Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS

Handle URI:
http://hdl.handle.net/10754/622029
Title:
Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS
Authors:
Wong, Yee-Chin; Abd El Ghany, Moataz; Naeem, Raeece ( 0000-0003-1734-1007 ) ; Lee, Kok-Wei; Tan, Yung-Chie; Pain, Arnab ( 0000-0002-1755-2819 ) ; Nathan, Sheila
Abstract:
Burkholderia cenocepacia infection often leads to fatal cepacia syndrome in cystic fibrosis patients. However, antibiotic therapy rarely results in complete eradication of the pathogen due to its intrinsic resistance to many clinically available antibiotics. Recent attention has turned to the identification of essential genes as the proteins encoded by these genes may serve as potential targets for development of novel antimicrobials. In this study, we utilized TraDIS (Transposon Directed Insertion-site Sequencing) as a genome-wide screening tool to facilitate the identification of B. cenocepacia genes essential for its growth and viability. A transposon mutant pool consisting of approximately 500,000 mutants was successfully constructed, with more than 400,000 unique transposon insertion sites identified by computational analysis of TraDIS datasets. The saturated library allowed for the identification of 383 genes that were predicted to be essential in B. cenocepacia. We extended the application of TraDIS to identify conditionally essential genes required for in vitro growth and revealed an additional repertoire of 439 genes to be crucial for B. cenocepacia growth under nutrient-depleted conditions. The library of B. cenocepacia mutants can subsequently be subjected to various biologically related conditions to facilitate the discovery of genes involved in niche adaptation as well as pathogenicity and virulence.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Wong Y-C, Abd El Ghany M, Naeem R, Lee K-W, Tan Y-C, et al. (2016) Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS. Frontiers in Microbiology 7. Available: http://dx.doi.org/10.3389/fmicb.2016.01288.
Publisher:
Frontiers Media SA
Journal:
Frontiers in Microbiology
Issue Date:
22-Aug-2016
DOI:
10.3389/fmicb.2016.01288
Type:
Article
ISSN:
1664-302X
Sponsors:
This study was supported by the grants 06-05-16-MB003 and Ap-004-2014 awarded to SN by the Ministry of Science, Technology and Innovation Malaysia and Universiti Kcbangsaan Malaysia. Y-CW was supported by a MyBrain15 Scholarship from the Ministry of Higher Education Malaysia. Part of this work was conducted in KAUST funded by faculty baseline funding from KAUST to AP.
Additional Links:
http://journal.frontiersin.org/article/10.3389/fmicb.2016.01288/full
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorWong, Yee-Chinen
dc.contributor.authorAbd El Ghany, Moatazen
dc.contributor.authorNaeem, Raeeceen
dc.contributor.authorLee, Kok-Weien
dc.contributor.authorTan, Yung-Chieen
dc.contributor.authorPain, Arnaben
dc.contributor.authorNathan, Sheilaen
dc.date.accessioned2016-12-18T13:36:59Z-
dc.date.available2016-12-18T13:36:59Z-
dc.date.issued2016-08-22en
dc.identifier.citationWong Y-C, Abd El Ghany M, Naeem R, Lee K-W, Tan Y-C, et al. (2016) Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS. Frontiers in Microbiology 7. Available: http://dx.doi.org/10.3389/fmicb.2016.01288.en
dc.identifier.issn1664-302Xen
dc.identifier.doi10.3389/fmicb.2016.01288en
dc.identifier.urihttp://hdl.handle.net/10754/622029-
dc.description.abstractBurkholderia cenocepacia infection often leads to fatal cepacia syndrome in cystic fibrosis patients. However, antibiotic therapy rarely results in complete eradication of the pathogen due to its intrinsic resistance to many clinically available antibiotics. Recent attention has turned to the identification of essential genes as the proteins encoded by these genes may serve as potential targets for development of novel antimicrobials. In this study, we utilized TraDIS (Transposon Directed Insertion-site Sequencing) as a genome-wide screening tool to facilitate the identification of B. cenocepacia genes essential for its growth and viability. A transposon mutant pool consisting of approximately 500,000 mutants was successfully constructed, with more than 400,000 unique transposon insertion sites identified by computational analysis of TraDIS datasets. The saturated library allowed for the identification of 383 genes that were predicted to be essential in B. cenocepacia. We extended the application of TraDIS to identify conditionally essential genes required for in vitro growth and revealed an additional repertoire of 439 genes to be crucial for B. cenocepacia growth under nutrient-depleted conditions. The library of B. cenocepacia mutants can subsequently be subjected to various biologically related conditions to facilitate the discovery of genes involved in niche adaptation as well as pathogenicity and virulence.en
dc.description.sponsorshipThis study was supported by the grants 06-05-16-MB003 and Ap-004-2014 awarded to SN by the Ministry of Science, Technology and Innovation Malaysia and Universiti Kcbangsaan Malaysia. Y-CW was supported by a MyBrain15 Scholarship from the Ministry of Higher Education Malaysia. Part of this work was conducted in KAUST funded by faculty baseline funding from KAUST to AP.en
dc.publisherFrontiers Media SAen
dc.relation.urlhttp://journal.frontiersin.org/article/10.3389/fmicb.2016.01288/fullen
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBurkholderia cenocepaciaen
dc.subjectessentialgenesen
dc.subjecttransposonen
dc.subjectmutagenesisen
dc.subjectTraDISen
dc.titleCandidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDISen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalFrontiers in Microbiologyen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionFaculty of Science and Technology, School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, Bangi, Malaysiaen
dc.contributor.institutionThe Westmead Institute for Medical Research, The Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australiaen
dc.contributor.institutionCodon Genomics SB, Selangor, Malaysiaen
kaust.authorAbd El Ghany, Moatazen
kaust.authorNaeem, Raeeceen
kaust.authorPain, Arnaben
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