Identification and characterization of simple sequence repeats in the genomes of Shigella species.
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.
Yang
Jian
J
Laboratory of Bioinformatics, Institute of Biophysics, CAS, Datun Road 15, Chaoyang District, 100101 Beijing, China.
Wang
Jinhua
J
Chen
Lihong
L
Yu
Jun
J
Dong
Jie
J
Yao
Zhi Jian
ZJ
Shen
Yan
Y
Jin
Qi
Q
Chen
Runsheng
R
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005287:Ferredoxin-NADP Reductase / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D018895:Microsatellite Repeats / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D011110:Polymorphism, Genetic; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D012703:Serotyping; D012760:Shigella / Q000145:classification / Q000235:genetics*; D012761:Shigella boydii / Q000235:genetics; D012762:Shigella dysenteriae / Q000235:genetics; D012763:Shigella flexneri / Q000235:genetics; D012764:Shigella sonnei / Q000235:genetics; D013045:Species Specificity
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D021122:Protein Subunits; D005287:Ferredoxin-NADP Reductase