SecY is the central channel-forming subunit of the bacterial SecYEG protein translocase complex. It forms a heterotrimeric complex with SecE and SecG that constitutes the core protein-conducting channel in the cytoplasmic membrane. SecY consists of 10 transmembrane helices organized into two halves (TMs 1-5 and TMs 6-10) that form a lateral gate, which can open to allow insertion of transmembrane segments into the lipid bilayer. The channel is sealed by a pore ring of hydrophobic residues and a plug helix on the extracellular side. SecY functions in two modes: (1) post-translational translocation of secretory proteins driven by the SecA ATPase, and (2) co-translational insertion of membrane proteins via the SRP (signal recognition particle) pathway. In B. subtilis, SecY localizes to the plasma membrane and is found in detergent-resistant membrane domains (membrane rafts), where it interacts with the flotillin homolog FloT. SecY is essential for protein secretion and membrane protein biogenesis in bacteria.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005886
plasma membrane
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: SecY is an integral membrane protein with 10 transmembrane helices that localizes to the cytoplasmic (plasma) membrane of B. subtilis. UniProt reports cell membrane localization based on experimental evidence from PMID:23651456, which demonstrated SecY presence in the B. subtilis membrane.
Reason: This is a core annotation for SecY. The protein is an integral component of the plasma membrane where it forms the protein-conducting channel of the Sec translocon. The deep research confirms SecY is localized to the cytoplasmic membrane, and UniProt cites experimental evidence (PMID:23651456) for cell membrane localization. IBA inference is consistent with extensive biochemical and structural data across bacteria.
Supporting Evidence:
UniProt:P16336
SUBCELLULAR LOCATION: Cell membrane
file:BACSU/secY/secY-deep-research-falcon.md
SecY is the channel-forming subunit of the bacterial SecYEG translocon
|
|
GO:0005048
signal sequence binding
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: SecY binds to signal sequences on preproteins during translocation. The signal sequence interacts with the lateral gate of SecY, which can open to release transmembrane segments into the lipid bilayer.
Reason: This is a core molecular function of SecY. Signal sequence binding is integral to SecY's role in recognizing and translocating secretory proteins. Structural studies have shown that signal sequences interact with the lateral gate region of SecY between TMs 2 and 7. The deep research confirms that substrates are signal peptide-bearing preproteins.
Supporting Evidence:
file:BACSU/secY/secY-deep-research-falcon.md
Substrates are unfolded polypeptides bearing N-terminal signal peptides (secretory proteins) or topogenic sequences (membrane protein TM helices)
UniProt:P16336
These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7
|
|
GO:0006616
SRP-dependent cotranslational protein targeting to membrane, translocation
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: SecY participates in co-translational protein targeting via the SRP pathway. The ribosome-nascent chain complex is targeted to SecYEG by SRP and its receptor, and SecY mediates insertion of transmembrane segments into the membrane.
Reason: This is a well-established function of SecY. While post-translational translocation (SecA-dependent) is the dominant mode for secretory proteins, membrane protein insertion is typically co-translational and SRP-dependent. SecY functions as the translocon in both pathways. The deep research explicitly states that co-translational insertion is mediated by SRP-ribosome targeting.
Supporting Evidence:
file:BACSU/secY/secY-deep-research-falcon.md
co-translational routes can also target substrates to SecYEG via SRP-ribosome interactions
file:BACSU/secY/secY-deep-research-falcon.md
membrane protein insertion is typically co-translational
|
|
GO:0008320
protein transmembrane transporter activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: SecY has protein transmembrane transporter activity, enabling the transfer of unfolded polypeptides across the cytoplasmic membrane. This is the central molecular function of the SecY channel.
Reason: This is the core molecular function of SecY. The protein forms the actual channel through which preproteins are translocated. The GO term definition "Enables the transfer of a protein from one side of a membrane to the other" precisely describes SecY's function as the protein-conducting channel of the Sec translocon.
Supporting Evidence:
file:BACSU/secY/secY-deep-research-falcon.md
SecY is the channel-forming subunit of the bacterial SecYEG translocon. It conducts preproteins across the cytoplasmic membrane (secretion) and supports insertion of membrane proteins
UniProt:P16336
The central subunit of the protein translocation channel SecYEG
|
|
GO:0031522
cell envelope Sec protein transport complex
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: SecY is a core component of the cell envelope Sec protein transport complex (SecYEG translocon). This complex includes SecY, SecE, SecG, and associated factors like SecA and SecDF.
Reason: This is the appropriate cellular component annotation for SecY. The GO term definition explicitly mentions SecY as a component of the Sec complex. SecY forms the heterotrimeric SecYEG complex with SecE and SecG, which is the core translocon.
Supporting Evidence:
file:BACSU/secY/secY-deep-research-falcon.md
SecY is the channel-forming subunit of the bacterial SecYEG translocon
UniProt:P16336
Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits
|
|
GO:0005886
plasma membrane
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: IEA annotation for plasma membrane localization, which is consistent with the experimentally validated IBA annotation above.
Reason: This annotation is redundant with the IBA annotation but is not incorrect. SecY is indeed an integral plasma membrane protein. The IEA annotation provides additional automated support for what is well-established experimentally.
Supporting Evidence:
UniProt:P16336
SUBCELLULAR LOCATION: Cell membrane
|
|
GO:0006605
protein targeting
|
IEA
GO_REF:0000104 |
KEEP AS NON CORE |
Summary: SecY participates in protein targeting by receiving signal sequence-bearing proteins targeted by the SRP pathway or post-translationally by SecA.
Reason: While SecY is involved in protein targeting as part of the translocation machinery, this term is quite general. The more specific terms like GO:0043952 (protein transport by the Sec complex) and GO:0006616 (SRP-dependent cotranslational protein targeting) are more informative. This annotation is not wrong but represents a higher-level categorization rather than a core specific function.
Supporting Evidence:
file:BACSU/secY/secY-deep-research-falcon.md
Substrates are signal peptide-bearing preproteins (secretory) or nascent TM helices (membrane proteins)
|
|
GO:0015031
protein transport
|
IEA
GO_REF:0000120 |
KEEP AS NON CORE |
Summary: SecY is involved in protein transport across the cytoplasmic membrane.
Reason: This is a general parent term for the more specific protein transport processes that SecY participates in. While accurate, the more specific terms (GO:0043952, GO:0006616, GO:0065002) are more informative about SecY's actual role. Keeping as non-core since it is not incorrect, just less specific.
Supporting Evidence:
UniProt:P16336
The central subunit of the protein translocation channel SecYEG
|
|
GO:0016020
membrane
|
IEA
GO_REF:0000120 |
KEEP AS NON CORE |
Summary: SecY is a membrane protein.
Reason: This is a very general cellular component term. While accurate, the more specific term GO:0005886 (plasma membrane) provides more informative localization. This annotation is acceptable but not a core annotation as it lacks specificity.
Supporting Evidence:
UniProt:P16336
Multi-pass membrane protein
|
|
GO:0043952
protein transport by the Sec complex
|
IEA
GO_REF:0000104 |
ACCEPT |
Summary: SecY is a core component of the Sec complex and directly participates in protein transport by this complex. This biological process term accurately describes SecY's role in translocating unfolded proteins across the membrane via the SecYEG translocon.
Reason: This is a highly appropriate and specific annotation for SecY. The GO term definition explicitly mentions that it is for annotating proteins that compose the transport complex. SecY is the central channel subunit and directly conducts proteins across the membrane as part of the Sec complex.
Supporting Evidence:
file:BACSU/secY/secY-deep-research-falcon.md
SecY is the channel-forming subunit of the bacterial SecYEG translocon. It conducts preproteins across the cytoplasmic membrane
UniProt:P16336
Component of the Sec protein translocase complex
|
|
GO:0045121
membrane raft
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: SecY localizes to membrane rafts (detergent-resistant membrane domains) in B. subtilis. This is based on experimental evidence from Bach & Bramkamp 2013 (PMID:23651456) which showed SecY is found in DRM fractions and interacts with the flotillin homolog FloT.
Reason: This annotation is supported by experimental evidence in B. subtilis. UniProt cites PMID:23651456 which demonstrated that SecY is present in detergent-resistant membrane fractions (bacterial membrane rafts) and interacts with FloT. While membrane rafts are a secondary localization relative to plasma membrane, this is a valid specific annotation.
Supporting Evidence:
UniProt:P16336
Present in detergent-resistant membrane (DRM) fractions that may be equivalent to eukaryotic membrane rafts
UniProt:P16336
Interacts with FloT (PubMed:23651456)
|
|
GO:0065002
intracellular protein transmembrane transport
|
IEA
GO_REF:0000104 |
ACCEPT |
Summary: SecY mediates the translocation of proteins across the cytoplasmic membrane, which constitutes intracellular protein transmembrane transport.
Reason: This is an accurate biological process annotation for SecY. The term describes the directed movement of proteins across a membrane, which is exactly what SecY does as the protein-conducting channel. In bacteria, this involves transport from the cytoplasm across the plasma membrane to the periplasm or cell exterior.
Supporting Evidence:
file:BACSU/secY/secY-deep-research-falcon.md
conducts preproteins across the cytoplasmic membrane (secretion)
file:BACSU/secY/secY-deep-research-falcon.md
AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex
|
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template_file: templates/gene_research_go_focused.md
template_variables:
organism: BACSU
gene_id: secY
gene_symbol: secY
uniprot_accession: P16336
protein_description: 'RecName: Full=Protein translocase subunit SecY {ECO:0000255|HAMAP-Rule:MF_01465};'
gene_info: Name=secY {ECO:0000255|HAMAP-Rule:MF_01465}; OrderedLocusNames=BSU01360;
organism_full: Bacillus subtilis (strain 168).
protein_family: Belongs to the SecY/SEC61-alpha family. {ECO:0000255|HAMAP-
protein_domains: SecY. (IPR026593); SecY/SEC61-alpha. (IPR002208); SecY_CS. (IPR030659);
SecY_dom_sf. (IPR023201); SecY (PF00344)
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citation_count: 23
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'secY' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene secY (gene ID: secY, UniProt: P16336) in BACSU.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'secY' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene secY (gene ID: secY, UniProt: P16336) in BACSU.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Research plan and verification summary
- Identity verification: The target is Bacillus subtilis (strain 168) secY (UniProt P16336), encoding the core membrane-channel subunit of the SecYEG translocon, a member of the conserved SecY/SEC61-alpha family. Contemporary reviews and structural/mechanistic studies confirm SecY as the protein-conducting channel that operates with SecE and SecG in bacteria, and with SecA as the ATPase motor (Open Biology review, 2023; https://doi.org/10.1098/rsob.230166, published Aug 30, 2023) (allen2023aunifyingmechanism pages 1-2, allen2023aunifyingmechanism pages 12-13). No conflicting gene symbol usages were detected for Bacillus subtilis.
Comprehensive research report
1) Key concepts and definitions with current understanding
- Core role: SecY is the channel-forming subunit of the bacterial SecYEG translocon. It conducts preproteins across the cytoplasmic membrane (secretion) and supports insertion of membrane proteins, functioning with SecE and SecG as a heterotrimer and energized primarily by the SecA ATPase for post-translational transport; co-translational routes can also target substrates to SecYEG via SRP–ribosome interactions (Open Biology review, 2023; URL: https://doi.org/10.1098/rsob.230166; published Aug 30, 2023) (allen2023aunifyingmechanism pages 1-2, allen2023aunifyingmechanism pages 2-3). SecY is homologous to the eukaryotic Sec61α subunit of the ER translocon (allen2023aunifyingmechanism pages 1-2).
- Transport substrate and type: Substrates are unfolded polypeptides bearing N‑terminal signal peptides (secretory proteins) or topogenic sequences (membrane protein TM helices). Bacterial secretion is largely post‑translational and driven by SecA; membrane protein insertion is typically co‑translational (Open Biology review, 2023; https://doi.org/10.1098/rsob.230166) (allen2023aunifyingmechanism pages 1-2, allen2023aunifyingmechanism pages 2-3).
- Energetics: In vitro, SecA + ATP with membrane‑embedded SecYEG suffices for transport, but in vivo the proton‑motive force (PMF) accelerates export (Open Biology review, 2023; https://doi.org/10.1098/rsob.230166) (allen2023aunifyingmechanism pages 2-3).
2) Recent developments and latest research (2023–2024 prioritized)
- Mechanism of SecA–SecY–substrate translocation: Cryo‑EM structures of an active complex with substrate in ADP vs ATP states show a helicase‑like translocation mechanism by SecA (two‑helix finger and clamp dynamics) that advances polypeptide through SecY; the study used B. subtilis SecA and bacterial SecYE (PNAS, 2023; https://doi.org/10.1073/pnas.2208070120; published Jan 4, 2023) (dong2023structuralbasisof pages 1-2).
- Unified mechanistic framework: A 2023 review synthesizes structural, single‑molecule, and biochemical advances to propose a unifying mechanism for bacterial SecYEG operation, cataloging the roles of SecA, SecDF (PMF‑coupled enhancer), and YidC as interacting partners with SecYEG (Open Biology, 2023; https://doi.org/10.1098/rsob.230166; published Aug 30, 2023) (allen2023aunifyingmechanism pages 12-13, allen2023aunifyingmechanism pages 2-3).
- Gram‑positive secretion architecture in vivo: In B. subtilis and B. licheniformis, fluorescently tagged secreted α‑amylase (AmyE‑mCherry) accumulates at discrete, low‑mobility “secretion zones” within the cell wall during overexpression; lysozyme conversion to spheroplasts removes most envelope‑associated signal, indicating wall association; these zones persist minutes and shift laterally only tens of nanometers per minute (BMC Biology, 2023; https://doi.org/10.1186/s12915-023-01684-1; published Oct 6, 2023) (strach2023proteinsecretionzones pages 3-7, strach2023proteinsecretionzones pages 14-16).
- SecA dynamics in B. subtilis under high secretion demand: Single‑molecule tracking in the same study shows SecA and SecDF partition into static, medium‑mobile, and free fractions; the static (translocon‑engaged) SecA fraction increases under AmyE overexpression, consistent with elevated SecYEG engagement (BMC Biology, 2023; https://doi.org/10.1186/s12915-023-01684-1) (strach2023proteinsecretionzones pages 14-16).
- Methodological progress: Single‑cell technologies to monitor secretion heterogeneity and stress responses in Bacillus and other hosts have matured, enabling quantitative and high‑throughput readouts of Sec‑dependent secretion performance (Trends in Biotechnology, 2024; https://doi.org/10.1016/j.tibtech.2024.02.011; published Sep 2024) (hartmann2024singlecelltechnologies pages 17-17).
- Direct visualization of single SecYEG–SecA translocation events: High‑speed AFM visualized substrate translocation through single SecYEG–SecA nanodiscs, supporting one active unit sufficiency and nucleotide‑dependent SecA conformational changes (Nat. Commun., 2025; https://doi.org/10.1038/s41467-024-54875-x; published Jan 23, 2025). Although 2025, this work reinforces 2023–2024 mechanistic models (kanaoka2025afmobservationof pages 9-10).
3) Current applications and real‑world implementations
- Industrial secretion in Bacillus: B. subtilis is widely used for secretion of industrial enzymes. Secretion heterogeneity and stress responses (e.g., CssRS) are operational constraints; single‑cell tools and signal peptide engineering are emphasized as levers for optimizing Sec‑dependent export and culture‑level yields (Trends in Biotechnology, 2024; https://doi.org/10.1016/j.tibtech.2024.02.011) (hartmann2024singlecelltechnologies pages 17-17). The identification of secretion zones and SecA engagement dynamics in Bacillus informs strain/process engineering to alleviate wall passage bottlenecks and tune translocon load (BMC Biology, 2023; https://doi.org/10.1186/s12915-023-01684-1) (strach2023proteinsecretionzones pages 3-7, strach2023proteinsecretionzones pages 14-16).
- Antibacterial target potential: The active SecA–SecY complex shows commonalities with other antibiotic‑targeted translocation systems; structural work argues SecA/SecY as compelling antibacterial targets across Gram‑positives and Gram‑negatives (PNAS, 2023; https://doi.org/10.1073/pnas.2208070120) (dong2023structuralbasisof pages 1-2). Mechanistic syntheses underscore the pharmaceutical potential of modulating SecYEG function (Open Biology, 2023; https://doi.org/10.1098/rsob.230166) (allen2023aunifyingmechanism pages 12-13).
4) Expert opinions and analysis from authoritative sources
- Unified mechanism and open questions: Allen & Collinson (2023) weigh evidence for power‑stroke vs Brownian ratchet components, argue for a largely complete mechanism integrating structural and single‑molecule data, and discuss the roles of accessory factors (SecDF, YidC) that modulate SecYEG performance, especially under native PMF (Open Biology, 2023; https://doi.org/10.1098/rsob.230166) (allen2023aunifyingmechanism pages 12-13, allen2023aunifyingmechanism pages 2-3).
- Mechanistic details from structure: Dong et al. (2023) interpret ATP‑state cryo‑EM to support a helicase‑like driving motion by SecA that advances substrate through SecY and strengthens the case for targeting the active complex pharmaceutically (PNAS, 2023; https://doi.org/10.1073/pnas.2208070120) (dong2023structuralbasisof pages 1-2).
- Host‑level perspective on secretion: Hartmann et al. (2024) review single‑cell secretion analyses, emphasizing that process‑level optimization in Bacillus should address heterogeneity, secretion stress, and signal peptide–substrate–translocon matching (Trends in Biotechnology, 2024; https://doi.org/10.1016/j.tibtech.2024.02.011) (hartmann2024singlecelltechnologies pages 17-17).
5) Relevant statistics and data from recent studies
- B. subtilis secretion zones and kinetics: In Bacillus, secretion zones appear in a subset of cells under AmyE overexpression (e.g., ~19% of B. subtilis cells in stationary phase exhibited visible peripheral puncta), persist for minutes, and show small lateral displacements (∼70 nm per 60 s frame) in the cell wall; lysozyme treatment converted >90% of cells to spheroplasts and removed most envelope‑associated fluorescence, indicating wall association (BMC Biology, 2023; https://doi.org/10.1186/s12915-023-01684-1) (strach2023proteinsecretionzones pages 3-7, strach2023proteinsecretionzones pages 14-16).
- SecA single‑molecule dynamics in B. subtilis: Diffusion coefficients partitioned as Dstatic ≈ 0.03–0.04 μm2/s, Dmobile ≈ 0.11–0.15 μm2/s, and Dfree ≈ 0.60–0.70 μm2/s; the static (putative translocon‑bound) fraction increased from ~21% (WT) to ~29% under AmyE overproduction, with bi‑exponential dwell times τ1 ≈ 0.24 s and τ2 ≈ 0.43–0.45 s (BMC Biology, 2023; https://doi.org/10.1186/s12915-023-01684-1) (strach2023proteinsecretionzones pages 14-16).
- Energetic contribution of PMF: In vivo PMF accelerates Sec‑dependent export beyond ATP‑alone reconstitutions in vitro (Open Biology, 2023; https://doi.org/10.1098/rsob.230166) (allen2023aunifyingmechanism pages 2-3).
- Structural/functional visualization: High‑speed AFM directly visualized single SecYEG–SecA‑mediated translocation events and nucleotide‑dependent SecA domain changes, demonstrating sufficiency of one SecYEG–SecA unit for transport (Nat. Commun., 2025; https://doi.org/10.1038/s41467-024-54875-x) (kanaoka2025afmobservationof pages 9-10).
Functional annotation for secY (B. subtilis 168)
- Primary function: Channel subunit of the SecYEG translocon that conducts unfolded polypeptides across the cytoplasmic membrane (secretion) and supports insertion of transmembrane segments of membrane proteins. Substrates are signal peptide–bearing preproteins (secretory) or nascent TM helices (membrane proteins) (Open Biology, 2023; https://doi.org/10.1098/rsob.230166) (allen2023aunifyingmechanism pages 1-2, allen2023aunifyingmechanism pages 2-3).
- Partners and pathway: Operates as SecYEG with SecA ATPase, frequently in concert with accessory factors such as SecDF (PMF‑coupled enhancer) and YidC (insertase/chaperone) in bacteria (Open Biology, 2023; https://doi.org/10.1098/rsob.230166) (allen2023aunifyingmechanism pages 12-13, allen2023aunifyingmechanism pages 2-3). In B. subtilis, SecA and SecDF dynamics increase under high secretion load, supporting increased SecYEG engagement (BMC Biology, 2023; https://doi.org/10.1186/s12915-023-01684-1) (strach2023proteinsecretionzones pages 14-16).
- Localization: Plasma (cytoplasmic) membrane of B. subtilis; organism‑specific imaging places secretion events at discrete, long‑lived zones within the Gram‑positive cell wall beyond the membrane translocation step (BMC Biology, 2023; https://doi.org/10.1186/s12915-023-01684-1) (strach2023proteinsecretionzones pages 3-7, strach2023proteinsecretionzones pages 14-16).
- Mechanism and energetics: Post‑translational translocation is driven by SecA ATPase cycles that advance substrate through SecY via helicase‑like motions; co‑translational insertion is mediated by SRP‑ribosome targeting. PMF enhances translocation efficiency/velocity in vivo (PNAS, 2023; https://doi.org/10.1073/pnas.2208070120; Open Biology, 2023; https://doi.org/10.1098/rsob.230166) (dong2023structuralbasisof pages 1-2, allen2023aunifyingmechanism pages 2-3).
Organism‑specific insights (Bacillus subtilis 168)
- SecA/SecDF dynamics and secretion zones during high production: Bacillus cells show heterogeneity; secretion zones are spatially discrete and long‑lived in the cell wall; SecA’s static fraction increases under load, consistent with more SecYEG engagement (BMC Biology, 2023; https://doi.org/10.1186/s12915-023-01684-1) (strach2023proteinsecretionzones pages 3-7, strach2023proteinsecretionzones pages 14-16).
- Process implications: Secretion heterogeneity and stress responses are key for industrial strain/process design; single‑cell analyses provide actionable levers (Trends in Biotechnology, 2024; https://doi.org/10.1016/j.tibtech.2024.02.011) (hartmann2024singlecelltechnologies pages 17-17).
Limitations and open questions
- While mechanistic principles are well‑established, quantitative partitioning of ATP vs PMF contributions and accessory factor roles (e.g., SecDF, YidC) in Gram‑positive bacteria in vivo remain areas of active study, as highlighted by expert analyses (Open Biology, 2023; https://doi.org/10.1098/rsob.230166) (allen2023aunifyingmechanism pages 12-13, allen2023aunifyingmechanism pages 2-3).
References (with URLs and publication dates)
- Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biology. Published Aug 30, 2023. URL: https://doi.org/10.1098/rsob.230166 (allen2023aunifyingmechanism pages 1-2, allen2023aunifyingmechanism pages 12-13, allen2023aunifyingmechanism pages 2-3).
- Dong L, Yang S, Chen J, et al. Structural basis of SecA-mediated protein translocation. PNAS. Published Jan 4, 2023. URL: https://doi.org/10.1073/pnas.2208070120 (dong2023structuralbasisof pages 1-2).
- Strach M, Koch F, Fiedler S, et al. Protein secretion zones during overexpression of amylase within the Gram-positive cell wall. BMC Biology. Published Oct 6, 2023. URL: https://doi.org/10.1186/s12915-023-01684-1 (strach2023proteinsecretionzones pages 3-7, strach2023proteinsecretionzones pages 14-16).
- Hartmann FSF, Grégoire M, Renzi F, Delvigne F. Single cell technologies for monitoring protein secretion heterogeneity. Trends in Biotechnology. Published Sep 2024. URL: https://doi.org/10.1016/j.tibtech.2024.02.011 (hartmann2024singlecelltechnologies pages 17-17).
- Kanaoka Y, Mori T, Nagaike W, et al. AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex. Nature Communications. Published Jan 23, 2025. URL: https://doi.org/10.1038/s41467-024-54875-x (kanaoka2025afmobservationof pages 9-10).
Compliance with mandatory verification steps
- Gene symbol and identity: The research above pertains to bacterial SecY, which matches the UniProt P16336 designation (B. subtilis 168 secY), and aligns with SecY/SEC61-alpha family membership and the SecY domain annotations. No alternative gene with the same symbol was used (allen2023aunifyingmechanism pages 1-2, allen2023aunifyingmechanism pages 12-13).
References
(allen2023aunifyingmechanism pages 1-2): William J. Allen and Ian Collinson. A unifying mechanism for protein transport through the core bacterial sec machinery. Open Biology, Aug 2023. URL: https://doi.org/10.1098/rsob.230166, doi:10.1098/rsob.230166. This article has 12 citations and is from a peer-reviewed journal.
(allen2023aunifyingmechanism pages 12-13): William J. Allen and Ian Collinson. A unifying mechanism for protein transport through the core bacterial sec machinery. Open Biology, Aug 2023. URL: https://doi.org/10.1098/rsob.230166, doi:10.1098/rsob.230166. This article has 12 citations and is from a peer-reviewed journal.
(allen2023aunifyingmechanism pages 2-3): William J. Allen and Ian Collinson. A unifying mechanism for protein transport through the core bacterial sec machinery. Open Biology, Aug 2023. URL: https://doi.org/10.1098/rsob.230166, doi:10.1098/rsob.230166. This article has 12 citations and is from a peer-reviewed journal.
(dong2023structuralbasisof pages 1-2): Linlin Dong, Song Yang, Jingxia Chen, Xiaofei Wu, Dongjie Sun, Chen Song, and Long Li. Structural basis of seca-mediated protein translocation. Proceedings of the National Academy of Sciences of the United States of America, Jan 2023. URL: https://doi.org/10.1073/pnas.2208070120, doi:10.1073/pnas.2208070120. This article has 20 citations and is from a highest quality peer-reviewed journal.
(strach2023proteinsecretionzones pages 3-7): Manuel Strach, Felicitas Koch, Svenja Fiedler, Klaus Liebeton, and Peter L. Graumann. Protein secretion zones during overexpression of amylase within the gram-positive cell wall. BMC Biology, Oct 2023. URL: https://doi.org/10.1186/s12915-023-01684-1, doi:10.1186/s12915-023-01684-1. This article has 10 citations and is from a domain leading peer-reviewed journal.
(strach2023proteinsecretionzones pages 14-16): Manuel Strach, Felicitas Koch, Svenja Fiedler, Klaus Liebeton, and Peter L. Graumann. Protein secretion zones during overexpression of amylase within the gram-positive cell wall. BMC Biology, Oct 2023. URL: https://doi.org/10.1186/s12915-023-01684-1, doi:10.1186/s12915-023-01684-1. This article has 10 citations and is from a domain leading peer-reviewed journal.
(hartmann2024singlecelltechnologies pages 17-17): Fabian Stefan Franz Hartmann, Mélanie Grégoire, Francesco Renzi, and Frank Delvigne. Single cell technologies for monitoring protein secretion heterogeneity. Trends in Biotechnology, 42:1144-1160, Sep 2024. URL: https://doi.org/10.1016/j.tibtech.2024.02.011, doi:10.1016/j.tibtech.2024.02.011. This article has 4 citations and is from a domain leading peer-reviewed journal.
(kanaoka2025afmobservationof pages 9-10): Yui Kanaoka, Takaharu Mori, Wataru Nagaike, Seira Itaya, Yuto Nonaka, Hidetaka Kohga, Takamitsu Haruyama, Yasunori Sugano, Ryoji Miyazaki, Muneyoshi Ichikawa, Takayuki Uchihashi, and Tomoya Tsukazaki. Afm observation of protein translocation mediated by one unit of secyeg-seca complex. Nature Communications, Jan 2025. URL: https://doi.org/10.1038/s41467-024-54875-x, doi:10.1038/s41467-024-54875-x. This article has 7 citations and is from a highest quality peer-reviewed journal.
id: P16336
gene_symbol: secY
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:224308
label: Bacillus subtilis (strain 168)
description: >-
SecY is the central channel-forming subunit of the bacterial SecYEG protein translocase complex.
It forms a heterotrimeric complex with SecE and SecG that constitutes the core protein-conducting
channel in the cytoplasmic membrane. SecY consists of 10 transmembrane helices organized into
two halves (TMs 1-5 and TMs 6-10) that form a lateral gate, which can open to allow insertion
of transmembrane segments into the lipid bilayer. The channel is sealed by a pore ring of
hydrophobic residues and a plug helix on the extracellular side. SecY functions in two modes:
(1) post-translational translocation of secretory proteins driven by the SecA ATPase, and
(2) co-translational insertion of membrane proteins via the SRP (signal recognition particle)
pathway. In B. subtilis, SecY localizes to the plasma membrane and is found in detergent-resistant
membrane domains (membrane rafts), where it interacts with the flotillin homolog FloT. SecY is
essential for protein secretion and membrane protein biogenesis in bacteria.
existing_annotations:
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
SecY is an integral membrane protein with 10 transmembrane helices that localizes to the
cytoplasmic (plasma) membrane of B. subtilis. UniProt reports cell membrane localization
based on experimental evidence from PMID:23651456, which demonstrated SecY presence in the
B. subtilis membrane.
action: ACCEPT
reason: >-
This is a core annotation for SecY. The protein is an integral component of the plasma
membrane where it forms the protein-conducting channel of the Sec translocon. The deep
research confirms SecY is localized to the cytoplasmic membrane, and UniProt cites
experimental evidence (PMID:23651456) for cell membrane localization. IBA inference is
consistent with extensive biochemical and structural data across bacteria.
supported_by:
- reference_id: UniProt:P16336
supporting_text: "SUBCELLULAR LOCATION: Cell membrane"
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "SecY is the channel-forming subunit of the bacterial SecYEG translocon"
- term:
id: GO:0005048
label: signal sequence binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
SecY binds to signal sequences on preproteins during translocation. The signal sequence
interacts with the lateral gate of SecY, which can open to release transmembrane segments
into the lipid bilayer.
action: ACCEPT
reason: >-
This is a core molecular function of SecY. Signal sequence binding is integral to SecY's
role in recognizing and translocating secretory proteins. Structural studies have shown
that signal sequences interact with the lateral gate region of SecY between TMs 2 and 7.
The deep research confirms that substrates are signal peptide-bearing preproteins.
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "Substrates are unfolded polypeptides bearing N-terminal signal peptides (secretory proteins) or topogenic sequences (membrane protein TM helices)"
- reference_id: UniProt:P16336
supporting_text: "These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7"
- term:
id: GO:0006616
label: SRP-dependent cotranslational protein targeting to membrane, translocation
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
SecY participates in co-translational protein targeting via the SRP pathway. The ribosome-nascent
chain complex is targeted to SecYEG by SRP and its receptor, and SecY mediates insertion of
transmembrane segments into the membrane.
action: ACCEPT
reason: >-
This is a well-established function of SecY. While post-translational translocation (SecA-dependent)
is the dominant mode for secretory proteins, membrane protein insertion is typically co-translational
and SRP-dependent. SecY functions as the translocon in both pathways. The deep research explicitly
states that co-translational insertion is mediated by SRP-ribosome targeting.
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "co-translational routes can also target substrates to SecYEG via SRP-ribosome interactions"
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "membrane protein insertion is typically co-translational"
- term:
id: GO:0008320
label: protein transmembrane transporter activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
SecY has protein transmembrane transporter activity, enabling the transfer of unfolded
polypeptides across the cytoplasmic membrane. This is the central molecular function
of the SecY channel.
action: ACCEPT
reason: >-
This is the core molecular function of SecY. The protein forms the actual channel through
which preproteins are translocated. The GO term definition "Enables the transfer of a protein
from one side of a membrane to the other" precisely describes SecY's function as the
protein-conducting channel of the Sec translocon.
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "SecY is the channel-forming subunit of the bacterial SecYEG translocon. It conducts preproteins across the cytoplasmic membrane (secretion) and supports insertion of membrane proteins"
- reference_id: UniProt:P16336
supporting_text: "The central subunit of the protein translocation channel SecYEG"
- term:
id: GO:0031522
label: cell envelope Sec protein transport complex
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
SecY is a core component of the cell envelope Sec protein transport complex (SecYEG translocon).
This complex includes SecY, SecE, SecG, and associated factors like SecA and SecDF.
action: ACCEPT
reason: >-
This is the appropriate cellular component annotation for SecY. The GO term definition
explicitly mentions SecY as a component of the Sec complex. SecY forms the heterotrimeric
SecYEG complex with SecE and SecG, which is the core translocon.
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "SecY is the channel-forming subunit of the bacterial SecYEG translocon"
- reference_id: UniProt:P16336
supporting_text: "Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits"
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
IEA annotation for plasma membrane localization, which is consistent with the experimentally
validated IBA annotation above.
action: ACCEPT
reason: >-
This annotation is redundant with the IBA annotation but is not incorrect. SecY is indeed
an integral plasma membrane protein. The IEA annotation provides additional automated
support for what is well-established experimentally.
supported_by:
- reference_id: UniProt:P16336
supporting_text: "SUBCELLULAR LOCATION: Cell membrane"
- term:
id: GO:0006605
label: protein targeting
evidence_type: IEA
original_reference_id: GO_REF:0000104
review:
summary: >-
SecY participates in protein targeting by receiving signal sequence-bearing proteins
targeted by the SRP pathway or post-translationally by SecA.
action: KEEP_AS_NON_CORE
reason: >-
While SecY is involved in protein targeting as part of the translocation machinery, this
term is quite general. The more specific terms like GO:0043952 (protein transport by the
Sec complex) and GO:0006616 (SRP-dependent cotranslational protein targeting) are more
informative. This annotation is not wrong but represents a higher-level categorization
rather than a core specific function.
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "Substrates are signal peptide-bearing preproteins (secretory) or nascent TM helices (membrane proteins)"
- term:
id: GO:0015031
label: protein transport
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
SecY is involved in protein transport across the cytoplasmic membrane.
action: KEEP_AS_NON_CORE
reason: >-
This is a general parent term for the more specific protein transport processes that SecY
participates in. While accurate, the more specific terms (GO:0043952, GO:0006616, GO:0065002)
are more informative about SecY's actual role. Keeping as non-core since it is not incorrect,
just less specific.
supported_by:
- reference_id: UniProt:P16336
supporting_text: "The central subunit of the protein translocation channel SecYEG"
- term:
id: GO:0016020
label: membrane
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
SecY is a membrane protein.
action: KEEP_AS_NON_CORE
reason: >-
This is a very general cellular component term. While accurate, the more specific term
GO:0005886 (plasma membrane) provides more informative localization. This annotation
is acceptable but not a core annotation as it lacks specificity.
supported_by:
- reference_id: UniProt:P16336
supporting_text: "Multi-pass membrane protein"
- term:
id: GO:0043952
label: protein transport by the Sec complex
evidence_type: IEA
original_reference_id: GO_REF:0000104
review:
summary: >-
SecY is a core component of the Sec complex and directly participates in protein transport
by this complex. This biological process term accurately describes SecY's role in
translocating unfolded proteins across the membrane via the SecYEG translocon.
action: ACCEPT
reason: >-
This is a highly appropriate and specific annotation for SecY. The GO term definition
explicitly mentions that it is for annotating proteins that compose the transport complex.
SecY is the central channel subunit and directly conducts proteins across the membrane
as part of the Sec complex.
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "SecY is the channel-forming subunit of the bacterial SecYEG translocon. It conducts preproteins across the cytoplasmic membrane"
- reference_id: UniProt:P16336
supporting_text: "Component of the Sec protein translocase complex"
- term:
id: GO:0045121
label: membrane raft
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
SecY localizes to membrane rafts (detergent-resistant membrane domains) in B. subtilis.
This is based on experimental evidence from Bach & Bramkamp 2013 (PMID:23651456) which
showed SecY is found in DRM fractions and interacts with the flotillin homolog FloT.
action: ACCEPT
reason: >-
This annotation is supported by experimental evidence in B. subtilis. UniProt cites
PMID:23651456 which demonstrated that SecY is present in detergent-resistant membrane
fractions (bacterial membrane rafts) and interacts with FloT. While membrane rafts are
a secondary localization relative to plasma membrane, this is a valid specific annotation.
supported_by:
- reference_id: UniProt:P16336
supporting_text: "Present in detergent-resistant membrane (DRM) fractions that may be equivalent to eukaryotic membrane rafts"
- reference_id: UniProt:P16336
supporting_text: "Interacts with FloT (PubMed:23651456)"
- term:
id: GO:0065002
label: intracellular protein transmembrane transport
evidence_type: IEA
original_reference_id: GO_REF:0000104
review:
summary: >-
SecY mediates the translocation of proteins across the cytoplasmic membrane, which
constitutes intracellular protein transmembrane transport.
action: ACCEPT
reason: >-
This is an accurate biological process annotation for SecY. The term describes the
directed movement of proteins across a membrane, which is exactly what SecY does as
the protein-conducting channel. In bacteria, this involves transport from the cytoplasm
across the plasma membrane to the periplasm or cell exterior.
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "conducts preproteins across the cytoplasmic membrane (secretion)"
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex"
references:
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings:
- statement: SecY annotations are inferred from well-characterized orthologs through phylogenetic analysis
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
findings:
- statement: Membrane raft localization inferred from UniProt subcellular location annotation
- id: GO_REF:0000104
title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins
findings:
- statement: Annotations transferred based on shared sequence features with characterized Sec translocon subunits
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings:
- statement: Automated annotations consistent with known SecY function
- id: PMID:23651456
title: Flotillins functionally organize the bacterial membrane
full_text_unavailable: true
findings: []
- id: UniProt:P16336
title: UniProt entry for B. subtilis SecY
findings:
- statement: SecY is a 431 amino acid multi-pass membrane protein
supporting_text: "SECY_BACSU Reviewed; 431 AA"
- statement: Forms heterotrimer with SecE and SecG
supporting_text: "Heterotrimer consisting of SecY, SecE and SecG subunits"
- statement: Interacts with SecA, SecDF, and the ribosome
supporting_text: "Interacts with the ribosome. Interacts with SecDF"
- statement: Interacts with FloT and localizes to membrane rafts
supporting_text: "Interacts with FloT (PubMed:23651456)"
- statement: Member of SecY/SEC61-alpha family
supporting_text: "Belongs to the SecY/SEC61-alpha family"
- id: file:BACSU/secY/secY-deep-research-falcon.md
title: Deep research review for B. subtilis SecY
findings:
- statement: SecY is the channel-forming subunit of the SecYEG translocon
supporting_text: "SecY is the channel-forming subunit of the bacterial SecYEG translocon"
- statement: SecY conducts preproteins across the cytoplasmic membrane
supporting_text: "conducts preproteins across the cytoplasmic membrane (secretion)"
- statement: SecY supports both post-translational and co-translational transport
supporting_text: "co-translational routes can also target substrates to SecYEG via SRP-ribosome interactions"
- statement: SecYEG operates with SecA ATPase for post-translational secretion
supporting_text: "Operates as SecYEG with SecA ATPase"
- statement: Proton-motive force enhances translocation efficiency in vivo
supporting_text: "the proton-motive force (PMF) accelerates export"
core_functions:
- molecular_function:
id: GO:0008320
label: protein transmembrane transporter activity
description: >-
SecY forms the protein-conducting channel of the SecYEG translocon, enabling direct
transfer of unfolded polypeptides across the cytoplasmic membrane. Functions with
SecA ATPase for post-translational translocation.
locations:
- id: GO:0005886
label: plasma membrane
in_complex:
id: GO:0031522
label: cell envelope Sec protein transport complex
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "SecY is the channel-forming subunit of the bacterial SecYEG translocon. It conducts preproteins across the cytoplasmic membrane (secretion) and supports insertion of membrane proteins"
- reference_id: UniProt:P16336
supporting_text: "The central subunit of the protein translocation channel SecYEG"
- molecular_function:
id: GO:0005048
label: signal sequence binding
description: >-
SecY recognizes and binds signal peptides on preproteins. Signal sequences interact
with the lateral gate of SecY (between TMs 2 and 7), which is required for substrate
recognition and translocation initiation.
locations:
- id: GO:0005886
label: plasma membrane
in_complex:
id: GO:0031522
label: cell envelope Sec protein transport complex
supported_by:
- reference_id: file:BACSU/secY/secY-deep-research-falcon.md
supporting_text: "Substrates are unfolded polypeptides bearing N-terminal signal peptides (secretory proteins) or topogenic sequences (membrane protein TM helices)"
- reference_id: UniProt:P16336
supporting_text: "These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7"