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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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.
The che-11 gene (ORF name C27A7.4; UniProt P90757) of Caenorhabditis elegans encodes a WD-repeat- and TPR-domain-containing protein that is the ortholog of human intraflagellar transport protein 140 (IFT140). Multiple independent studies have confirmed this orthology based on sequence conservation, domain architecture, and functional complementation experiments (scheidel2018intraflagellartransportcomplex pages 1-3, blacque2006thewdrepeatcontaining pages 6-8, jensen2016wholeorganismdevelopmentalexpression pages 8-9). The gene was originally identified through forward genetic screens for chemotaxis-defective mutants in C. elegans, hence the "che" designation (scheidel2018intraflagellartransportcomplex pages 1-3).
The following table summarizes the key properties of CHE-11/IFT140:
| Property | Description |
|---|---|
| Gene name | che-11; the provided UniProt annotation and C. elegans literature align che-11 with the IFT140 ortholog in sensory cilia (scheidel2018intraflagellartransportcomplex pages 1-3, brocalruiz2023forkheadtranscriptionfactor pages 3-5) |
| Protein name | CHE-11 / IFT-140; a WD-repeat/TPR-containing intraflagellar transport protein and core IFT-A subunit (blacque2006thewdrepeatcontaining pages 6-8, picariello2019aglobalanalysis pages 4-6) |
| UniProt ID | P90757 (provided target identity) |
| Organism | Caenorhabditis elegans (worm) (scheidel2018intraflagellartransportcomplex pages 1-3, brocalruiz2023forkheadtranscriptionfactor pages 3-5) |
| ORF name | C27A7.4 (provided target identity) |
| Human ortholog | IFT140; che-11 is identified as the C. elegans ortholog of mammalian/human IFT140 (scheidel2018intraflagellartransportcomplex pages 1-3, OpenTargets Search: -IFT140) |
| Protein complex | IFT-A core complex; IFT140/CHE-11 belongs to the IFT-A core together with IFT122 and IFT144 (meleppattu2022mechanismofifta pages 3-5, nakayama2018ciliaryproteintrafficking pages 3-3) |
| Key domains | N-terminal WD repeats / β-propeller domains plus C-terminal TPR domains; WD repeats contribute to membrane-associated cargo transport and retrograde transport performance, whereas TPR domains stabilize IFT-A assembly and mediate core subunit interactions (picariello2019aglobalanalysis pages 6-8, picariello2019aglobalanalysis pages 13-15, meleppattu2022mechanismofifta pages 3-5) |
| Molecular function | Structural/adaptor subunit of the IFT-A complex required for retrograde intraflagellar transport and for proper assembly/stability of IFT-A; broader comparative work indicates IFT140-containing IFT-A also specializes in trafficking membrane-associated ciliary cargoes (blacque2006thewdrepeatcontaining pages 6-8, blacque2006thewdrepeatcontaining pages 8-9, picariello2019aglobalanalysis pages 6-8, picariello2019aglobalanalysis pages 1-4) |
| Subcellular localization | Localizes to sensory cilia, including the axoneme and ciliary region visualized in phasmid/amphid neurons; genetic evidence also places IFT-A/CHE-11 function at the transition zone/periciliary gating interface, and in some mutant contexts CHE-11 can become restricted near the transition zone (scheidel2018intraflagellartransportcomplex pages 3-4, efimenko2006caenorhabditiselegansdyf2an pages 6-8, scheidel2018intraflagellartransportcomplex pages 4-6) |
| Expression pattern | Expressed broadly in the ciliated sensory neuron system, with reporter activity in ~30 or more ciliated neurons (brocalruiz2023forkheadtranscriptionfactor pages 3-5) |
| Mutant phenotypes | Truncated/short cilia, defective retrograde IFT with accumulation of IFT material in cilia, dye-filling defects, and chemotaxis/sensory defects; cell-type-specific defects include collapsed AWC cilia and CEP abnormalities (blacque2006thewdrepeatcontaining pages 6-8, jensen2016wholeorganismdevelopmentalexpression pages 8-9, scheidel2018intraflagellartransportcomplex pages 1-3) |
| Transcriptional regulation | Regulated by DAF-19/RFX, with additional cooperative input from FKH-8; che-11 contains validated X-box regulatory elements and retains partial expression in daf-19 mutants, indicating combinatorial control (brocalruiz2023forkheadtranscriptionfactor pages 3-5, brocalruiz2023forkheadtranscriptionfactor pages 2-3) |
| Human disease associations | Human IFT140 is associated with ciliopathies including Mainzer-Saldino syndrome, Jeune syndrome, short-rib thoracic dysplasia, retinitis pigmentosa, and cystic kidney disease / polycystic kidney disease (OpenTargets Search: -IFT140) |
Table: This table summarizes the core identifiers, molecular role, localization, regulation, mutant phenotypes, and human disease relevance of C. elegans che-11/CHE-11. It is useful as a quick reference for the full research report.
CHE-11 functions as a core structural and adaptor subunit of the intraflagellar transport complex A (IFT-A). It is not an enzyme; rather, it serves as a scaffold protein within the IFT-A macromolecular assembly that is essential for retrograde intraflagellar transport (IFT)—the directed movement of protein cargo from the ciliary tip back to the ciliary base (blacque2006thewdrepeatcontaining pages 6-8, blacque2006thewdrepeatcontaining pages 8-9).
The IFT-A complex is a six-subunit assembly organized into two modules. CHE-11/IFT140 resides in the core (A1) subcomplex together with IFT144 (DYF-2 in C. elegans) and IFT122 (DAF-10). The peripheral (A2) module contains IFT139, IFT121, and IFT43 (meleppattu2022mechanismofifta pages 3-5, nakayama2018ciliaryproteintrafficking pages 3-3). Cryo-electron microscopy and integrative modeling studies have revealed that IFT140 and IFT144 form a heterodimer through antiparallel TPR-TPR interactions involving the first five helices of their respective TPR domains, creating a characteristic V-shaped architecture with their tandem β-propeller domains splayed approximately 50 Å apart (meleppattu2022mechanismofifta pages 3-5). IFT122 serves as a linker, bridging the A1 and A2 modules by extending its TPR domain to engage both IFT140 and IFT144 at the apex of the V-shape (meleppattu2022mechanismofifta pages 5-6).
| Subunit Name | C. elegans Ortholog | Subcomplex | Domain Architecture | Key Function |
|---|---|---|---|---|
| IFT140 | CHE-11 | Core / A1 | N-terminal WD repeats / β-propellers plus C-terminal TPR domains | Stabilizes the IFT-A complex, contributes to retrograde IFT, and supports transport of membrane-associated ciliary cargoes (meleppattu2022mechanismofifta pages 3-5, picariello2019aglobalanalysis pages 6-8, picariello2019aglobalanalysis pages 13-15) |
| IFT144 | DYF-2 | Core / A1 | WD repeats / β-propellers plus TPR domains | Forms a heterodimeric core unit with IFT140 through TPR-mediated interactions and helps build the A1 V-shaped architecture (meleppattu2022mechanismofifta pages 3-5, meleppattu2022mechanismofifta pages 5-6) |
| IFT122 | DAF-10 / IFT-122 | Core linker between A1 and A2 | WD repeats / β-propellers plus TPR domains | Bridges the core and peripheral modules; its TPR region extends to contact IFT140 and IFT144, linking A1 and A2 (meleppattu2022mechanismofifta pages 3-5, meleppattu2022mechanismofifta pages 5-6, nakayama2018ciliaryproteintrafficking pages 3-3) |
| IFT139 | IFT-139 | Peripheral / A2 | TPR domains throughout | Peripheral IFT-A component important for peripheral module stability and retrograde IFT-related organization (picariello2019aglobalanalysis pages 4-6, scheidel2018intraflagellartransportcomplex pages 4-6) |
| IFT121 | IFT-121 | Peripheral / A2 | WD repeats / β-propellers plus TPR domains | Peripheral component of A2; interacts with IFT43 and contacts the core via IFT122 (meleppattu2022mechanismofifta pages 5-6, nakayama2018ciliaryproteintrafficking pages 3-3) |
| IFT43 | IFT-43 | Peripheral / A2 | Coiled-coil domain | Peripheral component that directly interacts with IFT121 and supports A2 integrity and localization (nakayama2018ciliaryproteintrafficking pages 3-3, zhu2017functionalexplorationof pages 9-12) |
Table: This table summarizes the six-subunit IFT-A complex with emphasis on the CHE-11/IFT140-containing core module, domain architecture, and inferred functional roles. It is useful for linking the worm che-11 gene to conserved IFT-A assembly and cargo-transport mechanisms.
The CHE-11/IFT140 protein contains two principal functional regions:
N-terminal WD-repeat (β-propeller) domains: Studies in Chlamydomonas reinhardtii using a truncated IFT140 lacking the N-terminal WD repeats demonstrated that these domains are required for proper retrograde IFT velocity, likely by affecting dynein-1b motor activation or IFT train–motor interaction (picariello2019aglobalanalysis pages 13-15). Critically, the WD repeats are also essential for proper trafficking of membrane-associated proteins—including small GTPases, lipid-anchored proteins (myristoylated and geranylgeranylated), and cell signaling components—into cilia (picariello2019aglobalanalysis pages 6-8, picariello2019aglobalanalysis pages 13-15). When the WD repeats are absent, the truncated protein still supports half-length flagella with normal axonemal ultrastructure, but these flagella show dramatic decreases in membrane-associated signaling proteins (picariello2019aglobalanalysis pages 1-4, picariello2019aglobalanalysis pages 17-19).
C-terminal TPR domains: These tetratricopeptide repeat domains are sufficient to stabilize IFT-A complex assembly. Expression of only the TPR region of IFT140 partially rescues IFT-A formation and supports partial flagellar assembly, indicating that the TPR domains mediate the essential protein–protein interactions within the IFT-A core (picariello2019aglobalanalysis pages 13-15, picariello2019aglobalanalysis pages 4-6).
A landmark study by Picariello et al. (2019) using Chlamydomonas IFT140 null mutants revealed a key functional specialization of IFT-A: it is specifically dedicated to importing membrane-associated proteins into cilia, while IFT-B handles the import of axonemal structural proteins (picariello2019aglobalanalysis pages 1-4, picariello2019aglobalanalysis pages 17-19). The IFT-A complex, via IFT140, transports G protein-coupled receptors (GPCRs), Smoothened, rhodopsin/opsin, Arl13b, and various lipid-modified signaling proteins into the ciliary compartment (picariello2019aglobalanalysis pages 17-19). This is accomplished in part through the adaptor protein TULP3, which bridges IFT-A core subunits (including IFT140) and membrane phosphoinositides (nakayama2018ciliaryproteintrafficking pages 3-3).
CHE-11 protein localizes to the sensory cilia of C. elegans ciliated neurons. Using GFP-tagged CHE-11 constructs, the protein has been visualized in both amphid and phasmid sensory cilia, where it undergoes bidirectional IFT—moving anterogradely from the ciliary base to tip and retrogradely from tip to base (scheidel2018intraflagellartransportcomplex pages 3-4). In C. elegans, IFT-A (including CHE-11) travels at the slow speed characteristic of heterotrimeric kinesin-II (~0.5 μm/s) during anterograde transport, while IFT-B moves at faster speeds characteristic of the homodimeric kinesin OSM-3 (blacque2006thewdrepeatcontaining pages 6-8, taschner2016theintraflagellartransport pages 12-13). The BBSome is responsible for holding IFT-A and IFT-B subcomplexes together during transport; in BBS mutant backgrounds, CHE-11/IFT-A and IFT-B separate and move independently at their respective motor speeds (taschner2016theintraflagellartransport pages 12-13, bhogaraju2013intraflagellartransportcomplex pages 6-7).
In dyf-2 (IFT144) mutant backgrounds, CHE-11 protein becomes restricted to the transition zone and is unable to enter the ciliary axoneme, demonstrating the dependence of CHE-11 ciliary entry on other core IFT-A components (efimenko2006caenorhabditiselegansdyf2an pages 6-8).
The primary biological process in which CHE-11 participates is retrograde IFT. Loss of CHE-11 function phenocopies classic retrograde IFT defects: IFT machinery components accumulate within the ciliary axoneme, retrograde motility is severely abrogated, and cilia become truncated (blacque2006thewdrepeatcontaining pages 6-8, blacque2006thewdrepeatcontaining pages 8-9). CHE-11 is also required for proper incorporation of other IFT components—such as IFTA-1—into the IFT machinery. In che-11 mutants, IFTA-1 fails to localize to ciliary structures (blacque2006thewdrepeatcontaining pages 6-8, blacque2006thewdrepeatcontaining pages 8-9).
CHE-11/IFT-140 plays a cell-type-specific role in transition zone (TZ) function. The TZ is a specialized ciliary gate at the base of the cilium that regulates protein entry and exit. Scheidel and Blacque (2018) demonstrated that IFT-A genes differentially regulate TZ gating in C. elegans: while non-core IFT-A genes (IFT-43, IFT-121, IFT-139) control ciliary removal of MKS module proteins, IFT-140 controls the ciliary entry/accumulation of MKS module proteins into cilia in these non-core mutant backgrounds (scheidel2018intraflagellartransportcomplex pages 4-6). IFT-140 also targets the peripheral component IFT-121 to cilia and mediates IFT-139's association with IFT trains (scheidel2018intraflagellartransportcomplex pages 4-6). These findings reveal that IFT-A maintains, rather than initially establishes, TZ restriction of gating proteins.
CHE-11 is essential for cilium formation across all examined cilium types in C. elegans. Mutants display cell-type-specific structural defects: for example, ift-140 mutants show collapsed wing-shaped AWC cilia and abnormal rod-shaped CEP cilia (scheidel2018intraflagellartransportcomplex pages 1-3). The interaction between IFT-A and MKS module components works synergistically to determine cilium structure (scheidel2018intraflagellartransportcomplex pages 1-3).
Because CHE-11 is essential for proper ciliary structure and composition, its loss leads to defective sensory behaviors including chemotaxis defects (hence the gene name "che") and dye-filling defects—a hallmark phenotype of ciliary structural compromise in C. elegans sensory neurons (scheidel2018intraflagellartransportcomplex pages 1-3, blacque2006thewdrepeatcontaining pages 6-8). Additionally, IFT-A's role in transporting membrane-associated signaling receptors implies that CHE-11 is indirectly required for sensory signal transduction through its role in localizing receptors and signaling components to the ciliary membrane (picariello2019aglobalanalysis pages 17-19).
Studies in Chlamydomonas have identified a novel role for IFT-A, including IFT140, in mobilizing ciliary precursors from the cytoplasmic pool to the peri-basal body region prior to their entry into the cilium. In ift140 null mutants, the peri-basal body localization of IFT-A proteins is disrupted, and flagellar regeneration requiring recruitment of preexisting precursors is blocked (zhu2017functionalexplorationof pages 9-12).
The che-11 gene is expressed in essentially all ciliated sensory neurons in C. elegans (~30+ neurons), as shown by reporter gene analysis (brocalruiz2023forkheadtranscriptionfactor pages 3-5). Its expression is regulated in part by the DAF-19/RFX transcription factor, an evolutionarily conserved master regulator of ciliome genes, acting through X-box regulatory elements in the che-11 promoter. Loss of DAF-19 dramatically reduces but does not eliminate che-11 expression, indicating that additional transcription factors cooperate in its regulation (brocalruiz2023forkheadtranscriptionfactor pages 3-5). The Forkhead transcription factor FKH-8 has been identified as an additional direct co-regulator that works synergistically with DAF-19/RFX to control ciliome gene expression, including che-11 (brocalruiz2023forkheadtranscriptionfactor pages 2-3, brocalruiz2023forkheadtranscriptionfactor pages 3-5).
IFT140 is highly conserved across eukaryotes. The human ortholog IFT140 is strongly associated with multiple ciliopathies, as documented by OpenTargets disease-target associations (OpenTargets Search: -IFT140). Mutations in human IFT140 cause Mainzer-Saldino syndrome (characterized by retinitis pigmentosa, cerebellar ataxia, and renal disease), Jeune asphyxiating thoracic dystrophy (short-rib thoracic dysplasia with or without polydactyly), retinitis pigmentosa, and autosomal dominant polycystic kidney disease (OpenTargets Search: -IFT140). The pleiotropic nature of these ciliopathies can be explained by IFT-A's specialized role in transporting membrane-associated signaling proteins into cilia: abnormal levels of these proteins would disrupt multiple ciliary signaling pathways across diverse tissues (picariello2019aglobalanalysis pages 1-4, picariello2019aglobalanalysis pages 17-19).
CHE-11 (UniProt P90757) is the C. elegans ortholog of IFT140, a core structural subunit of the IFT-A complex essential for retrograde intraflagellar transport and ciliary membrane protein import. It is not an enzyme but rather serves as a multi-domain scaffold within the IFT-A core, using its C-terminal TPR domains for complex assembly and its N-terminal WD-repeat/β-propeller domains for cargo recognition and retrograde motor regulation. CHE-11 localizes to the axoneme and transition zone region of all sensory cilia in C. elegans, where it undergoes bidirectional IFT movement. Its loss results in truncated cilia, disrupted retrograde IFT, defective transition zone gating, dye-filling defects, and chemotaxis behavioral impairment. Transcriptional regulation of che-11 involves the cooperative action of DAF-19/RFX and FKH-8 transcription factors. The deep conservation of IFT140 from worms to humans, and its association with multiple human ciliopathies, underscores the fundamental importance of this protein in ciliary biology.
References
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