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Simple sequence repeats in prokaryotic genomes.

Jan Mrázek1, Xiangxue Guo, Apurva Shah

  • 1Department of Microbiology, University of Georgia, Athens, GA 30602, USA. mrazek@uga.edu

Proceedings of the National Academy of Sciences of the United States of America
|May 9, 2007
PubMed
Summary
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Long simple sequence repeats (SSRs) in prokaryotes differ based on length. Short SSRs (LSSR(1-4)) are found in pathogens and likely selected, while longer SSRs (LSSR(5-11)) are common in nonpathogens.

Area of Science:

  • Genomics
  • Microbial genetics
  • Bioinformatics

Background:

  • Simple sequence repeats (SSRs) are repetitive DNA sequences with potential functional and structural roles.
  • Long SSRs (LSSRs) are prevalent in eukaryotes but scarce in prokaryotes.
  • SSRs can influence pathogen evolution by modulating antigenic variance against host immunity.

Purpose of the Study:

  • To analyze SSR distribution across >300 prokaryotic genomes.
  • To investigate differences in SSR types and their prevalence among prokaryotes.
  • To correlate SSR characteristics with prokaryotic lifestyles (pathogenic vs. nonpathogenic).

Main Methods:

  • Bioinformatic analysis of SSRs in a large dataset of prokaryotic genomes.
  • Classification of SSRs based on oligonucleotide repeat length (1-4 bp for LSSR(1-4) and 5-11 bp for LSSR(5-11)).

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  • Comparative analysis of SSR frequencies in relation to genome size and host adaptation.

    • Main Results:

    • Significant variations in SSR representation were observed among different prokaryotic species and SSR types.
    • LSSR(1-4) were predominantly found in host-adapted pathogens with reduced genomes.
    • LSSR(5-11) were more common in nonpathogens and opportunistic pathogens with larger genomes.

    Conclusions:

    • LSSR(1-4) appear to be maintained by selection, potentially for antigenic variation in pathogens.
    • The abundance of LSSR(5-11) may be due to general DNA expansion rather than specific adaptive roles.
    • SSR patterns provide insights into prokaryotic genome evolution and adaptation strategies.