Gep4 (YHR100C) is the mitochondrial phosphatidylglycerophosphate (PGP) phosphatase of Saccharomyces cerevisiae, a HAD-superfamily phosphatase of the PGPP1/Gep4 family. It is a peripheral protein on the matrix side of the mitochondrial inner membrane, where it dephosphorylates phosphatidylglycerophosphate (made from CDP-diacylglycerol and glycerol-3-phosphate by Pgs1) to phosphatidylglycerol (EC 3.1.3.27), the second step of the mitochondrial phosphatidylglycerol branch and an obligatory step for cardiolipin synthesis by Crd1. Loss of Gep4 causes accumulation of PGP and loss of phosphatidylglycerol and cardiolipin; a mitochondrially targeted E. coli PgpA restores cardiolipin, showing functional conservation with the bacterial PGP phosphatases. gep4 mutants are sensitive to elevated temperature and ethidium bromide and are synthetically sick with loss of prohibitins.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MODIFY | Summary: Deep PAINT node (PTN002711682, with bacterial PgpA and other HAD phosphatases) propagates 'cytoplasm'. For Gep4 the active site faces the mitochondrial matrix; cytoplasm is formally a superset but misleading. Reason: Gep4 activity is in the mitochondrial matrix; the lineage-specific node already gives mitochondrion. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN002711682 · deep HAD PGP-phosphatase node incl. E. coli PgpA (P0AF24) and human PTPMT1-like members SUPPORTS SOURCE BUT NOT TARGET Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Gep4 detected in the purified mitochondrial proteome (PROMITO); consistent with the matrix-side inner membrane localisation. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS file:yeast/GEP4/GEP4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Gep4-subfamily PAINT node; mitochondrial localisation is experimentally established. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location (inner membrane, peripheral, matrix side) mapping; correct. Supporting Evidence: file:yeast/GEP4/GEP4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane file:yeast/GEP4/GEP4-uniprot.txt membrane protein {ECO:0000269|PubMed:16823961, |
| GO:0005759 mitochondrial matrix | IDA PMID:20485265 A mitochondrial phosphatase required for cardiolipin biosynt... | ACCEPT | Summary: Osman et al. localised Gep4 to the mitochondrial matrix space; this is where PGP dephosphorylation occurs. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways converts PHOS-PWY with the default 'cytosol' compartment on every step. Gep4 is a mitochondrial matrix-side inner-membrane protein; there is no evidence for cytosolic activity. Reason: Default YeastCyc compartment contradicted by experimental localisation to the mitochondrial matrix side of the inner membrane. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis file:yeast/GEP4/GEP4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane |
| GO:0006655 phosphatidylglycerol biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway UPA00084 mapping (phosphatidylglycerol from CDP-diacylglycerol, step 2/2); Gep4 catalyses exactly this step. Supporting Evidence: file:yeast/GEP4/GEP4-uniprot.txt PATHWAY: Phospholipid metabolism; phosphatidylglycerol biosynthesis; PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis |
| GO:0008654 phospholipid biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways PHOS-PWY superpathway assigns the general 'phospholipid biosynthetic process'. True but uninformative; Gep4's step is the PG/CL branch. Reason: Replace the superpathway-level term by the specific branch Gep4 acts in. Proposed replacements: phosphatidylglycerol biosynthetic process Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis file:yeast/GEP4/GEP4-uniprot.txt PATHWAY: Phospholipid metabolism; phosphatidylglycerol biosynthesis; |
| GO:0008962 phosphatidylglycerophosphatase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN001060726 (Gep4 subfamily, seeded by the SGD experimental annotation) places PGP phosphatase activity on Gep4; consistent with the biochemical identification. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis file:yeast/GEP4/GEP4-uniprot.txt EC=3.1.3.27; |
| GO:0008962 phosphatidylglycerophosphatase activity | IDA PMID:20485265 A mitochondrial phosphatase required for cardiolipin biosynt... | ACCEPT | Summary: Osman et al. showed that Gep4 dephosphorylates PGP to PG; this is the defining catalytic activity of the protein. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis PMID:20485265 Expression of a mitochondrially targeted variant of Escherichia coli phosphatase PgpA restores CL levels in Gep4-deficient cells, indicating functional conservation |
| GO:0008962 phosphatidylglycerophosphatase activity | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro PGPP1/Gep4 (IPR010021, IPR027706) and EC 3.1.3.27 mapping; correct for Gep4. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis file:yeast/GEP4/GEP4-uniprot.txt EC=3.1.3.27; |
| GO:0008962 phosphatidylglycerophosphatase activity | IGI PMID:20485265 A mitochondrial phosphatase required for cardiolipin biosynt... | ACCEPT | Summary: Genetic interaction with PGS1 (S000002301) places Gep4 immediately downstream of PGP synthase, supporting the PGP phosphatase activity. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis PMID:20485265 A genetic epistasis analysis combined with the identification of intermediates of CL biosynthesis allowed us to integrate Gep4 in the CL-biosynthetic pathway |
| GO:0008962 phosphatidylglycerophosphatase activity | IMP PMID:20485265 A mitochondrial phosphatase required for cardiolipin biosynt... | ACCEPT | Summary: gep4 deletion causes PGP accumulation and loss of PG/CL, consistent with loss of the PGP phosphatase step. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis PMID:20485265 Expression of a mitochondrially targeted variant of Escherichia coli phosphatase PgpA restores CL levels in Gep4-deficient cells, indicating functional conservation |
| GO:0031314 extrinsic component of mitochondrial inner membrane | IDA PMID:20485265 A mitochondrial phosphatase required for cardiolipin biosynt... | ACCEPT | Summary: Gep4 is a peripheral protein on the matrix face of the inner membrane (UniProt, citing Osman et al.), consistent with acting on membrane-embedded PGP. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis file:yeast/GEP4/GEP4-uniprot.txt membrane protein {ECO:0000269|PubMed:16823961, |
| GO:0032049 cardiolipin biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference for Gep4 subfamily; Gep4 performs the PGP to PG step that cardiolipin synthesis requires, so it is directly involved in cardiolipin biosynthesis. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis |
| GO:0032049 cardiolipin biosynthetic process | IMP PMID:20485265 A mitochondrial phosphatase required for cardiolipin biosynt... | ACCEPT | Summary: gep4 cells lack cardiolipin, restored by mitochondrial PgpA; Gep4 catalyses an obligatory step of the CL pathway. Supporting Evidence: PMID:20485265 we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis PMID:20485265 Expression of a mitochondrially targeted variant of Escherichia coli phosphatase PgpA restores CL levels in Gep4-deficient cells, indicating functional conservation |
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Download this section (compressed HTML)Q: Does Gep4 have substrates other than PGP in vivo (HAD phosphatases are often promiscuous), and does it act on the lyso-PGP or other glycerophospholipid phosphates?
Q: Is Gep4 activity regulated by Tam41/Pgs1 levels or by respiratory growth, given the requirement for CL in supercomplex stability?
Experiment: Purify recombinant Gep4 and measure steady-state kinetics with PGP versus other phosphomonoester lipids and soluble phosphates to define its substrate range.
Mitochondrial phosphatidylglycerophosphatase (PGP phosphatase); dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during cardiolipin biosynthesis; null mutant is sensitive to tunicamycin, DTT
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