Please use this identifier to cite or link to this item: https://www.arca.fiocruz.br/handle/icict/33145
Title: Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
Authors: Antunes, Deborah
Jorge, Natasha Andressa Nogueira
Costa, Mauricio Garcia de Souza
Passetti, Fabio
Caffarena, Ernesto Raul
Affilliation: 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. 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.
Abstract: 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.
Keywords: Post-Transcriptional
RNA Processing
Thiamine Pyrophosphate
Bacteria
Plants
Keywords in spanish: Procesamiento Postranscripcional del ARN
Bacterias
keywords: Riboswitch
DeCS: Processamento Pós-Transcricional do RNA
Tiamina Pirofosfato
Escherichia coli
Arabidopsis
Bactérias
Plantas
Issue Date: 2019
Publisher: Nature Research
Citation: 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.
DOI: 10.1038/s41598-019-40875-1
ISSN: 2045-2322
Copyright: open access
Appears in Collections:Presidência Fiocruz - PROCC - Artigos de Periódicos
IOC - Artigos de Periódicos
PR - ICC - Artigos de Periódicos

Files in This Item:
File Description SizeFormat 
41598_2019_Article_40875.pdf7.85 MBAdobe PDFView/Open



FacebookTwitterDeliciousLinkedInGoogle BookmarksBibTex Format mendeley Endnote DiggMySpace

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.