Mrázek Jan
Department of Microbiology and Institute of Bioinformatics, University of Georgia, USA.
Mol Biol Evol. 2006 Jul;23(7):1370-85. doi: 10.1093/molbev/msk023. Epub 2006 Apr 17.
Simple sequence repeats (SSRs) composed of extensive tandem iterations of a single nucleotide or a short oligonucleotide are rare in most bacterial genomes, but they are common among Mycoplasma. Some of these repeats act as contingency loci in association with families of surface antigens. By contraction or expansion during replication, these SSRs increase genetic variance of the population and facilitate avoidance of the immune response of the host. Occurrence and distribution of SSRs are analyzed in complete genomes of 11 Mycoplasma and 3 related Mollicutes in order to gain insights into functional and evolutionary diversity of the SSRs in Mycoplasma. The results revealed an unexpected variety of SSRs with respect to their distribution and composition and suggest that it is unlikely that all SSRs function as contingency loci or recombination hot spots. Various types of SSRs are most abundant in Mycoplasma hyopneumoniae, whereas Mycoplasma penetrans, Mycoplasma mobile, and Mycoplasma synoviae do not contain unusually long SSRs. Mycoplasma hyopneumoniae and Mycoplasma pulmonis feature abundant short adenine and thymine runs periodically spaced at 11 and 12 bp, respectively, which likely affect the supercoiling propensities of the DNA molecule. Physiological roles of long adenine and thymine runs in M. hyopneumoniae appear independent of location upstream or downstream of genes, unlike contingency loci that are typically located in protein-coding regions or upstream regulatory regions. Comparisons among 3 M. hyopneumoniae strains suggest that the adenine and thymine runs are rarely involved in genome rearrangements. The results indicate that the SSRs in the Mycoplasma genomes play diverse roles, including modulating gene expression as contingency loci, facilitating genome rearrangements via recombination, affecting protein structure and possibly protein-protein interactions, and contributing to the organization of the DNA molecule in the cell.
由单个核苷酸或短寡核苷酸的广泛串联重复组成的简单序列重复（SSRs）在大多数细菌基因组中很少见，但在支原体中很常见。其中一些重复序列作为与表面抗原家族相关的应急位点。通过复制过程中的收缩或扩展，这些SSRs增加了群体的遗传变异，并有助于避免宿主的免疫反应。分析了11种支原体和3种相关柔膜菌纲细菌的全基因组中SSRs的发生和分布情况，以便深入了解支原体中SSRs的功能和进化多样性。结果揭示了SSRs在分布和组成方面出人意料的多样性，并表明并非所有的SSRs都作为应急位点或重组热点发挥作用。各种类型的SSRs在猪肺炎支原体中最为丰富，而穿透支原体、运动支原体和滑膜支原体则不含有异常长的SSRs。猪肺炎支原体和肺支原体的特征是分别以11和12个碱基对的间隔周期性出现丰富的短腺嘌呤和胸腺嘧啶序列，这可能会影响DNA分子的超螺旋倾向。与通常位于蛋白质编码区或上游调控区的应急位点不同，猪肺炎支原体中长腺嘌呤和胸腺嘧啶序列的生理作用似乎与基因上游或下游的位置无关。对3株猪肺炎支原体菌株的比较表明，腺嘌呤和胸腺嘧啶序列很少参与基因组重排。结果表明，支原体基因组中的SSRs发挥着多种作用，包括作为应急位点调节基因表达、通过重组促进基因组重排、影响蛋白质结构以及可能的蛋白质-蛋白质相互作用，以及有助于细胞中DNA分子的组织。
