Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.

Transposon mutagenesis, in combination with parallel sequencing, is becoming a powerful tool for en-masse mutant analysis. A probability generating function was used to explain observed miniHimar transposon insertion patterns, and gene essentiality calls were made by transposon insertion frequency a...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Hong Yang, Elias W Krumholz, Evan D Brutinel, Nagendra P Palani, Michael J Sadowsky, Andrew M Odlyzko, Jeffrey A Gralnick, Igor G L Libourel
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/07abc409acf04af58d95ec660176f4de
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:07abc409acf04af58d95ec660176f4de
record_format	dspace
spelling	oai:doaj.org-article:07abc409acf04af58d95ec660176f4de2021-11-25T05:40:44ZGenome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.1553-734X1553-735810.1371/journal.pcbi.1003848https://doaj.org/article/07abc409acf04af58d95ec660176f4de2014-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1003848https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Transposon mutagenesis, in combination with parallel sequencing, is becoming a powerful tool for en-masse mutant analysis. A probability generating function was used to explain observed miniHimar transposon insertion patterns, and gene essentiality calls were made by transposon insertion frequency analysis (TIFA). TIFA incorporated the observed genome and sequence motif bias of the miniHimar transposon. The gene essentiality calls were compared to: 1) previous genome-wide direct gene-essentiality assignments; and, 2) flux balance analysis (FBA) predictions from an existing genome-scale metabolic model of Shewanella oneidensis MR-1. A three-way comparison between FBA, TIFA, and the direct essentiality calls was made to validate the TIFA approach. The refinement in the interpretation of observed transposon insertions demonstrated that genes without insertions are not necessarily essential, and that genes that contain insertions are not always nonessential. The TIFA calls were in reasonable agreement with direct essentiality calls for S. oneidensis, but agreed more closely with E. coli essentiality calls for orthologs. The TIFA gene essentiality calls were in good agreement with the MR-1 FBA essentiality predictions, and the agreement between TIFA and FBA predictions was substantially better than between the FBA and the direct gene essentiality predictions.Hong YangElias W KrumholzEvan D BrutinelNagendra P PalaniMichael J SadowskyAndrew M OdlyzkoJeffrey A GralnickIgor G L LibourelPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 10, Iss 9, p e1003848 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Hong Yang Elias W Krumholz Evan D Brutinel Nagendra P Palani Michael J Sadowsky Andrew M Odlyzko Jeffrey A Gralnick Igor G L Libourel Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.
description	Transposon mutagenesis, in combination with parallel sequencing, is becoming a powerful tool for en-masse mutant analysis. A probability generating function was used to explain observed miniHimar transposon insertion patterns, and gene essentiality calls were made by transposon insertion frequency analysis (TIFA). TIFA incorporated the observed genome and sequence motif bias of the miniHimar transposon. The gene essentiality calls were compared to: 1) previous genome-wide direct gene-essentiality assignments; and, 2) flux balance analysis (FBA) predictions from an existing genome-scale metabolic model of Shewanella oneidensis MR-1. A three-way comparison between FBA, TIFA, and the direct essentiality calls was made to validate the TIFA approach. The refinement in the interpretation of observed transposon insertions demonstrated that genes without insertions are not necessarily essential, and that genes that contain insertions are not always nonessential. The TIFA calls were in reasonable agreement with direct essentiality calls for S. oneidensis, but agreed more closely with E. coli essentiality calls for orthologs. The TIFA gene essentiality calls were in good agreement with the MR-1 FBA essentiality predictions, and the agreement between TIFA and FBA predictions was substantially better than between the FBA and the direct gene essentiality predictions.
format	article
author	Hong Yang Elias W Krumholz Evan D Brutinel Nagendra P Palani Michael J Sadowsky Andrew M Odlyzko Jeffrey A Gralnick Igor G L Libourel
author_facet	Hong Yang Elias W Krumholz Evan D Brutinel Nagendra P Palani Michael J Sadowsky Andrew M Odlyzko Jeffrey A Gralnick Igor G L Libourel
author_sort	Hong Yang
title	Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.
title_short	Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.
title_full	Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.
title_fullStr	Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.
title_full_unstemmed	Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.
title_sort	genome-scale metabolic network validation of shewanella oneidensis using transposon insertion frequency analysis.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/07abc409acf04af58d95ec660176f4de
work_keys_str_mv	AT hongyang genomescalemetabolicnetworkvalidationofshewanellaoneidensisusingtransposoninsertionfrequencyanalysis AT eliaswkrumholz genomescalemetabolicnetworkvalidationofshewanellaoneidensisusingtransposoninsertionfrequencyanalysis AT evandbrutinel genomescalemetabolicnetworkvalidationofshewanellaoneidensisusingtransposoninsertionfrequencyanalysis AT nagendrappalani genomescalemetabolicnetworkvalidationofshewanellaoneidensisusingtransposoninsertionfrequencyanalysis AT michaeljsadowsky genomescalemetabolicnetworkvalidationofshewanellaoneidensisusingtransposoninsertionfrequencyanalysis AT andrewmodlyzko genomescalemetabolicnetworkvalidationofshewanellaoneidensisusingtransposoninsertionfrequencyanalysis AT jeffreyagralnick genomescalemetabolicnetworkvalidationofshewanellaoneidensisusingtransposoninsertionfrequencyanalysis AT igorgllibourel genomescalemetabolicnetworkvalidationofshewanellaoneidensisusingtransposoninsertionfrequencyanalysis
_version_	1718414500199137280

Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.

Ejemplares similares