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Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition.
Hoffmann, Ute A; Heyl, Florian; Rogh, Said N; Wallner, Thomas; Backofen, Rolf; Hess, Wolfgang R; Steglich, Claudia; Wilde, Annegret.
Afiliação
  • Hoffmann UA; Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany.
  • Heyl F; Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.
  • Rogh SN; Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany.
  • Wallner T; Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany.
  • Backofen R; Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.
  • Hess WR; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.
  • Steglich C; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
  • Wilde A; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
Nucleic Acids Res ; 49(22): 13075-13091, 2021 12 16.
Article em En | MEDLINE | ID: mdl-34871439
Ribonucleases are crucial enzymes in RNA metabolism and post-transcriptional regulatory processes in bacteria. Cyanobacteria encode the two essential ribonucleases RNase E and RNase J. Cyanobacterial RNase E is shorter than homologues in other groups of bacteria and lacks both the chloroplast-specific N-terminal extension as well as the C-terminal domain typical for RNase E of enterobacteria. In order to investigate the function of RNase E in the model cyanobacterium Synechocystis sp. PCC 6803, we engineered a temperature-sensitive RNase E mutant by introducing two site-specific mutations, I65F and the spontaneously occurred V94A. This enabled us to perform RNA-seq after the transient inactivation of RNase E by a temperature shift (TIER-seq) and to map 1472 RNase-E-dependent cleavage sites. We inferred a dominating cleavage signature consisting of an adenine at the -3 and a uridine at the +2 position within a single-stranded segment of the RNA. The data identified mRNAs likely regulated jointly by RNase E and an sRNA and potential 3' end-derived sRNAs. Our findings substantiate the pivotal role of RNase E in post-transcriptional regulation and suggest the redundant or concerted action of RNase E and RNase J in cyanobacteria.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteínas de Bactérias / Cianobactérias / Perfilação da Expressão Gênica / Endorribonucleases / Transcriptoma Tipo de estudo: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Alemanha

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteínas de Bactérias / Cianobactérias / Perfilação da Expressão Gênica / Endorribonucleases / Transcriptoma Tipo de estudo: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Alemanha