RppH (PA0336) is the Nudix-family RNA pyrophosphohydrolase of Pseudomonas aeruginosa. By homology with Escherichia coli RppH it removes pyrophosphate from the 5' end of triphosphorylated (or diphosphorylated) primary transcripts, leaving a 5'-monophosphate that stimulates RNase E-dependent decay. The P. aeruginosa protein substitutes for RppH in E. coli. Loss of PA0336 alters the abundance of several hundred transcripts, raises pyocyanin production and increases virulence in Caenorhabditis elegans, and the pyocyanin phenotype needs the catalytic activity, so RppH acts as a broad post-transcriptional regulator through mRNA turnover.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN000561806, seeded only by eukaryotic Dcp2-type decapping enzymes (yeast, fission yeast, fly, worm). Bacteria have no nucleus, no m7G cap and no deadenylation-dependent decay pathway. Reason: Taxon mismatch. The term describes a nuclear-transcribed mRNA decay pathway of eukaryotes; the bacterial RppH acts on 5'-triphosphorylated primary transcripts upstream of RNase E. The bacterial counterpart of the process is captured by GO:0006402 mRNA catabolic process (core function). Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH Sources checked: PANTHER:PTN000561806 · PTN000561806 SUPPORTS SOURCE BUT NOT TARGET Deep Nudix node whose IBD seeds are all eukaryotic decapping enzymes; the process term is right for them but not for a bacterial leaf. SGD:S000005062 · S. cerevisiae DCP2 SUPPORTS SOURCE BUT NOT TARGET Eukaryotic mRNA decapping enzyme. PomBase:SPAC19A8.12 · S. pombe dcp2 SUPPORTS SOURCE BUT NOT TARGET Eukaryotic mRNA decapping enzyme. Supporting Evidence: file:PSEAE/rppH/rppH-uniprot.txt Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the same eukaryote-seeded node. For a soluble bacterial enzyme without signal peptide or TM segment acting on cellular RNA, the cytoplasm is nonetheless correct. Reason: Correct location; RppH acts on cytoplasmic transcripts in a bacterium, where there is no nuclear compartment to separate. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO from the Nudix box signature. Reason: Entailed by GO:0034353, accepted below. |
| GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides | IEA GO_REF:0000104 | TOO GENERAL | Summary: UniRule transfer. Reason: Entailed by GO:0034353 (is_a GO:0016462 pyrophosphatase activity, is_a GO:0016818). |
| GO:0034353 mRNA 5'-triphosphate diphosphatase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001500664 (bacterial RppH clade, 11 leaf IBAs), seeded by E. coli RppH (IDA PMID:18202662) and by Q9X4P2 itself (expected, not circular). The IBD stands on the E. coli seed alone. Reason: Core activity, consistent with HAMAP and the complementation data. Supporting Evidence: file:PSEAE/rppH/rppH-uniprot.txt Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA PMID:28833678 Trans-complementation experiments showed that the P. aeruginosa enzyme can functionally substitute for RppH in E. coli cells |
| GO:0034353 mRNA 5'-triphosphate diphosphatase activity | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of the same activity. Reason: Same claim as the accepted IBA and IMP rows. Supporting Evidence: file:PSEAE/rppH/rppH-uniprot.txt Belongs to the Nudix hydrolase family. RppH subfamily. |
| GO:0034353 mRNA 5'-triphosphate diphosphatase activity | IMP PMID:28833678 Nudix-type RNA pyrophosphohydrolase provides homeostasis of ... | ACCEPT | Summary: PseudoCAP seed row for PTN001500664. The abstract reports that PA0336 complements E. coli RppH and that a catalytically inactive variant fails to complement the pyocyanin phenotype. Seed verdict SOUND. Reason: Functional complementation of the E. coli RNA pyrophosphohydrolase plus the catalytic-mutant control directly ties the activity to PA0336. The term suits the bacterial RppH clade. Supporting Evidence: PMID:28833678 Trans-complementation experiments showed that the P. aeruginosa enzyme can functionally substitute for RppH in E. coli cells indicating that, similar to RppH, the Pseudomonas hydrolase mediates RNA turnover in vivo. PMID:28833678 This phenotype was reversed by complementation with the wild type but not catalytically inactive PA0336 |
| GO:0006402 mRNA catabolic process | IMP PMID:28833678 Nudix-type RNA pyrophosphohydrolase provides homeostasis of ... | NEW | Summary: Proposed. PA0336 complements the RNA-turnover function of E. coli RppH, and loss of PA0336 changes the levels of 537 transcripts. Reason: RppH performs the rate-setting 5'-end conversion step of 5'-end-dependent mRNA decay, so it does work in the process; E. coli RppH carries the same term. Replaces the removed eukaryote-specific GO:0000290. Supporting Evidence: PMID:28833678 Trans-complementation experiments showed that the P. aeruginosa enzyme can functionally substitute for RppH in E. coli cells indicating that, similar to RppH, the Pseudomonas hydrolase mediates RNA turnover in vivo. |
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Download this section (compressed HTML)Q: Does P. aeruginosa RppH, like E. coli RppH, prefer 5'-diphosphorylated RNA generated by a separate kinase/phosphatase step, and which PA0336-dependent transcripts (for example phz operon mRNAs) are its direct substrates?
Experiment: Measure 5'-end phosphorylation state and half-life of pyocyanin-pathway transcripts in wild type and a PA0336 catalytic mutant (PPP/PP/P-RNA sequencing), and assay purified PA0336 on 5'-triphosphate and 5'-diphosphate RNA substrates.
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