Simple sequence repeats in mycobacterial genomes.

Area of Science:

• Genomics
• Molecular Biology
• Microbial Genetics

Background:

• Simple sequence repeats (SSRs), also known as microsatellites, are repetitive DNA sequences found across all life forms.
• Microsatellites are prone to mutations, particularly insertions and deletions (INDELs), which can alter genome structure and plasticity.
• Prokaryotic genomes typically possess DNA repair systems, like MutL, MutH, and MutS, to manage microsatellite instability.

Purpose of the Study:

• To investigate the distribution and abundance of SSRs in key mycobacterial genomes.
• To explore the potential for microsatellite polymorphism in mycobacteria.
• To understand how mycobacterial genomes manage microsatellite stability in the absence of canonical post-replicative repair enzymes.

Main Methods:

• Bioinformatic analysis of available mycobacterial genomes (Mycobacterium avium, M. leprae, M. bovis, and two strains of M. tuberculosis).
• Quantification of SSR frequencies and abundance across the genomes.
• Comparative analysis of SSR distribution patterns.

Main Results:

• SSRs are prevalent in mycobacterial genomes, averaging 220-230 tracts per kb.
• Specific genomic regions exhibit unusually high or low microsatellite densities.
• Despite lacking MutL/MutH/MutS repair systems, mycobacterial genomes show a marked scarcity of long microsatellites.

Conclusions:

• The absence of long microsatellites in mycobacteria is likely due to strong selective pressures against unstable sequences.
• While GC-content and point mutations may play a role, selection appears to be the primary driver of microsatellite tract length regulation.
• The occasional presence of long SSRs in coding and non-coding regions may contribute to limited genome plasticity in mycobacteria.