PNPase (CG11337) is the Drosophila mitochondrial polynucleotide phosphorylase, a trimeric phosphorolytic 3'-5' exoribonuclease of the PNPase/RNase PH family with KH and S1 RNA-binding domains. With the helicase SUV3 it forms the mitochondrial degradosome, which degrades mitochondrial mRNAs that are not protected by LRPPRC and rapidly removes non-coding antisense transcripts generated by bidirectional mitochondrial transcription. Loss of PNPase in flies stabilizes mitochondrial mRNAs and antisense RNAs, impairs respiratory chain function and leads to accumulation of mitochondrial double-stranded RNA, some of which escapes to the cytosol.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000175 3'-5'-RNA exonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: PNPase is a 3'-5' exoribonuclease. Reason: PNPase degrades RNA phosphorolytically from the 3' end, a conserved family activity; fly PNPase is required for decay of mitochondrial mRNAs and antisense RNAs. GO's exonuclease branch is defined by hydrolysis, so this term describes the outcome (3'-5' removal of nucleotides) rather than the phosphorolytic mechanism, which is captured by the polyribonucleotide nucleotidyltransferase activity row. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000134193 SUPPORTS TRANSFER PNPase is a canonical member of the PNPase family, which is a phosphorolytic 3'-5' exoribonuclease from bacteria to animal mitochondria. Supporting Evidence: PMID:31365523 Besides degrading mRNAs, loss of the degradosome also resulted in the accumulation of antisense RNA, suggesting that PNPase and SUV3 are also responsible for degrading these RNAs |
| GO:0000957 mitochondrial RNA catabolic process | IMP PMID:31365523 Defects of mitochondrial RNA turnover lead to the accumulati... | ACCEPT | Summary: PNPase degrades mitochondrial RNAs. Reason: Loss of fly PNPase stabilizes mitochondrial mRNAs and antisense transcripts. Supporting Evidence: PMID:26152302 In agreement, silencing of both DmSUV3 and DmPNPase resulted in increased mitochondrial mRNA stability PMID:31365523 Besides degrading mRNAs, loss of the degradosome also resulted in the accumulation of antisense RNA, suggesting that PNPase and SUV3 are also responsible for degrading these RNAs |
| GO:0000957 mitochondrial RNA catabolic process | ISS GO_REF:0000024 | ACCEPT | Summary: PNPase degrades mitochondrial RNAs. Reason: Loss of fly PNPase stabilizes mitochondrial mRNAs and antisense transcripts. Supporting Evidence: PMID:26152302 In agreement, silencing of both DmSUV3 and DmPNPase resulted in increased mitochondrial mRNA stability PMID:31365523 Besides degrading mRNAs, loss of the degradosome also resulted in the accumulation of antisense RNA, suggesting that PNPase and SUV3 are also responsible for degrading these RNAs |
| GO:0000958 mitochondrial mRNA catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: PNPase degrades mitochondrial mRNAs. Reason: Silencing of DmPNPase increases mitochondrial mRNA stability; LRPPRC protects mRNAs from degradosome-mediated decay. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000134194 SUPPORTS TRANSFER Mitochondrial mRNA decay by PNPase is conserved in metazoan mitochondrial PNPases and experimentally established in the fly. Supporting Evidence: PMID:26152302 In agreement, silencing of both DmSUV3 and DmPNPase resulted in increased mitochondrial mRNA stability PMID:31365523 suggesting that indeed, LRPPRC functions as a physical barrier, protecting mRNAs from degradation by the degradosome |
| GO:0000958 mitochondrial mRNA catabolic process | IMP PMID:26152302 SUV3 helicase is required for correct processing of mitochon... | ACCEPT | Summary: PNPase degrades mitochondrial mRNAs. Reason: Silencing of DmPNPase increases mitochondrial mRNA stability; LRPPRC protects mRNAs from degradosome-mediated decay. Supporting Evidence: PMID:26152302 In agreement, silencing of both DmSUV3 and DmPNPase resulted in increased mitochondrial mRNA stability PMID:31365523 suggesting that indeed, LRPPRC functions as a physical barrier, protecting mRNAs from degradation by the degradosome |
| GO:0000965 mitochondrial RNA 3'-end processing | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Mitochondrial RNA 3'-end processing inherited from human PNPT1. Reason: In Drosophila the processing of polycistronic mitochondrial transcripts depends on SUV3 but was shown to be independent of PNPase, and PNPase loss mainly stabilizes mRNAs and antisense RNAs. A role for fly PNPase in 3'-end processing is not supported. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000134194 SUPPORTS SOURCE BUT NOT TARGET The processing role is seeded from human PNPT1; fly genetics place precursor processing on SUV3 independently of PNPase. Supporting Evidence: PMID:26152302 our results propose that SUV3 is predominantly required for the processing of mitochondrial polycistronic transcripts in metazoan and that this function is independent of PNPase |
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | MODIFY | Summary: PNPase binds RNA. Reason: PNPase carries KH and S1 RNA-binding domains; correct but general, so MODIFY to RNA binding, which PNPase already carries (IEA). Proposed replacements: RNA binding Supporting Evidence: file:DROME/PNPase/PNPase-uniprot.txt Belongs to the polyribonucleotide nucleotidyltransferase family |
| GO:0003723 RNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: PNPase binds RNA. Reason: PNPase carries KH and S1 RNA-binding domains (PROSITE KH_TYPE_1 and S1 matches in the UniProt record; domain composition also reported for the fly protein in PMID:31365523). No more specific RNA-binding term is supported, so RNA binding is as precise as the evidence allows. Supporting Evidence: PMID:31365523 identified the PNPase family-defining RNase PH, KH, and S1 domains file:DROME/PNPase/PNPase-uniprot.txt DR PROSITE; PS50084; KH_TYPE_1; 1. file:DROME/PNPase/PNPase-uniprot.txt DR PROSITE; PS50126; S1; 1. |
| GO:0004654 polyribonucleotide nucleotidyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PNPase has polyribonucleotide nucleotidyltransferase activity. Reason: Defining activity of the PNPase family (phosphorolysis and the reverse polymerization). Fly PNPase matches the PNPase family signatures (InterPro IPR012162, NCBIfam TIGR03591), and the fly study PMID:31365523 describes PNPase as a phosphorolytic 3'-5' exoribonuclease; this activity has not been assayed biochemically on the fly protein itself, so the claim rests on family membership. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000134193 SUPPORTS TRANSFER PNPase is a canonical member of the PNPase family, which is a phosphorolytic 3'-5' exoribonuclease from bacteria to animal mitochondria. Supporting Evidence: PMID:31365523 PNPase has phosphorolytic 3′ to 5′ exoribonuclease activity file:DROME/PNPase/PNPase-uniprot.txt DR InterPro; IPR012162; PNPase. file:DROME/PNPase/PNPase-uniprot.txt DR NCBIfam; TIGR03591; polynuc_phos; 1. |
| GO:0004654 polyribonucleotide nucleotidyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: PNPase has polyribonucleotide nucleotidyltransferase activity. Reason: Defining activity of the PNPase family (phosphorolysis and the reverse polymerization). Fly PNPase matches the PNPase family signatures (InterPro IPR012162, NCBIfam TIGR03591), and the fly study PMID:31365523 describes PNPase as a phosphorolytic 3'-5' exoribonuclease; this activity has not been assayed biochemically on the fly protein itself, so the claim rests on family membership. Supporting Evidence: PMID:31365523 PNPase has phosphorolytic 3′ to 5′ exoribonuclease activity file:DROME/PNPase/PNPase-uniprot.txt DR InterPro; IPR012162; PNPase. file:DROME/PNPase/PNPase-uniprot.txt DR NCBIfam; TIGR03591; polynuc_phos; 1. |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: Cytoplasm from a family-level ARBA rule. Reason: The rule reflects bacterial PNPases. Mitochondria are formally part of the cytoplasm in GO, but the fly protein functions inside mitochondria in the degradosome, so this generic assignment adds nothing and can be misread as a cytosolic location. Supporting Evidence: PMID:31365523 we manipulated the mitochondrial mRNA degrading complex in Drosophila melanogaster models |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PNPase is active in mitochondria. Reason: Fly PNPase functions in mitochondrial RNA turnover; fractionation was used in the dsRNA study. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000134194 SUPPORTS TRANSFER Mitochondrial localization is conserved in animal and plant PNPases. Supporting Evidence: PMID:31365523 Western blot analysis of total (T), cytosolic (C) and mitochondrial (M) fractions from control, dmsuv3KD, dmpnpaseKO, and dmmtpapKO protein extracts PMID:31365523 suggesting that indeed, LRPPRC functions as a physical barrier, protecting mRNAs from degradation by the degradosome |
| GO:0005739 mitochondrion | IDA PMID:31365523 Defects of mitochondrial RNA turnover lead to the accumulati... | ACCEPT | Summary: PNPase is active in mitochondria. Reason: Fly PNPase functions in mitochondrial RNA turnover; fractionation was used in the dsRNA study. Supporting Evidence: PMID:31365523 Western blot analysis of total (T), cytosolic (C) and mitochondrial (M) fractions from control, dmsuv3KD, dmpnpaseKO, and dmmtpapKO protein extracts PMID:31365523 suggesting that indeed, LRPPRC functions as a physical barrier, protecting mRNAs from degradation by the degradosome |
| GO:0005759 mitochondrial matrix | ISS GO_REF:0000024 | ACCEPT | Summary: PNPase in the mitochondrial matrix (by similarity to human PNPT1). Reason: Degradosome-mediated decay of mitochondrial transcripts takes place in the matrix with SUV3. Supporting Evidence: PMID:26152302 Studies in yeast and human cell lines have indicated that the mitochondrial helicase SUV3, together with the polynucleotide phosphorylase, PNPase, composes the mitochondrial degradosome |
| GO:0005829 cytosol | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Cytosol inherited across the PNPase family. Reason: The node includes bacterial PNPase, which is cytosolic. Fly PNPase acts in mitochondrial RNA decay; mitochondrial dsRNA escapes to the cytosol when PNPase is lost, but there is no evidence that PNPase itself functions in the fly cytosol. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000134193 SUPPORTS SOURCE BUT NOT TARGET Cytosol is appropriate for bacterial PNPase; the animal mitochondrial PNPase clade acts in mitochondria. Supporting Evidence: PMID:31365523 suggesting that indeed, LRPPRC functions as a physical barrier, protecting mRNAs from degradation by the degradosome PMID:31365523 indicating that mitochondrial-derived dsRNA can be released from mitochondria in flies |
| GO:0006396 RNA processing | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: RNA processing (InterPro mapping); fly PNPase acts in RNA degradation, not maturation. Reason: RNA processing in GO is the conversion of primary transcripts into mature RNAs, and RNA catabolism is not part of it. The InterPro mapping reflects processing roles of some PNPase family members, but in the fly the degradosome processing defects are attributable to SUV3, as dmpnpase larvae showed increased mRNA levels but no processing intermediates and normal tRNA levels (PMID:26152302). The degradative role is captured by the mitochondrial RNA/mRNA catabolic process rows. Consistent with the mitochondrial RNA 3'-end processing row, this is treated as an over-annotation. Supporting Evidence: PMID:26152302 we failed to detect processing intermediates in dmpnpase larvae, nor did we detect reduced tRNA levels |
| GO:0006402 mRNA catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: mRNA catabolic process (InterPro). Reason: Correct; the specific process is mitochondrial mRNA catabolism. Supporting Evidence: PMID:26152302 In agreement, silencing of both DmSUV3 and DmPNPase resulted in increased mitochondrial mRNA stability |
| GO:0045025 mitochondrial degradosome | IGI PMID:31365523 Defects of mitochondrial RNA turnover lead to the accumulati... | ACCEPT | Summary: PNPase is part of the mitochondrial degradosome with SUV3. Reason: Genetic interaction data in flies support a SUV3/PNPase degradosome for mRNA and antisense RNA decay. Supporting Evidence: PMID:31365523 are therefore rapidly degraded in a SUV3/PNPase-dependent manner PMID:26152302 Studies in yeast and human cell lines have indicated that the mitochondrial helicase SUV3, together with the polynucleotide phosphorylase, PNPase, composes the mitochondrial degradosome |
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Download this section (compressed HTML)Q: Does fly PNPase, like human PNPT1, also occupy the intermembrane space and contribute to RNA import into mitochondria, or is it exclusively a matrix degradosome component?
Experiment: Rescue dmpnpase knockout larvae with wild-type or phosphorolysis-dead PNPase and quantify antisense RNA, J2-positive dsRNA in mitochondrial and cytosolic fractions, and immune gene induction.
Hypothesis: Fly PNPase catalytic activity, not only its presence, is required to prevent mitochondrial dsRNA accumulation and release.
Type: genetic rescue
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Download this section (compressed HTML)Polynucleotide phosphorylase (PNPase) encodes an enzyme involved in the regulation of mitochondrial mRNA stability.
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