OmcE (locus GSU0618) is a tetraheme c-type cytochrome of Geobacter sulfurreducens that sits on the outer cell surface and can polymerize into extracellular filaments. The 232-residue precursor carries a cleavable signal peptide and no transmembrane segment or lipid anchor; four CXXCH motifs bind its hemes, the last two forming the paired motif recognised as Pfam PF09699. The protein was first recovered, at around 30 kDa, among the cytochromes most readily sheared from the outer surface of intact cells. Cryo-electron microscopy of filaments later showed OmcE forming an appendage about 40 angstroms across, thinner than the OmcS filament, in which hemes stack along the fibre axis and one heme per subunit is coordinated by a histidine donated from the neighbouring subunit. That arrangement is shared with OmcS even though the two proteins have no detectable sequence or backbone similarity, which led to the proposal that conductive bacterial appendages form a class defined by heme packing rather than by homology. The filament surface carries extra densities, hypothesised but not shown to be glycans. Loss of omcE abolishes reduction of insoluble Fe(III) oxide while leaving soluble acceptors, anode respiration and interspecies electron transfer essentially unaffected, which sets OmcE apart from OmcS and from the electrode-specific OmcZ. OmcE is also the specific target of the artificial electron mediator resorufin, which binds the isolated protein with submicromolar affinity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0020037 heme binding | IDA PMID:35798889 Cryo-EM structure of an extracellular Geobacter OmcE cytochr... | NEW | Summary: OmcE carries four covalently attached c-type hemes. The cryo-EM structure of the filament resolves them, with each heme iron bis-coordinated by histidines, and the sequence carries exactly four CXXCH motifs. Reason: GOA holds nothing at all for this protein, and heme binding is the best evidenced thing about it. The hemes are resolved in PDB 7TFS and UniProt records the corresponding binding sites from that structure; the authors note that of the candidate cytochromes considered, only OmcE has the eight histidines needed to bis-coordinate four hemes, which is what identified the filament as OmcE in the first place. The count is independently consistent with the four CXXCH motifs in the sequence and with the tetraheme prediction made when the protein was first described. Supporting Evidence: PMID:35798889 Of these four cytochromes, only OmcE has eight histidine residues near the Fe densities to assemble bis-coordinated hemes PMID:16332857 The other abundant c-type cytochrome sheared from the outer surface of G. sulfurreducens, designated OmcE, has a molecular mass of ca. 30 kDa and is predicted to be an outer membrane tetraheme c-type cytochrome. |
| GO:0009055 electron transfer activity | IC PMID:35798889 Cryo-EM structure of an extracellular Geobacter OmcE cytochr... | NEW | Summary: Inferred by the reviewer rather than measured. Three lines converge: the structure shows four hemes stacked along the filament with bis-histidine coordination and cross-subunit heme ligation, the aligned inter-heme distances match those of the OmcS filament, and losing omcE costs the cell its ability to reduce insoluble Fe(III) oxide. The artificial mediator resorufin binds the purified protein at a heme. Reason: Recorded as IC, not IDA, and the distinction is the point. Unlike OmcS and OmcZ, OmcE has never been purified and shown to reduce an acceptor, and the 2022 structure paper did not measure the filament's conductivity either; it inferred similar electron transport from matching heme geometry and warned in the same breath that conductivity attributed to a particular protein needs treating with caution. What is directly shown is a stacked, bis-histidine-coordinated heme chain, which is the structural signature of an electron conduit, together with a genetic phenotype that only makes sense if electrons reach an extracellular acceptor through this protein. That is a sound inference and a weak measurement, so the evidence code says so. An experiment to close the gap is suggested below. Supporting Evidence: PMID:35798889 Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. PMID:16332857 When either omcS or omcE was deleted, G. sulfurreducens could no longer reduce Fe(III) oxide but could still reduce soluble electron acceptors, including Fe(III) citrate. PMID:39278116 By using heterologously expressed OmcE monomers in Escherichia coli, it was found that RR bonded with OmcE monomers with a moderate intensity (dissociation constant of 720 nM) |
| GO:0019645 anaerobic electron transport chain | IMP PMID:16332857 Outer membrane c-type cytochromes required for Fe(III) and M... | NEW | Summary: Deleting omcE leaves the cell unable to reduce insoluble Fe(III) oxide while growth on soluble acceptors including Fe(III) citrate is unaffected, and expressing omcE in trans restores the capacity. Reason: The gene product does part of the work rather than merely being required for it: it is itself a heme-bearing carrier on the outer surface, so the perturbation result is read together with the structure rather than on its own. The specificity of the phenotype is what places OmcE in the extracellular branch of the chain rather than upstream, and complementation rules out a polar effect. The same term is used across the other Geobacter and Shewanella envelope and surface cytochromes reviewed here (ImcH, CbcL, OmcS, OmcZ, OmcA), and GO has nothing narrower for respiration on an extracellular solid acceptor. Note the contrast with OmcS and OmcZ: the omcE phenotype does not extend to anodes or to interspecies transfer. Supporting Evidence: PMID:16332857 When either omcS or omcE was deleted, G. sulfurreducens could no longer reduce Fe(III) oxide but could still reduce soluble electron acceptors, including Fe(III) citrate. PMID:16332857 Expressing omcS or omcE in trans restored the capacity for Fe(III) oxide reduction. PMID:37881251 Deletion of omcE also impaired bacterial ability to reduce ferrihydrite, but its impacts on the ability for anode reduction and the co-culture of G. metallireducens-G. sulfurreducens were minimal. |
| GO:0051258 protein polymerization | IDA PMID:35798889 Cryo-EM structure of an extracellular Geobacter OmcE cytochr... | NEW | Summary: OmcE subunits polymerize into an extracellular filament about 40 angstroms across, resolved by cryo-EM at 4.3 angstroms. The subunit interface is made by OmcE itself, including a heme coordinated by a histidine from the adjacent subunit. Reason: The protein makes its own polymer: the filament contains no other subunit, and the contact that holds consecutive subunits together is a heme-histidine ligation across the interface, which the authors describe as unique among c-type cytochrome structures. One caveat belongs in the record rather than in a footnote. The filaments were enriched from strains carrying omcS mutations, and the authors read that as the cell compensating for loss of OmcS function, so what is established is that OmcE can polymerize and does so in cells, not how much filament a wild-type cell makes. The annotation is for the capability, which is directly observed; the abundance question is recorded as a knowledge gap and an experiment. Supporting Evidence: PMID:35798889 Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. PMID:35798889 To the best of our knowledge, the coordination of a heme in one subunit by a histidine in an adjacent subunit in both the OmcE and OmcS filaments seems to be unique among all c-type cytochrome structures solved to date. PMID:35798889 a serendipitous outcome was that these omcS mutations resulted in an enrichment of extracellular OmcE filaments |
| GO:0009986 cell surface | IDA PMID:16332857 Outer membrane c-type cytochromes required for Fe(III) and M... | NEW | Summary: OmcE was among the most abundant proteins sheared from the outer surfaces of intact cells, and the filaments it forms are extracellular. Reason: Shearing intact cells recovers what is accessible on the outside without breaking the envelope, and the later structural work took OmcE from extracellular preparations, so two methods agree. GO:0009986 covers products attached integrally or loosely to the envelope, which is what this is. The outer membrane term GO:0009279 was deliberately not proposed: the entry records no transmembrane segment and no lipid anchor, and in the OmcS review the equivalent rows were judged over-annotated for the same reasons. GO:0005576 extracellular region was also declined, since its GO comment reserves it for products not attached to the cell surface. Supporting Evidence: PMID:16332857 The other abundant c-type cytochrome sheared from the outer surface of G. sulfurreducens, designated OmcE, has a molecular mass of ca. 30 kDa and is predicted to be an outer membrane tetraheme c-type cytochrome. PMID:35798889 The multiheme c-type cytochromes OmcE, OmcS, and OmcZ are typically the most abundant proteins sheared from G. sulfurreducens cell surfaces after growth with metal oxides or electrode surfaces |
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Download this section (compressed HTML)Q: Does a wild-type cell make OmcE filaments at all, or only monomeric surface OmcE? The structure came from omcS-mutant strains in which the filaments were enriched, and the authors read that as compensation.
Q: Is the Fe(III) oxide phenotype a property of the filament or of monomeric OmcE? A polymerization-deficient but folded OmcE would separate the two.
Q: Why does this organism maintain three unrelated polymerizing cytochromes whose deletion phenotypes barely overlap, with OmcE confined to insoluble iron, OmcS covering iron and interspecies transfer, and OmcZ owning the electrode?
Q: Is PANTHER's placement of OmcE in PTHR35038:SF6 defensible? The family is named for a dissimilatory sulfite reductase and the subfamily for a decaheme lipoprotein, while OmcE is a tetraheme cytochrome with no lipid anchor, and the same subfamily also holds MtrA and a hydroxylamine oxidoreductase.
Q: Are the surface densities on the OmcE filament really glycans, and if so are they O-linked? The protein contains no N-X-S/T sequon, so a canonical N-linked modification is not available to it.
Experiment: Purify OmcE, reduce it with dithionite and follow its reoxidation by Fe(III) oxide, Mn(IV) oxide, chelated Fe(III) and AQDS by stopped flow, exactly as was done for OmcS. That comparison would convert the molecular-function row here from an inference to a measurement and would place OmcE on the same scale as the other two cytochromes.
Hypothesis: OmcE itself transfers electrons to insoluble Fe(III) oxide, rather than only holding a mediator or a partner in place.
Type: electron transfer assay on purified protein
Experiment: Compare wild type with the omcS mutants side by side, measuring the abundance of filamentous versus monomeric OmcE in sheared surface fractions by quantitative mass spectrometry and counting filament species by cryo-EM with DNase treatment throughout. If wild-type cells carry few OmcE filaments, the structure describes a stress state and the physiological unit is monomeric surface OmcE.
Hypothesis: OmcE filaments are a compensatory response to loss of OmcS rather than a constitutive feature of wild-type cells.
Type: quantitative imaging and proteomics across strains
Experiment: Mutate the cross-subunit histidine that ligates the interfacial heme, together with other interface residues identified in 7TFS, to produce a folded, heme-loaded OmcE that cannot polymerize. Test Fe(III) oxide reduction in that strain. A mutant that keeps its hemes but loses the filament and also loses the phenotype would show the polymer is the functional unit.
Hypothesis: Polymerization is required for OmcE to support Fe(III) oxide reduction.
Type: structure-guided separation-of-function mutagenesis
Experiment: Determine the modification by mass spectrometry of OmcE purified from wild type and from deletions of the glycosyltransferases in the downstream 17-gene cluster, looking specifically at S83, N86, N87, N132 and T184. The absence of any N-X-S/T sequon makes this worth settling rather than assuming.
Hypothesis: The extra densities on the filament surface are O-linked glycans installed by the gene cluster downstream of omcE.
Type: glycoproteomics with targeted deletions
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