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High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria

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 signa...

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Autores principales: Huang, Qianli, Cheng, Xuanjin, Cheung, Man Kit, Kiselev, Sergey S., Ozoline, Olga N., Kwan, Hoi Shan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3309015/
https://www.ncbi.nlm.nih.gov/pubmed/22448273
http://dx.doi.org/10.1371/journal.pone.0033759
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author Huang, Qianli
Cheng, Xuanjin
Cheung, Man Kit
Kiselev, Sergey S.
Ozoline, Olga N.
Kwan, Hoi Shan
author_facet Huang, Qianli
Cheng, Xuanjin
Cheung, Man Kit
Kiselev, Sergey S.
Ozoline, Olga N.
Kwan, Hoi Shan
author_sort Huang, Qianli
collection PubMed
description 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.
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spelling pubmed-33090152012-03-23 High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria Huang, Qianli Cheng, Xuanjin Cheung, Man Kit Kiselev, Sergey S. Ozoline, Olga N. Kwan, Hoi Shan PLoS One Research Article 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. Public Library of Science 2012-03-20 /pmc/articles/PMC3309015/ /pubmed/22448273 http://dx.doi.org/10.1371/journal.pone.0033759 Text en Huang et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Huang, Qianli
Cheng, Xuanjin
Cheung, Man Kit
Kiselev, Sergey S.
Ozoline, Olga N.
Kwan, Hoi Shan
High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria
title High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria
title_full High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria
title_fullStr High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria
title_full_unstemmed High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria
title_short High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria
title_sort high-density transcriptional initiation signals underline genomic islands in bacteria
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3309015/
https://www.ncbi.nlm.nih.gov/pubmed/22448273
http://dx.doi.org/10.1371/journal.pone.0033759
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