title: Mapping of internal monophosphate 5' ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains.
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 exonucleolytic versus endonucleolytic nature of 16S rRNA maturation.
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Jeanne M
authors.initials: JM
authors.lastname: DiChiara
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.affiliation: CNRS UMR8261 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Sabine
authors.initials: S
authors.lastname: Figaro
authors.affiliation: CNRS UMR8261 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Ciarán
authors.initials: C
authors.lastname: Condon
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029, USA david.bechhofer@mssm.edu.
authors.forename: David H
authors.initials: DH
authors.lastname: Bechhofer
mesh_terms: D026921:Amino Acid Transport Systems, Neutral / Q000235:genetics; D001412:Bacillus subtilis / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D005095:Exoribonucleases / Q000378:metabolism*; D009154:Mutation; D009876:Operon; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D020733:RNA, Small Cytoplasmic / Q000378:metabolism; D043244:Ribonuclease III / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D026921:Amino Acid Transport Systems, Neutral; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D020733:RNA, Small Cytoplasmic; D005095:Exoribonucleases; D043244:Ribonuclease III