SecF is a multi-pass inner membrane protein that forms the SecDF accessory complex together with SecD. As part of the Sec protein translocase, SecDF uses the proton motive force (PMF) to enhance protein translocation across the cytoplasmic membrane after the ATP-dependent function of SecA. SecDF undergoes PMF-driven conformational cycles that pull preproteins through the SecYEG channel into the periplasm, functioning as a membrane-integrated chaperone that works independently of ATP. In P. aeruginosa, the SecD-SecF complex has been directly demonstrated by in vivo cross-linking mass spectrometry.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for plasma membrane localization inferred from phylogenetic analysis (PANTHER). SecF is well established as an integral inner membrane protein in bacteria. In P. aeruginosa, the inner membrane corresponds to the plasma membrane. UniProt confirms cell inner membrane localization via HAMAP rule MF_01464. Reason: SecF is an integral inner membrane protein with six predicted transmembrane helices. Plasma membrane localization is consistent with all structural and functional evidence for SecDF family members across bacteria. Supporting Evidence: PMID:21562494 Here, we determined the crystal structure of Thermus thermophilus SecDF at 3.3 Å resolution, revealing a pseudo-symmetrical, 12-helix transmembrane domain belonging to the RND superfamily and two major periplasmic domains, P1 and P4 PMID:7507921 TnphoA fusions have been used to analyze the topology of SecD in the inner membrane; the protein contains six transmembrane stretches and a large periplasmic domain |
| GO:0015031 protein transport | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA annotation for involvement in protein transport, inferred from phylogeny. SecF is part of the Sec translocase that mediates protein export across the bacterial inner membrane. This is correct but very general. Reason: Protein transport is accurate but too broad. The more specific term GO:0043952 (protein transport by the Sec complex) is also annotated and better captures the biological context. This annotation is redundant with the more specific terms. Supporting Evidence: PMID:29718185 The bacterial membrane protein SecDF enhances protein translocation across the membrane driven by the complex of SecA ATPase and SecYEG |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for plasma membrane from combined automated methods (UniProt subcellular location mapping). Correct and consistent with the IBA annotation above. Reason: Redundant with the IBA annotation but independently correct. SecF is an integral inner membrane protein confirmed by topology studies and crystal structures. Supporting Evidence: PMID:21562494 Here, we determined the crystal structure of Thermus thermophilus SecDF at 3.3 Å resolution, revealing a pseudo-symmetrical, 12-helix transmembrane domain belonging to the RND superfamily and two major periplasmic domains, P1 and P4 |
| GO:0006605 protein targeting | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: IEA annotation from UniRule for involvement in protein targeting. SecDF enhances the translocation of preproteins across the membrane, which is part of the protein targeting process. However, SecDF functions specifically in the translocation step rather than in the targeting/recognition step per se. Reason: Protein targeting is a broader process that includes signal recognition and membrane targeting. SecDF specifically functions in the translocation step, after the preprotein has already been targeted to the membrane. This annotation is not incorrect but is less precise than the Sec-complex-specific terms. Supporting Evidence: PMID:29718185 SecDF is proposed to undergo repeated conformational transitions to pull out the precursor protein from the SecYEG channel into the periplasm |
| GO:0006886 intracellular protein transport | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: IEA annotation from InterPro2GO mapping (IPR005665 SecF bacterial family). SecF is involved in transporting preproteins from the cytoplasm across the inner membrane to the periplasm, which is intracellular protein transport in the context of Gram-negative bacteria. Reason: Correct but general. The term captures the overall transport function but does not specify the Sec pathway or the PMF-dependent mechanism. More specific terms are available and already annotated. Supporting Evidence: PMID:21562494 Protein translocation across the bacterial membrane, mediated by the secretory translocon SecYEG and the SecA ATPase, is enhanced by proton motive force and membrane-integrated SecDF |
| GO:0015450 protein-transporting ATPase activity | IEA GO_REF:0000002 | MODIFY | Summary: IEA annotation from InterPro2GO mapping (IPR005665). This is an incorrect annotation for SecF. SecF does not have ATPase activity. The ATPase function in the Sec translocase belongs to SecA. SecDF instead uses the proton motive force to drive conformational changes that enhance translocation. Reason: SecF/SecDF is explicitly not an ATPase. Multiple structural and biochemical studies demonstrate that SecDF uses the proton motive force, not ATP hydrolysis, to enhance translocation. Tsukazaki et al. (2011) identified an ATP-independent translocation step requiring SecDF and PMF. The appropriate MF term is GO:0009977 (proton motive force dependent protein transmembrane transporter activity), as SecDF conducts protons coupled to polypeptide movement. SecF contributes to the translocase complex activity but does not independently enable ATPase activity. Proposed replacements: proton motive force dependent protein transmembrane transporter activity Supporting Evidence: PMID:21562494 we propose that SecDF functions as a membrane-integrated chaperone, powered by proton motive force, to achieve ATP-independent protein translocation PMID:29718185 Once SecDF captures the precursor protein on the periplasmic surface, SecDF can complete protein translocation even if SecA function is inactivated by ATP depletion, implying that SecDF is a protein-translocation motor that works independent of SecA PMID:28467902 SecDF in I form can generate a tunnel that penetrates the transmembrane region and functions as a proton pathway regulated by a conserved Asp residue |
| GO:0043952 protein transport by the Sec complex | IEA GO_REF:0000104 | ACCEPT | Summary: IEA annotation from UniRule for involvement in protein transport by the Sec complex. This is the most specific and appropriate BP term for SecF function. SecDF is an integral component of the Sec translocase that enhances protein export. Reason: This is the most specific and accurate BP annotation for SecF. SecDF is a well-characterized component of the Sec protein translocation machinery. Multiple structural and biochemical studies confirm this role across bacterial species. Supporting Evidence: PMID:21562494 Protein translocation across the bacterial membrane, mediated by the secretory translocon SecYEG and the SecA ATPase, is enhanced by proton motive force and membrane-integrated SecDF, which associates with SecYEG PMID:24550475 The SecY/61 complex forms the protein-channel component of the ubiquitous protein secretion and membrane protein insertion apparatus. The bacterial version SecYEG interacts with the highly conserved YidC and SecDF-YajC subcomplex, which facilitates translocation into and across the membrane |
| GO:0065002 intracellular protein transmembrane transport | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: IEA annotation from UniRule for intracellular protein transmembrane transport. SecF facilitates the transport of preproteins across the inner membrane, which is intracellular protein transmembrane transport. Reason: Correct and somewhat more specific than GO:0006886 (intracellular protein transport) in that it specifies transmembrane transport. However, GO:0043952 (protein transport by the Sec complex) is the most informative annotation. This is a valid parent-level annotation that is kept but not core. Supporting Evidence: PMID:29718185 Many newly synthesized proteins in the cytoplasm are programmed to be translocated to the periplasm via the narrow channel that is formed in the center of SecYEG |
| GO:0031522 cell envelope Sec protein transport complex | ISS PMID:25800553 Probing the protein interaction network of Pseudomonas aerug... | NEW | Summary: SecF is a component of the cell envelope Sec protein transport complex. In P. aeruginosa, the SecD-SecF physical interaction has been directly demonstrated by in vivo chemical cross-linking mass spectrometry. The SecDF subcomplex associates with SecYEG to form the Sec translocon, and with YidC to form the holo-translocon. This annotation is supported by deep research findings in secF-deep-research-bioreason-sft.md which correctly identifies SecF as part of the Sec protein secretion complex. Reason: GO:0031522 (cell envelope Sec protein transport complex) is the most specific CC term for SecF and captures its role as a subunit of the Sec translocase complex. This is supported by direct cross-linking evidence in P. aeruginosa (PMID:25800553) and extensive structural evidence from E. coli and T. thermophilus. Supporting Evidence: PMID:25800553 Structures of three membrane proteins, namely, SecD-SecF, OprF, and OprI are predicted using in vivo cross-linked sites PMID:24550475 The bacterial version SecYEG interacts with the highly conserved YidC and SecDF-YajC subcomplex, which facilitates translocation into and across the membrane file:PSEAE/secF/secF-deep-research-bioreason-sft.md [BioReason SFT] A multi-pass inner-membrane component of the bacterial Sec pathway |
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Download this section (compressed HTML)Q: Has SecF or SecDF been directly studied for essentiality or translocation activity in P. aeruginosa, or is all functional evidence transferred from E. coli and T. thermophilus?
Suggested experts: James E Bruce
Q: Does the SecDF complex in P. aeruginosa interact with YidC and participate in membrane protein insertion as part of a holo-translocon, similar to E. coli?
Experiment: Construct a secF deletion mutant in P. aeruginosa PAO1 and measure protein export efficiency (e.g., secretion of alkaline phosphatase or beta-lactamase) in the presence and absence of PMF (using CCCP). Compare translocation rates to wild type and to secD mutants.
Hypothesis: SecF in P. aeruginosa forms a functional SecDF complex that enhances PMF-dependent protein translocation, analogous to E. coli and T. thermophilus.
Experiment: Generate point mutations in the conserved Asp and Arg residues of P. aeruginosa SecF (identified by alignment with T. thermophilus SecDF). Assay protein export and proton conductance in reconstituted proteoliposomes.
Hypothesis: The conserved Asp and Arg residues in the SecF transmembrane region are essential for proton-coupled translocation in P. aeruginosa.
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