Bergholz Teresa M, Tarr Cheryl L, Christensen Lisa M, Betting David J, Whittam Thomas S
Microbial Evolution Laboratory, National Food Safety & Toxicology Center, Michigan State University, East Lansing, USA.
Mol Biol Evol. 2007 Oct;24(10):2323-33. doi: 10.1093/molbev/msm163. Epub 2007 Aug 4.
Escherichia coli have evolved adaptive systems to resist strongly acidic habitats in part through the production of 2 biochemically identical isoforms of glutamate decarboxylase (GAD), encoded by the gadA and gadB genes. These genes occur in E. coli and other members of the genospecies (e.g., Shigella spp.) and originated as part of a genomic fitness island acquired early in Escherichia evolution. The present duplicated gad loci are widely spaced on the E. coli chromosome, and the 2 genes are 97% similar in sequence. Comparison of the nucleotide sequences of the gadA and gadB in 16 strains of pathogenic E. coli revealed 3.8% and 5.0% polymorphism in the 2 genes, respectively. Alignment of the homologous genes identified a total of 120 variable sites, including 21 fixed nucleotide differences between the loci within the first 82 codons of the genes. Twenty-three phylogenetically informative sites were polymorphic for the same nucleotides in both genes suggesting recent gene conversions or intergenic recombination. Phylogenetic analysis based on the synonymous substitutions per synonymous site indicated 2 cases in which specific gadA and gadB alleles were more closely related to one another than to other alleles at the corresponding locus. The results indicate that at least 3 gene conversion events have occurred after the gad gene duplication in the evolution of E. coli. Despite multiple gene conversion events, the upstream regulatory regions and the 5' end of each gene remains distinct, suggesting that maintaining functionally different gad genes is important in this acid-resistance mechanism in pathogenic E. coli.
大肠杆菌已经进化出适应性系统来抵抗强酸性环境，部分原因是通过产生由gadA和gadB基因编码的两种生化性质相同的谷氨酸脱羧酶（GAD）同工型。这些基因存在于大肠杆菌和该基因种的其他成员（如志贺氏菌属）中，并且起源于大肠杆菌进化早期获得的基因组适应性岛的一部分。目前重复的gad基因座在大肠杆菌染色体上相距很远，并且这两个基因的序列相似度为97%。对16株致病性大肠杆菌的gadA和gadB核苷酸序列进行比较，发现这两个基因的多态性分别为3.8%和5.0%。同源基因比对共鉴定出120个可变位点，包括在基因前82个密码子内两个基因座之间的21个固定核苷酸差异。23个系统发育信息位点在两个基因中相同核苷酸处呈多态性，表明最近发生了基因转换或基因间重组。基于每个同义位点的同义替换进行的系统发育分析表明，在2个案例中，特定的gadA和gadB等位基因彼此之间的关系比与相应基因座的其他等位基因更为密切。结果表明，在大肠杆菌进化过程中，gad基因复制后至少发生了3次基因转换事件。尽管发生了多次基因转换事件，但每个基因的上游调控区和5'端仍然不同，这表明在致病性大肠杆菌的这种抗酸机制中，维持功能不同的gad基因很重要。
