Beyond the Limits: tRNA Array Units in Mycobacterium Genomes

Detalhes bibliográficos
Autor(a) principal: Morgado, Sergio M.
Data de Publicação: 2018
Outros Autores: Vicente, Ana C. P.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/31738
Resumo: Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microorganismos. Rio de Janeiro, RJ. Brasil.
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spelling Morgado, Sergio M.Vicente, Ana C. P.2019-02-19T12:26:15Z2019-02-19T12:26:15Z2018MORGADO, Sergio M.; VICENTE, Ana C. P. Beyond the Limits: tRNA Array Units in Mycobacterium Genomes. Frontiers in Microbiology, v. 9, p. 1-9, May 2018.1664-302Xhttps://www.arca.fiocruz.br/handle/icict/3173810.3389/fmicb.2018.01042engFrontiers MediaMicobactériasMicobacteriófagosMicobactérias plasmídeosBioinformáticaEndonuclease HNHCódigo: PerlMycobacteriatRNA array unitsCode:PerlMycobacteriophagesMycobacteria plasmidstmRNA and structured RNABioinformaticsHNH endonucleaseBeyond the Limits: tRNA Array Units in Mycobacterium Genomesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microorganismos. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microorganismos. Rio de Janeiro, RJ. Brasil.tRNA array unit, a genomic region presenting an intriguing high tRNA gene number and density, was supposed to occur only in few bacteria phyla, particularly Firmicutes. Here, we identified and characterized an abundance and diversity of tRNA array units in Mycobacterium associated genomes. These genomes comprised chromosome, bacteriophages and plasmids from mycobacteria. Firstly, we had identified 32 tRNA genes organized in an array unit within a mycobacteria plasmid genome and therefore, we hypothesized the presence of such structures in Mycobacterium genus. However, at the time, bioinformatics tools only predict tRNA genes, not characterizing their arrangement as arrays. In order to test our hypothesis, we developed and applied an in-house Perl script that identified tRNA genes organization as an array unit. This survey included a total of 7,670 complete and drafts genomes of Mycobacterium genus, 4312 mycobacteriophage genomes and 40 mycobacteria plasmids. We showed that tRNA array units are abundant in genomes associated to the Mycobacterium genus, mainly in Mycobacterium abscessus complex species, being spread in chromosome, prophage, and plasmid genomes. Moreover, other non-coding RNA species (tmRNA and structured RNA) were also identified in these regions. Our results revealed that tRNA array units are not restrict, as previously assumed, to few bacteria phyla and genomes being present in one of the most diverse bacteria genus. We also provide a bioinformatics tool that allows further exploration of this issue in huge genomic databases. The presence of tRNA array units in plasmids and bacteriophages, associated with horizontal gene transfer, and in a bacteria genus that explores diverse niches, are indicatives that tRNA array units have impact in the bacteria biology.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/31738/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALsergiomorgado_ACPvicente_IOC_2018.pdfsergiomorgado_ACPvicente_IOC_2018.pdfapplication/pdf3864737https://www.arca.fiocruz.br/bitstream/icict/31738/2/sergiomorgado_ACPvicente_IOC_2018.pdf20bc6a9b09af614a376646abb071525bMD52TEXTsergiomorgado_ACPvicente_IOC_2018.pdf.txtsergiomorgado_ACPvicente_IOC_2018.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv Beyond the Limits: tRNA Array Units in Mycobacterium Genomes
title Beyond the Limits: tRNA Array Units in Mycobacterium Genomes
spellingShingle Beyond the Limits: tRNA Array Units in Mycobacterium Genomes
Morgado, Sergio M.
Micobactérias
Micobacteriófagos
Micobactérias plasmídeos
Bioinformática
Endonuclease HNH
Código: Perl
Mycobacteria
tRNA array units
Code:Perl
Mycobacteriophages
Mycobacteria plasmids
tmRNA and structured RNA
Bioinformatics
HNH endonuclease
title_short Beyond the Limits: tRNA Array Units in Mycobacterium Genomes
title_full Beyond the Limits: tRNA Array Units in Mycobacterium Genomes
title_fullStr Beyond the Limits: tRNA Array Units in Mycobacterium Genomes
title_full_unstemmed Beyond the Limits: tRNA Array Units in Mycobacterium Genomes
title_sort Beyond the Limits: tRNA Array Units in Mycobacterium Genomes
author Morgado, Sergio M.
author_facet Morgado, Sergio M.
Vicente, Ana C. P.
author_role author
author2 Vicente, Ana C. P.
author2_role author
dc.contributor.author.fl_str_mv Morgado, Sergio M.
Vicente, Ana C. P.
dc.subject.other.pt_BR.fl_str_mv Micobactérias
Micobacteriófagos
Micobactérias plasmídeos
Bioinformática
Endonuclease HNH
Código: Perl
topic Micobactérias
Micobacteriófagos
Micobactérias plasmídeos
Bioinformática
Endonuclease HNH
Código: Perl
Mycobacteria
tRNA array units
Code:Perl
Mycobacteriophages
Mycobacteria plasmids
tmRNA and structured RNA
Bioinformatics
HNH endonuclease
dc.subject.en.pt_BR.fl_str_mv Mycobacteria
tRNA array units
Code:Perl
Mycobacteriophages
Mycobacteria plasmids
tmRNA and structured RNA
Bioinformatics
HNH endonuclease
description Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microorganismos. Rio de Janeiro, RJ. Brasil.
publishDate 2018
dc.date.issued.fl_str_mv 2018
dc.date.accessioned.fl_str_mv 2019-02-19T12:26:15Z
dc.date.available.fl_str_mv 2019-02-19T12:26:15Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv MORGADO, Sergio M.; VICENTE, Ana C. P. Beyond the Limits: tRNA Array Units in Mycobacterium Genomes. Frontiers in Microbiology, v. 9, p. 1-9, May 2018.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/31738
dc.identifier.issn.pt_BR.fl_str_mv 1664-302X
dc.identifier.doi.none.fl_str_mv 10.3389/fmicb.2018.01042
identifier_str_mv MORGADO, Sergio M.; VICENTE, Ana C. P. Beyond the Limits: tRNA Array Units in Mycobacterium Genomes. Frontiers in Microbiology, v. 9, p. 1-9, May 2018.
1664-302X
10.3389/fmicb.2018.01042
url https://www.arca.fiocruz.br/handle/icict/31738
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/31738/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/31738/2/sergiomorgado_ACPvicente_IOC_2018.pdf
https://www.arca.fiocruz.br/bitstream/icict/31738/3/sergiomorgado_ACPvicente_IOC_2018.pdf.txt
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