Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mapping of the local proteome of the Arabidopsis chloroplast intermembrane space by proximity labelling

ABSTRACT: The chloroplast intermembrane space, located between the outer and inner envelope membranes, plays key roles in protein and lipid trafficking. Currently, the proteome of the intermembrane space is largely uncharacterized, with only a relatively few protein players identified, and thus limiting our understanding of the functional relevance of this region. Here, we used a biotin proximity labelling technique, based on the TurboID enzyme (a modified biotin ligase), to define the chloroplast intermembrane space proteome in Arabidopsis thaliana. TurboID was targeted to the intermembrane space when fused with the chloroplast transit peptide (cTP) of A. thaliana Tic22, a 22-kDa protein component of the translocon at the inner chloroplast membrane. Localization of the Tic22cTP fusion protein in the intermembrane space was confirmed by confocal microscopy and protease protection assays of isolated intact chloroplasts. Following optimization of biotinylation, mass spectrometry analysis revealed a distinct set of candidate intermembrane space-localized proteins, including known components of protein import and lipid trafficking pathways, as well as several other novel proteins.

INSTRUMENT(S):

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Leaf

SUBMITTER: Yang Xu

LAB HEAD: Yang Xu

PROVIDER: PXD072271 | Pride | 2026-07-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MSF_619_C1.raw	Raw
	MSF_619_C2.raw	Raw
	MSF_619_C3.raw	Raw
	MSF_619_D1.raw	Raw
	MSF_619_D2.raw	Raw

Items per page:

1 - 5 of 28

Similar Datasets

Mapping the protein interactome of mitochondrial intermembrane space proteases identifies a novel function for HTRA2

Project description:Data contains LC-MS data of proximity-based biotin labeling assay (BioID) to generate the protein interaction network of mitochondrial intermembrane space proteases fused with BirAFlag (C-terminal tag) and expressed in T-REx HEK293 cells.

2018-11-14 | MSV000083140 | MassIVE

Small heat shock proteins operate as molecular chaperones in the mitochondrial intermembrane space

Project description:Mitochondria are complex organelles with different compartments, each harboring their own protein quality control factors. While the chaperones of the mitochondrial matrix have been well characterized, it is poorly understood which chaperones protect the mitochondrial intermembrane space. We show that cytosolic small heat shock proteins are imported under basal conditions into the mitochondrial intermembrane space, where they operate as molecular chaperones. To identify chaperone substrates with MS/MS, we used a molecular trap variant of HSPB1/Hsp27 (S135F mutant). Through affinity-enrichment co-immunoprecipitation we identified significantly enriched substrates versus GFP-negative control.

2022-12-12 | PXD038275 | Pride

CLPB disaggregase dysfunction impacts the functional integrity of the proteolytic SPY complex

Project description:CLPB is a mitochondrial intermembrane space AAA+ domain–containing disaggregase. CLPB mutations are associated with 3-methylglutaconic aciduria and neutropenia; however, the molecular mechanism underscoring disease and the contribution of CLPB substrates to disease pathology remains unknown. Interactions between CLPB and mitochondrial quality control (QC) factors, including PARL and OPA1, have been reported, hinting at dysregulation of organelle QC in disease. Utilizing proteomic and biochemical approaches, we define a stress-specific aggregation phenotype in a CLPB-null environment and define the CLPB substrate profile. We show an interplay between intermembrane space proteins including CLPB, HAX1, HTRA2, and the inner membrane quality control proteins (STOML2, PARL, YME1L1; SPY complex), with CLPB deficiency impeding SPY complex function by virtue of protein aggregation in the intermembrane space. We conclude that there is an interdependency of mitochondrial QC components at the intermembrane space/inner membrane interface, and perturbations to this network may underscore CLPB disease pathology.

2024-01-18 | PXD042313 | Pride

HYPOXIA RESCUES COMPLEX 1-ASSOCIATED DISEASE CAUSED BY PROTEOSTATIC DEFECTS

Project description:Impaired mitochondrial proteostasis underlies a broad spectrum of diseases, yet effective therapies remain limited. Here, we show that deficiency of HTRA2, a mitochondrial intermembrane space protease, can be rescued by hypoxia therapy. Using an Htra2 mutant mouse model that displays severe neurodegeneration and early lethality, we find that continuous hypoxia rescues striatal degeneration and extends lifespan. Mechanistically, we demonstrate that HTRA2 forms a functional complex with the disaggregase CLPB. Loss of function of either protein drives aggregation of intermembrane space–facing subunits of complex I of the electron transport chain, resulting in secondary complex I dysfunction. These changes impair tissue oxygen consumption and likely cause pathological hyperoxia, which is corrected by hypoxia. Together, these findings define a proteostasis pathway linking intermembrane space quality control to complex I function and expand the potential of hypoxia therapy to secondary complex I disease.

2026-05-29 | GSE327486 | GEO

Total RNA Sequencing analysis of total RNA and RNA isolated from mitochondrial pellets in CSDE1-knockdown sensory neurons

Project description:CSDE1 is an RNA-binding protein that associates with a subset of mitochondria-related transcripts. We previously observed that RNAs encoding mitochondrial proteins localized to the mitochondrial inner membrane (MIM), intermembrane space (IMS), matrix, and outer membrane (MOM) are enriched within the CSDE1-bound RNA pool. To determine whether CSDE1 regulates the abundance and mitochondrial localization of mitochondria-associated RNAs in sensory neurons, we performed RNA sequencing of both total RNA and RNA extracted from isolated mitochondria isolated from CSDE1-knockdown sensory neurons. CSDE1 knockdown was achieved using lentiviral transduction, and sequencing results were compared with control neurons infected with empty vector (pLKO).

2026-03-12 | GSE324285 | GEO

Dysfunctional mitochondria trap proteins in the intermembrane space - Data set 1: proximity labelling

Project description:Mitochondria consist of hundreds of proteins which are initially synthesized in the cytosol as ‘precursors’ and imported into the organelle. The accumulation of precursors in the cytosol due to mitochondrial dysfunction compromises cellular proteostasis and is a hallmark of diseases. How cells counteract the accumulation of potentially toxic precursors in the cytosol is poorly understood. Using a proximity labeling-based assay to globally monitor the intramitochondrial location of proteins, we show, that upon mitochondrial dysfunction many mitochondrial matrix proteins are sequestered in the intermembrane space (IMS). This Mitochondrial Triage of Precursor proteins (MitoTraP) was not simply the result of a general translocation block at the level of the inner membrane. Rather, MitoTraP specifically directs a defined subgroup of matrix proteins into the IMS, most of which being constituents of the mitochondrial ribosome. Using the mitoribosomal protein Mrp17 (bS6m) as a model, we found that the targeting into the IMS prevents the mistargeting to the nucleolus and the interference with ribosome assembly. Thus, MitoTraP represents a novel, so far unknown mechanism of the eukaryotic quality control system that protects the cellular proteome against toxic effects of non-imported mitochondrial precursor proteins.

2025-05-21 | PXD057245 | Pride

Dysfunctional mitochondria trap proteins in the intermembrane space - Data set 5: MRP17 - AP-MS

Project description:Mitochondria consist of hundreds of proteins which are initially synthesized in the cytosol as ‘precursors’ and imported into the organelle. The accumulation of precursors in the cytosol due to mitochondrial dysfunction compromises cellular proteostasis and is a hallmark of diseases. How cells counteract the accumulation of potentially toxic precursors in the cytosol is poorly understood. Using a proximity labeling-based assay to globally monitor the intramitochondrial location of proteins, we show, that upon mitochondrial dysfunction many mitochondrial matrix proteins are sequestered in the intermembrane space (IMS). This Mitochondrial Triage of Precursor proteins (MitoTraP) was not simply the result of a general translocation block at the level of the inner membrane. Rather, MitoTraP specifically directs a defined subgroup of matrix proteins into the IMS, most of which being constituents of the mitochondrial ribosome. Using the mitoribosomal protein Mrp17 (bS6m) as a model, we found that the targeting into the IMS prevents the mistargeting to the nucleolus and the interference with ribosome assembly. Thus, MitoTraP represents a novel, so far unknown mechanism of the eukaryotic quality control system that protects the cellular proteome again toxic effects of non-imported mitochondrial precursor proteins.

2025-05-21 | PXD054381 | Pride

Human Tim8a, Tim8b and Tim13 are auxiliary assembly factors of mature Complex IV

Project description:Human Tim8a and Tim8b are paralogous intermembrane space proteins of the small TIM chaperone family. Yeast small TIMs function in the trafficking of proteins to the outer and inner mitochondrial membranes. This putative import function for hTim8a and hTim8b has been challenged in human models, but their true molecular function in cells has not been defined. Likewise, why human cells possess two Tim8 proteins and any potential redundancy is not clear. We demonstrate that hTim8a and hTim8b function in the assembly of cytochrome c oxidase (Complex IV). Using affinity enrichment mass spectrometry, we catalogue the interaction network of hTim8a, hTim8b and hTim13, identifying subunits and assembly factors of the Complex IV COX2 module. hTim8-deficient cells have a COX2/COX3 module defect, albeit less severe than a COX17KO cell line, and exhibit an accumulation of the S2 subcomplex. This suggests that hTim8a and hTim8b are required for assembly of Complex IV via interactions with intermembrane-space exposed subunits. We propose hTim8-hTim13 complexes act as chaperones to stabilise the intermediate S3 subcomplex, promoting assembly of monomeric Complex IV.

2023-05-10 | PXD037906 | Pride

Gene expression of iPSC-derived neurons from patient with Mohr-Tranebjaerg syndrome and healthy control

Project description:Mohr-Tranebjaerg syndrome (MTS) is a neurodegenerative disease caused by mutations in Translocase of Inner Mitochondrial Membrane 8A/Deafness Dystonia Protein 1 (TIMM8A/DDP1), which encodes TIMM8a/DDP1 located in the intermembrane space (IMS) of mitochondria. Up to now, the pathophysiology of MTS remains unclear. In this study, we established induced pluripotent stem cells (iPSCs) derived from MTS patient carrying the TIMM8a loss-of-function pathogenic variant, p.Q75fs95* to study the mechanism of MTS. We found that MTS-iPSCs presented defects in neuronal differentiation, exhibited smaller somata, fewer branches and shorter neurites, accompanied by mitochondrial dysfunction including fragmented mitochondria, reduced ATP and elevated ROS.

2025-03-19 | GSE284292 | GEO

Dysfunctional mitochondria trap proteins in the intermembrane space - Data set 4: AP-MS for Apj1, Pwp2 and Utp18

Project description:Mitochondria consist of hundreds of proteins which are initially synthesized in the cytosol as ‘precursors’ and imported into the organelle. The accumulation of precursors in the cytosol due to mitochondrial dysfunction compromises cellular proteostasis and is a hallmark of diseases. How cells counteract the accumulation of potentially toxic precursors in the cytosol is poorly understood. Using a proximity labeling-based assay to globally monitor the intramitochondrial location of proteins, we show, that upon mitochondrial dysfunction many mitochondrial matrix proteins are sequestered in the intermembrane space (IMS). This Mitochondrial Triage of Precursor proteins (MitoTraP) was not simply the result of a general translocation block at the level of the inner membrane. Rather, MitoTraP specifically directs a defined subgroup of matrix proteins into the IMS, most of which being constituents of the mitochondrial ribosome. Using the mitoribosomal protein Mrp17 (bS6m) as a model, we found that the targeting into the IMS prevents the mistargeting to the nucleolus and the interference with ribosome assembly. Thus, MitoTraP represents a novel, so far unknown mechanism of the eukaryotic quality control system that protects the cellular proteome again toxic effects of non-imported mitochondrial precursor proteins.

2025-05-21 | PXD062600 | 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