An integrated approach for finding overlooked genes in Shigella.

<h4>Background</h4>The completion of numerous genome sequences introduced an era of whole-genome study. However, many genes are missed during genome annotation, including small RNAs (sRNAs) and small open reading frames (sORFs). In order to improve genome annotation, we aimed to identify...

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Autores principales:	Junping Peng, Jian Yang, Qi Jin
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/aa45bfabfbe84e9aa348367efb5935ac
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spelling	oai:doaj.org-article:aa45bfabfbe84e9aa348367efb5935ac2021-11-18T06:56:12ZAn integrated approach for finding overlooked genes in Shigella.1932-620310.1371/journal.pone.0018509https://doaj.org/article/aa45bfabfbe84e9aa348367efb5935ac2011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21483688/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>The completion of numerous genome sequences introduced an era of whole-genome study. However, many genes are missed during genome annotation, including small RNAs (sRNAs) and small open reading frames (sORFs). In order to improve genome annotation, we aimed to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery.<h4>Methodology/principal findings</h4>We identified 64 sRNAs in Shigella, which were experimentally validated in other bacteria based on sequence conservation. We employed computer-based and tiling array-based methods to search for sRNAs, followed by RT-PCR and northern blots, to identify nine sRNAs in Shigella flexneri strain 301 (Sf301) and 256 regions containing possible sRNA genes. We found 29 candidate sORFs using bioinformatic prediction, array hybridization and RT-PCR verification. We experimentally validated 557 (57.9%) DOOR operon predictions in the chromosomes of Sf301 and 46 (76.7%) in virulence plasmid.We found 40 additional co-expressed gene pairs that were not predicted by DOOR.<h4>Conclusions/significance</h4>We provide an updated and comprehensive annotation of the Shigella genome. Our study increased the expected numbers of sORFs and sRNAs, which will impact on future functional genomics and proteomics studies. Our method can be used for large scale reannotation of sRNAs and sORFs in any microbe with a known genome sequence.Junping PengJian YangQi JinPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e18509 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Junping Peng Jian Yang Qi Jin An integrated approach for finding overlooked genes in Shigella.
description	<h4>Background</h4>The completion of numerous genome sequences introduced an era of whole-genome study. However, many genes are missed during genome annotation, including small RNAs (sRNAs) and small open reading frames (sORFs). In order to improve genome annotation, we aimed to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery.<h4>Methodology/principal findings</h4>We identified 64 sRNAs in Shigella, which were experimentally validated in other bacteria based on sequence conservation. We employed computer-based and tiling array-based methods to search for sRNAs, followed by RT-PCR and northern blots, to identify nine sRNAs in Shigella flexneri strain 301 (Sf301) and 256 regions containing possible sRNA genes. We found 29 candidate sORFs using bioinformatic prediction, array hybridization and RT-PCR verification. We experimentally validated 557 (57.9%) DOOR operon predictions in the chromosomes of Sf301 and 46 (76.7%) in virulence plasmid.We found 40 additional co-expressed gene pairs that were not predicted by DOOR.<h4>Conclusions/significance</h4>We provide an updated and comprehensive annotation of the Shigella genome. Our study increased the expected numbers of sORFs and sRNAs, which will impact on future functional genomics and proteomics studies. Our method can be used for large scale reannotation of sRNAs and sORFs in any microbe with a known genome sequence.
format	article
author	Junping Peng Jian Yang Qi Jin
author_facet	Junping Peng Jian Yang Qi Jin
author_sort	Junping Peng
title	An integrated approach for finding overlooked genes in Shigella.
title_short	An integrated approach for finding overlooked genes in Shigella.
title_full	An integrated approach for finding overlooked genes in Shigella.
title_fullStr	An integrated approach for finding overlooked genes in Shigella.
title_full_unstemmed	An integrated approach for finding overlooked genes in Shigella.
title_sort	integrated approach for finding overlooked genes in shigella.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/aa45bfabfbe84e9aa348367efb5935ac
work_keys_str_mv	AT junpingpeng anintegratedapproachforfindingoverlookedgenesinshigella AT jianyang anintegratedapproachforfindingoverlookedgenesinshigella AT qijin anintegratedapproachforfindingoverlookedgenesinshigella AT junpingpeng integratedapproachforfindingoverlookedgenesinshigella AT jianyang integratedapproachforfindingoverlookedgenesinshigella AT qijin integratedapproachforfindingoverlookedgenesinshigella
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An integrated approach for finding overlooked genes in Shigella.

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