Identification and characterization of simple sequence repeats in the genomes of Shigella species

Jian Yang, Jinhua Wang, Lihong Chen, Jun Yu, Jie Dong, Zhi Jian Yao, Yan Shen, Qi Jin, Runsheng Chen

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

A variety of simple sequence repeats (SSRs) have been identified in the genome of Shigella flexneri serotype 2a (strain Sf301), an enteric pathogen that causes bacillary dysentery in man. The distribution of SSRs, with unit length ranging from 1 to 9 nucleotides, was biased in different regions of the genome. The tri-, tetra- and hexanucleotide SSRs prevailed in the coding regions while the mono- and dinucleotide SSRs were more common in the noncoding regions. Many intergenic SSRs are less than 30 bp away from the downstream open reading frames (ORFs), suggesting a potential role in transcriptional regulation. To study polymorphism of SSRs, we compared 17 coding-region SSRs from strain Sf301 with the corresponding sequences from 23 other strains of four Shigella species. Five chromosomal loci were found to be polymorphic, of which those from S. flexneri strains were most variable. Particularly interesting is the C5-1 locus in the coding sequence of the hcaD gene encoding a subunit of ferredoxin reductase. Depending on the insertion of variable numbers of the unit sequence (CGCAG), the Shigella hcaD genes can encode truncated products due to premature stop codons or frame shifts, or products with extended core alpha helices that leads to radical alterations in the predicted tertiary structure. Hence, SSRs may serve as genotyping markers for epidemiological investigations, and may offer insights into evolutionary adaptation of the pathogens.

Original languageEnglish (US)
Pages (from-to)85-92
Number of pages8
JournalGene
Volume322
Issue number1-2
DOIs
StatePublished - Dec 11 2003

Bibliographical note

Funding Information:
We thank Moqing Liu, Hong Liu and Fan Yang for their technical assistance, and Peadar O'Gaora and Kathy Smollett for their critical reading of the manuscript. This work is supported by the Chinese Academy of Sciences (grant no. KSCX2-2-07), and the National High Technology Development Program of China (grant no. 2002AA231031).

Keywords

  • Distribution
  • Polymorphism
  • SSR
  • Tandem repeat

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