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Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
- Source :
- Nucleic Acids Research
- Publication Year :
- 2016
- Publisher :
- Oxford University Press, 2016.
-
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.
- Subjects :
- 0301 basic medicine
Ribonuclease III
RNase P
030106 microbiology
Endoribonuclease
RNase PH
03 medical and health sciences
RNA, Ribosomal, 16S
Operon
RNA, Small Cytoplasmic
Genetics
Ribonuclease
RNA, Messenger
RNA Processing, Post-Transcriptional
biology
Sequence Analysis, RNA
RNA
Ribosomal RNA
Molecular biology
RNase MRP
RNA, Bacterial
Amino Acid Transport Systems, Neutral
RNA, Ribosomal
Exoribonucleases
Mutation
biology.protein
Bacillus subtilis
Subjects
Details
- Language :
- English
- ISSN :
- 13624962 and 03051048
- Volume :
- 44
- Issue :
- 7
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....b277762102dcc9d2845b6d8104283205