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The gene xbx-1 (X-box regulated gene 1; systematic name F02D8.3, UniProt Q19119) encodes the cytoplasmic dynein 2 light intermediate chain 1 (DYNC2LI1 ortholog) in Caenorhabditis elegans. The gene name derives from its regulation by the X-box DNA motif, which is recognized by the RFX-family transcription factor DAF-19 (perrone2003anoveldynein pages 1-2, chu2012finetuningof pages 4-5). XBX-1 belongs to the dynein light intermediate chain family and contains a P-loop NTPase domain and a DLIC (dynein light intermediate chain) domain, consistent with its classification as a structural and regulatory subunit of the IFT-dynein (cytoplasmic dynein-2) motor complex (hao2011theretrogradeift pages 5-7, hao2011theretrogradeift pages 1-2).
XBX-1 is the light intermediate chain (LIC) of the IFT-dynein complex (also known as cytoplasmic dynein-2), the minus-end-directed microtubule motor responsible for retrograde intraflagellar transport (IFT) within cilia. In C. elegans, the conventional IFT-dynein complex comprises the heavy chain CHE-3 (DYNC2H1 ortholog), the light intermediate chain XBX-1 (DYNC2LI1 ortholog), and several light chains including DYLT-1, DYLT-2 (Tctex-type), and DYRB-1 (Roadblock-type) (hao2011theretrogradeift pages 5-7, hao2011theretrogradeift pages 3-5). XBX-1 is an essential component of this complex: loss-of-function mutations in xbx-1 produce short cilia filled with accumulated IFT particle subunits, a hallmark phenotype of retrograde IFT failure (hao2011theretrogradeift pages 1-2, perrone2003anoveldynein pages 1-2).
The primary function of XBX-1/DYNC2LI1 is not enzymatic per se—it does not catalyze a chemical reaction—but rather structural and regulatory: it is required for the assembly and function of the dynein-2 motor complex that powers the retrograde movement of IFT trains from the ciliary tip back to the ciliary base (hao2011theretrogradeift pages 5-7, hao2011theretrogradeift pages 9-9). Without functional XBX-1, retrograde IFT is disrupted while anterograde transport continues, leading to progressive accumulation of IFT components at the ciliary tip and consequent ciliary structural defects (hao2011theretrogradeift pages 1-2).
Structural studies of the mammalian dynein-2 complex, informed by cryo-electron microscopy, reveal that the holocomplex comprises 11 subunits that can be divided into three subcomplexes: (1) the DYNC2H1–DYNC2LI1 core, (2) the WDR34–DYNLL1/DYNLL2–DYNLRB1/DYNLRB2 module, and (3) the WDR60–TCTEX1D2–DYNLT1/DYNLT3 module (tsurumi2019interactionsofthe pages 1-2). DYNC2LI1 (the XBX-1 ortholog) binds directly to the N-terminal nonmotor tail region of DYNC2H1, and each dynein-2 complex contains two DYNC2H1 molecules that adopt asymmetric conformations, each binding one copy of DYNC2LI1, yielding a 2:2:1:1 stoichiometry for DYNC2H1:DYNC2LI1:WDR60:WDR34 (qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 2-3). DYNC2LI1 thus serves as a critical structural bridge between the heavy chain motor and the intermediate/light chain assembly that organizes the tail of the dynein-2 complex (qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 3-4).
The following table summarizes the dynein-2 complex subunit composition:
| Subunit type | C. elegans gene name | Human ortholog | Role in complex | Key references |
|---|---|---|---|---|
| Heavy chain | che-3 | DYNC2H1 | Core dynein-2 motor subunit; provides the ATPase/motor domain that powers retrograde intraflagellar transport (IFT) from ciliary tip to base. In C. elegans, CHE-3 is the essential conventional IFT-dynein heavy chain; in human dynein-2, two DYNC2H1 heavy chains form the motor core. (hao2011theretrogradeift pages 5-7, qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 2-3) | Hao et al. 2011; Qiu et al. 2022; Hiyamizu et al. 2023 (hao2011theretrogradeift pages 5-7, qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 2-3) |
| Light intermediate chain | xbx-1 | DYNC2LI1 | Dynein-2 light intermediate chain; binds the N-terminal/nonmotor tail of DYNC2H1 and helps bridge the heavy chain to intermediate-chain modules. In C. elegans, XBX-1 is an essential component of IFT-dynein required for retrograde IFT and cilia assembly. In human dynein-2, DYNC2LI1 is part of the DYNC2H1-DYNC2LI1 core subcomplex; the human complex has a reported 2:2:1:1 stoichiometry for DYNC2H1:DYNC2LI1:WDR60:WDR34. (hao2011theretrogradeift pages 5-7, qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 2-3) | Hao et al. 2011; Qiu et al. 2022; Hiyamizu et al. 2023 (hao2011theretrogradeift pages 5-7, qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 2-3) |
| Intermediate chain | No clearly established named equivalent in the retrieved C. elegans xbx-1-focused literature | WDR60 (DYNC2I1) | One of the two dynein-2 intermediate chains. Associates with the DYNC2H1-DYNC2LI1 core through WD40-domain interactions and contributes to assembly of the heteromeric dynein-2 tail; also mediates functionally important interactions with IFT-B subunits such as IFT54. (hiyamizu2023multipleinteractionsof pages 2-3, hiyamizu2023multipleinteractionsof pages 1-2, tsurumi2019interactionsofthe pages 1-2, hiyamizu2023multipleinteractionsof pages 3-4) | Tsurumi et al. 2019; Hiyamizu et al. 2023 (hiyamizu2023multipleinteractionsof pages 2-3, hiyamizu2023multipleinteractionsof pages 1-2, tsurumi2019interactionsofthe pages 1-2, hiyamizu2023multipleinteractionsof pages 3-4) |
| Intermediate chain | No clearly established named equivalent in the retrieved C. elegans xbx-1-focused literature | WDR34 (DYNC2I2) | Second dynein-2 intermediate chain. Works with WDR60 to organize the asymmetric tail region of dynein-2; associates with light-chain arrays and is required for proper dynein-2 assembly and retrograde ciliary trafficking. (qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2, hiyamizu2023multipleinteractionsof pages 3-4) | Qiu et al. 2022; Tsurumi et al. 2019; Hiyamizu et al. 2023 (qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2, hiyamizu2023multipleinteractionsof pages 3-4) |
| Light chain | dylt-1 / dylt-2 | DYNLT family / TCTEX1D2-associated light-chain module | Tctex-type light chains associated with the dynein-2 complex in C. elegans; bidirectional IFT behavior supports their participation in the IFT-dynein motor. In vertebrate/human dynein-2, TCTEX1D2 is a dynein-2-specific light chain associated with the WDR60 module. (hao2011theretrogradeift pages 3-5, hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2) | Hao et al. 2011; Tsurumi et al. 2019; Hiyamizu et al. 2023 (hao2011theretrogradeift pages 3-5, hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2) |
| Light chain | dyrb-1 | DYNLRB1 / DYNLRB2 | Roadblock-type light chain associated with IFT-dynein in C. elegans; contributes to dynein-2 light-chain architecture. In human dynein-2, roadblock-family dimers are incorporated into the intermediate-chain/light-chain modules. (hao2011theretrogradeift pages 3-5, hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2) | Hao et al. 2011; Tsurumi et al. 2019; Hiyamizu et al. 2023 (hao2011theretrogradeift pages 3-5, hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2) |
| Light chain | Various/not clearly resolved in the retrieved C. elegans xbx-1-focused literature | DYNLL1 / DYNLL2 | LC8-family light chains that help heterodimerize and stabilize intermediate-chain subcomplexes in human dynein-2, especially the WDR34-associated module. Specific C. elegans one-to-one orthology was not clearly established in the retrieved evidence set. (hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2) | Tsurumi et al. 2019; Hiyamizu et al. 2023 (hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2) |
Table: This table compares the dynein-2 complex across C. elegans and humans, highlighting where xbx-1/DYNC2LI1 fits within the motor. It is useful for linking worm functional genetics to current structural and ciliopathy-focused understanding of human dynein-2.
XBX-1 is expressed exclusively in ciliated sensory neurons in C. elegans, consistent with its function as part of the cilium-specific IFT machinery (hao2011theretrogradeift pages 5-7, hao2011theretrogradeift pages 1-2). Using fluorescently tagged reporters (XBX-1::YFP, XBX-1::RFP, XBX-1::tdTomato), the protein has been localized to the ciliary axonemes of both amphid (head) and phasmid (tail) sensory neurons (scheidel2018intraflagellartransportcomplex pages 3-4, hao2011theretrogradeift pages 1-2). XBX-1 is commonly used as a ciliary marker in C. elegans research, demarcating the transition zone and axonemal regions by its characteristic fluorescence pattern (scheidel2018intraflagellartransportcomplex pages 3-4).
Live imaging of XBX-1::YFP has revealed that the protein undergoes bidirectional transport within cilia, being carried anterogradely as cargo by kinesin-2 motors (kinesin-II and OSM-3) to the distal tip of the cilium, and then powering retrograde transport back toward the base as part of the active dynein-2 motor (hao2011theretrogradeift pages 3-5, hao2011theretrogradeift pages 5-7).
A key finding from quantitative IFT studies is that XBX-1 is transported along cilia independently of the IFT particle subcomplexes (IFT-A and IFT-B) and the BBSome. In wild-type amphid cilia, XBX-1::YFP moves anterogradely at approximately 0.776 ± 0.08 µm/s in the middle (doublet microtubule) segment and 1.30 ± 0.18 µm/s in the distal (singlet microtubule) segment (hao2011theretrogradeift pages 5-7). These rates correspond to transport by the coordinated action of kinesin-II and OSM-3 in the middle segment, and by OSM-3 alone in the distal segment, mirroring the behavior of other IFT components (hao2011theretrogradeift pages 3-5, hao2011theretrogradeift pages 5-7). However, unlike IFT-A and IFT-B subunits, XBX-1 transport rates are not affected by loss of BBSome (BBS) subunits, suggesting that IFT-dynein is carried as an independent cargo that binds directly to anterograde motors rather than being coupled through the IFT particle/BBSome complex (hao2011theretrogradeift pages 3-5, hao2011theretrogradeift pages 5-7, wei2012thebbsomecontrols pages 14-16).
The xbx-1(ok279) deletion allele disrupts retrograde IFT and produces several well-characterized phenotypes:
XBX-1 functions within the intraflagellar transport pathway, a bidirectional trafficking system essential for cilium assembly, maintenance, and signaling. In this pathway, anterograde IFT trains are assembled at the ciliary base, transported to the ciliary tip by kinesin-2 motors, and then remodeled at the tip for retrograde return driven by the dynein-2 motor complex containing XBX-1 (hao2011theretrogradeift pages 5-7, hiyamizu2023multipleinteractionsof pages 1-2). The dynein-2 complex must be transported as inactive cargo during anterograde transport and then activated at the ciliary tip for retrograde transport (hao2011theretrogradeift pages 3-5). Multiple interactions between dynein-2 subunits (including DYNC2H1–DYNC2LI1 and WDR60) and IFT-B subunits (particularly IFT54 and IFT57) are essential for properly coupling the motor to IFT trains (hiyamizu2023multipleinteractionsof pages 1-2).
Beyond its role in retrograde IFT, the dynein-2 complex containing XBX-1 has been implicated in transition zone (TZ) assembly and ciliary gating. Using a temperature-sensitive IFT-dynein mutant (che-3 ts) in C. elegans, Jensen et al. (2018) demonstrated that retrograde IFT is required for proper assembly and maintenance of the TZ—a ciliary gate at the base of the cilium that controls protein entry and exit (jensen2018roleforintraflagellar pages 1-2, jensen2018roleforintraflagellar pages 3-5). When IFT-dynein function is disrupted, TZ proteins such as NPHP-4, MKS-6, and CEP-290 mislocalize ectopically into the ciliary axoneme, and the gating function that excludes periciliary membrane proteins from the cilium is compromised (jensen2018roleforintraflagellar pages 3-5). Importantly, restoring IFT function in adult animals reverses these TZ defects, demonstrating that active IFT-dynein-mediated transport is continuously required for TZ maintenance, although this capacity declines with age (jensen2018roleforintraflagellar pages 1-2).
An interesting finding relevant to xbx-1 is the discovery that the outer labial quadrant (OLQ) neurons of C. elegans can assemble cilia independently of the conventional CHE-3/XBX-1-based IFT-dynein complex, implying the existence of a second IFT-dynein in these specific neurons (hao2011theretrogradeift pages 5-7). A novel dynein heavy chain, DHC-3, along with additional light chains, may constitute this alternative IFT-dynein complex in OLQ cilia (hao2011theretrogradeift pages 5-7).
The promoter of xbx-1 contains an X-box motif (consensus sequence GTTTCCATGGTAAC), which is recognized by the RFX-family transcription factor DAF-19, the master regulator of ciliogenesis gene expression in C. elegans (chu2012finetuningof pages 4-5, perrone2003anoveldynein pages 1-2). DAF-19 activates the expression of xbx-1 and dozens of other ciliome genes in ciliated sensory neurons.
Recent work (2023) has revealed that DAF-19 does not act alone: the Forkhead transcription factor FKH-8 cooperates with DAF-19/RFX as a direct co-regulator of ciliome genes, including xbx-1. FKH-8 is expressed in all ciliated sensory neurons, binds regulatory regions of ciliome genes near X-box motifs, and physically interacts with DAF-19 (brocalruiz2023forkheadtranscriptionfactor pages 1-2, brocalruiz2023forkheadtranscriptionfactor pages 6-7, brocalruiz2023forkheadtranscriptionfactor pages 7-8). ChIP-seq analysis showed that FKH-8 binding peaks are associated with 49% of ciliome genes and preferentially with core ciliome genes (75%), with approximately 62% of core ciliome genes containing both X-box motifs and FKH-8 binding sites (brocalruiz2023forkheadtranscriptionfactor pages 5-6). Point mutations disrupting FKH binding sites in the xbx-1 regulatory region result in expression defects, confirming a direct regulatory role (brocalruiz2023forkheadtranscriptionfactor pages 9-10). This cooperative FKH-8/DAF-19 regulatory logic may represent an ancient trait predating functional cilia sub-specialization, as FKH-8 function can be replaced by mouse FOXJ1 and FOXN4 (brocalruiz2023forkheadtranscriptionfactor pages 1-2).
The human ortholog of XBX-1, DYNC2LI1 (also known as LIC3 or D2LIC), is associated with skeletal ciliopathies when mutated. Pathogenic variants in DYNC2LI1 cause short-rib thoracic dystrophy (SRTD), a form of Jeune asphyxiating thoracic dystrophy, as well as Ellis-van Creveld syndrome and short-rib polydactyly syndrome (OpenTargets Search: -DYNC2LI1, qiu2022combinationsofdeletion pages 2-4). Several pathogenic DYNC2LI1 variants, including p.(Leu117Val), p.(Ser302_Ile332del), and p.(Trp124*), have been shown to impair binding to DYNC2H1 and WDR60 (qiu2022combinationsofdeletion pages 2-4). In cell-based assays, combinations of deletion and missense variants—mimicking compound heterozygosity seen in patients—cause ciliary defects, whereas individual missense variants alone often do not produce substantial abnormalities (qiu2022combinationsofdeletion pages 2-4). These findings underscore the conservation of DYNC2LI1/XBX-1 function from nematodes to humans and its essential role in cilium biogenesis.
The following table provides a concise overview of the experimentally supported functional annotations for xbx-1:
| Functional aspect | Finding | Evidence type | Reference |
|---|---|---|---|
| Molecular function | XBX-1 is the light intermediate chain of the IFT-dynein (dynein-2) complex and is essential for retrograde intraflagellar transport in C. elegans sensory cilia. (hao2011theretrogradeift pages 5-7, hao2011theretrogradeift pages 1-2, hao2011theretrogradeift pages 9-9) | Genetic/biochemical | Hao et al. 2011 |
| Expression pattern | xbx-1 is expressed in most or all ciliated sensory neurons and is an X-box-regulated ciliome gene under DAF-19/RFX control; more recent work supports cooperative regulation with FKH-8. (perrone2003anoveldynein pages 1-2, chu2012finetuningof pages 4-5, brocalruiz2023forkheadtranscriptionfactor pages 9-10, brocalruiz2023forkheadtranscriptionfactor pages 1-2) | Reporter assays, transcription factor analysis | Perrone et al. 2003; Chu et al. 2012; Brocal-Ruiz et al. 2023 |
| Subcellular localization | XBX-1 localizes to ciliary axonemes of amphid and phasmid neurons, visualized with XBX-1::YFP/RFP/tdTomato reporters and knock-ins. (scheidel2018intraflagellartransportcomplex pages 3-4, hao2011theretrogradeift pages 1-2) | XBX-1::YFP/tdTomato imaging | Hao et al. 2011; Scheidel et al. 2018 |
| Transport properties | XBX-1 is transported anterogradely at ~0.776 ± 0.08 µm/s in the middle segment and ~1.30 ± 0.18 µm/s in the distal segment; its movement is largely independent of IFT particle/BBSome coupling. (hao2011theretrogradeift pages 3-5, hao2011theretrogradeift pages 5-7) | IFT velocity measurements | Hao et al. 2011 |
| Loss-of-function phenotype | xbx-1(ok279) and related loss-of-function conditions cause highly abnormal phasmid cilia, dye-filling defects, and short/swollen cilia that accumulate IFT material, consistent with retrograde IFT failure. (hao2011theretrogradeift pages 1-2, perrone2003anoveldynein pages 1-2, williams2008functionalredundancyof pages 4-6) | Mutant phenotyping, dye-fill assays, cilia morphology analysis | Hao et al. 2011; Perrone et al. 2003; Williams et al. 2008 |
| Complex membership | XBX-1/DYNC2LI1 forms the DYNC2H1-DYNC2LI1 core dynein-2 subcomplex and bridges the heavy chain tail to intermediate-chain modules in the holocomplex. (qiu2022combinationsofdeletion pages 1-2, hiyamizu2023multipleinteractionsof pages 2-3, tsurumi2019interactionsofthe pages 1-2, hiyamizu2023multipleinteractionsof pages 3-4) | Structural analysis, cryo-EM, biochemical complex mapping | Qiu et al. 2022; Tsurumi et al. 2019; Hiyamizu et al. 2023 |
| Transcriptional regulation | xbx-1 is co-regulated by FKH-8 and DAF-19/RFX through nearby FKH-binding and X-box regulatory elements, supporting a cooperative ciliome transcription program. (brocalruiz2023forkheadtranscriptionfactor pages 9-10, brocalruiz2023forkheadtranscriptionfactor pages 3-5, brocalruiz2023forkheadtranscriptionfactor pages 6-7, brocalruiz2023forkheadtranscriptionfactor pages 7-8) | ChIP-seq, reporter assays, cis-regulatory analysis | Brocal-Ruiz et al. 2023 |
| Human disease relevance | The human ortholog DYNC2LI1 is implicated in skeletal ciliopathies, including short-rib thoracic dysplasia, and pathogenic variants can impair dynein-2 assembly and ciliary function. (qiu2022combinationsofdeletion pages 2-4, OpenTargets Search: -DYNC2LI1) | Human genetics, cell-based functional studies | Qiu et al. 2022; Open Targets context |
Table: This table summarizes the main experimentally supported functional findings for C. elegans xbx-1, including molecular role, localization, transport behavior, regulation, phenotype, and human ortholog relevance. It is useful as a compact evidence map for the gene’s annotation.
xbx-1 encodes the light intermediate chain of the IFT-dynein (cytoplasmic dynein-2) complex in C. elegans. Its primary function is structural: it forms a core subcomplex with the dynein heavy chain CHE-3 (DYNC2H1), bridging it to intermediate and light chain modules that together constitute the retrograde IFT motor. XBX-1 is essential for retrograde intraflagellar transport—the recycling of IFT components and associated cargo from the ciliary tip back to the base—and its loss results in structurally abnormal, truncated cilia. The protein localizes exclusively to sensory cilia, where it undergoes bidirectional transport, and it is uniquely transported as cargo independently of IFT particle subcomplexes and the BBSome. Beyond retrograde transport, the dynein-2 complex containing XBX-1 contributes to transition zone assembly, ciliary gating, and ciliary maintenance. Transcriptionally, xbx-1 is co-regulated by DAF-19/RFX and FKH-8, representing a conserved ciliome gene regulatory program. The human ortholog DYNC2LI1 is mutated in skeletal ciliopathies, confirming the deep evolutionary conservation of this gene's function in cilium biology.
References
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(hao2011theretrogradeift pages 5-7): Limin Hao, Evgeni Efimenko, Peter Swoboda, and Jonathan M. Scholey. The retrograde ift machinery of c. elegans cilia: two ift dynein complexes? PLoS ONE, 6:e20995, Jun 2011. URL: https://doi.org/10.1371/journal.pone.0020995, doi:10.1371/journal.pone.0020995. This article has 59 citations and is from a peer-reviewed journal.
(hao2011theretrogradeift pages 1-2): Limin Hao, Evgeni Efimenko, Peter Swoboda, and Jonathan M. Scholey. The retrograde ift machinery of c. elegans cilia: two ift dynein complexes? PLoS ONE, 6:e20995, Jun 2011. URL: https://doi.org/10.1371/journal.pone.0020995, doi:10.1371/journal.pone.0020995. This article has 59 citations and is from a peer-reviewed journal.
(hao2011theretrogradeift pages 3-5): Limin Hao, Evgeni Efimenko, Peter Swoboda, and Jonathan M. Scholey. The retrograde ift machinery of c. elegans cilia: two ift dynein complexes? PLoS ONE, 6:e20995, Jun 2011. URL: https://doi.org/10.1371/journal.pone.0020995, doi:10.1371/journal.pone.0020995. This article has 59 citations and is from a peer-reviewed journal.
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(tsurumi2019interactionsofthe pages 1-2): Yuta Tsurumi, Yuki Hamada, Yohei Katoh, and Kazuhisa Nakayama. Interactions of the dynein-2 intermediate chain wdr34 with the light chains are required for ciliary retrograde protein trafficking. Mar 2019. URL: https://doi.org/10.1091/mbc.e18-10-0678, doi:10.1091/mbc.e18-10-0678. This article has 47 citations and is from a domain leading peer-reviewed journal.
(qiu2022combinationsofdeletion pages 1-2): Hantian Qiu, Yuta Tsurumi, Yohei Katoh, and Kazuhisa Nakayama. Combinations of deletion and missense variations of the dynein-2 dync2li1 subunit found in skeletal ciliopathies cause ciliary defects. Scientific Reports, Jan 2022. URL: https://doi.org/10.1038/s41598-021-03950-0, doi:10.1038/s41598-021-03950-0. This article has 14 citations and is from a peer-reviewed journal.
(hiyamizu2023multipleinteractionsof pages 2-3): Shunya Hiyamizu, Hantian Qiu, Laura Vuolo, Nicola L. Stevenson, Caroline Shak, Kate J. Heesom, Yuki Hamada, Yuta Tsurumi, Shuhei Chiba, Yohei Katoh, David J. Stephens, and Kazuhisa Nakayama. Multiple interactions of the dynein-2 complex with the ift-b complex are required for effective intraflagellar transport. Journal of Cell Science, Feb 2023. URL: https://doi.org/10.1242/jcs.260462, doi:10.1242/jcs.260462. This article has 18 citations and is from a domain leading peer-reviewed journal.
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