Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition.

Autor:	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.; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany., Hess WR; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany., Steglich C; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany., Wilde A; Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2021 Dec 16; Vol. 49 (22), pp. 13075-13091.
DOI:	10.1093/nar/gkab1161
Abstrakt:	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. (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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