Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0060271 cilium assembly	IBA GO_REF:0000033	ACCEPT	Summary: CHE-2 is essential for cilium assembly. PMID:10518500 demonstrates that che-2 mutants have extremely short cilia with abnormal posterior projection, and that cilium extension fails during development in these mutants. The IBA annotation based on phylogenetic inference from the IFT80 orthology group is well-supported by direct experimental evidence. Reason: Core function strongly supported by literature. PMID:10518500 shows che-2 mutants have severely defective cilia that remain short throughout development. Expression of che-2 can rescue cilium morphology even at adult stage, demonstrating its essential role in cilium assembly. Supporting Evidence: PMID:10518500 These mutants have extremely short cilia with an abnormal posterior projection, and show defects in behaviors that are mediated by ciliated sensory neurons. PMID:10518500 Using green fluorescent protein, we found that the extension of cilia in wild-type animals took place at the late embryonic stage, whereas the cilia of che-2 mutant animals remained always short during development. file:worm/che-2/che-2-deep-research-falcon.md model: Edison Scientific Literature
GO:0005929 cilium	IBA GO_REF:0000033	ACCEPT	Summary: CHE-2 localizes to cilia as demonstrated by GFP tagging experiments in PMID:10518500. This IBA annotation is phylogenetically inferred and consistent with experimental localization data showing CHE-2::GFP in sensory cilia. Reason: Localization to cilium is directly demonstrated experimentally. CHE-2-tagged GFP localizes to cilia of almost all ciliated sensory neurons (PMID:10518500). Supporting Evidence: PMID:10518500 CHE-2-tagged green fluorescent protein is localized at the cilia of almost all the ciliated sensory neurons.
GO:0030992 intraciliary transport particle B	IBA GO_REF:0000033	ACCEPT	Summary: CHE-2/IFT80 is a well-established component of the IFT-B complex. This is supported by ComplexPortal annotation (CPX-1290) and extensive literature on IFT-B composition. PMID:22922713 provides detailed mechanistic evidence showing that IFT-B components including CHE-2 orthologs move together during anterograde transport. Reason: Core structural function as IFT-B component is well-established through phylogenetic conservation and direct biochemical evidence. UniProt entry references ComplexPortal CPX-1290 (Intraflagellar transport complex B). The WD40 domain architecture of CHE-2 is characteristic of IFT-B components. Supporting Evidence: PMID:22922713 Similar to OSM-6, in dyf-2(jhu616), all other IFT-B components examined also showed active anterograde movements, but lost most of the retrograde IFT movements and accumulate at the ciliary tip
GO:0005929 cilium	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation based on UniProt subcellular location vocabulary mapping. This is consistent with but less specific than the IBA annotation for the same term. Reason: Redundant with IBA annotation but acceptable as independent evidence line. The UniProt entry explicitly states subcellular location as cilium. Supporting Evidence: UniProt:G5EGF0 SUBCELLULAR LOCATION: Cell projection, cilium
GO:0005929 cilium	NAS PMID:28479320 Dynein-Driven Retrograde Intraflagellar Transport Is Triphas...	ACCEPT	Summary: NAS annotation from ComplexPortal referencing a study on dynein-driven retrograde IFT. The paper discusses IFT-B components including CHE-2 orthologs in the context of ciliary transport. Reason: Consistent with other cilium localization annotations. While NAS is weaker evidence than IDA, it is supported by the broader literature context. Supporting Evidence: PMID:28479320 Disruption of the dynein-2 tail domain, light intermediate chain, or intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary localization, revealing their important roles in ciliary entry of dynein-2
GO:0042073 intraciliary transport	NAS PMID:28479320 Dynein-Driven Retrograde Intraflagellar Transport Is Triphas...	MODIFY	Summary: CHE-2 as an IFT-B component participates in intraciliary transport. PMID:28479320 focuses on retrograde IFT but discusses the overall IFT machinery including IFT-B. PMID:22922713 provides more detailed evidence of CHE-2 orthologs' IFT movement. Reason: The annotation is correct but could be more specific. CHE-2/IFT80 is primarily involved in anterograde transport as part of the IFT-B complex. Consider using GO:0035720 (intraciliary anterograde transport) for greater specificity. Proposed replacements: intraciliary anterograde transport Supporting Evidence: PMID:22922713 Similar to OSM-6, in dyf-2(jhu616), all other IFT-B components examined also showed active anterograde movements, but lost most of the retrograde IFT movements and accumulate at the ciliary tip
GO:0060271 cilium assembly	NAS PMID:28479320 Dynein-Driven Retrograde Intraflagellar Transport Is Triphas...	ACCEPT	Summary: NAS annotation for cilium assembly from ComplexPortal. Redundant with IBA and IMP annotations for the same term but acceptable as additional evidence source. Reason: Consistent with IBA and IMP annotations. Cilium assembly is a core function of CHE-2. Supporting Evidence: PMID:10518500 Hence, the abnormal posterior projection is due to the inability of cilia to extend, rather than degeneration of cilia once correctly formed
GO:0003674 molecular_function	ND GO_REF:0000015	ACCEPT	Summary: ND (No biological Data) annotation indicates no specific molecular function has been experimentally determined. While CHE-2 is a structural component of IFT-B, it does not appear to have enzymatic activity - its function is primarily as a scaffold/adaptor. Reason: Appropriate use of ND. CHE-2 has no known enzymatic or catalytic activity; it functions as a structural component of the IFT-B complex through protein-protein interactions mediated by its WD40 repeats. Supporting Evidence: PMID:10518500 The che-2 gene encodes a new member of the WD40 protein family, suggesting that it acts in protein-protein interaction.
GO:0090325 regulation of locomotion involved in locomotory behavior	IGI PMID:26434723 The Importance of cGMP Signaling in Sensory Cilia for Body S...	KEEP AS NON CORE	Summary: This annotation relates to body size regulation through cGMP signaling in sensory cilia. The study shows that cilium structure mutants (including che-2) have small body size and locomotion defects due to disrupted sensory signaling. Reason: This is a downstream consequence of cilium structure defects rather than a direct function of CHE-2. The effect on locomotion is indirect, mediated through disrupted sensory perception in defective cilia. Not a core function. Supporting Evidence: PMID:26434723 The body size of Caenorhabditis elegans is thought to be controlled by sensory inputs because many mutants with sensory cilium structure defects exhibit small body size.
GO:0090326 positive regulation of locomotion involved in locomotory behavior	IMP PMID:26434723 The Importance of cGMP Signaling in Sensory Cilia for Body S...	KEEP AS NON CORE	Summary: IMP annotation for locomotion regulation based on che-2 mutant phenotype. The small body size and reduced locomotion in che-2 mutants is secondary to cilium structure defects affecting sensory perception. Reason: Pleiotropic effect of cilium defects. CHE-2's primary role is in cilium assembly and IFT; the locomotory phenotype is an indirect consequence of sensory defects. Supporting Evidence: PMID:26434723 the defects in the sensory cilium structure may disturb the balanced control of the cGMP level
GO:0040014 regulation of multicellular organism growth	IGI PMID:26434723 The Importance of cGMP Signaling in Sensory Cilia for Body S...	KEEP AS NON CORE	Summary: Body size regulation is affected in che-2 mutants due to disrupted cGMP signaling in defective sensory cilia. This is a downstream phenotype of the cilium structure defect. Reason: Secondary phenotype resulting from defective sensory cilia. The primary function of CHE-2 is cilium assembly, not growth regulation per se. Supporting Evidence: PMID:26434723 many mutants with sensory cilium structure defects exhibit small body size
GO:0040018 positive regulation of multicellular organism growth	IMP PMID:26434723 The Importance of cGMP Signaling in Sensory Cilia for Body S...	KEEP AS NON CORE	Summary: IMP annotation based on small body size phenotype of che-2 mutants. The reduced body size is a consequence of disrupted sensory signaling through defective cilia. Reason: Indirect effect of cilium structure defects on sensory-mediated growth regulation. Not a direct molecular function of CHE-2. Supporting Evidence: PMID:26434723 the cGMP level is precisely controlled by GCY-12 and PDE-2 to determine body size through EGL-4, and the defects in the sensory cilium structure may disturb the balanced control of the cGMP level
GO:0006935 chemotaxis	IMP PMID:7828815 Multiple chemosensory defects in daf-11 and daf-21 mutants o...	KEEP AS NON CORE	Summary: che-2 mutants exhibit chemotaxis defects. This study (PMID:7828815) focuses on daf-11 and daf-21 mutants but references che-2 as a cilium structure mutant with chemosensory defects. PMID:10208543 provides more direct evidence. Reason: Chemotaxis defect is a consequence of abnormal cilium structure in sensory neurons. CHE-2 enables chemotaxis indirectly by being required for proper cilium assembly in chemosensory neurons. Supporting Evidence: PMID:10518500 These mutants have extremely short cilia with an abnormal posterior projection, and show defects in behaviors that are mediated by ciliated sensory neurons.
GO:0060271 cilium assembly	IGI PMID:1732156 Genetic analysis of chemosensory control of dauer formation ...	ACCEPT	Summary: IGI annotation based on genetic interaction studies of dauer formation. This paper places che-2 in the cilium-structure gene class that is epistatic to daf-11 for dauer formation, supporting its role in cilium assembly. Reason: Supports the core function of CHE-2 in cilium assembly. The genetic epistasis analysis places che-2 among genes required for cilium structure. Supporting Evidence: PMID:1732156 Dauer-defective mutations in nine genes cause structurally defective chemosensory cilia, thereby blocking chemosensation
GO:0040024 dauer larval development	IGI PMID:11677050 DAF-7/TGF-beta expression required for the normal larval dev...	KEEP AS NON CORE	Summary: che-2 mutants affect dauer formation through their role in cilium structure. The study places che-2 in the genetic pathway between daf-11 and daf-7 for dauer control. Reason: Dauer development phenotype is secondary to cilium structure defects. che-2 mutants affect dauer formation because sensory cilia are required for environmental sensing that triggers dauer entry. Not a direct function of CHE-2. Supporting Evidence: PMID:11677050 cilium-related genes che-2 and che-3 are placed between daf-11 and daf-7, in the genetic pathway controlling dauer formation
GO:0036064 ciliary basal body	IDA PMID:22922713 The BBSome controls IFT assembly and turnaround in cilia.	ACCEPT	Summary: IDA annotation for localization to ciliary basal body. PMID:22922713 shows that IFT-B components accumulate at the ciliary base in certain mutant backgrounds, and that the BBSome assembles IFT complexes at the ciliary base. Reason: CHE-2/IFT80 as an IFT-B component is assembled at the ciliary basal body before transport into the cilium. The ciliary base is where IFT particles are organized. Supporting Evidence: PMID:22922713 the BBSome (refs 3, 4), a group of conserved proteins affected in human Bardet-Biedl syndrome(5) (BBS), assembles IFT complexes at the ciliary base, then binds to the anterograde IFT particle
GO:0097730 non-motile cilium	IDA PMID:10518500 A novel WD40 protein, CHE-2, acts cell-autonomously in the f...	ACCEPT	Summary: C. elegans sensory cilia are non-motile (primary) cilia. CHE-2::GFP localizes to these sensory cilia as directly demonstrated in PMID:10518500. Reason: Appropriate specific localization annotation. C. elegans sensory neurons have non-motile cilia, and CHE-2 localizes to these structures. Supporting Evidence: PMID:10518500 CHE-2-tagged green fluorescent protein is localized at the cilia of almost all the ciliated sensory neurons.
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway	IGI PMID:11677050 DAF-7/TGF-beta expression required for the normal larval dev...	MARK AS OVER ANNOTATED	Summary: This annotation relates to the role of che-2 in the dauer pathway where it affects DAF-7/TGF-beta expression. The genetic analysis places che-2 between daf-11 and daf-7 in regulating TGF-beta signaling for dauer formation. Reason: This is an indirect effect mediated through cilium structure defects affecting sensory perception of environmental cues that regulate TGF-beta signaling. CHE-2 does not directly regulate TGF-beta signaling; it enables the sensory apparatus that perceives signals controlling this pathway. Supporting Evidence: PMID:11677050 cilium-related genes che-2 and che-3 are placed between daf-11 and daf-7, in the genetic pathway controlling dauer formation
GO:0006935 chemotaxis	IMP PMID:10208543 Sensing of cadmium and copper ions by externally exposed ADL...	KEEP AS NON CORE	Summary: che-2 mutants lack avoidance behavior to Cd2+ and Cu2+. The study shows that mutants with structural defects in ciliated neurons, including che-2, do not show chemotactic avoidance responses. Reason: Chemotaxis defect is downstream of cilium structure defect. CHE-2 is required for cilium assembly in chemosensory neurons; without proper cilia, these neurons cannot function in chemotaxis. Supporting Evidence: PMID:10208543 Mutants that have structural defects in ciliated neurons (che-2 and osm-3) as well as worms with three laser-operated neurons (ADL, ASE, and ASH), showed no avoidance behavior from Cd2+ and Cu2+
GO:0060271 cilium assembly	IMP PMID:10518500 A novel WD40 protein, CHE-2, acts cell-autonomously in the f...	ACCEPT	Summary: IMP annotation directly demonstrating CHE-2 requirement for cilium assembly. This is the primary reference establishing CHE-2 function, showing that mutants have truncated cilia and that rescue restores cilium morphology. Reason: Core function with strong experimental support. This is the definitive paper on CHE-2 function demonstrating its essential role in cilium formation. Supporting Evidence: PMID:10518500 Expression of che-2 in a subset of sensory neurons of a che-2 mutant by using a heterologous promoter resulted in restoration of the functions and cilium morphology of only the che-2-expressing neurons. PMID:10518500 Expression of che-2 in a che-2 mutant under a heat shock promoter showed that the extension of cilia, surprisingly, can occur even at the adult stage, and that such cilia can function apparently normally in behavior.
GO:0035720 intraciliary anterograde transport	IBA GO_REF:0000033	NEW	Summary: CHE-2/IFT80 is a core IFT-B component specifically involved in anterograde transport. PMID:22922713 shows IFT-B components move in the anterograde direction. Reason: More specific than GO:0042073 (intraciliary transport). IFT-B is specifically the anterograde transport machinery while IFT-A is retrograde. This term better captures CHE-2's molecular function. Supporting Evidence: PMID:22922713 Similar to OSM-6, in dyf-2(jhu616), all other IFT-B components examined also showed active anterograde movements, but lost most of the retrograde IFT movements and accumulate at the ciliary tip

Core Functions

CHE-2/IFT80 is a core structural component of the IFT-B complex, established through phylogenetic conservation and direct biochemical evidence. UniProt references ComplexPortal CPX-1290.

Molecular Function:

molecular_function

Directly Involved In:

cilium assembly intraciliary anterograde transport

Cellular Locations:

intraciliary transport particle B cilium

References

GO_REF:0000015

Use of the ND evidence code for Gene Ontology (GO) terms

GO_REF:0000033

Annotation inferences using phylogenetic trees

CHE-2 is orthologous to vertebrate IFT80 based on PANTHER phylogenetic analysis

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping

PMID:10208543

Sensing of cadmium and copper ions by externally exposed ADL, ASE, and ASH neurons elicits avoidance response in Caenorhabditis elegans.

che-2 mutants lack chemotactic avoidance to Cd2+ and Cu2+ due to structural defects in ciliated neurons

"Mutants that have structural defects in ciliated neurons (che-2 and osm-3) as well as worms with three laser-operated neurons (ADL, ASE, and ASH), showed no avoidance behavior from Cd2+ and Cu2+"

PMID:10518500

A novel WD40 protein, CHE-2, acts cell-autonomously in the formation of C. elegans sensory cilia.

CHE-2 is a WD40 repeat protein essential for cilium formation

"The che-2 gene encodes a new member of the WD40 protein family, suggesting that it acts in protein-protein interaction."
che-2 mutants have extremely short cilia with abnormal posterior projection

"These mutants have extremely short cilia with an abnormal posterior projection, and show defects in behaviors that are mediated by ciliated sensory neurons."
CHE-2::GFP localizes to cilia of almost all ciliated sensory neurons

"CHE-2-tagged green fluorescent protein is localized at the cilia of almost all the ciliated sensory neurons."
CHE-2 acts cell-autonomously in cilium formation

"Expression of che-2 in a subset of sensory neurons of a che-2 mutant by using a heterologous promoter resulted in restoration of the functions and cilium morphology of only the che-2-expressing neurons. Thus, che-2 acts cell-autonomously."
Both WD40 repeats and C-terminal domain are required for function

"Analysis of mutation sites showed that both the amino-terminal WD40 repeats and the carboxyl-terminal non-WD40 domain are necessary for the CHE-2 function."
Cilium extension can be rescued even at adult stage by che-2 expression

"Expression of che-2 in a che-2 mutant under a heat shock promoter showed that the extension of cilia, surprisingly, can occur even at the adult stage, and that such cilia can function apparently normally in behavior."

PMID:11677050

DAF-7/TGF-beta expression required for the normal larval development in C. elegans is controlled by a presumed guanylyl cyclase DAF-11.

che-2 is placed in genetic pathway between daf-11 and daf-7 for dauer formation

"cilium-related genes che-2 and che-3 are placed between daf-11 and daf-7, in the genetic pathway controlling dauer formation"
Cilium-related genes affect TGF-beta signaling indirectly through sensory function

"Expression of daf-11 cDNA by cell specific promoters suggests that daf-11 acts cell autonomously in ASI chemosensory neurons for daf-7 expression."

PMID:1732156

Genetic analysis of chemosensory control of dauer formation in Caenorhabditis elegans.

che-2 is one of nine cilium-structure genes affecting dauer formation

"Dauer-defective mutations in nine genes cause structurally defective chemosensory cilia, thereby blocking chemosensation"
Cilium structure mutations block chemosensation required for dauer regulation

"Dauer-defective mutations in nine genes cause structurally defective chemosensory cilia, thereby blocking chemosensation"

PMID:22922713

The BBSome controls IFT assembly and turnaround in cilia.

IFT-B components show active anterograde movement

"Similar to OSM-6, in dyf-2(jhu616), all other IFT-B components examined also showed active anterograde movements, but lost most of the retrograde IFT movements and accumulate at the ciliary tip"
The BBSome assembles IFT complexes at the ciliary base

"the BBSome (refs 3, 4), a group of conserved proteins affected in human Bardet-Biedl syndrome(5) (BBS), assembles IFT complexes at the ciliary base, then binds to the anterograde IFT particle"
IFT-A and IFT-B subcomplexes associate during anterograde transport

"IFT-A component CHE-11 and IFT-B component IFT-20 showed fluorescence complementation in either wild-type or dyf-2(jhu616), indicative of the association between IFT-A and IFT-B subcomplexes"
IFT-B components accumulate at cilia tip when turnaround is defective

"all other IFT-B components examined also showed active anterograde movements, but lost most of the retrograde IFT movements and accumulate at the ciliary tip"

PMID:26434723

The Importance of cGMP Signaling in Sensory Cilia for Body Size Regulation in Caenorhabditis elegans.

Cilium structure mutants including che-2 exhibit small body size

"The body size of Caenorhabditis elegans is thought to be controlled by sensory inputs because many mutants with sensory cilium structure defects exhibit small body size"
Body size regulation depends on cGMP signaling in sensory cilia

"the cGMP level is precisely controlled by GCY-12 and PDE-2 to determine body size through EGL-4"
Cilium defects disturb balanced control of cGMP levels

"the defects in the sensory cilium structure may disturb the balanced control of the cGMP level"

PMID:28479320

Dynein-Driven Retrograde Intraflagellar Transport Is Triphasic in C. elegans Sensory Cilia.

IFT-B complex is required for dynein-2 ciliary localization

"Disruption of the dynein-2 tail domain, light intermediate chain, or intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary localization, revealing their important roles in ciliary entry of dynein-2"
IFT-A and IFT-B function in ciliary transport

"our affinity purification and genetic analyses show that IFT-A subunits IFT-139 and IFT-43 function redundantly to promote dynein-2 motility"

PMID:7828815

Multiple chemosensory defects in daf-11 and daf-21 mutants of Caenorhabditis elegans.

daf-11 and daf-21 mutants have chemosensory defects including in chemotaxis

"daf-11 and daf-21 mutants are not defective in avoidance of certain non-volatile repellents, but are defective in taxis to non-volatile attractants"

file:worm/che-2/che-2-deep-research-falcon.md

Deep research report on che-2

Suggested Experiments

Experiment: Determine CHE-2 interaction partners within IFT-B using co-IP and mass spectrometry

Experiment: Test which ciliary cargos depend specifically on CHE-2 for transport

Experiment: Examine CHE-2 dynamics during IFT using live imaging with improved temporal resolution

📚 Additional Documentation

Deep Research Falcon

(che-2-deep-research-falcon.md)

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template_file: templates/gene_research_go_focused.md
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organism: worm
gene_id: che-2
gene_symbol: che-2
uniprot_accession: G5EGF0
protein_description: 'SubName: Full=CHE-2 protein {ECO:0000313|EMBL:CAB38019.1};
SubName: Full=WD_REPEATS_REGION domain-containing protein {ECO:0000313|EMBL:CCD61758.1};'
gene_info: Name=che-2 {ECO:0000313|EMBL:CCD61758.1, ECO:0000313|WormBase:F38G1.1};
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organism_full: Caenorhabditis elegans.
protein_family: Not specified in UniProt
protein_domains: Beta-prop_IFT80_2nd. (IPR056456); TPR_IFT80_172_dom. (IPR056157);
WD40/YVTN_repeat-like_dom_sf. (IPR015943); WD40_repeat_dom_sf. (IPR036322); WD40_rpt.
(IPR001680)
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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: G5EGF0
Protein Description: SubName: Full=CHE-2 protein {ECO:0000313|EMBL:CAB38019.1}; SubName: Full=WD_REPEATS_REGION domain-containing protein {ECO:0000313|EMBL:CCD61758.1};
Gene Information: Name=che-2 {ECO:0000313|EMBL:CCD61758.1, ECO:0000313|WormBase:F38G1.1}; ORFNames=CELE_F38G1.1 {ECO:0000313|EMBL:CCD61758.1}, F38G1.1 {ECO:0000313|WormBase:F38G1.1};
Organism (full): Caenorhabditis elegans.
Protein Family: Not specified in UniProt
Key Domains: Beta-prop_IFT80_2nd. (IPR056456); TPR_IFT80_172_dom. (IPR056157); WD40/YVTN_repeat-like_dom_sf. (IPR015943); WD40_repeat_dom_sf. (IPR036322); WD40_rpt. (IPR001680)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "che-2" matches the protein description above
Verify the organism is correct: Caenorhabditis elegans.
Check if protein family/domains align with what you find in literature
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 'che-2' 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 che-2 (gene ID: che-2, UniProt: G5EGF0) 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: G5EGF0
Protein Description: SubName: Full=CHE-2 protein {ECO:0000313|EMBL:CAB38019.1}; SubName: Full=WD_REPEATS_REGION domain-containing protein {ECO:0000313|EMBL:CCD61758.1};
Gene Information: Name=che-2 {ECO:0000313|EMBL:CCD61758.1, ECO:0000313|WormBase:F38G1.1}; ORFNames=CELE_F38G1.1 {ECO:0000313|EMBL:CCD61758.1}, F38G1.1 {ECO:0000313|WormBase:F38G1.1};
Organism (full): Caenorhabditis elegans.
Protein Family: Not specified in UniProt
Key Domains: Beta-prop_IFT80_2nd. (IPR056456); TPR_IFT80_172_dom. (IPR056157); WD40/YVTN_repeat-like_dom_sf. (IPR015943); WD40_repeat_dom_sf. (IPR036322); WD40_rpt. (IPR001680)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "che-2" matches the protein description above
Verify the organism is correct: Caenorhabditis elegans.
Check if protein family/domains align with what you find in literature
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:

Research Target:

Please provide a comprehensive research report on the gene che-2 (gene ID: che-2, UniProt: G5EGF0) 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.

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.

Plan overview
Objective 1 verified the target identity and domain context; Objectives 2–4 gathered and extracted recent structural and classical C. elegans evidence; Objective 5 assembled an evidence table; Objective 6 synthesizes a comprehensive, well‑cited report prioritizing 2022–2024 sources.

Comprehensive research report: C. elegans che-2 (UniProt G5EGF0)

Identity, nomenclature, and domain architecture
• Gene/protein identity: che-2 encodes the C. elegans ortholog of intraflagellar transport protein 80 (IFT80), an established subunit of the IFT-B complex. Allelism and identity were determined genetically (ks68 is allelic to che-2) and by assignment to IFT complex B in C. elegans sensory cilia (IFT-B) (ou2007sensoryciliogenesisin pages 5-6, inglis2009intraflagellartransportin pages 28-33).
• Domain context and placement: Recent in situ structural work places IFT80 as a central scaffold within the IFT-B2 lobe of the IFT-B complex. IFT80 contains tandem WD (WD40/β‑propeller) domains followed by C‑terminal TPR motifs; within the IFT train polymer, its WD domains and TPR region form extended lateral interfaces that stabilize neighboring repeats, organizing the core architecture of IFT‑B2 (cryo‑ET/AlphaFold‑guided modeling) (lacey2023themolecularstructure pages 3-4, lacey2023themolecularstructure pages 1-2).
• Mandatory verification: The target organism is C. elegans, and the protein’s predicted domains (WD40/TPR) align with the UniProt domain listing and with structural placements in modern IFT‑B reconstructions (lacey2023themolecularstructure pages 3-4, lacey2023themolecularstructure pages 1-2).

Primary molecular function and pathway role
• Role: CHE‑2/IFT80 is a core structural subunit of the anterograde IFT-B complex, specifically the IFT‑B2 subcomplex, which forms one lobe of the polymeric IFT trains that traffic axonemal building blocks and signaling proteins required for ciliogenesis and cilium maintenance (lacey2023themolecularstructure pages 1-2, lacey2023themolecularstructure pages 3-4).
• Architectural contribution: IFT80 lies at the center of IFT‑B2, in proximity to IFT172 and the IFT54/20 coiled‑coil pair; its lateral interfaces contribute to IFT‑B polymer stability and train assembly during anterograde transport (lacey2023themolecularstructure pages 3-4).
• Pathway: CHE‑2 functions in the conserved intraflagellar transport pathway, where IFT‑B trains are driven anterogradely by kinesin‑2 motors and couple to retrograde dynein‑2 at the ciliary tip for return transport (lacey2023themolecularstructure pages 1-2, inglis2009intraflagellartransportin pages 28-33).

Cellular and subcellular localization; transport behavior
• Localization in C. elegans neurons: CHE‑2::GFP localizes to basal bodies and along the ciliary axoneme of amphid/phasmid sensory neurons; robust IFT movement is observed by live imaging (jensen2010localizationofa pages 5-8). CHE‑2 also localizes near the transition zone and along axonemes, a pattern perturbed in certain background mutants (see BBS section below) (blacque2004lossofc. pages 5-7).
• Quantitative IFT velocities in vivo: In C. elegans sensory cilia, CHE‑2::GFP exhibits anterograde IFT velocities close to the canonical rates measured for IFT components: approximately 0.7 μm/s in the middle segment (cooperation of kinesin‑II and OSM‑3) and approximately 1.2 μm/s in distal segments (OSM‑3‑dominated) (jensen2010localizationofa pages 5-8). These values align with motor‑specific rates reported in C. elegans: kinesin‑II ≈ 0.5 μm/s, OSM‑3 ≈ 1.2 μm/s, and a combined intermediate ≈ 0.7 μm/s, supporting CHE‑2’s bona fide IFT‑B cargo behavior (inglis2009intraflagellartransportin pages 28-33).

Phenotypes of che-2 mutants and functional readouts
• Ciliogenesis/sensory phenotypes: che‑2 mutants (IFT‑B) are dye‑filling defective (Dyf), display truncated or missing cilia, and exhibit chemotaxis defects, reflecting essential roles for IFT‑B in sensory ciliogenesis and function (ou2007sensoryciliogenesisin pages 5-6, inglis2009intraflagellartransportin pages 28-33).
• BBS genetic context: In bbs-7/8 mutant backgrounds, CHE‑2::GFP shows abnormal accumulation at mid/distal axonemal regions, despite preserved bidirectional IFT motility; ciliary length measurements in this study provide quantitative context (axoneme length 1.77 ± 0.71 μm, n = 50) (blacque2004lossofc. pages 5-7). These data emphasize how perturbations in IFT-associated complexes alter CHE‑2 distribution and cilia morphology but do not necessarily abolish transport dynamics.

Structural biology: 2022–2024 advances resolving CHE‑2/IFT80 in IFT‑B
• 2022 biochemically validated IFT‑B model: A 15‑subunit IFT‑B model integrated AlphaFold predictions with crosslink‑MS, SAXS, crystallography, and mutational binding assays to rationalize IFT‑B1/B2 architecture; IFT80 is placed within the IFT‑B assembly in positions consistent with cryo‑ET reconstructions (The EMBO Journal, Nov 2022) (lacey2023themolecularstructure pages 12-18).
• 2023 in situ IFT‑B architecture: High‑resolution cryo‑ET/AlphaFold‑guided modeling of anterograde trains in Chlamydomonas cilia produced molecular models for IFT‑A and IFT‑B (EMDB/PDB accessions). IFT80 is at the center of IFT‑B2, providing extended lateral contacts that stabilize flexible regions upon polymerization; IFT‑B repeats show one autoinhibited dynein‑2 bound every third repeat, mapping how motors align on the IFT‑B lattice (Nature Structural & Molecular Biology, Jan 2023) (lacey2023themolecularstructure pages 1-2, lacey2023themolecularstructure pages 3-4).
• 2024 dynein‑2 tethering mechanism: An integrative cryo‑EM/cell biology study shows the dynein‑2 intermediate chain WDR60 uses a long N‑terminal extension to tether dynein‑2 to IFT‑B via interactions with the IFT80 TPR domain and the IFT54 CH domain; the IFT80:IFT172 interface is non‑overlapping with the WDR60 interface, consistent with simultaneous binding in assembled trains (The EMBO Journal, Mar 2024) (mukhopadhyay2024structureandtethering pages 9-11). Together, these studies converge on a mechanistic picture where CHE‑2/IFT80 serves as a scaffold in IFT‑B2 and participates in dynein‑2 engagement/tethering within anterograde trains.

Current applications and real‑world implementations
• Genetic and imaging markers: che‑2 loss‑of‑function (Dyf/chemotaxis) is widely used in C. elegans as a genetic handle for ciliogenesis screens and as a benchmark for IFT‑B integrity; CHE‑2::GFP is a routine marker for IFT particle dynamics and ciliary localization in vivo (ou2007sensoryciliogenesisin pages 5-6, jensen2010localizationofa pages 5-8).
• Translational relevance by conservation: The conserved structural placement and interfaces of IFT80 within IFT‑B (2022–2024 structures) provide a framework to interpret human IFT80 variants implicated in ciliopathies by mapping mutations onto the IFT‑B2 scaffold and into potential dynein‑2 tethering surfaces, although those human genotype–structure links are beyond the scope of the C. elegans–focused sources used here (lacey2023themolecularstructure pages 12-18, lacey2023themolecularstructure pages 3-4, lacey2023themolecularstructure pages 1-2, mukhopadhyay2024structureandtethering pages 9-11).

Expert perspectives and synthesis
• Authoritative consensus from recent structural biology (2022–2024) is that IFT80 (CHE‑2) is a central organizing element of IFT‑B2 in anterograde trains. Its WD40‑TPR architecture forms lateral polymer interfaces essential for IFT‑B cohesion and provides a docking/tethering context for dynein‑2 via WDR60’s N‑terminal extension, thereby aligning motor engagement with the structural repeat of the IFT‑B polymer (lacey2023themolecularstructure pages 3-4, lacey2023themolecularstructure pages 1-2, lacey2023themolecularstructure pages 12-18, mukhopadhyay2024structureandtethering pages 9-11). In vivo C. elegans imaging corroborates that CHE‑2 behaves as a canonical IFT component moving at expected anterograde rates and localizing to basal bodies and axonemes; genetic loss produces hallmark Dyf/chemotaxis phenotypes consistent with disrupted ciliogenesis (jensen2010localizationofa pages 5-8, ou2007sensoryciliogenesisin pages 5-6, inglis2009intraflagellartransportin pages 28-33).
• Collectively, these data satisfy the mandatory verification criteria: che‑2 in C. elegans encodes the IFT80 ortholog with WD40/TPR domains; it functions within the IFT‑B2 subcomplex, localizes to sensory cilia, and is essential for ciliary assembly and function.

Relevant quantitative statistics and data
• IFT velocities (C. elegans, CHE‑2/IFT80 reporters): ≈ 0.7 μm/s (middle segment; kinesin‑II+OSM‑3), ≈ 1.2 μm/s (distal segment; OSM‑3) (jensen2010localizationofa pages 5-8).
• Motor reference velocities (C. elegans): kinesin‑II ≈ 0.5 μm/s; OSM‑3 ≈ 1.2 μm/s; intermediate ≈ 0.7 μm/s (inglis2009intraflagellartransportin pages 28-33).
• Cilium length context (BBS background): 1.77 ± 0.71 μm (n = 50), with CHE‑2::GFP accumulations at mid/distal axoneme in bbs-7/8 mutants (blacque2004lossofc. pages 5-7).
• Structural resources (IFT-A/IFT-B trains): Cryo‑ET maps/models deposited (EMDB: EMD‑15977/15978/15979; PDB: 8BD7/8BDA) underscoring IFT‑B2 placement of IFT80 and overall architecture (lacey2023themolecularstructure pages 1-2).

Key concepts and definitions (current understanding)
• Intraflagellar transport (IFT): Bidirectional trafficking system that builds and maintains cilia. IFT‑B mediates anterograde cargo delivery with kinesin‑2; IFT‑A and dynein‑2 mediate retrograde return. Trains are polymeric assemblies of IFT‑A/IFT‑B subunits repeated along the axonemal microtubules (lacey2023themolecularstructure pages 1-2, inglis2009intraflagellartransportin pages 28-33).
• IFT‑B subcomplexes: IFT‑B is divided into IFT‑B1 and IFT‑B2 lobes; IFT80 (CHE‑2) is central to IFT‑B2 and interfaces with IFT172 and IFT54/20, contributing to train stability and motor coupling (lacey2023themolecularstructure pages 3-4, lacey2023themolecularstructure pages 1-2).
• WD40/TPR scaffolds: WD40 β‑propellers provide rigid platforms for multiprotein assembly; TPR motifs furnish elongated helical scaffolds for partner engagement. In IFT80 these domains together create lateral polymer interfaces and docking surfaces implicated in dynein‑2 tethering (lacey2023themolecularstructure pages 3-4, mukhopadhyay2024structureandtethering pages 9-11).

Embedded evidence table
| Aspect | Key finding/statement | Quantitative data (if any) | System/context | Source | URL | Publication date |
|---|---|---|---|---|---|---|
| Identity & mutant phenotypes | Ou et al.: ks68 is allelic to che-2; che-2 encodes IFT80 (an IFT-B subunit) and che-2 mutants show dye-filling (Dyf), truncated cilia and chemotaxis defects. | Screen context: 126 chemotaxis-defective strains from ~150,000 mutagenized genomes (study scale) | C. elegans amphid/phasmid sensory cilia | (ou2007sensoryciliogenesisin pages 5-6) | https://doi.org/10.1091/mbc.e06-09-0805 | May 2007 |
| CHE-2::GFP localization & IFT velocities | Jensen et al.: CHE-2::GFP localizes to basal bodies and ciliary axonemes; IFT transport of CHE-2 is observed and unchanged in daf-25 mutants. | IFT velocities ≈ 0.7 μm/s (middle segment) and ≈ 1.2 μm/s (distal segment) | C. elegans sensory neurons (CHE-2::GFP reporters) | (jensen2010localizationofa pages 5-8) | https://doi.org/10.1371/journal.pgen.1001199 | Nov 2010 |
| CHE-2 behavior in BBS mutants | Blacque et al.: CHE-2::GFP localizes to the transition zone and along axonemes; in bbs-7/8 mutants CHE-2 shows abnormal accumulations at mid/distal axoneme regions. | Cilium length reported 1.77 ± 0.71 μm (n = 50) | C. elegans amphid/phasmid cilia; BBS mutant background | (blacque2004lossofc. pages 5-7) | https://doi.org/10.1101/gad.1194004 | Jul 2004 |
| Anterograde motor velocities & Dyf/chemotaxis context | Inglis (review): Two anterograde kinesin-2 motors (kinesin-II and OSM-3) cooperate to drive IFT; IFT mutants produce Dyf and chemotaxis phenotypes. | kinesin-II ≈ 0.5 μm/s; OSM-3 ≈ 1.2 μm/s; combined/intermediate ≈ 0.7 μm/s | C. elegans IFT dynamics and behavioral phenotypes | (inglis2009intraflagellartransportin pages 28-33) | (no DOI available in excerpt) | 2009 |
| IFT-B architecture: IFT80 in IFT-B2 | Lacey et al.: Cryo-ET models place IFT80 at the center of the IFT-B2 subcomplex; IFT80 organizes core IFT-B2 architecture and provides lateral interfaces that stabilize repeats upon polymerization. | EMDB maps: EMD-15977/15978/15979; PDB models: 8BD7, 8BDA | In situ cryo-ET of anterograde IFT trains (Chlamydomonas; conserved architecture) | (lacey2023themolecularstructure pages 12-18) | https://doi.org/10.1038/s41594-022-00905-5 | Jan 2023 |
| Biochemically validated 15‑subunit IFT‑B model | Petriman et al.: An AlphaFold-guided 15‑subunit IFT‑B structural model was biochemically validated (crosslink‑MS, SAXS) and places IFT80 within the IFT‑B assembly to explain interfaces. | 15-subunit model; crosslinking/MS and SAXS validation reported | Reconstituted IFT-B complexes (structural + biochemical validation) | (lacey2023themolecularstructure pages 12-18) | https://doi.org/10.15252/embj.2022112440 | Nov 2022 |
| Dynein-2 tethering via IFT80 TPR | Mukhopadhyay et al.: Dynein-2 intermediate chain WDR60 N-terminal extension contacts the IFT80 TPR and the IFT54 CH domain, suggesting IFT80 contributes to tethering dynein‑2 to the IFT-B polymer. | Cryo-EM structure reported at ~3.9 Å resolution for dynein-2 intermediate chain interactions | Mammalian dynein-2 / IFT-B structural analysis with conserved interface implications | (mukhopadhyay2024structureandtethering pages 9-11) | https://doi.org/10.1038/s44318-024-00060-1 | Mar 2024 |

Table: Compact, citable summary of experimental and structural evidence for C. elegans CHE-2 (IFT80), showing identity, localization, mutant phenotypes, measured IFT velocities, and recent structural insights into IFT‑B and dynein‑2 tethering.

Citations with URLs and publication dates
• Ou et al., Sensory ciliogenesis in C. elegans: assignment of IFT components into distinct modules. Mol Biol Cell. May 2007. https://doi.org/10.1091/mbc.e06-09-0805 (ou2007sensoryciliogenesisin pages 5-6).
• Jensen et al., Localization of a guanylyl cyclase to chemosensory cilia requires DAF‑25. PLoS Genet. Nov 2010. https://doi.org/10.1371/journal.pgen.1001199 (jensen2010localizationofa pages 5-8).
• Blacque et al., Loss of C. elegans BBS‑7 and BBS‑8 results in cilia defects and compromised IFT. Genes Dev. Jul 2004. https://doi.org/10.1101/gad.1194004 (blacque2004lossofc. pages 5-7).
• Inglis, Intraflagellar transport in C. elegans: identification of novel proteins and behavioural functions. 2009. (URL not present in excerpt) (inglis2009intraflagellartransportin pages 28-33).
• Lacey et al., The molecular structure of IFT‑A and IFT‑B in anterograde IFT trains. Nat Struct Mol Biol. Jan 2023. https://doi.org/10.1038/s41594-022-00905-5 (lacey2023themolecularstructure pages 1-2, lacey2023themolecularstructure pages 3-4, lacey2023themolecularstructure pages 8-9).
• Petriman et al., Biochemically validated structural model of the 15‑subunit IFT‑B complex. EMBO J. Nov 2022. https://doi.org/10.15252/embj.2022112440 (lacey2023themolecularstructure pages 12-18).
• Mukhopadhyay et al., Structure and tethering mechanism of dynein‑2 intermediate chains in IFT. EMBO J. Mar 2024. https://doi.org/10.1038/s44318-024-00060-1 (mukhopadhyay2024structureandtethering pages 9-11).

Conclusion
All mandatory verification criteria are satisfied. CHE‑2 in C. elegans is the IFT80 ortholog with WD40/TPR domains, positioned centrally in the IFT‑B2 lobe where it scaffolds IFT‑B polymerization and contributes to dynein‑2 tethering. In vivo, CHE‑2 localizes to basal bodies and axonemes and moves with canonical anterograde IFT velocities; che‑2 loss causes Dyf and chemotaxis defects consistent with a primary role in sensory ciliogenesis and IFT (lacey2023themolecularstructure pages 3-4, lacey2023themolecularstructure pages 1-2, lacey2023themolecularstructure pages 12-18, jensen2010localizationofa pages 5-8, ou2007sensoryciliogenesisin pages 5-6, inglis2009intraflagellartransportin pages 28-33).

References

(ou2007sensoryciliogenesisin pages 5-6): Guangshuo Ou, Makato Koga, Oliver E. Blacque, Takashi Murayama, Yasumi Ohshima, Jenny C. Schafer, Chunmei Li, Bradley K. Yoder, Michel R. Leroux, and Jonathan M. Scholey. Sensory ciliogenesis in caenorhabditis elegans: assignment of ift components into distinct modules based on transport and phenotypic profiles. Molecular biology of the cell, 18 5:1554-69, May 2007. URL: https://doi.org/10.1091/mbc.e06-09-0805, doi:10.1091/mbc.e06-09-0805. This article has 120 citations and is from a domain leading peer-reviewed journal.
(inglis2009intraflagellartransportin pages 28-33): PN Inglis. Intraflagellar transport in caenorhabditis elegans: identification of novel proteins and behavioural functions. Unknown journal, 2009.
(lacey2023themolecularstructure pages 3-4): Samuel E. Lacey, Helen E. Foster, and Gaia Pigino. The molecular structure of ift-a and ift-b in anterograde intraflagellar transport trains. Nature Structural & Molecular Biology, 30:584-593, Jan 2023. URL: https://doi.org/10.1038/s41594-022-00905-5, doi:10.1038/s41594-022-00905-5. This article has 101 citations and is from a highest quality peer-reviewed journal.
(lacey2023themolecularstructure pages 1-2): Samuel E. Lacey, Helen E. Foster, and Gaia Pigino. The molecular structure of ift-a and ift-b in anterograde intraflagellar transport trains. Nature Structural & Molecular Biology, 30:584-593, Jan 2023. URL: https://doi.org/10.1038/s41594-022-00905-5, doi:10.1038/s41594-022-00905-5. This article has 101 citations and is from a highest quality peer-reviewed journal.
(jensen2010localizationofa pages 5-8): Victor L. Jensen, Nathan J. Bialas, Sharon L. Bishop-Hurley, Laurie L. Molday, Katarzyna Kida, Phuong Anh T. Nguyen, Oliver E. Blacque, Robert S. Molday, Michel R. Leroux, and Donald L. Riddle. Localization of a guanylyl cyclase to chemosensory cilia requires the novel ciliary mynd domain protein daf-25. PLoS Genetics, 6:e1001199, Nov 2010. URL: https://doi.org/10.1371/journal.pgen.1001199, doi:10.1371/journal.pgen.1001199. This article has 29 citations and is from a domain leading peer-reviewed journal.
(blacque2004lossofc. pages 5-7): Oliver E. Blacque, Michael J. Reardon, Chunmei Li, Jonathan McCarthy, Moe R. Mahjoub, Stephen J. Ansley, Jose L. Badano, Allan K. Mah, Philip L. Beales, William S. Davidson, Robert C. Johnsen, Mark Audeh, Ronald H.A. Plasterk, David L. Baillie, Nicholas Katsanis, Lynne M. Quarmby, Stephen R. Wicks, and Michel R. Leroux. Loss of c. elegans bbs-7 and bbs-8 protein function results in cilia defects and compromised intraflagellar transport. Genes & development, 18 13:1630-42, Jul 2004. URL: https://doi.org/10.1101/gad.1194004, doi:10.1101/gad.1194004. This article has 463 citations and is from a highest quality peer-reviewed journal.
(lacey2023themolecularstructure pages 12-18): Samuel E. Lacey, Helen E. Foster, and Gaia Pigino. The molecular structure of ift-a and ift-b in anterograde intraflagellar transport trains. Nature Structural & Molecular Biology, 30:584-593, Jan 2023. URL: https://doi.org/10.1038/s41594-022-00905-5, doi:10.1038/s41594-022-00905-5. This article has 101 citations and is from a highest quality peer-reviewed journal.
(mukhopadhyay2024structureandtethering pages 9-11): Aakash G Mukhopadhyay, Katerina Toropova, Lydia Daly, Jennifer N Wells, Laura Vuolo, Miroslav Mladenov, Marian Seda, Dagan Jenkins, David J Stephens, and Anthony J Roberts. Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport. The EMBO Journal, 43:1257-1272, Mar 2024. URL: https://doi.org/10.1038/s44318-024-00060-1, doi:10.1038/s44318-024-00060-1. This article has 11 citations.
(lacey2023themolecularstructure pages 8-9): Samuel E. Lacey, Helen E. Foster, and Gaia Pigino. The molecular structure of ift-a and ift-b in anterograde intraflagellar transport trains. Nature Structural & Molecular Biology, 30:584-593, Jan 2023. URL: https://doi.org/10.1038/s41594-022-00905-5, doi:10.1038/s41594-022-00905-5. This article has 101 citations and is from a highest quality peer-reviewed journal.

Citations

lacey2023themolecularstructure pages 3-4
jensen2010localizationofa pages 5-8
inglis2009intraflagellartransportin pages 28-33
lacey2023themolecularstructure pages 12-18
mukhopadhyay2024structureandtethering pages 9-11
lacey2023themolecularstructure pages 1-2
ou2007sensoryciliogenesisin pages 5-6
lacey2023themolecularstructure pages 8-9
https://doi.org/10.1091/mbc.e06-09-0805
https://doi.org/10.1371/journal.pgen.1001199
https://doi.org/10.1101/gad.1194004
https://doi.org/10.1038/s41594-022-00905-5
https://doi.org/10.15252/embj.2022112440
https://doi.org/10.1038/s44318-024-00060-1
https://doi.org/10.1091/mbc.e06-09-0805,
https://doi.org/10.1038/s41594-022-00905-5,
https://doi.org/10.1371/journal.pgen.1001199,
https://doi.org/10.1101/gad.1194004,
https://doi.org/10.1038/s44318-024-00060-1,

📄 View Raw YAML

id: G5EGF0
gene_symbol: che-2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: CHE-2 is the C. elegans ortholog of vertebrate IFT80, a WD40 
  repeat-containing protein that is a core component of the intraflagellar 
  transport particle B (IFT-B) complex. CHE-2 is essential for the assembly and 
  maintenance of sensory cilia in C. elegans. The protein localizes to sensory 
  cilia where it participates in anterograde intraflagellar transport, carrying 
  cargo proteins from the base to the tip of cilia. che-2 mutants exhibit 
  severely truncated cilia, chemotaxis defects, and dye-filling defects 
  characteristic of cilium structure mutants. The protein acts cell-autonomously
  in ciliated sensory neurons for proper cilium formation and sensory function.
existing_annotations:
  - term:
      id: GO:0060271
      label: cilium assembly
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CHE-2 is essential for cilium assembly. PMID:10518500 
        demonstrates that che-2 mutants have extremely short cilia with abnormal
        posterior projection, and that cilium extension fails during development
        in these mutants. The IBA annotation based on phylogenetic inference 
        from the IFT80 orthology group is well-supported by direct experimental 
        evidence.
      action: ACCEPT
      reason: Core function strongly supported by literature. PMID:10518500 
        shows che-2 mutants have severely defective cilia that remain short 
        throughout development. Expression of che-2 can rescue cilium morphology
        even at adult stage, demonstrating its essential role in cilium 
        assembly.
      supported_by:
        - reference_id: PMID:10518500
          supporting_text: These mutants have extremely short cilia with an 
            abnormal posterior projection, and show defects in behaviors that 
            are mediated by ciliated sensory neurons.
        - reference_id: PMID:10518500
          supporting_text: Using green fluorescent protein, we found that the 
            extension of cilia in wild-type animals took place at the late 
            embryonic stage, whereas the cilia of che-2 mutant animals remained 
            always short during development.
        - reference_id: file:worm/che-2/che-2-deep-research-falcon.md
          supporting_text: 'model: Edison Scientific Literature'
  - term:
      id: GO:0005929
      label: cilium
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CHE-2 localizes to cilia as demonstrated by GFP tagging 
        experiments in PMID:10518500. This IBA annotation is phylogenetically 
        inferred and consistent with experimental localization data showing 
        CHE-2::GFP in sensory cilia.
      action: ACCEPT
      reason: Localization to cilium is directly demonstrated experimentally. 
        CHE-2-tagged GFP localizes to cilia of almost all ciliated sensory 
        neurons (PMID:10518500).
      supported_by:
        - reference_id: PMID:10518500
          supporting_text: CHE-2-tagged green fluorescent protein is localized 
            at the cilia of almost all the ciliated sensory neurons.
  - term:
      id: GO:0030992
      label: intraciliary transport particle B
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CHE-2/IFT80 is a well-established component of the IFT-B complex.
        This is supported by ComplexPortal annotation (CPX-1290) and extensive 
        literature on IFT-B composition. PMID:22922713 provides detailed 
        mechanistic evidence showing that IFT-B components including CHE-2 
        orthologs move together during anterograde transport.
      action: ACCEPT
      reason: Core structural function as IFT-B component is well-established 
        through phylogenetic conservation and direct biochemical evidence. 
        UniProt entry references ComplexPortal CPX-1290 (Intraflagellar 
        transport complex B). The WD40 domain architecture of CHE-2 is 
        characteristic of IFT-B components.
      supported_by:
        - reference_id: PMID:22922713
          supporting_text: Similar to OSM-6, in dyf-2(jhu616), all other IFT-B 
            components examined also showed active anterograde movements, but 
            lost most of the retrograde IFT movements and accumulate at the 
            ciliary tip
  - term:
      id: GO:0005929
      label: cilium
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: IEA annotation based on UniProt subcellular location vocabulary 
        mapping. This is consistent with but less specific than the IBA 
        annotation for the same term.
      action: ACCEPT
      reason: Redundant with IBA annotation but acceptable as independent 
        evidence line. The UniProt entry explicitly states subcellular location 
        as cilium.
      supported_by:
        - reference_id: UniProt:G5EGF0
          supporting_text: 'SUBCELLULAR LOCATION: Cell projection, cilium'
  - term:
      id: GO:0005929
      label: cilium
    evidence_type: NAS
    original_reference_id: PMID:28479320
    review:
      summary: NAS annotation from ComplexPortal referencing a study on 
        dynein-driven retrograde IFT. The paper discusses IFT-B components 
        including CHE-2 orthologs in the context of ciliary transport.
      action: ACCEPT
      reason: Consistent with other cilium localization annotations. While NAS 
        is weaker evidence than IDA, it is supported by the broader literature 
        context.
      supported_by:
        - reference_id: PMID:28479320
          supporting_text: Disruption of the dynein-2 tail domain, light 
            intermediate chain, or intraflagellar transport (IFT)-B complex 
            abolishes dynein-2's ciliary localization, revealing their important
            roles in ciliary entry of dynein-2
  - term:
      id: GO:0042073
      label: intraciliary transport
    evidence_type: NAS
    original_reference_id: PMID:28479320
    review:
      summary: CHE-2 as an IFT-B component participates in intraciliary 
        transport. PMID:28479320 focuses on retrograde IFT but discusses the 
        overall IFT machinery including IFT-B. PMID:22922713 provides more 
        detailed evidence of CHE-2 orthologs' IFT movement.
      action: MODIFY
      reason: The annotation is correct but could be more specific. CHE-2/IFT80 
        is primarily involved in anterograde transport as part of the IFT-B 
        complex. Consider using GO:0035720 (intraciliary anterograde transport) 
        for greater specificity.
      proposed_replacement_terms:
        - id: GO:0035720
          label: intraciliary anterograde transport
      supported_by:
        - reference_id: PMID:22922713
          supporting_text: Similar to OSM-6, in dyf-2(jhu616), all other IFT-B 
            components examined also showed active anterograde movements, but 
            lost most of the retrograde IFT movements and accumulate at the 
            ciliary tip
  - term:
      id: GO:0060271
      label: cilium assembly
    evidence_type: NAS
    original_reference_id: PMID:28479320
    review:
      summary: NAS annotation for cilium assembly from ComplexPortal. Redundant 
        with IBA and IMP annotations for the same term but acceptable as 
        additional evidence source.
      action: ACCEPT
      reason: Consistent with IBA and IMP annotations. Cilium assembly is a core
        function of CHE-2.
      supported_by:
        - reference_id: PMID:10518500
          supporting_text: Hence, the abnormal posterior projection is due to 
            the inability of cilia to extend, rather than degeneration of cilia 
            once correctly formed
  - term:
      id: GO:0003674
      label: molecular_function
    evidence_type: ND
    original_reference_id: GO_REF:0000015
    review:
      summary: ND (No biological Data) annotation indicates no specific 
        molecular function has been experimentally determined. While CHE-2 is a 
        structural component of IFT-B, it does not appear to have enzymatic 
        activity - its function is primarily as a scaffold/adaptor.
      action: ACCEPT
      reason: Appropriate use of ND. CHE-2 has no known enzymatic or catalytic 
        activity; it functions as a structural component of the IFT-B complex 
        through protein-protein interactions mediated by its WD40 repeats.
      supported_by:
        - reference_id: PMID:10518500
          supporting_text: The che-2 gene encodes a new member of the WD40 
            protein family, suggesting that it acts in protein-protein 
            interaction.
  - term:
      id: GO:0090325
      label: regulation of locomotion involved in locomotory behavior
    evidence_type: IGI
    original_reference_id: PMID:26434723
    review:
      summary: This annotation relates to body size regulation through cGMP 
        signaling in sensory cilia. The study shows that cilium structure 
        mutants (including che-2) have small body size and locomotion defects 
        due to disrupted sensory signaling.
      action: KEEP_AS_NON_CORE
      reason: This is a downstream consequence of cilium structure defects 
        rather than a direct function of CHE-2. The effect on locomotion is 
        indirect, mediated through disrupted sensory perception in defective 
        cilia. Not a core function.
      supported_by:
        - reference_id: PMID:26434723
          supporting_text: The body size of Caenorhabditis elegans is thought to
            be controlled by sensory inputs because many mutants with sensory 
            cilium structure defects exhibit small body size.
  - term:
      id: GO:0090326
      label: positive regulation of locomotion involved in locomotory behavior
    evidence_type: IMP
    original_reference_id: PMID:26434723
    review:
      summary: IMP annotation for locomotion regulation based on che-2 mutant 
        phenotype. The small body size and reduced locomotion in che-2 mutants 
        is secondary to cilium structure defects affecting sensory perception.
      action: KEEP_AS_NON_CORE
      reason: Pleiotropic effect of cilium defects. CHE-2's primary role is in 
        cilium assembly and IFT; the locomotory phenotype is an indirect 
        consequence of sensory defects.
      supported_by:
        - reference_id: PMID:26434723
          supporting_text: the defects in the sensory cilium structure may 
            disturb the balanced control of the cGMP level
  - term:
      id: GO:0040014
      label: regulation of multicellular organism growth
    evidence_type: IGI
    original_reference_id: PMID:26434723
    review:
      summary: Body size regulation is affected in che-2 mutants due to 
        disrupted cGMP signaling in defective sensory cilia. This is a 
        downstream phenotype of the cilium structure defect.
      action: KEEP_AS_NON_CORE
      reason: Secondary phenotype resulting from defective sensory cilia. The 
        primary function of CHE-2 is cilium assembly, not growth regulation per 
        se.
      supported_by:
        - reference_id: PMID:26434723
          supporting_text: many mutants with sensory cilium structure defects 
            exhibit small body size
  - term:
      id: GO:0040018
      label: positive regulation of multicellular organism growth
    evidence_type: IMP
    original_reference_id: PMID:26434723
    review:
      summary: IMP annotation based on small body size phenotype of che-2 
        mutants. The reduced body size is a consequence of disrupted sensory 
        signaling through defective cilia.
      action: KEEP_AS_NON_CORE
      reason: Indirect effect of cilium structure defects on sensory-mediated 
        growth regulation. Not a direct molecular function of CHE-2.
      supported_by:
        - reference_id: PMID:26434723
          supporting_text: the cGMP level is precisely controlled by GCY-12 and 
            PDE-2 to determine body size through EGL-4, and the defects in the 
            sensory cilium structure may disturb the balanced control of the 
            cGMP level
  - term:
      id: GO:0006935
      label: chemotaxis
    evidence_type: IMP
    original_reference_id: PMID:7828815
    review:
      summary: che-2 mutants exhibit chemotaxis defects. This study 
        (PMID:7828815) focuses on daf-11 and daf-21 mutants but references che-2
        as a cilium structure mutant with chemosensory defects. PMID:10208543 
        provides more direct evidence.
      action: KEEP_AS_NON_CORE
      reason: Chemotaxis defect is a consequence of abnormal cilium structure in
        sensory neurons. CHE-2 enables chemotaxis indirectly by being required 
        for proper cilium assembly in chemosensory neurons.
      supported_by:
        - reference_id: PMID:10518500
          supporting_text: These mutants have extremely short cilia with an 
            abnormal posterior projection, and show defects in behaviors that 
            are mediated by ciliated sensory neurons.
  - term:
      id: GO:0060271
      label: cilium assembly
    evidence_type: IGI
    original_reference_id: PMID:1732156
    review:
      summary: IGI annotation based on genetic interaction studies of dauer 
        formation. This paper places che-2 in the cilium-structure gene class 
        that is epistatic to daf-11 for dauer formation, supporting its role in 
        cilium assembly.
      action: ACCEPT
      reason: Supports the core function of CHE-2 in cilium assembly. The 
        genetic epistasis analysis places che-2 among genes required for cilium 
        structure.
      supported_by:
        - reference_id: PMID:1732156
          supporting_text: Dauer-defective mutations in nine genes cause 
            structurally defective chemosensory cilia, thereby blocking 
            chemosensation
  - term:
      id: GO:0040024
      label: dauer larval development
    evidence_type: IGI
    original_reference_id: PMID:11677050
    review:
      summary: che-2 mutants affect dauer formation through their role in cilium
        structure. The study places che-2 in the genetic pathway between daf-11 
        and daf-7 for dauer control.
      action: KEEP_AS_NON_CORE
      reason: Dauer development phenotype is secondary to cilium structure 
        defects. che-2 mutants affect dauer formation because sensory cilia are 
        required for environmental sensing that triggers dauer entry. Not a 
        direct function of CHE-2.
      supported_by:
        - reference_id: PMID:11677050
          supporting_text: cilium-related genes che-2 and che-3 are placed 
            between daf-11 and daf-7, in the genetic pathway controlling dauer 
            formation
  - term:
      id: GO:0036064
      label: ciliary basal body
    evidence_type: IDA
    original_reference_id: PMID:22922713
    review:
      summary: IDA annotation for localization to ciliary basal body. 
        PMID:22922713 shows that IFT-B components accumulate at the ciliary base
        in certain mutant backgrounds, and that the BBSome assembles IFT 
        complexes at the ciliary base.
      action: ACCEPT
      reason: CHE-2/IFT80 as an IFT-B component is assembled at the ciliary 
        basal body before transport into the cilium. The ciliary base is where 
        IFT particles are organized.
      supported_by:
        - reference_id: PMID:22922713
          supporting_text: the BBSome (refs 3, 4), a group of conserved proteins
            affected in human Bardet-Biedl syndrome(5) (BBS), assembles IFT 
            complexes at the ciliary base, then binds to the anterograde IFT 
            particle
  - term:
      id: GO:0097730
      label: non-motile cilium
    evidence_type: IDA
    original_reference_id: PMID:10518500
    review:
      summary: C. elegans sensory cilia are non-motile (primary) cilia. 
        CHE-2::GFP localizes to these sensory cilia as directly demonstrated in 
        PMID:10518500.
      action: ACCEPT
      reason: Appropriate specific localization annotation. C. elegans sensory 
        neurons have non-motile cilia, and CHE-2 localizes to these structures.
      supported_by:
        - reference_id: PMID:10518500
          supporting_text: CHE-2-tagged green fluorescent protein is localized 
            at the cilia of almost all the ciliated sensory neurons.
  - term:
      id: GO:0030512
      label: negative regulation of transforming growth factor beta receptor 
        signaling pathway
    evidence_type: IGI
    original_reference_id: PMID:11677050
    review:
      summary: This annotation relates to the role of che-2 in the dauer pathway
        where it affects DAF-7/TGF-beta expression. The genetic analysis places 
        che-2 between daf-11 and daf-7 in regulating TGF-beta signaling for 
        dauer formation.
      action: MARK_AS_OVER_ANNOTATED
      reason: This is an indirect effect mediated through cilium structure 
        defects affecting sensory perception of environmental cues that regulate
        TGF-beta signaling. CHE-2 does not directly regulate TGF-beta signaling;
        it enables the sensory apparatus that perceives signals controlling this
        pathway.
      supported_by:
        - reference_id: PMID:11677050
          supporting_text: cilium-related genes che-2 and che-3 are placed 
            between daf-11 and daf-7, in the genetic pathway controlling dauer 
            formation
  - term:
      id: GO:0006935
      label: chemotaxis
    evidence_type: IMP
    original_reference_id: PMID:10208543
    review:
      summary: che-2 mutants lack avoidance behavior to Cd2+ and Cu2+. The study
        shows that mutants with structural defects in ciliated neurons, 
        including che-2, do not show chemotactic avoidance responses.
      action: KEEP_AS_NON_CORE
      reason: Chemotaxis defect is downstream of cilium structure defect. CHE-2 
        is required for cilium assembly in chemosensory neurons; without proper 
        cilia, these neurons cannot function in chemotaxis.
      supported_by:
        - reference_id: PMID:10208543
          supporting_text: Mutants that have structural defects in ciliated 
            neurons (che-2 and osm-3) as well as worms with three laser-operated
            neurons (ADL, ASE, and ASH), showed no avoidance behavior from Cd2+ 
            and Cu2+
  - term:
      id: GO:0060271
      label: cilium assembly
    evidence_type: IMP
    original_reference_id: PMID:10518500
    review:
      summary: IMP annotation directly demonstrating CHE-2 requirement for 
        cilium assembly. This is the primary reference establishing CHE-2 
        function, showing that mutants have truncated cilia and that rescue 
        restores cilium morphology.
      action: ACCEPT
      reason: Core function with strong experimental support. This is the 
        definitive paper on CHE-2 function demonstrating its essential role in 
        cilium formation.
      supported_by:
        - reference_id: PMID:10518500
          supporting_text: Expression of che-2 in a subset of sensory neurons of
            a che-2 mutant by using a heterologous promoter resulted in 
            restoration of the functions and cilium morphology of only the 
            che-2-expressing neurons.
        - reference_id: PMID:10518500
          supporting_text: Expression of che-2 in a che-2 mutant under a heat 
            shock promoter showed that the extension of cilia, surprisingly, can
            occur even at the adult stage, and that such cilia can function 
            apparently normally in behavior.
  - term:
      id: GO:0035720
      label: intraciliary anterograde transport
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CHE-2/IFT80 is a core IFT-B component specifically involved in 
        anterograde transport. PMID:22922713 shows IFT-B components move in the 
        anterograde direction.
      action: NEW
      reason: More specific than GO:0042073 (intraciliary transport). IFT-B is 
        specifically the anterograde transport machinery while IFT-A is 
        retrograde. This term better captures CHE-2's molecular function.
      supported_by:
        - reference_id: PMID:22922713
          supporting_text: Similar to OSM-6, in dyf-2(jhu616), all other IFT-B 
            components examined also showed active anterograde movements, but 
            lost most of the retrograde IFT movements and accumulate at the 
            ciliary tip
references:
  - id: GO_REF:0000015
    title: Use of the ND evidence code for Gene Ontology (GO) terms
    findings: []
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings:
      - statement: CHE-2 is orthologous to vertebrate IFT80 based on PANTHER 
          phylogenetic analysis
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular 
      Location vocabulary mapping
    findings: []
  - id: PMID:10208543
    title: Sensing of cadmium and copper ions by externally exposed ADL, ASE, 
      and ASH neurons elicits avoidance response in Caenorhabditis elegans.
    findings:
      - statement: che-2 mutants lack chemotactic avoidance to Cd2+ and Cu2+ due
          to structural defects in ciliated neurons
        supporting_text: Mutants that have structural defects in ciliated 
          neurons (che-2 and osm-3) as well as worms with three laser-operated 
          neurons (ADL, ASE, and ASH), showed no avoidance behavior from Cd2+ 
          and Cu2+
  - id: PMID:10518500
    title: A novel WD40 protein, CHE-2, acts cell-autonomously in the formation 
      of C. elegans sensory cilia.
    findings:
      - statement: CHE-2 is a WD40 repeat protein essential for cilium formation
        supporting_text: The che-2 gene encodes a new member of the WD40 protein
          family, suggesting that it acts in protein-protein interaction.
      - statement: che-2 mutants have extremely short cilia with abnormal 
          posterior projection
        supporting_text: These mutants have extremely short cilia with an 
          abnormal posterior projection, and show defects in behaviors that are 
          mediated by ciliated sensory neurons.
      - statement: CHE-2::GFP localizes to cilia of almost all ciliated sensory 
          neurons
        supporting_text: CHE-2-tagged green fluorescent protein is localized at 
          the cilia of almost all the ciliated sensory neurons.
      - statement: CHE-2 acts cell-autonomously in cilium formation
        supporting_text: Expression of che-2 in a subset of sensory neurons of a
          che-2 mutant by using a heterologous promoter resulted in restoration 
          of the functions and cilium morphology of only the che-2-expressing 
          neurons. Thus, che-2 acts cell-autonomously.
      - statement: Both WD40 repeats and C-terminal domain are required for 
          function
        supporting_text: Analysis of mutation sites showed that both the 
          amino-terminal WD40 repeats and the carboxyl-terminal non-WD40 domain 
          are necessary for the CHE-2 function.
      - statement: Cilium extension can be rescued even at adult stage by che-2 
          expression
        supporting_text: Expression of che-2 in a che-2 mutant under a heat 
          shock promoter showed that the extension of cilia, surprisingly, can 
          occur even at the adult stage, and that such cilia can function 
          apparently normally in behavior.
  - id: PMID:11677050
    title: DAF-7/TGF-beta expression required for the normal larval development 
      in C. elegans is controlled by a presumed guanylyl cyclase DAF-11.
    findings:
      - statement: che-2 is placed in genetic pathway between daf-11 and daf-7 
          for dauer formation
        supporting_text: cilium-related genes che-2 and che-3 are placed between
          daf-11 and daf-7, in the genetic pathway controlling dauer formation
      - statement: Cilium-related genes affect TGF-beta signaling indirectly 
          through sensory function
        supporting_text: Expression of daf-11 cDNA by cell specific promoters 
          suggests that daf-11 acts cell autonomously in ASI chemosensory 
          neurons for daf-7 expression.
  - id: PMID:1732156
    title: Genetic analysis of chemosensory control of dauer formation in 
      Caenorhabditis elegans.
    findings:
      - statement: che-2 is one of nine cilium-structure genes affecting dauer 
          formation
        supporting_text: Dauer-defective mutations in nine genes cause 
          structurally defective chemosensory cilia, thereby blocking 
          chemosensation
      - statement: Cilium structure mutations block chemosensation required for 
          dauer regulation
        supporting_text: Dauer-defective mutations in nine genes cause 
          structurally defective chemosensory cilia, thereby blocking 
          chemosensation
  - id: PMID:22922713
    title: The BBSome controls IFT assembly and turnaround in cilia.
    findings:
      - statement: IFT-B components show active anterograde movement
        supporting_text: Similar to OSM-6, in dyf-2(jhu616), all other IFT-B 
          components examined also showed active anterograde movements, but lost
          most of the retrograde IFT movements and accumulate at the ciliary tip
      - statement: The BBSome assembles IFT complexes at the ciliary base
        supporting_text: the BBSome (refs 3, 4), a group of conserved proteins 
          affected in human Bardet-Biedl syndrome(5) (BBS), assembles IFT 
          complexes at the ciliary base, then binds to the anterograde IFT 
          particle
      - statement: IFT-A and IFT-B subcomplexes associate during anterograde 
          transport
        supporting_text: IFT-A component CHE-11 and IFT-B component IFT-20 
          showed fluorescence complementation in either wild-type or 
          dyf-2(jhu616), indicative of the association between IFT-A and IFT-B 
          subcomplexes
      - statement: IFT-B components accumulate at cilia tip when turnaround is 
          defective
        supporting_text: all other IFT-B components examined also showed active 
          anterograde movements, but lost most of the retrograde IFT movements 
          and accumulate at the ciliary tip
  - id: PMID:26434723
    title: The Importance of cGMP Signaling in Sensory Cilia for Body Size 
      Regulation in Caenorhabditis elegans.
    findings:
      - statement: Cilium structure mutants including che-2 exhibit small body 
          size
        supporting_text: The body size of Caenorhabditis elegans is thought to 
          be controlled by sensory inputs because many mutants with sensory 
          cilium structure defects exhibit small body size
      - statement: Body size regulation depends on cGMP signaling in sensory 
          cilia
        supporting_text: the cGMP level is precisely controlled by GCY-12 and 
          PDE-2 to determine body size through EGL-4
      - statement: Cilium defects disturb balanced control of cGMP levels
        supporting_text: the defects in the sensory cilium structure may disturb
          the balanced control of the cGMP level
  - id: PMID:28479320
    title: Dynein-Driven Retrograde Intraflagellar Transport Is Triphasic in C. 
      elegans Sensory Cilia.
    findings:
      - statement: IFT-B complex is required for dynein-2 ciliary localization
        supporting_text: Disruption of the dynein-2 tail domain, light 
          intermediate chain, or intraflagellar transport (IFT)-B complex 
          abolishes dynein-2's ciliary localization, revealing their important 
          roles in ciliary entry of dynein-2
      - statement: IFT-A and IFT-B function in ciliary transport
        supporting_text: our affinity purification and genetic analyses show 
          that IFT-A subunits IFT-139 and IFT-43 function redundantly to promote
          dynein-2 motility
  - id: PMID:7828815
    title: Multiple chemosensory defects in daf-11 and daf-21 mutants of 
      Caenorhabditis elegans.
    findings:
      - statement: daf-11 and daf-21 mutants have chemosensory defects including
          in chemotaxis
        supporting_text: daf-11 and daf-21 mutants are not defective in 
          avoidance of certain non-volatile repellents, but are defective in 
          taxis to non-volatile attractants
  - id: file:worm/che-2/che-2-deep-research-falcon.md
    title: Deep research report on che-2
    findings: []
core_functions:
  - description: CHE-2/IFT80 is a core structural component of the IFT-B 
      complex, established through phylogenetic conservation and direct 
      biochemical evidence. UniProt references ComplexPortal CPX-1290.
    molecular_function:
      id: GO:0003674
      label: molecular_function
    locations:
      - id: GO:0030992
        label: intraciliary transport particle B
      - id: GO:0005929
        label: cilium
    directly_involved_in:
      - id: GO:0060271
        label: cilium assembly
      - id: GO:0035720
        label: intraciliary anterograde transport
proposed_new_terms: []
suggested_questions:
  - question: Does CHE-2 have any cargo-binding specificity within the IFT-B 
      complex?
  - question: What is the structural basis for CHE-2 interaction with other 
      IFT-B components?
  - question: Are there tissue-specific differences in CHE-2 requirement for 
      different sensory cilia types?
suggested_experiments:
  - description: Determine CHE-2 interaction partners within IFT-B using co-IP 
      and mass spectrometry
  - description: Test which ciliary cargos depend specifically on CHE-2 for 
      transport
  - description: Examine CHE-2 dynamics during IFT using live imaging with 
      improved temporal resolution
tags:
  - caeel-ciliopathy

che-2

Gene Description

Existing Annotations Review

Core Functions

CHE-2/IFT80 is a core structural component of the IFT-B complex, established through phylogenetic conservation and direct biochemical evidence. UniProt references ComplexPortal CPX-1290.

References

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Deep Research Falcon

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Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

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

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Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

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

Research Target:

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