ArticleProceedings of the National Academy of Sciences of the United States of America2013
Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 38 citations in OpenAlex.
- Mycobacterium tuberculosis MutT4/RppH is an RNA pyrophosphohydrolase that forms condensate-like bodies and impacts mRNA degradation.Nucleic acids research · 2026Article
- Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.Nature communications · 2024Article
- Article
- Multifaceted impact of a nucleoside monophosphate kinase on 5'-end-dependent mRNA degradation in bacteria.Nucleic acids research · 2021Article
- Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.Nucleic acids research · 2020Article
- Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs inRNA (New York, N.Y.) · 2020Article
- YvcI fromThe Journal of biological chemistry · 2019Article
- Bacterial ribonucleases and their roles in RNA metabolism.Critical reviews in biochemistry and molecular biology · 2019Review
- Noncanonical features and modifications on the 5'-end of bacterial sRNAs and mRNAs.Wiley interdisciplinary reviews. RNA · 2019Review
- sRNA-mediated activation of gene expression by inhibition of 5'-3' exonucleolytic mRNA degradation.eLife · 2017Article
- Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets.The Journal of biological chemistry · 2017Article
- Expression, maturation and turnover of DrrS, an unusually stable, DosR regulated small RNA in Mycobacterium tuberculosis.PloS one · 2017Article
- Unknown unknowns: essential genes in quest for function.Microbial biotechnology · 2016Review
- Structural basis of prokaryotic NAD-RNA decapping by NudC.Cell research · 2016Article
- Mapping of internal monophosphate 5' ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains.Nucleic acids research · 2016Article
- Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA.Journal of molecular biology · 2015Article
- Structures of RNA complexes with the Escherichia coli RNA pyrophosphohydrolase RppH unveil the basis for specific 5'-end-dependent mRNA decay.The Journal of biological chemistry · 2015Article
- Specificity and evolutionary conservation of the Escherichia coli RNA pyrophosphohydrolase RppH.The Journal of biological chemistry · 2015Article
- RNA Degradation in Staphylococcus aureus: Diversity of Ribonucleases and Their Impact.International journal of genomics · 2015Review
- RppH-dependent pyrophosphohydrolysis of mRNAs is regulated by direct interaction with DapF in Escherichia coli.Nucleic acids research · 2014Article
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10 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The initiation of mRNA degradation often requires deprotection of its 5' end. In eukaryotes, the 5'-methylguanosine (cap) structure is principally removed by the Nudix family decapping enzyme Dcp2, yielding a 5'-monophosphorylated RNA that is a substrate for 5' exoribonucleases. In bacteria, the 5'-triphosphate group of primary transcripts is also converted to a 5' monophosphate by a Nudix protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5' exoribonucleases. Here we present the crystal structures of Bacillus subtilis RppH (BsRppH) bound to GTP and to a triphosphorylated dinucleotide RNA. In contrast to Bdellovibrio bacteriovorus RppH, which recognizes the first nucleotide of its RNA targets, the B. subtilis enzyme has a binding pocket that prefers guanosine residues in the second position of its substrates. The identification of sequence specificity for RppH in an internal position was a highly unexpected result. NMR chemical shift mapping in solution shows that at least three nucleotides are required for unambiguous binding of RNA. Biochemical assays of BsRppH on RNA substrates with single-base-mutation changes in the first four nucleotides confirm the importance of guanosine in position two for optimal enzyme activity. Our experiments highlight important structural and functional differences between BsRppH and the RNA deprotection enzymes of distantly related bacteria.
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