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 transcripti...

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Autores principales:	Qianli Huang, Xuanjin Cheng, Man Kit Cheung, Sergey S Kiselev, Olga N Ozoline, Hoi Shan Kwan
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0ca80cb5ba604760b225b4eeb6d8fc4e
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spelling	oai:doaj.org-article:0ca80cb5ba604760b225b4eeb6d8fc4e2021-11-18T07:24:39ZHigh-density transcriptional initiation signals underline genomic islands in bacteria.1932-620310.1371/journal.pone.0033759https://doaj.org/article/0ca80cb5ba604760b225b4eeb6d8fc4e2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22448273/?tool=EBIhttps://doaj.org/toc/1932-6203Genomic 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.Qianli HuangXuanjin ChengMan Kit CheungSergey S KiselevOlga N OzolineHoi Shan KwanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e33759 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qianli Huang Xuanjin Cheng Man Kit Cheung Sergey S Kiselev Olga N Ozoline Hoi Shan Kwan High-density transcriptional initiation signals underline genomic islands in bacteria.
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.
format	article
author	Qianli Huang Xuanjin Cheng Man Kit Cheung Sergey S Kiselev Olga N Ozoline Hoi Shan Kwan
author_facet	Qianli Huang Xuanjin Cheng Man Kit Cheung Sergey S Kiselev Olga N Ozoline Hoi Shan Kwan
author_sort	Qianli Huang
title	High-density transcriptional initiation signals underline genomic islands in bacteria.
title_short	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_sort	high-density transcriptional initiation signals underline genomic islands in bacteria.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/0ca80cb5ba604760b225b4eeb6d8fc4e
work_keys_str_mv	AT qianlihuang highdensitytranscriptionalinitiationsignalsunderlinegenomicislandsinbacteria AT xuanjincheng highdensitytranscriptionalinitiationsignalsunderlinegenomicislandsinbacteria AT mankitcheung highdensitytranscriptionalinitiationsignalsunderlinegenomicislandsinbacteria AT sergeyskiselev highdensitytranscriptionalinitiationsignalsunderlinegenomicislandsinbacteria AT olganozoline highdensitytranscriptionalinitiationsignalsunderlinegenomicislandsinbacteria AT hoishankwan highdensitytranscriptionalinitiationsignalsunderlinegenomicislandsinbacteria
_version_	1718423454361845760

High-density transcriptional initiation signals underline genomic islands in bacteria.

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