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dc.contributor.authorGallant, James
dc.contributor.authorMouton, Jomien
dc.contributor.authorUmmels, Roy
dc.contributor.authorten Hagen-Jongman, Corinne
dc.contributor.authorKriel, Nastassja
dc.contributor.authorPain, Arnab
dc.contributor.authorWarren, Robin M
dc.contributor.authorBitter, Wilbert
dc.contributor.authorHeunis, Tiaan
dc.contributor.authorSampson, Samantha L
dc.date.accessioned2020-05-21T11:30:56Z
dc.date.available2020-05-21T11:30:56Z
dc.date.issued2020-05-18
dc.date.submitted2020-02-06
dc.identifier.citationGallant, J., Mouton, J., Ummels, R., ten Hagen-Jongman, C., Kriel, N., Pain, A., … Sampson, S. L. (2020). Identification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins. NAR Genomics and Bioinformatics, 2(2). doi:10.1093/nargab/lqaa033
dc.identifier.issn2631-9268
dc.identifier.doi10.1093/nargab/lqaa033
dc.identifier.urihttp://hdl.handle.net/10754/662901
dc.description.abstractAbstract Mycobacterium tuberculosis is a facultative intracellular pathogen responsible for causing tuberculosis. The harsh environment in which M. tuberculosis survives requires this pathogen to continuously adapt in order to maintain an evolutionary advantage. However, the apparent absence of horizontal gene transfer in M. tuberculosis imposes restrictions in the ways by which evolution can occur. Large-scale changes in the genome can be introduced through genome reduction, recombination events and structural variation. Here, we identify a functional chimeric protein in the ppe38–71 locus, the absence of which is known to have an impact on protein secretion and virulence. To examine whether this approach was used more often by this pathogen, we further develop software that detects potential gene fusion events from multigene deletions using whole genome sequencing data. With this software we could identify a number of other putative gene fusion events within the genomes of M. tuberculosis isolates. We were able to demonstrate the expression of one of these gene fusions at the protein level using mass spectrometry. Therefore, gene fusions may provide an additional means of evolution for M. tuberculosis in its natural environment whereby novel chimeric proteins and functions can arise.
dc.description.sponsorshipNational Research Foundation/Vrije Universiteit Amsterdam Desmond Tutu Doctoral Training Program [to J.G.]; Financial support was provided by the South African Medical Research Council Centre for Tuberculosis Research and DST/NRF Centre of Excellence for Biomedical Tuberculosis Research [to S.S, J.G, J.M, N.K]; South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation (NRF) of South Africa [UID 86539 to S.S.]; KAUST faculty baseline grant [BAS/1/1020-01-01 to A.P.]. Conflict of interest statement. None declared.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/nargab/article/doi/10.1093/nargab/lqaa033/5838823
dc.relation.urlhttps://academic.oup.com/nargab/article-pdf/2/2/lqaa033/33227562/lqaa033.pdf
dc.rightsThis is a pre-copyedited, author-produced PDF of an article accepted for publication in NAR Genomics and Bioinformatics following peer review. The version of record is available online at: https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqaa033/5838823.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleIdentification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalNAR Genomics and Bioinformatics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
dc.contributor.institutionSection of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
dc.contributor.institutionMedical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
dc.contributor.institutionGlobal Station for Zoonosis Control, GI-CoRE, Hokkaido University, 001-0020, N20 W10 Kita-ku, Sapporo, Japan
dc.contributor.institutionBiosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
dc.identifier.volume2
dc.identifier.issue2
kaust.personPain, Arnab
kaust.grant.numberBAS/1/1020-01-01
dc.date.accepted2020-05-05
dc.relation.issupplementedbygithub:JamesGallant/Genomics
refterms.dateFOA2020-05-21T11:33:29Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Software]</i> <br/> Title: JamesGallant/Genomics: Pipeline for calling SNV/SV's and gene fusions from paired end illumina reads. Publication Date: 2016-11-28. github: <a href="https://github.com/JamesGallant/Genomics" >JamesGallant/Genomics</a> Handle: <a href="http://hdl.handle.net/10754/667868" >10754/667868</a></a></li></ul>
dc.date.published-online2020-05-18
dc.date.published-print2020-06-01


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This is a pre-copyedited, author-produced PDF of an article accepted for publication in NAR Genomics and Bioinformatics following peer review. The version of record is available online at: https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqaa033/5838823.
Except where otherwise noted, this item's license is described as This is a pre-copyedited, author-produced PDF of an article accepted for publication in NAR Genomics and Bioinformatics following peer review. The version of record is available online at: https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqaa033/5838823.