ARL3 GTPases facilitate ODA16 unloading from IFT in motile cilia
Ontology highlight
ABSTRACT:
INSTRUMENT(S): TripleTOF 5600
ORGANISM(S): Trypanosoma Brucei
TISSUE(S): Eukaryotic Cell
DISEASE(S): Trypanosomiasis
SUBMITTER: 
Yameng Huang
LAB HEAD: Cynthia Y. He
PROVIDER: PXD053760 | Pride | 2024-09-05
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 20-10-21_2010S05_T0_1hr.group | Other | |||
| 20-10-21_2010S05_T0_1hr.wiff | Wiff | |||
| 20-10-21_2010S05_T0_1hr.wiff.scan | Wiff | |||
| 20-10-21_2010S05_T48_1hr.group | Other | |||
| 20-10-21_2010S05_T48_1hr.wiff | Wiff |
Items per page: 5 1 - 5 of 11 |
Similar Datasets
Project description:Study Smoking and COPD are associated with decreased mucociliary clearance and healthy smokers have shorter cilia in the large airway than nonsmokers. Intraflagellar transport (IFT) is the process by which cilia are produced and maintained. We assessed expression of IFT-related genes in smokers and nonsmokers and evaluated cilia length in the large and small airway of nonsmokers, healthy smokers, and smokers with COPD. Methods Airway epithelium was obtained via bronchoscopic brushing. Affymetrix microarrays were used to evaluate IFT gene expression in 2 independent data sets from large and small airway. Cilia length was assessed by measuring 100 cilia (10 cilia on each of 10 cells) per subject. Results All 40 IFT genes were expressed in the human large and small airway epithelium. In the large airway, 10 IFT genes were down-regulated and 1 up-regulated in smokers. In the small airway, 11 genes were down-regulated and 3 up-regulated in smokers. A set of 8 IFT genes was down-regulated in both data sets. In the large and small airway epithelium, cilia were significantly shorter in healthy smokers than nonsmokers, and significantly shorter in COPD smokers than in both healthy smokers and nonsmokers. Answer to the Question These results support the concept that loss of cilia length contributes to defective mucociliary clearance in COPD, and that smoking-induced changes in expression of IFT genes may be one mechanism of abnormally short cilia in smokers. Strategies to normalize cilia length may be an important avenue for novel COPD therapies. Gene expression was assessed for 40 intraflagellar transport related genes in the LAE of nonsmokers (n=21) and healthy smokers (n=31) and the SAE of an independent group of nonsmokers (n=28) and healthy smokers (n=69). Cilia length was assessed in a total of 228 airway epithelium samples, including 120 LAE samples and 108 SAE samples; a subset of the 228 samples is represented among the 149 samples in this Series.
2014-02-03 | E-GEOD-43939 | biostudies-arrayexpress
Project description:Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo inside cilia. However, the mechanism of selective transport of cargo to cilia and entry across the diffusion barrier is not well understood. WDR35/IFT121 is a component of the IFT-A complex, best known for ciliary retrograde transport. Small Wdr35 mutant cilia are formed but fail to enrich in diverse classes of ciliary membrane proteins. Whilst the assembly of the IFT-B complex is unaffected, these exhibit retrograde trafficking defects in Wdr35 mutants. In contrast, the IFT-A peripheral components are degraded and core components remain stuck at the cilia base. The deep sequence homology and structural similarity of WDR35 and other IFT-As to the coatomer COPI proteins α and ß’, and accumulation of electron-light vesicles around Wdr35 mutant cilia, suggest that WDR35 is required to form coated vesicles delivering cargo from the Golgi necessary for cilia elongation. This is the first insitu proof towards a novel coatomer function for WDR35 and likely other IFT-A proteins in transporting ciliary membrane proteins from the Golgi.
2021-05-03 | PXD022652 | Pride
Project description:Study Smoking and COPD are associated with decreased mucociliary clearance and healthy smokers have shorter cilia in the large airway than nonsmokers. Intraflagellar transport (IFT) is the process by which cilia are produced and maintained. We assessed expression of IFT-related genes in smokers and nonsmokers and evaluated cilia length in the large and small airway of nonsmokers, healthy smokers, and smokers with COPD. Methods Airway epithelium was obtained via bronchoscopic brushing. Affymetrix microarrays were used to evaluate IFT gene expression in 2 independent data sets from large and small airway. Cilia length was assessed by measuring 100 cilia (10 cilia on each of 10 cells) per subject. Results All 40 IFT genes were expressed in the human large and small airway epithelium. In the large airway, 10 IFT genes were down-regulated and 1 up-regulated in smokers. In the small airway, 11 genes were down-regulated and 3 up-regulated in smokers. A set of 8 IFT genes was down-regulated in both data sets. In the large and small airway epithelium, cilia were significantly shorter in healthy smokers than nonsmokers, and significantly shorter in COPD smokers than in both healthy smokers and nonsmokers. Answer to the Question These results support the concept that loss of cilia length contributes to defective mucociliary clearance in COPD, and that smoking-induced changes in expression of IFT genes may be one mechanism of abnormally short cilia in smokers. Strategies to normalize cilia length may be an important avenue for novel COPD therapies.
2014-02-03 | GSE43939 | GEO
Project description:Cilia are ubiquitous eukaryotic organelles impotant for cellular motility, signaling, and sensory reception. Cilium formation requires intraflagellar transport of structural and signaling components and involves 22 different proteins organized into intraflagellar transport (IFT) complexes IFT-A and IFT-B that are transported by molecular motors. The IFT-B complex constitutes the backbone of polymeric IFT trains carrying cargo between the cilium and the cell body. Currently, high-resolution structures are only available for smaller IFT-B subcomplexes leaving > 50% structurally uncharacterized. Here, we used Alphafold to structurally model the 15-subunit IFT-B complex. The model was validated using cross-linking/mass-spectrometry data on reconstituted IFT-B complexes, X-ray scattering in solution, diffraction from crystals as well as site-directed mutagenesis and protein-binding assays. The IFT-B structure reveals an elongated and highly flexible complex consistent with cryo-electron tomographic reconstructions of IFT trains. The IFT-B complex organizes into IFT-B1 and IFT-B2 parts with binding sites for ciliary cargo and the inactive IFT dynein motor, respectively. Interestingly, our results are consistent with two different binding sites for IFT81/74 on IFT88/70/52/46 suggesting the possibility of different structural architectures for the IFT-B1 complex. Our data present a structural framework to understand IFT-B complex assembly, function, and ciliopathy variants.
2022-12-02 | PXD037049 | Pride
Project description:Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney caused causes ciliary elongation and cystogenesis, and cell-based proximity labelling proteomics and fluorescence microscopy showed alterations in the ciliary proteome upon loss of DLG1. Specifically, the retromer-associated protein SDCCAG3, IFT20 and polycystin-2 (PC2) were are reduced in cilia of DLG1 deficient cells compared to control cells. This phenotype was is recapitulated in vivo and rescuable by re-expression of wildtype DLG1, but not a Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)-associated DLG1 variant, p.T489R. Finally, biochemical approaches and Alpha Fold modelling suggested that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Our work identifies a key role for DLG1 in regulating ciliary protein composition and suggests that ciliary dysfunction of the p.T489R DLG1 variant may contribute to CAKUT.
2024-05-14 | PXD051912 | Pride
Project description:Intraflagellar transport (IFT) is a microtubule-based system that supports the assembly and maintenance of cilia, an essential organelle for development and maintenance of cellular integrity. Dysfunction of IFT was shown to lead to a wide spectrum of disease phenotypes, so called ciliopathies of variable severity. In previous studies two distinct complexes (IFT-A; IFT-B) were identified, containing multiple proteins that are part of the IFT machinery. Two of the IFT-B components are TTC30A and TTC30B and in contrast to all other IFT components, only these two are paralogues. To investigate whether these two proteins have a similar and essential ciliary or constitute redundant functions, CRIPSR/Cas9 was used to specifically knock-out TTC30A or B and to generate a double knock-out. Localization studies showed a redundancy of both proteins in ciliogenesis while polyglutamylation of cilia was affected by both single knockouts. Further, the localization of other IFT components was not affected by the depletion of a single paralogue. A loss of both proteins led to a severe ciliogenesis defect, resulting in no cilia formation which can be rescued by expression of TTC30A or B. The redundancy can be explained by highly similar interaction patterns of both paralogues, both equally interact with the IFT-B machinery. In summary our study demonstrates that a loss of one TTC30 paralogue can mostly compensate severe ciliary defects, due to redundancy. However, cells assemble shorter cilia which are potentially limited in their functions, especially because of impaired polyglutamylation. A complete loss of both proteins leads to a deficit in IFT complex B integrity followed by disrupted IFT and subsequently no cilia.
2023-12-28 | PXD033614 | Pride
Project description:Intraflagellar transport (IFT) is a microtubule-based system that supports the assembly and maintenance of cilia, an essential organelle for development and maintenance of cellular integrity. Dysfunction of IFT was shown to lead to a wide spectrum of disease phenotypes, so called ciliopathies of variable severity. In previous studies two distinct complexes (IFT-A; IFT-B) were identified, containing multiple proteins that are part of the IFT machinery. Two of the IFT-B components are TTC30A and TTC30B and in contrast to all other IFT components, only these two are paralogues. To investigate whether these two proteins have a similar and essential ciliary or constitute redundant functions, CRIPSR/Cas9 was used to specifically knock-out TTC30A or B and to generate a double knock-out. Localization studies showed a redundancy of both proteins in ciliogenesis while polyglutamylation of cilia was affected by both single knockouts. Further, the localization of other IFT components was not affected by the depletion of a single paralogue. A loss of both proteins led to a severe ciliogenesis defect, resulting in no cilia formation which can be rescued by expression of TTC30A or B. The redundancy can be explained by highly similar interaction patterns of both paralogues, both equally interact with the IFT-B machinery. In summary our study demonstrates that a loss of one TTC30 paralogue can mostly compensate severe ciliary defects, due to redundancy. However, cells assemble shorter cilia which are potentially limited in their functions, especially because of impaired polyglutamylation. A complete loss of both proteins leads to a deficit in IFT complex B integrity followed by disrupted IFT and subsequently no cilia formation
2022-08-12 | PXD034412 | Pride
Project description:Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, referred to as anterograde and retrograde IFT “trains”. Anterograde trains deliver cargoes from the cell to the ciliary tip, then remodel into retrograde trains for cargo export. We set out to understand how the structure of these trains changes at the tip, and thus how the same IFT complexes can perform opposing transport roles. We use cryo-electron tomography, subtomogram averaging and in-situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains, and compare with the known anterograde train structure. We show that the retrograde train is a two-fold symmetric polymer organised around a central thread of IFTA complexes. We conclude that the structural differences between anterograde and retrograde trains can only be achieved through de novo polymerisation of the retrograde train from individual IFTA/B complexes. Finally we describe how conformational changes to cargo binding sites allow for unidirectional cargo transport in a bidirectional system.
2024-08-21 | PXD049195 | JPOST Repository
Project description:Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, referred to as anterograde and retrograde IFT “trains”. Anterograde trains deliver cargoes from the cell to the ciliary tip, then remodel into retrograde trains for cargo export. We set out to understand how the structure of these trains changes at the tip, and thus how the same IFT complexes can perform opposing transport roles. We use cryo-electron tomography, subtomogram averaging and in-situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains, and compare with the known anterograde train structure. We show that the retrograde train is a two-fold symmetric polymer organised around a central thread of IFTA complexes. We conclude that the structural differences between anterograde and retrograde trains can only be achieved through de novo polymerisation of the retrograde train from individual IFTA/B complexes. Finally we describe how conformational changes to cargo binding sites allow for unidirectional cargo transport in a bidirectional system.
2024-08-21 | PXD049260 | JPOST Repository
Project description:DSSO crosslinking data from two Tetrahymena thermophila samples: IEX fractions from chromatography of a cilia extract, and IFT-A-enriched fractions from preparative SEC of cilia extract.
2022-03-25 | MSV000089131 | MassIVE