Analysis of distribution indicates diverse functions of simple sequence repeats in Mycoplasma genomes

• Published in: Molecular biology and evolution Vol. 23; no. 7; pp. 1370 - 1385
• Main Author: Mrazek, Jan
• Format: Journal Article
• Language: English
• Published: United States 01-07-2006
• Subjects: Base Sequence; Databases, Nucleic Acid; Evolution, Molecular; Genes, Bacterial - genetics; Genome, Bacterial - genetics; Molecular Sequence Data; Mollicutes; Mycoplasma - genetics; Mycoplasma hyopneumoniae; Mycoplasma hyopneumoniae - genetics; Mycoplasma mobile; Mycoplasma penetrans; Mycoplasma pulmonis; Mycoplasma pulmonis - genetics; Mycoplasma synoviae; Open Reading Frames - genetics; Repetitive Sequences, Nucleic Acid - genetics
• ISSN: 0737-4038; 1537-1719
• DOI: 10.1093/molbev/msk023

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.