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organism: worm
gene_id: clec-60
gene_symbol: clec-60
uniprot_accession: Q23564
protein_description: 'SubName: Full=VWFA domain-containing protein {ECO:0000313|EMBL:CAA88985.1};'
gene_info: Name=clec-60 {ECO:0000313|EMBL:CAA88985.1, ECO:0000313|WormBase:ZK666.6};
ORFNames=CELE_ZK666.6 {ECO:0000313|EMBL:CAA88985.1}, ZK666.6 {ECO:0000313|WormBase:ZK666.6};
organism_full: Caenorhabditis elegans.
protein_family: Not specified in UniProt
protein_domains: C-type_lectin-like. (IPR001304); C-type_lectin-like/link_sf. (IPR016186);
CTDL_fold. (IPR016187); VWF_A. (IPR002035); vWFA_dom_sf. (IPR036465)
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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.

Target Gene/Protein Identity (from UniProt):

• UniProt Accession: Q23564
• Protein Description: SubName: Full=VWFA domain-containing protein {ECO:0000313|EMBL:CAA88985.1};
• Gene Information: Name=clec-60 {ECO:0000313|EMBL:CAA88985.1, ECO:0000313|WormBase:ZK666.6}; ORFNames=CELE_ZK666.6 {ECO:0000313|EMBL:CAA88985.1}, ZK666.6 {ECO:0000313|WormBase:ZK666.6};
• Organism (full): Caenorhabditis elegans.
• Protein Family: Not specified in UniProt
• Key Domains: C-type_lectin-like. (IPR001304); C-type_lectin-like/link_sf. (IPR016186); CTDL_fold. (IPR016187); VWF_A. (IPR002035); vWFA_dom_sf. (IPR036465)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "clec-60" matches the protein description above
2. Verify the organism is correct: Caenorhabditis elegans.
3. Check if protein family/domains align with what you find in literature
4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'clec-60' 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

Research Target:

Please provide a comprehensive research report on the gene clec-60 (gene ID: clec-60, UniProt: Q23564) in worm.

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.

Output

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.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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.

Target Gene/Protein Identity (from UniProt):

• UniProt Accession: Q23564
• Protein Description: SubName: Full=VWFA domain-containing protein {ECO:0000313|EMBL:CAA88985.1};
• Gene Information: Name=clec-60 {ECO:0000313|EMBL:CAA88985.1, ECO:0000313|WormBase:ZK666.6}; ORFNames=CELE_ZK666.6 {ECO:0000313|EMBL:CAA88985.1}, ZK666.6 {ECO:0000313|WormBase:ZK666.6};
• Organism (full): Caenorhabditis elegans.
• Protein Family: Not specified in UniProt
• Key Domains: C-type_lectin-like. (IPR001304); C-type_lectin-like/link_sf. (IPR016186); CTDL_fold. (IPR016187); VWF_A. (IPR002035); vWFA_dom_sf. (IPR036465)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "clec-60" matches the protein description above
2. Verify the organism is correct: Caenorhabditis elegans.
3. Check if protein family/domains align with what you find in literature
4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'clec-60' 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

Research Target:

Please provide a comprehensive research report on the gene clec-60 (gene ID: clec-60, UniProt: Q23564) in worm.

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 report: Functional annotation of C. elegans clec-60 (ZK666.6; UniProt Q23564)

Executive summary
- Identity verified: clec-60 is a Caenorhabditis elegans gene (locus ZK666.6) encoding a secreted protein with an N-terminal signal peptide, a von Willebrand factor A (vWFA) domain, and a C-type lectin-like domain (CTLD), consistent with UniProt Q23564 and primary literature. Induced in the intestine during infection with Microbacterium nematophilum; intestinal reporter expression has been demonstrated. Perturbation studies implicate roles during infection, with RNAi causing a hyper-deformed anal region (Dar) phenotype and constipation under M. nematophilum, and overexpression of the clec-60/61 cluster increasing susceptibility to Pseudomonas aeruginosa. Regulation intersects with innate immune signaling modules; in Enterotoxigenic E. coli (ETEC) contexts, clec-60 responds to p38 MAPK and DAF/IGF signaling perturbations. No direct enzymatic or ligand-binding biochemistry has been reported for CLEC-60 to date. (o′rourke2006genomicclustersputative pages 3-4, pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10, zhou2018cellsignalingof pages 7-9)

1) Key concepts and definitions
- Gene/protein identity and domains. clec-60 (ZK666.6) encodes a secreted protein with a hydrophobic signal peptide and no predicted membrane anchor, indicating a soluble extracellular protein. Domain architecture includes a von Willebrand factor A (vWFA) domain followed by a C-type lectin-like domain (CTLD), aligning with the C-type lectin-like family in C. elegans. These features were cataloged in the context of pathogen-induced gene clusters. Publication: O’Rourke et al., Genome Research, Aug 2006; URL: https://doi.org/10.1101/gr.50823006 (o′rourke2006genomicclustersputative pages 3-4).
- Family context. clec genes comprise a large and diverse CTLD gene family in C. elegans associated with innate immunity. Comparative analyses emphasize diversification and immune specificity among CTLD proteins, situating clec-60 within this immune effector/regulator landscape. Publication: Pees et al., Journal of Innate Immunity, Nov 2016; URL: https://doi.org/10.1159/000441475 (pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10). Pan et al. (mBio, Oct 2021) curated infection-responsive clec genes and annotated secretory features; clec-60 (406 aa) is predicted secreted and differentially regulated across pathogens (see section 2). URL: https://doi.org/10.1128/mbio.02579-21 (pan2021identificationandfunctional pages 2-3).

2) Recent developments and latest research (emphasis 2023–2024)
- Targeted literature specifically on clec-60 in 2023–2024 appears limited; however, recent syntheses of C. elegans CLEC proteins and infection-responsive repertoires include clec-60 annotations. Pan et al. (2021, mBio) aggregated 38 infection-responsive clec genes; for clec-60 they report pathogen-dependent regulation: induction by Microbacterium nematophilum and Staphylococcus aureus, and suppression by Pseudomonas aeruginosa, alongside prediction of a signal peptide/secretory status (methods using SignalP/TMHMM). URL: https://doi.org/10.1128/mbio.02579-21 (pan2021identificationandfunctional pages 2-3). This updates earlier pathogen-response catalogs by confirming clec-60 as a secreted, infection-responsive CTLD protein. Where 2023–2024 sources are lacking specifically for clec-60, we prioritize the most recent high-quality sources that mention clec-60 directly and provide curated, cross-pathogen comparisons (Pan 2021) (pan2021identificationandfunctional pages 2-3).

3) Current applications and real-world implementations
- Reporter and marker usage. clec-60 promoter GFP reporters (pclec-60::GFP) have been used to visualize intestinal expression during infection paradigms, serving as markers of intestinal immune activation. Summary tables cite intestinal fluorescence in promoter-fusion experiments during Staphylococcus aureus exposure, consistent with gut-localized innate immune responses. Publication: Pees et al., 2016; URL: https://doi.org/10.1159/000441475 (pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10).
- Genetic perturbation assays in infection models. RNAi knockdown of clec-60 produces a hyper-deformed anal region (Dar) phenotype and severe constipation during Microbacterium nematophilum infection, linking clec-60 to the characteristic posterior swelling response to bacterial attachment at the rectal/anal epithelium. Overexpression of the clec-60/61 cluster renders animals more susceptible in survival assays to Pseudomonas aeruginosa, suggesting dosage-sensitive roles in host–pathogen dynamics. Publication summaries compiled in Pees et al., 2016; URL: https://doi.org/10.1159/000441475 (pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10).

4) Expert opinions and analysis from authoritative sources
- Infection-induced secreted effector/regulator. O’Rourke et al. (Genome Research) identified clec-60 among genes robustly induced by M. nematophilum infection and emphasized secreted lectin-like proteins with N-terminal signal peptides lacking membrane anchors, consistent with extracellular effectors or modulators in the intestinal lumen or apical surfaces. URL: https://doi.org/10.1101/gr.50823006 (o′rourke2006genomicclustersputative pages 3-4).
- CTLD diversification and immune specificity. Reviews of CTLD proteins in invertebrates highlight how diversification underlies pathogen specificity; tabulated phenotypes place clec-60 within intestinally expressed CTLDs affecting infection outcomes and epithelial responses (Dar), aligning clec-60 with effector/regulator roles rather than catalytic enzymes. URL: https://doi.org/10.1159/000441475 (pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10).
- Signaling architecture insights. In ETEC infection/beneficial microbe contexts, Zhou et al. show that defense genes including clec-60 are modulated by p38 MAPK (NSY-1/SEK-1/PMK-1) and DAF/IGF (DAF-16) pathways, with expression down in nsy-1 or daf-16 mutants and up in dbl-1 or age-1 mutants, indicating that clec-60 is integrated within canonical innate immune signaling circuits. URL: https://doi.org/10.3389/fimmu.2018.01745 (zhou2018cellsignalingof pages 7-9).

5) Relevant statistics and data from recent studies
- Pathogen induction magnitude and tissue annotation (M. nematophilum). clec-60 is induced 6.6-fold after 6 h of infection with virulent M. nematophilum strain CBX102 compared with avirulent UV336; induction was confirmed by semiquantitative RT–PCR. The protein is annotated as secreted (signal peptide; no transmembrane anchor), with intestinal expression. Publication date: Aug 2006. URL: https://doi.org/10.1101/gr.50823006 (o′rourke2006genomicclustersputative pages 3-4).
- Pathogen-dependent regulation. curation across datasets indicates clec-60 is induced by M. nematophilum and S. aureus, and suppressed by P. aeruginosa; predicted to be secretory based on SignalP/TMHMM analysis of CLEC proteins (37/38 infection-responsive CLECs predicted secreted). Publication date: Oct 2021. URL: https://doi.org/10.1128/mbio.02579-21 (pan2021identificationandfunctional pages 2-3).
- Reporter/phenotype summaries. pclec-60::GFP fluorescence localizes to intestine; clec-60 RNAi yields Dar and severe constipation in M. nematophilum infection; clec-60/61 overexpression increases susceptibility to P. aeruginosa in survival assays. Publication date: Nov 2016. URL: https://doi.org/10.1159/000441475 (pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10).
- Signaling modulation. In ETEC infection paradigms, clec-60 expression is positively regulated by p38 MAPK and DAF/IGF axis; expression is down in nsy-1 or daf-16 mutants and elevated in dbl-1 or age-1 mutants (qRT-PCR analyzed by 2−ΔΔCt, day 2 sampling). Publication date: Sep 2018. URL: https://doi.org/10.3389/fimmu.2018.01745 (zhou2018cellsignalingof pages 7-9).

Functional and mechanistic interpretation
- Primary function. CLEC-60 is a secreted CTLD-containing protein likely acting as an innate immune effector and/or regulator in the intestinal epithelium, responding to bacterial colonization at the rectal/intestinal interface. The vWFA+CTLD arrangement suggests potential extracellular protein–protein or carbohydrate-mediated interactions with microbial surfaces or host matrices; however, no direct biochemical binding/catalytic activity has been experimentally demonstrated for CLEC-60 itself. The lack of enzymatic motifs and the presence of a secretory signal peptide support a non-enzymatic, extracellular role. (o′rourke2006genomicclustersputative pages 3-4, pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10).
- Cellular and subcellular localization. Reporter and annotation data indicate intestinal expression and secretion to the lumen or apical surface, consistent with a role in the gut’s barrier/immune environment. (o′rourke2006genomicclustersputative pages 3-4, pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10).
- Pathway context. clec-60 expression is induced by M. nematophilum and modulated by conserved innate immunity pathways, including p38 MAPK and insulin/DAF-16 signaling in ETEC contexts, indicating integration with canonical stress/immune transcriptional programs. (o′rourke2006genomicclustersputative pages 3-4, zhou2018cellsignalingof pages 7-9, pan2021identificationandfunctional pages 2-3).
- Phenotypic evidence. RNAi knockdown during M. nematophilum infection causes Dar and severe constipation, indicative of compromised epithelial/immune response to pathogen attachment at the anus. Overexpression of clec-60/61 increases susceptibility to P. aeruginosa, suggesting that balanced CLEC-60 dosage is critical and that overexpression may dysregulate immune or behavioral responses leading to reduced survival on PA. (pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10).

Limitations and open questions
- Direct biochemical activity for CLEC-60 has not been shown; ligand specificity and binding partners remain to be defined. Quantitative localization (e.g., secretion dynamics, apical vs basolateral) and structural data for CLEC-60 are lacking in current literature. While pathway influences are established in ETEC paradigms, direct transcriptional regulators (specific TFs binding the clec-60 promoter) and pathogen-specific upstream signaling for M. nematophilum and P. aeruginosa have not been pinpointed for clec-60.

Citations
- O’Rourke D, et al. Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum. Genome Research. 2006-08. https://doi.org/10.1101/gr.50823006 (o′rourke2006genomicclustersputative pages 3-4).
- Pees B, et al. High Innate Immune Specificity through Diversified C-Type Lectin-Like Domain Proteins in Invertebrates. Journal of Innate Immunity. 2016-11. https://doi.org/10.1159/000441475 (pees2016highinnateimmune pages 7-9, pees2016highinnateimmune pages 9-10).
- Pan W, et al. Identification and Functional Analysis of Cytokine-Like Protein CLEC-47 in Caenorhabditis elegans. mBio. 2021-10. https://doi.org/10.1128/mbio.02579-21 (contextual curation of clec-60 regulation and secretory prediction among infection-responsive CLECs). (pan2021identificationandfunctional pages 2-3).
- Zhou M, et al. Cell Signaling of Caenorhabditis elegans in Response to Enterotoxigenic Escherichia coli Infection and Lactobacillus zeae Protection. Frontiers in Immunology. 2018-09. https://doi.org/10.3389/fimmu.2018.01745 (pathway-dependent modulation of clec-60 expression). (zhou2018cellsignalingof pages 7-9).

Verification checklist (MANDATORY STEPS)
- Symbol and identity: clec-60 matches ZK666.6; literature mapping confirms a secreted vWFA+CTLD protein consistent with UniProt Q23564 (C. elegans). (o′rourke2006genomicclustersputative pages 3-4).
- Organism: Caenorhabditis elegans throughout. (o′rourke2006genomicclustersputative pages 3-4, pees2016highinnateimmune pages 7-9, pan2021identificationandfunctional pages 2-3, zhou2018cellsignalingof pages 7-9).
- Domains/family: CTLD and vWFA domains in the literature and family-level analyses; signal peptide indicates secreted status. (o′rourke2006genomicclustersputative pages 3-4, pan2021identificationandfunctional pages 2-3, pees2016highinnateimmune pages 7-9).
- Ambiguity check: No conflicting gene symbol usage identified across organisms; all references map to the C. elegans clec-60 locus. (o′rourke2006genomicclustersputative pages 3-4, pees2016highinnateimmune pages 7-9, pan2021identificationandfunctional pages 2-3).

References

1. (o′rourke2006genomicclustersputative pages 3-4): D. O′Rourke, D. Baban, M. Demidova, R. Mott, and J. Hodgkin. Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of c. elegans with m. nematophilum. Genome research, 16 8:1005-16, Aug 2006. URL: https://doi.org/10.1101/gr.50823006, doi:10.1101/gr.50823006. This article has 296 citations and is from a highest quality peer-reviewed journal.

2. (pees2016highinnateimmune pages 7-9): Barbara Pees, Wentao Yang, Alejandra Zárate-Potes, Hinrich Schulenburg, and Katja Dierking. High innate immune specificity through diversified c-type lectin-like domain proteins in invertebrates. Journal of Innate Immunity, 8:129-142, Nov 2016. URL: https://doi.org/10.1159/000441475, doi:10.1159/000441475. This article has 164 citations and is from a peer-reviewed journal.

3. (pees2016highinnateimmune pages 9-10): Barbara Pees, Wentao Yang, Alejandra Zárate-Potes, Hinrich Schulenburg, and Katja Dierking. High innate immune specificity through diversified c-type lectin-like domain proteins in invertebrates. Journal of Innate Immunity, 8:129-142, Nov 2016. URL: https://doi.org/10.1159/000441475, doi:10.1159/000441475. This article has 164 citations and is from a peer-reviewed journal.

4. (zhou2018cellsignalingof pages 7-9): Mengzhou Zhou, Xiaozhen Liu, Hai Yu, Xianhua Yin, Shao-Ping Nie, Ming-Yong Xie, Wei Chen, and Joshua Gong. Cell signaling of caenorhabditis elegans in response to enterotoxigenic escherichia coli infection and lactobacillus zeae protection. Frontiers in Immunology, Sep 2018. URL: https://doi.org/10.3389/fimmu.2018.01745, doi:10.3389/fimmu.2018.01745. This article has 49 citations and is from a peer-reviewed journal.

5. (pan2021identificationandfunctional pages 2-3): Wen Pan, Xiaowen Huang, Zeyuan Guo, Rekha Nagarajan, and Eleftherios Mylonakis. Identification and functional analysis of cytokine-like protein clec-47 in caenorhabditis elegans. mBio, Oct 2021. URL: https://doi.org/10.1128/mbio.02579-21, doi:10.1128/mbio.02579-21. This article has 9 citations and is from a domain leading peer-reviewed journal.

Citations

1. pan2021identificationandfunctional pages 2-3
2. zhou2018cellsignalingof pages 7-9
3. pees2016highinnateimmune pages 7-9
4. pees2016highinnateimmune pages 9-10
5. https://doi.org/10.1101/gr.50823006
6. https://doi.org/10.1159/000441475
7. https://doi.org/10.1128/mbio.02579-21
8. https://doi.org/10.3389/fimmu.2018.01745
9. https://doi.org/10.1101/gr.50823006,
10. https://doi.org/10.1159/000441475,
11. https://doi.org/10.3389/fimmu.2018.01745,
12. https://doi.org/10.1128/mbio.02579-21,