CcmC is a six-transmembrane inner-membrane protein of the System I cytochrome c maturation (Ccm) pathway. As the heme-handling subunit of the CcmABCD ABC-type complex, it binds heme through a conserved periplasmic tryptophan-rich (WWD/WxWD) domain and presents it for covalent attachment to the periplasmic heme chaperone CcmE; ATP hydrolysis by CcmA then releases holo-CcmE, which delivers heme to the CcmFH heme lyase for attachment to apocytochromes c. In P. aeruginosa, loss of ccmC abolishes c-type cytochrome production and causes broad secondary phenotypes, including loss of pyoverdine and catalase activity, porphyrin accumulation, reduced [Fe-S] cluster content and altered quorum-sensing-regulated traits and motility.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | MARK AS OVER ANNOTATED | Summary: A P. aeruginosa ccmC mutant makes very little pyoverdine, but CcmC is not known to do any step of pyoverdine synthesis or maturation. The cited PMID is a Ccm biochemistry paper indexed under E. coli; the phenotype is reported by Baert et al. 2008. Reason: The pyoverdine defect of ccmC mutants is real (P. aeruginosa, PMID:18174132; P. fluorescens, PMID:9822820, PMID:12123798). It shows that ccmC is necessary, not that CcmC takes part in the process. The proposed explanation is indirect: ferribactin-to-pyoverdine conversion fails for lack of periplasmic oxidizing power, which depends on c-type cytochromes. In P. fluorescens some CcmC substitutions affect pyoverdine without affecting cytochrome c, so a more direct contribution cannot be excluded. That is not enough to assert participation. The cited reference also appears to be wrong (see source_defects). Supporting Evidence: PMID:18174132 The production of the siderophore pyoverdine was very low and growth under the condition of iron limitation was severely restricted PMID:12123798 We suggest that the conversion of ferribactin to pyoverdine does not take place in the DeltaccmC mutant because of lack of oxidizing power in the periplasm. PMID:9822820 Simultaneous replacements of residues Trp-115 and Gly-116 in the second periplasmic loop substantially affected pyoverdine production/utilization but not cytochrome c production. |
| GO:0004096 catalase activity | IBA GO_REF:0000033 | REMOVE | Summary: Catalase activity is propagated from PTN001247822, whose only seed is the PseudoCAP IMP row on this gene. That row records a mutant phenotype, so the IBD has nothing to rest on. Reason: CcmC proteins are heme-handling membrane subunits of the Ccm heme-delivery complex. They have no catalase domain or catalytic residues, and no family member has been shown to dismutate H2O2. The sole seed for this node is the PseudoCAP IMP row on ccmC, which turns the loss of catalase activity in a ccmC mutant into a molecular function of CcmC. That loss is explained by poor heme supply to the cell's heme catalases. With the seed unsound, the IBD at PTN001247822 and all its catalase-activity IBAs (143 leaves in 59 taxa) are unsupported. The same node's plasma membrane and cytochrome c biosynthesis IBDs are sound and are kept. Propagation Review Root cause: SOURCE BAD Failure modes: ROLE CONFLATION SOURCE MISCITATION Sources checked: PANTHER:PTN001247822 · PTN001247822 SOURCE BAD Catalase activity IBD with a single seed (PseudoCAP IMP on Q9I3N5); no other family member has catalase evidence. UniProtKB:Q9I3N5 · ccmC (PA1477) SOURCE BAD The seed is a mutant phenotype (loss of catalase activity from impaired heme supply) recorded as an MF, keyed to a Ccm biochemistry paper (PMID:16824107) whose abstract reports no catalase assay. Supporting Evidence: PMID:14663086 Significantly reduced resistance to oxidative stress mediated by haem-containing catalases was observed for the ccmC mutant. PMID:20599545 For the first time, evidence that the external WWD domain of CcmC interacts directly with heme is presented. |
| GO:0004096 catalase activity | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | REMOVE | Summary: A ccmC mutant has no detectable catalase activity. That phenotype shows that heme supply to the catalases depends on CcmC, not that CcmC is a catalase. The cited PMID also appears to be the wrong paper. Reason: A molecular function asserted from loss of an enzyme activity in a mutant extract is an indirect phenotype. The catalases of P. aeruginosa (KatA, KatB, KatE) are separate heme enzymes. CcmC is a polytopic membrane protein that binds heme for delivery to CcmE, and both papers that report the phenotype attribute it to heme deficiency or porphyrin accumulation. The row is also keyed to PMID:16824107, a Ccm biochemistry paper (indexed under E. coli) whose abstract reports no catalase assay. This row is the sole seed of the PAINT IBD at PTN001247822. Supporting Evidence: PMID:18174132 The ccmC mutant was also found to accumulate porphyrins, and catalase production was undetectable, consistent with the increased sensitivity to hydrogen peroxide. PMID:14663086 Significantly reduced resistance to oxidative stress mediated by haem-containing catalases was observed for the ccmC mutant. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: CcmC is a six-TM inner-membrane protein. This IBD is seeded by E. coli CcmC and another family member, not by PseudoCAP, and is sound. Reason: Six predicted TM helices and the experimental inner-membrane location of the CcmABCD complex in E. coli support the plasma membrane (bacterial inner membrane) as the site of activity. Supporting Evidence: file:PSEAE/ccmC/ccmC-uniprot.txt TRANSMEM 26..46 PMID:9822820 A topological model for CcmC, based on the analysis of alkaline phosphatase fusions, predicts six membrane-spanning regions with three periplasmic loops. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Inner (cytoplasmic) membrane location, consistent with topology. Reason: The inner-membrane location agrees with the six-TM topology established for P. fluorescens CcmC by phoA fusions and with the IBA row. Supporting Evidence: PMID:9822820 The inner membrane protein CcmC (CytA) of Pseudomonas fluorescens ATCC17400 |
| GO:0009247 glycolipid biosynthetic process | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | REMOVE | Summary: Lower rhamnolipid production in the ccmC mutant is one of several pleiotropic, quorum-sensing-regulated phenotypes, not participation in glycolipid synthesis. Reason: Rhamnolipid is made by the cytoplasmic RhlA/RhlB/RhlC enzymes. The abstract itself presents the rhamnolipid defect as one of several quorum-sensing-regulated traits secondarily affected by loss of cytochrome c maturation. CcmC does no step of glycolipid synthesis. The cited PMID also appears to be wrong. Supporting Evidence: PMID:18174132 we have demonstrated that CcmC is a key determinant for cytochrome c biogenesis, pyoverdine maturation, and expression of some quorum sensing-regulated traits |
| GO:0015232 heme transmembrane transporter activity | IEA GO_REF:0000002 | ACCEPT | Summary: CcmC is the heme-handling membrane subunit of the CcmABCD heme-export complex. Cryo-EM structures of the E. coli complex support ATP-driven heme translocation at the CcmB/CcmC interface and transfer to CcmE. Reason: This is the family-level function in the protein name (heme exporter protein C). Strictly, the transport activity belongs to the CcmABCD complex, in which CcmC binds the heme and CcmA hydrolyses ATP, and whether heme is translocated or only ligated to CcmE has been debated. The 2023 structure favours translocation at the CcmBC interfaces. Accepted as the best available MF term for the core role. Supporting Evidence: PMID:37626034 Our data suggest that the complex flops a heme group from the inner to the outer leaflet at its CcmBC interfaces, driven by ATP hydrolysis at CcmA. PMID:36307425 CcmABCD represents an ABC transporter complex using the energy of ATP hydrolysis for the transfer of heme from one binding partner (CcmC) to another (CcmE). |
| GO:0015886 heme transport | IEA GO_REF:0000002 | ACCEPT | Summary: CcmC takes part in moving heme to the periplasmic chaperone CcmE. Reason: CcmC binds heme and is needed and sufficient to load it onto CcmE, which carries it to the CcmFH lyase. This is heme trafficking in the direct sense. Supporting Evidence: PMID:11384983 We propose that CcmC, CcmE, and heme interact directly with each other, establishing a periplasmic heme delivery pathway for cytochrome c maturation. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: Correct but general; CcmC is in the inner (plasma) membrane. Reason: The gene already carries plasma membrane (IBA, IEA), which the topology evidence supports. Refined to that term. Proposed replacements: plasma membrane Supporting Evidence: PMID:9822820 The inner membrane protein CcmC (CytA) of Pseudomonas fluorescens ATCC17400 |
| GO:0017004 cytochrome complex assembly | IEA GO_REF:0000002 | MODIFY | Summary: CcmC acts in covalent heme attachment to c-type cytochromes, which is cytochrome c biosynthesis, not assembly of a multi-subunit cytochrome complex. Reason: The InterPro2GO mapping uses the general assembly term. The specific process CcmC takes part in is cytochrome c maturation, which the gene already carries as GO:1903607 cytochrome c biosynthetic process (IBA). In P. aeruginosa, the ccmC mutant alone of the ccm mutants tested completely loses cytochrome c. Proposed replacements: cytochrome c biosynthetic process Supporting Evidence: PMID:18174132 Only in the case of the ccmC mutant was cytochrome c production totally abrogated. |
| GO:0020037 heme binding | IEA GO_REF:0000002 | ACCEPT | Summary: CcmC binds heme directly through its periplasmic WWD domain (shown for the E. coli orthologue, including by cryo-EM). Reason: Direct heme binding by CcmC is well established in E. coli. The P. aeruginosa protein has the conserved WWD domain (IPR045062) and the same family membership. Supporting Evidence: PMID:20599545 For the first time, evidence that the external WWD domain of CcmC interacts directly with heme is presented. PMID:36307425 We locate the ATP-binding site in CcmA and the heme-binding site in CcmC. |
| GO:0043107 type IV pilus-dependent motility | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | REMOVE | Summary: Reduced twitching motility in the ccmC mutant is a pleiotropic phenotype of losing c-type cytochromes, not participation in type IV pilus motility. Reason: The abstract lists twitching motility among the secondary, quorum-sensing-associated traits affected by loss of cytochrome c maturation. CcmC is not a pilus or pilus-motor component. The cited PMID also appears to be wrong. Supporting Evidence: PMID:18174132 Interestingly, other traits were also strongly affected by the ccmC mutation, including the production of pyocyanin, swarming and twitching motility, and rhamnolipid production. |
| GO:0071977 bacterial-type flagellum-dependent swimming motility | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | MARK AS OVER ANNOTATED | Summary: Swimming is not among the phenotypes in the Baert et al. abstract, and the abstract of the cited paper describes no motility assay. Any swimming defect would at most be an indirect energetic phenotype. Reason: A swimming phenotype may be reported in the Baert et al. 2008 full text, which could not be read. Even so, a motility defect in a mutant lacking all c-type cytochromes (and so respiratory capacity) is a pleiotropic consequence, not participation in flagellar motility. Marked over-annotated rather than removed because the evidence behind the row could not be seen. Supporting Evidence: PMID:18174132 Only in the case of the ccmC mutant was cytochrome c production totally abrogated. |
| GO:0071978 bacterial-type flagellum-dependent swarming motility | IMP PMID:16824107 ABC transporter-mediated release of a haem chaperone allows ... | REMOVE | Summary: Reduced swarming in the ccmC mutant is a pleiotropic phenotype, not participation in swarming motility. Reason: The abstract groups swarming with pyocyanin, twitching and rhamnolipid as secondarily affected traits. Swarming also depends on rhamnolipid, which the mutant makes less of. CcmC is not a flagellar or motility component. The cited PMID also appears to be wrong. Supporting Evidence: PMID:18174132 Interestingly, other traits were also strongly affected by the ccmC mutation, including the production of pyocyanin, swarming and twitching motility, and rhamnolipid production. |
| GO:0098869 cellular oxidant detoxification | IEA GO_REF:0000108 | REMOVE | Summary: Inferred automatically from the catalase activity annotation, which is itself an indirect phenotype. It goes when that row goes. Reason: This GO_REF:0000108 inference rests entirely on GO:0004096 catalase activity, which is removed here (both the PseudoCAP IMP and the IBA from PTN001247822). CcmC does not detoxify oxidants. The mutant's H2O2 sensitivity comes from losing heme-catalase activity. Supporting Evidence: PMID:14663086 Significantly reduced resistance to oxidative stress mediated by haem-containing catalases was observed for the ccmC mutant. |
| GO:1903607 cytochrome c biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Core process. CcmC loads heme onto CcmE for attachment to apocytochromes c. The IBD is seeded by E. coli CcmC and is sound, and the P. aeruginosa ccmC mutant loses all cytochrome c. Reason: Strong evidence in E. coli for the mechanism, and P. aeruginosa genetics show CcmC is essential for c-type cytochrome production. CcmC does a step of this process itself (heme presentation and ligation to CcmE). Supporting Evidence: PMID:18174132 Only in the case of the ccmC mutant was cytochrome c production totally abrogated. PMID:11384983 CcmC is necessary and sufficient to incorporate heme into CcmE. |
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Download this section (compressed HTML)Q: Why does losing ccmC have a stronger effect on pyoverdine, catalase and porphyrin homeostasis than losing other ccm genes, and do some P. fluorescens CcmC substitutions (W115/G116) really affect pyoverdine without affecting cytochrome c? Is there a cytochrome c-independent role in heme or porphyrin export?
Q: Can GO Central withdraw the catalase activity IBD at PTN001247822, whose only seed was a PseudoCAP IMP mutant-phenotype row?
Experiment: Express P. aeruginosa CcmC point mutants that abolish CcmE heme loading but keep the protein stable, and measure pyoverdine, catalase activity and porphyrin accumulation. This tests whether every secondary phenotype follows from losing cytochrome c maturation or from a separate CcmC heme-export role.
Type: site-directed mutagenesis with phenotypic profiling
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