Abstract
Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of “alien” elements which probably undergo special temporal–spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these “exotic” regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased “non-optimal” codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for “alien” regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions.
Highlights
Since the publication of the first pathogenicity island (PAI) [1], originally described as clusters of virulence genes that were identified in uropathogenic E. coli but absent in closely related strains, various types of other islands, such as secretion islands and resistance islands, have been detected
We found significantly more transcription start points (TSPs) in the Genomic islands (GIs) regions of E. coli K-12 MG1655, and this demonstrates that the phenomenon is not confined to Salmonella enterica
Through the comparative analysis of known features associated with GIs and the application in analyzing the GIs of the German E. coli O104:H4 outbreak strain TY-2482, we found that our method is powerful in detecting GI-like regions
Summary
Since the publication of the first pathogenicity island (PAI) [1], originally described as clusters of virulence genes that were identified in uropathogenic E. coli but absent in closely related strains, various types of other islands, such as secretion islands and resistance islands, have been detected. We compared the corresponding transcription initiation signals, here denoted by the TSPs, between the GI regions and genomes of the nine Salmonella strains.
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