Lafay B, Lloyd A T, McLean M J, Devine K M, Sharp P M, Wolfe K H
Division of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
Nucleic Acids Res. 1999 Apr 1;27(7):1642-9. doi: 10.1093/nar/27.7.1642.
The genomes of the spirochaetes Borrelia burgdorferi and Treponema pallidum show strong strand-specific skews in nucleotide composition, with the leading strand in replication being richer in G and T than the lagging strand in both species. This mutation bias results in codon usage and amino acid composition patterns that are significantly different between genes encoded on the two strands, in both species. There are also substantial differences between the species, with T.pallidum having a much higher G+C content than B. burgdorferi. These changes in amino acid and codon compositions represent neutral sequence change that has been caused by strong strand- and species-specific mutation pressures. Genes that have been relocated between the leading and lagging strands since B. burgdorferi and T.pallidum diverged from a common ancestor now show codon and amino acid compositions typical of their current locations. There is no evidence that translational selection operates on codon usage in highly expressed genes in these species, and the primary influence on codon usage is whether a gene is transcribed in the same direction as replication, or opposite to it. The dnaA gene in both species has codon usage patterns distinctive of a lagging strand gene, indicating that the origin of replication lies downstream of this gene, possibly within dnaN. Our findings strongly suggest that gene-finding algorithms that ignore variability within the genome may be flawed.
疏螺旋体伯氏疏螺旋体和梅毒螺旋体的基因组在核苷酸组成上表现出强烈的链特异性偏倚，在这两个物种中，复制中的前导链比滞后链富含更多的鸟嘌呤（G）和胸腺嘧啶（T）。这种突变偏向导致了密码子使用和氨基酸组成模式在两条链上编码的基因之间存在显著差异，在这两个物种中都是如此。这两个物种之间也存在很大差异，梅毒螺旋体的鸟嘌呤与胞嘧啶（G+C）含量比伯氏疏螺旋体高得多。氨基酸和密码子组成的这些变化代表了由强烈的链特异性和物种特异性突变压力引起的中性序列变化。自伯氏疏螺旋体和梅毒螺旋体从共同祖先分化以来，在前导链和滞后链之间重新定位的基因现在显示出其当前位置典型的密码子和氨基酸组成。没有证据表明翻译选择作用于这些物种中高表达基因的密码子使用，对密码子使用的主要影响是基因转录方向与复制方向相同还是相反。这两个物种中的dnaA基因具有滞后链基因特有的密码子使用模式，表明复制起点位于该基因的下游，可能在dnaN内。我们的研究结果强烈表明，忽略基因组内变异性的基因寻找算法可能存在缺陷。
