Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases

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dc.citation.journalTitleBMC Research Noteseng
dc.contributor.authorMosquera-Rendón, J.
dc.contributor.authorCárdenas-Brito, S.
dc.contributor.authorPineda, J.D.
dc.contributor.authorCorredor, M.
dc.contributor.authorBenítez-Páez, A.
dc.contributor.departmentUniversidad EAFIT. Departamento de Ingeniería de Sistemasspa
dc.contributor.researchgroupI+D+I en Tecnologías de la Información y las Comunicacionesspa
dc.creatorMosquera-Rendón, J.
dc.creatorCárdenas-Brito, S.
dc.creatorPineda, J.D.
dc.creatorCorredor, M.
dc.creatorBenítez-Páez, A.
dc.date.accessioned2021-04-12T20:55:46Z
dc.date.available2021-04-12T20:55:46Z
dc.date.issued2014-01-01
dc.description.abstractBackground: RNA post-transcriptional modification is an exciting field of research that has evidenced this editing process as a sophisticated epigenetic mechanism to fine tune the ribosome function and to control gene expression. Although tRNA modifications seem to be more relevant for the ribosome function and cell physiology as a whole, some rRNA modifications have also been seen to play pivotal roles, essentially those located in central ribosome regions. RNA methylation at nucleobases and ribose moieties of nucleotides appear to frequently modulate its chemistry and structure. RNA methyltransferases comprise a superfamily of highly specialized enzymes that accomplish a wide variety of modifications. These enzymes exhibit a poor degree of sequence similarity in spite of using a common reaction cofactor and modifying the same substrate type. Results: Relationships and lineages of RNA methyltransferases have been extensively discussed, but no consensus has been reached. To shed light on this topic, we performed amino acid and codon-based sequence analyses to determine phylogenetic relationships and molecular evolution. We found that most Class I RNA MTases are evolutionarily related to protein and cofactor/vitamin biosynthesis methyltransferases. Additionally, we found that at least nine lineages explain the diversity of RNA MTases. We evidenced that RNA methyltransferases have high content of polar and positively charged amino acid, which coincides with the electrochemistry of their substrates. Conclusions: After studying almost 12,000 bacterial genomes and 2,000 patho-pangenomes, we revealed that molecular evolution of Class I methyltransferases matches the different rates of synonymous and non-synonymous substitutions along the coding region. Consequently, evolution on Class I methyltransferases selects against amino acid changes affecting the structure conformation. © 2014 Mosquera-Rendón et al.; licensee BioMed Central Ltd.eng
dc.identifierhttps://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=2008
dc.identifier.doi10.1186/1756-0500-7-440
dc.identifier.issn17560500
dc.identifier.otherPUBMED;25012753
dc.identifier.otherSCOPUS;2-s2.0-84903863048
dc.identifier.urihttp://hdl.handle.net/10784/28601
dc.language.isoengeng
dc.publisherBioMed Central Ltd.
dc.relationDOI;10.1186/1756-0500-7-440
dc.relationPUBMED;25012753
dc.relationSCOPUS;2-s2.0-84903863048
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84903863048&doi=10.1186%2f1756-0500-7-440&partnerID=40&md5=ebc5df12f9d51e0cc34866230c6d9871
dc.rightshttps://v2.sherpa.ac.uk/id/publication/issn/1756-0500
dc.sourceBMC Research Notes
dc.subjectbacterial proteineng
dc.subjectmethyltransferaseeng
dc.subjects adenosylmethionineeng
dc.subjectuntranslated RNAeng
dc.subjectamino acid sequenceeng
dc.subjectBacteriaeng
dc.subjectbacterial genomeeng
dc.subjectchemical structureeng
dc.subjectchemistryeng
dc.subjectclassificationeng
dc.subjectgenetic epigenesiseng
dc.subjectgeneticseng
dc.subjectmetabolismeng
dc.subjectmethylationeng
dc.subjectmolecular evolutioneng
dc.subjectmolecular geneticseng
dc.subjectnucleotide sequenceeng
dc.subjectphylogenyeng
dc.subjectRNA processingeng
dc.subjectsequence alignmenteng
dc.subjectbacteriumeng
dc.subjectAmino Acid Sequenceeng
dc.subjectBacteriaeng
dc.subjectBacterial Proteinseng
dc.subjectBase Sequenceeng
dc.subjectEpigenesiseng
dc.subjectGeneticeng
dc.subjectEvolutioneng
dc.subjectMoleculareng
dc.subjectGenomeeng
dc.subjectBacterialeng
dc.subjectMethylationeng
dc.subjectMethyltransferaseseng
dc.subjectModelseng
dc.subjectMoleculareng
dc.subjectMolecular Sequence Dataeng
dc.subjectPhylogenyeng
dc.subjectRNA Processingeng
dc.subjectPost-Transcriptionaleng
dc.subjectRNAeng
dc.subjectUntranslatedeng
dc.subjectS-Adenosylmethionineeng
dc.subjectSequence Alignmenteng
dc.titleEvolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferaseseng
dc.typeinfo:eu-repo/semantics/articleeng
dc.typearticleeng
dc.typeinfo:eu-repo/semantics/publishedVersioneng
dc.typepublishedVersioneng
dc.type.localArtículospa

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