Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Toward a Comprehensive Map of Rab-Mediated Cargo Transport to Migrasomes

ABSTRACT: Migrasomes are essential intermediates for intercellular communication, involved in critical processes such as embryonic development, angiogenesis, and blood coagulation. So far, a comprehensive understanding of the protein cargoes within migrasomes and their transport mechanisms, which is fundamental to advancing the understanding of migrasomes function, is still lacking. In this study, we investigated the Rab-mediated cargo transport network to migrasomes. Rabs selectively transported proteins to migrasomes that are enriched in intracellular vesicle trafficking pathways. By integrating migrasomes protein profiling and Rab-effectors under various Rab activations, we identified key driving proteins involved in Rab-mediated cargo delivery to migrasomes. Additionally, we uncovered and validated that Rabs transported plasma membrane-localized receptors and matrix metalloproteinase to migrasomes, providing new insights into their in vivo functions. The proteomic dataset and integrated approach can be applied in further investigation of migrasomes in both physiological and disease contexts.

ORGANISM(S): Mus Musculus

SUBMITTER: Yang Chen

PROVIDER: PXD062412 | iProX | Mon Mar 31 00:00:00 BST 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Rab10-CAV1 mediated intraluminal vesicles transport to migrasomes

Project description:Migrasomes, vesicular organelles generated on the retraction fibers of migrating cells, play a crucial role in migracytosis, mediating intercellular communication. The content cargoes determine the functional specificity of migrasomes. Migrasomes harbor numerous intraluminal vesicles, a pivotal component of their cargo. The mechanism underlying the transportation of these intraluminal vesicles to the migrasomes remain enigmatic. In this study, we identified a pathway by which Rab10-Caveolin1 mediates the transport of intraluminal vesicles to migrasomes. This intricate process necessitates the coordination of the motor protein Myosin Va, adaptor proteins RILPL2, facilitating vesicle transportation through retraction fibers to the migrasomes. Notably, the phosphorylation of Rab10 by the kinase LRRK2 augments this transport. Moreover, CSF-1 is selectively transported to migrasomes through this mechanism, subsequently fostering monocyte-macrophage differentiation in skin wound healing, which adds to our understanding of the physiological role of migrasomes.

2023-10-14 | PXD046146 |

Transcriptome-wide view of endosomal mRNP transport [RNA-Seq]

Project description:Spatiotemporal protein expression is mediated by active transport and local translation of mRNAs. Key factors of the transport machinery are RNA-binding proteins (RBPs) that recognise mRNAs as cargo for motor-based transport. However, a global view of transported mRNAs with cognate RBP binding sites is missing. Here, we cast a transcriptome-wide view on endosomal mRNP transport in Ustilago maydis by studying the newly identified endosomal RBP Grp1 and the key transport RBP Rrm4 in a comparative iCLIP approach. This uncovered thousand of cargo mRNAs bound by both RBPs.

2018-12-10 | GSE109560 | GEO

Transcriptome-wide view of endosomal mRNP transport [iCLIP ]

2018-12-10 | GSE109557 | GEO

Identification of TbUnc119-interacting proteins by proximity-based biotinylation

Project description:Both intraflagellar transport (IFT) and lipidated intraflagellar transport (LIFT) pathways are essential for cilia/flagella biogenesis, motility and sensory functions. In the LIFT pathway, lipidated cargoes are transported into the cilia through the coordinated actions of cargo carrier proteins such as Unc119 or PDE6δ, as well as small GTPases Arl13b and Arl3 in the cilium. Our previous studies revealed a single Arl13b ortholog in the evolutionarily divergent Trypanosoma brucei. TbArl13 catalyses two TbArl3 homologs, TbArl3A and TbArl3C, suggesting the presence of a conserved LIFT pathway in these protozoan parasites. Only a single homolog to the cargo carrier protein Unc119 was identified in T. brucei genome, but its function in lipidated protein transport has not been characterized. In this study, we exploited the proximity-based biotinylation approach to identify binding partners of TbUnc119 using an improved version of biotin ligase BioID2. The BioID2 tag was fused to either the N-terminus (3HA-BioID2-TbUnc119) or the C-terminus (TbUnc119-BioID2-HA) of TbUnc119 and expressed using a cumate-inducible expression system in the procyclic cells of T. brucei. We performed LC-MS/MS on the affinity-purified biotinylated samples followed by evaluation of emPAI score.

2020-06-25 | PXD019488 | Pride

Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport

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

Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport (Proteomics

2024-08-21 | PXD049260 | JPOST Repository

Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway

Project description:Xiao L, Pi X, Goss AC, El-Baba T, Ehrmann JF, Grinkevich E, Bazua-Valenti S, Padovano V, Alper SL, Carey D, Udeshi ND, Carr SA, Pablo JL, Robinson CV, Greka A, Wu H. 2024 Intracellular accumulation of misfolded proteins causes serious human proteinopathies. The transmembrane emp24 domain 9 (TMED9) cargo receptor promotes a general mechanism of cytotoxicity by entrapping misfolded protein cargoes in the early secretory pathway. However, the molecular basis for this TMED9-mediated cargo retention remains elusive. Here we report cryoEM structures of TMED9, which reveal its unexpected self-oligomerization into octamers, dodecamers and by extension, even higher-order oligomers. The TMED9 oligomerization is driven by an intrinsic symmetry mismatch between the trimeric coiled coil domain and the tetrameric transmembrane domain. Using frameshifted Mucin 1 as an example of aggregated disease-related protein cargo, we implicate a mode of direct interaction with the TMED9 luminal Golgi-dynamics (GOLD) domain. The structures suggest and we confirm that TMED9 oligomerization favors the recruitment of COPI, but not COPII coatomers, facilitating retrograde transport and explaining the observed cargo entrapment. Our work thus reveals a molecular basis for TMED9-mediated misfolded protein retention in the early secretory pathway.

2022-06-29 | MSV000089757 | MassIVE

SILAC-Tp (12 importins)

Project description:Importin-beta family proteins are nucleocytoplasmic transport receptors (NTRs), and they transport most nuclear proteins as their cargoes into and out of the nuclei. Human cells have 20 species of importin-beta family NTRs, of which 10 (importin-beta, transportin-1, -2, -SR, importin-4, -5, -7, -8, -9, and -11) are nuclear import receptors and 2 (importin-13, and exportin-4) are bi-directional receptors. Here, we identified the import cargo proteins of these 12 NTRs by a method called SILAC-Tp, which employs stable isotope labeling with amino acids in cell culture (SILAC), an in vitro reconstituted transport system, and LC-MS/MS.

2017-03-30 | MSV000080815 | MassIVE

Proteomics of motor enriched fraction (ATP releasate) from Dictyostelium discoideum

Project description:Intracellular transport is regulated by the presence of motor proteins and its adapters on cargoes. Here, we are investigating the role of specific lipid on cargo in recruitment of these motor proteins and adapters. The proteomics were conducted to catalog for the possible adaptors, regulators, and microtubule-associated proteins (MAPs) present in our motor-enriched fractions (referred to as ATP-releasate).

2024-05-16 | PXD051777 | Pride

Xpo7 is a broad-spectrum exportin and a nuclear import receptor

Project description:Cargo molecules which exceed the passive diffusion limit of ~5nm require active translocation to cross the nuclear pore complex (NPC). Such a facilitated transport is achieved by specialized nuclear transport receptors (NTRs), which are classified according to their shuttling direction. Exportins bind their cargo in a RanGTP-dependent manner inside the nucleus and release it in the cytoplasm. Importins, on the other hand, bind their cargo without RanGTP and transfer it in the opposite direction. CRM1/Xpo1 is one of the best-characterized NTRs mostly due to the availability of specific inhibitors, like leptomycin B, which allowed cargo validation in vivo. Such inhibitors have not been characterized for other NTRs, thus analysis of those lagged behind. Here, we developed nanobodies to specifically target exportin 7/Xpo7 and block its transport pathway. Moreover, in-depth MS/MS analysis of Xpo7 under nuclear (+RanGTP) and cytoplasmic conditions (-RanGTP) revealed novel binders including ~200 potential export substrates, but also ~30 nuclear import cargoes. Enrichment factors of a putative cargo were calculated using the iBAQ strategy to quantify detectable proteins in the input as well as in the import or export mimicking material. Validation of selected cargo molecules was then accomplished by anti-Xpo7 nanobodies causing cargo mislocalization when transfected into cultured cells. Collectively, the data establish Xpo7 as a bidirectional NTR with a broad substrate specificity.

2018-05-07 | PXD008746 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data