Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana

Detalhes bibliográficos
Autor(a) principal: Antunes, Deborah
Data de Publicação: 2019
Outros Autores: Jorge, Natasha Andressa Nogueira, Costa, Mauricio Garcia de Souza, Passetti, Fabio, Caffarena, Ernesto Raul
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/33145
Resumo: Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.
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spelling Antunes, DeborahJorge, Natasha Andressa NogueiraCosta, Mauricio Garcia de SouzaPassetti, FabioCaffarena, Ernesto Raul2019-05-20T15:06:54Z2019-05-20T15:06:54Z2019ANTUNES, Deborah et al. Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana. Scientific Reports, v. 9, p. 1-13, 2019.2045-2322https://www.arca.fiocruz.br/handle/icict/3314510.1038/s41598-019-40875-12045-2322engNature ResearchRiboswitchPost-TranscriptionalRNA ProcessingThiamine PyrophosphateBacteriaPlantsProcesamiento Postranscripcional del ARNBacteriasProcessamento Pós-Transcricional do RNATiamina PirofosfatoEscherichia coliArabidopsisBactériasPlantasUnraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thalianainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Regulação da Expressão Gênica. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.Riboswitches are RNA sensors that affect post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch class is the most widespread riboswitch occurring in all three domains of life. Even though it controls different genes involved in the synthesis or transport of thiamine and its phosphorylated derivatives in bacteria, archaea, fungi, and plants, the TPP aptamer has a conserved structure. In this study, we aimed at understanding differences in the structural dynamics of TPP riboswitches from Escherichia coli and Arabidopsis thaliana, based on their crystallographic structures (TPPswec and TPPswat, respectively) and dynamics in aqueous solution, both in apo and holo states. A combination of Molecular Dynamics Simulations and Network Analysis empowered to find out slight differences in the dynamical behavior of TPP riboswitches, although relevant for their dynamics in bacteria and plants species. Our results suggest that distinct interactions in the microenvironment surrounding nucleotide U36 of TPPswec (and U35 in TPPswat) are related to different responses to TPP. The network analysis showed that minor structural differences in the aptamer enable enhanced intramolecular communication in the presence of TPP in TPPswec, but not in TPPswat. TPP riboswitches of plants present subtler and slower regulation mechanisms than bacteria do.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83084https://www.arca.fiocruz.br/bitstream/icict/33145/1/license.txt783568c2893d2e25a99990b126be1772MD51ORIGINAL41598_2019_Article_40875.pdf41598_2019_Article_40875.pdfapplication/pdf8041209https://www.arca.fiocruz.br/bitstream/icict/33145/2/41598_2019_Article_40875.pdfa824ccf0635d7165f090a5ce2df9c212MD52TEXT41598_2019_Article_40875.pdf.txt41598_2019_Article_40875.pdf.txtExtracted texttext/plain52938https://www.arca.fiocruz.br/bitstream/icict/33145/3/41598_2019_Article_40875.pdf.txt5ce0047a90aaf4ad91e1c765a99605a8MD53icict/331452021-12-13 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dc.title.pt_BR.fl_str_mv Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
title Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
spellingShingle Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
Antunes, Deborah
Riboswitch
Post-Transcriptional
RNA Processing
Thiamine Pyrophosphate
Bacteria
Plants
Procesamiento Postranscripcional del ARN
Bacterias
Processamento Pós-Transcricional do RNA
Tiamina Pirofosfato
Escherichia coli
Arabidopsis
Bactérias
Plantas
title_short Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
title_full Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
title_fullStr Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
title_full_unstemmed Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
title_sort Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
author Antunes, Deborah
author_facet Antunes, Deborah
Jorge, Natasha Andressa Nogueira
Costa, Mauricio Garcia de Souza
Passetti, Fabio
Caffarena, Ernesto Raul
author_role author
author2 Jorge, Natasha Andressa Nogueira
Costa, Mauricio Garcia de Souza
Passetti, Fabio
Caffarena, Ernesto Raul
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Antunes, Deborah
Jorge, Natasha Andressa Nogueira
Costa, Mauricio Garcia de Souza
Passetti, Fabio
Caffarena, Ernesto Raul
dc.subject.other.pt_BR.fl_str_mv Riboswitch
topic Riboswitch
Post-Transcriptional
RNA Processing
Thiamine Pyrophosphate
Bacteria
Plants
Procesamiento Postranscripcional del ARN
Bacterias
Processamento Pós-Transcricional do RNA
Tiamina Pirofosfato
Escherichia coli
Arabidopsis
Bactérias
Plantas
dc.subject.en.pt_BR.fl_str_mv Post-Transcriptional
RNA Processing
Thiamine Pyrophosphate
Bacteria
Plants
dc.subject.es.pt_BR.fl_str_mv Procesamiento Postranscripcional del ARN
Bacterias
dc.subject.decs.pt_BR.fl_str_mv Processamento Pós-Transcricional do RNA
Tiamina Pirofosfato
Escherichia coli
Arabidopsis
Bactérias
Plantas
description Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.
publishDate 2019
dc.date.accessioned.fl_str_mv 2019-05-20T15:06:54Z
dc.date.available.fl_str_mv 2019-05-20T15:06:54Z
dc.date.issued.fl_str_mv 2019
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 ANTUNES, Deborah et al. Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana. Scientific Reports, v. 9, p. 1-13, 2019.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/33145
dc.identifier.issn.pt_BR.fl_str_mv 2045-2322
dc.identifier.doi.none.fl_str_mv 10.1038/s41598-019-40875-1
dc.identifier.eissn.none.fl_str_mv 2045-2322
identifier_str_mv ANTUNES, Deborah et al. Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana. Scientific Reports, v. 9, p. 1-13, 2019.
2045-2322
10.1038/s41598-019-40875-1
url https://www.arca.fiocruz.br/handle/icict/33145
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 Nature Research
publisher.none.fl_str_mv Nature Research
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/33145/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/33145/2/41598_2019_Article_40875.pdf
https://www.arca.fiocruz.br/bitstream/icict/33145/3/41598_2019_Article_40875.pdf.txt
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
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