Shapiro B Jesse, Alm Eric
Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
ISME J. 2009 Oct;3(10):1180-92. doi: 10.1038/ismej.2009.51. Epub 2009 May 21.
Different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. Thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. We used the ratio of substitutions in slow- versus fast-evolving sites (nucleotides in DNA, or amino acids in protein sequence) to quantify deviations from the typical pattern of selective constraint observed across bacterial lineages. We propose that elevated S:F in one branch (an excess of slow-site substitutions) can indicate a functionally relevant change, due to either positive selection or relaxed evolutionary constraint. In a genome-wide comparative study of gamma-proteobacterial proteins, we find that cell-surface proteins involved with motility and secretion functions often have high S:F ratios, whereas information-processing genes do not. Change in evolutionary constraints in some species is evidenced by increased S:F ratios within functionally related sets of genes (for example, energy production in Pseudomonas fluorescens), whereas other species apparently evolve mostly by drift (for example, uniformly elevated S:F across most genes in Buchnera spp.). Overall, S:F reveals several species-specific, protein-level changes with potential functional/ecological importance. As microbial genome projects yield more species-rich gene trees, the S:F ratio will become an increasingly powerful tool for uncovering functional genetic differences among species.
不同的微生物物种被认为占据着不同的生态位，每个物种都受到独特的选择限制，这可能会在它们的基因组中留下可识别的信号。因此，通过识别直系同源基因或蛋白质序列中不寻常的替换模式，有可能深入了解不同谱系间生态差异的遗传基础。我们使用慢进化位点与快进化位点（DNA中的核苷酸或蛋白质序列中的氨基酸）的替换率，来量化与细菌谱系中观察到的典型选择限制模式的偏差。我们提出，一个分支中S:F升高（慢位点替换过多）可能表明由于正选择或进化限制放松而导致的功能相关变化。在一项对γ-变形菌蛋白质的全基因组比较研究中，我们发现与运动和分泌功能相关的细胞表面蛋白通常具有较高的S:F比率，而信息处理基因则不然。一些物种中进化限制的变化表现为功能相关基因集内S:F比率增加（例如荧光假单胞菌中的能量产生），而其他物种显然主要通过漂变进化（例如布赫纳氏菌属大多数基因中S:F普遍升高）。总体而言，S:F揭示了几种具有潜在功能/生态重要性的物种特异性蛋白质水平变化。随着微生物基因组计划产生更多物种丰富的基因树，S:F比率将成为揭示物种间功能遗传差异的越来越强大的工具。
