In Escherichia coli, RNA degradation often begins with conversion of the 5'-terminal triphosphate to a monophosphate, creating a better substrate for internal cleavage by RNase E. Remarkably, no homolog of this key endonuclease is present in many bacterial species, such as Bacillus subtilis and various pathogens. Here, we report that the degradation of primary transcripts in B. subtilis can nevertheless be triggered by an analogous process to generate a short-lived, monophosphorylated intermediate. Like its E. coli counterpart, the B. subtilis RNA pyrophosphohydrolase that catalyzes this event is a Nudix protein that prefers unpaired 5' ends. However, in B. subtilis, this modification exposes transcripts to rapid 5' exonucleolytic degradation by RNase J, which is absent in E. coli but present in most bacteria lacking RNase E. This pathway, which closely resembles the mechanism by which deadenylated mRNA is degraded in eukaryotic cells, explains the stabilizing influence of 5'-terminal stem-loops in such bacteria.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176438 | PMC |
| http://dx.doi.org/10.1016/j.molcel.2011.07.023 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Post-transcriptional capping generates coenzyme A-linked RNA.
RNA Biol
January 2024
Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA.
Article Synopsis
- NAD can be co-transcriptionally inserted into RNA, but this doesn't work well for CoA-linked RNAs due to the scarcity of dpCoA.
- Researchers found that the enzyme PPAT can utilize RNA transcripts to add 4'-phosphopantetheine, resulting in CoA-RNA formed after transcription.
- The study highlights that RNAs with specific unpaired nucleotides can act as substrates for PPAT and identifies factors that influence the capping process, suggesting that CoA-RNA production occurs after transcription in bacteria.
Selective RNA Processing and Stabilization are Multi-Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli.
Adv Sci (Weinh)
November 2023
Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao, Shandong, 266237, China.
Selective RNA processing and stabilization (SRPS) facilitates the differential expression of multiple genes in polycistronic operons. However, how the coordinated actions of SRPS-related enzymes affect stoichiometric regulation remains unclear. In the present study, the first genome-wide targetome analysis is reported of these enzymes in Escherichia coli, at a single-nucleotide resolution.
View Article and Find Full Text PDFDynamics of high hydrostatic pressure resistance development in RpoS-deficient Escherichia coli.
Food Res Int
February 2023
Department of Microbial and Molecular Systems, KU Leuven, Faculty of Bioscience Engineering, Kasteelpark Arenberg 20, 3001 Leuven, Belgium. Electronic address:
High hydrostatic pressure (HHP) treatment is one of the most widely accepted non-thermal food processing methods, but HHP-resistance development in pathogenic or spoilage bacteria might compromise the safety and stability of HHP-treated foods. Charting the possible routes and mechanisms of HHP resistance development in foodborne bacteria is therefore essential to anticipate or prevent the appearance of resistant variants. While upregulation of the RpoS-governed general stress response is a well-established route for increased HHP resistance in Escherichia coli, previous work revealed that mutations causing attenuated cAMP/CRP activity or aggregation-prone TnaA variants can evolve to overcome the HHP-hypersensitivity of an E.
View Article and Find Full Text PDFA distinct RNA recognition mechanism governs Np decapping by RppH.
Proc Natl Acad Sci U S A
February 2022
Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016;
Dinucleoside tetraphosphates, often described as alarmones because their cellular concentration increases in response to stress, have recently been shown to function in bacteria as precursors to nucleoside tetraphosphate (Np) RNA caps. Removal of this cap is critical for initiating 5' end-dependent degradation of those RNAs, potentially affecting bacterial adaptability to stress; however, the predominant Np decapping enzyme in proteobacteria, ApaH, is inactivated by the very conditions of disulfide stress that enable Np-capped RNAs to accumulate to high levels. Here, we show that, in cells experiencing such stress, the RNA pyrophosphohydrolase RppH assumes a leading role in decapping those transcripts, preferring them as substrates over their triphosphorylated and diphosphorylated counterparts.
View Article and Find Full Text PDFcyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3' clic hosphates and 5' droxyl ends.
RNA Biol
November 2021
Department of Life Science, Institute for Biochemistry, Leipzig, Germany.
Self-cleaving ribozymes are catalytically active RNAs that cleave themselves into a 5'-fragment with a 2',3'-cyclic phosphate and a 3'-fragment with a 5'-hydroxyl. They are widely applied for the construction of synthetic RNA devices and RNA-based therapeutics. However, the targeted discovery of self-cleaving ribozymes remains a major challenge.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!