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PMID: 16493139 Published · epublish English Comparative Study Journal Article Research Support, N.I.H., Intramural

Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands.

Nucleic acids research ·Vol. 34 ·No. 4 ·2006-00-00 ·Pages 1133-47

Chen Z, Schneider TD

Abstract

Based on molecular information theory, 10 T7-like promoter models were built for the T7 group of phages and used to scan their host genomes and closely related genomes. 38 genomes were scanned and 12 clusters of tandem promoters were identified in nine enteropathogens. Comparative analysis of these tandem promoter-bearing regions reveals that they are similar to each other, forming prophage-like islands of 4-13 kb. Each island appears to contain two or three tandem T7-like promoters within a stretch of 150-620 bases, but there are no corresponding RNA polymerase (RNAP) genes. The promoters would transcribe two to five putative phage-related proteins, but none of these resemble known phage structural proteins. An integrase belonging to the Int family of site-specific recombinases is encoded upstream of the tandem promoters. A direct repeat of 17-24 bases was found on the ends of all 12 islands. Comparative analysis of the islands shows that these islands appear to have recombined with each other. These results suggest that the islands could encode a group of satellite phages. Activation and function of the islands may depend on transcription by a T7-like RNAP after infection by a T7-like phage or foreign DNA that encodes a T7-like RNAP.

MeSH Terms
Enterobacteriaceae/genetics,virology Genome, Bacterial Genomics Models, Genetic Podoviridae/genetics Promoter Regions, Genetic Salmonella/genetics Shigella flexneri/genetics
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Chen Zehua
National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, P.O. Box B, Frederick, MD 21702-1201, USA.
Schneider Thomas D
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkj511
Published
2006-00-00
Epub
2006-00-21
Pages
1133-47
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1380254
Subset
IM
Grants
Intramural NIH HHS · United States
External Links
PubMed source DOI: 10.1093/nar/gkj511 PMC Full Text View journal details
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