贡献者。然而，一些共生菌和自由生活细菌的基因组中也有显著的原噬菌体成分。含有多个序列相关原噬菌体的溶原菌可能会经历跨原噬菌体的细菌基因组重排，从而产生具有新基因组合的原噬菌体。转运RNA基因是首选的染色体整合位点，许多原噬菌体也携带转运RNA基因。原噬菌体整合到蛋白质编码序列中可能导致基因破坏或产生新蛋白质。噬菌体阻遏物、免疫和溶原转换基因经常从原噬菌体转录。后者的表达有时会整合到连接原噬菌体、溶原菌及其动物宿主的控制回路中。原噬菌体显然既容易从细菌染色体上获得，也容易丢失。原噬菌体基因的固定似乎仅限于那些其功能已被细菌宿主所利用的基因。
