Mapping of internal monophosphate 5' ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains

Nucleic Acids Research
Jeanne M DiChiaraDavid H Bechhofer

Abstract

The recent findings that the narrow-specificity endoribonuclease RNase III and the 5' exonuclease RNase J1 are not essential in the Gram-positive model organism, Bacillus subtilis, facilitated a global analysis of internal 5' ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5' monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions appeared to be direct targets of RNase III. These target sites were, in most cases, not associated with a known antisense RNA. The PARE analysis also revealed an accumulation of 3'-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. A significant result from the PARE analysis was the discovery of an endonuclease cleavage just 2 nts downstream of the 16S rRNA 3' end. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolyt...Continue Reading

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Citations

Aug 30, 2019·Critical Reviews in Biochemistry and Molecular Biology·David H Bechhofer, Murray P Deutscher
Aug 17, 2018·Nucleic Acids Research·Yael AltuviaHanah Margalit
May 26, 2018·Proceedings of the National Academy of Sciences of the United States of America·Aaron DeLougheryGene-Wei Li
Nov 18, 2020·BMC Genomics·Jochen BathkeGabriele Klug
Jan 15, 2020·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·Maxence Lejars, Eliane Hajnsdorf
Apr 14, 2018·Microbiology Spectrum·Sylvain Durand, Ciaran Condon
Aug 20, 2021·FEMS Microbiology Reviews·Colin R Harwood, Yoshimi Kikuchi
Sep 23, 2021·Nucleic Acids Research·Jana Wiedermannová, Libor Krásný
Aug 4, 2021·Annual Review of Microbiology·James C TaggartGene-Wei Li
Jun 4, 2021·Annual Review of Microbiology·Murray P Deutscher

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