Hershberg Ruth, Tang Hua, Petrov Dmitri A
Department of Biological Sciences, Stanford University, Serra Mall, Stanford, CA 94305, USA.
Genome Biol. 2007;8(8):R164. doi: 10.1186/gb-2007-8-8-r164.
Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given to the causes of increased gene loss in facultative pathogens.
We examined in detail the rate of gene loss in two groups of facultative pathogenic bacteria: pathogenic Escherichia coli, and Shigella. We show that Shigella strains are losing genes at an accelerated rate relative to pathogenic E. coli. We demonstrate that a genome-wide reduction in the effectiveness of selection contributes to the observed increase in the rate of gene loss in Shigella.
When compared with their closely related pathogenic E. coli relatives, the more niche-limited Shigella strains appear to be losing genes at a significantly accelerated rate. A genome-wide reduction in the effectiveness of purifying selection plays a role in creating this observed difference. Our results demonstrate that differences in the effectiveness of selection contribute to differences in rate of gene loss in facultative pathogenic bacteria. We discuss how the lifestyle and pathogenicity of Shigella may alter the effectiveness of selection, thus influencing the rate of gene loss.
与兼性病原菌相比，专性病原菌丢失的基因更多，而兼性病原菌丢失的基因又比自由生活的细菌更多。有人提出，专性病原菌中基因丢失增加可能是由于纯化选择效率降低所致。对于兼性病原菌中基因丢失增加的原因关注较少。
我们详细研究了两组兼性病原菌的基因丢失率：致病性大肠杆菌和志贺氏菌。我们发现，相对于致病性大肠杆菌，志贺氏菌菌株的基因丢失速度正在加快。我们证明，全基因组选择效率的降低导致了志贺氏菌中观察到的基因丢失率增加。
与亲缘关系密切的致病性大肠杆菌相比，生态位限制更强的志贺氏菌菌株似乎正在以显著加快的速度丢失基因。全基因组纯化选择效率的降低在造成这种观察到的差异中起了作用。我们的结果表明，选择效率的差异导致了兼性病原菌基因丢失率的差异。我们讨论了志贺氏菌的生活方式和致病性如何改变选择效率，从而影响基因丢失率。
