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Definition of the human mitochondrial TOM interactome reveals TRABD as new interacting protein (TRABD IP data)

ABSTRACT: The mitochondrial proteome arises from dual genetic origin. Nuclear-encoded proteins need to be transported across or inserted into two distinguished membranes, and the TOM complex represents the main translocase in the outer mitochondrial membrane. Its composition and regulations have been extensively investigated within yeast cells. However, we have little knowledge of the TOM complex composition within human cells. Here, we have defined the TOM interactome in a comprehensive manner using biochemical approaches to isolate the TOM complex in combination with quantitative mass spectrometry analyses. Within these studies, we defined the pleiotropic nature of the human TOM complex, including new interactors, such as TRABD. Our studies provide a framework to understand the various biogenesis pathways that merge at the TOM complex within human cells.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Julian Bender

LAB HEAD: Bettina Warscheid

PROVIDER: PXD062440 | Pride | 2025-04-15

REPOSITORIES: Pride

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			Action	DRS
	Oxidation_M_Sites.txt	Txt
	QEplus036720.raw	Raw
	QEplus036721.raw	Raw
	QEplus036723.raw	Raw
	QEplus036724.raw	Raw

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Definition of the human mitochondrial TOM interactome reveals TRABD as new interacting protein (TOM20 IP data)

Project description:The mitochondrial proteome arises from dual genetic origin. Nuclear-encoded proteins need to be transported across or inserted into two distinguished membranes, and the TOM complex represents the main translocase in the outer mitochondrial membrane. Its composition and regulations have been extensively investigated within yeast cells. However, we have little knowledge of the TOM complex composition within human cells. Here, we have defined the TOM interactome in a comprehensive manner using biochemical approaches to isolate the TOM complex in combination with quantitative mass spectrometry analyses. Within these studies, we defined the pleiotropic nature of the human TOM complex, including new interactors, such as TRABD. Our studies provide a framework to understand the various biogenesis pathways that merge at the TOM complex within human cells.

2025-04-15 | PXD062418 | Pride

Definition of the human mitochondrial TOM interactome reveals TRABD as new interacting protein (MAPL IP data)

2025-04-15 | PXD062420 | Pride

Definition of the human mitochondrial TOM interactome reveals TRABD as new interacting protein (TRABD siRNA data)

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Receptor-mediated recruitment of cytosolic J-proteins to the mitochondrial outer membrane promotes assembly of preprotein translocases

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2018-11-26 | PXD008203 | Pride

Tom20 gates PINK1 activity and mediates its tethering of the TOM and TIM23 translocases upon mitochondrial stress

Project description:Mutations in PTEN-induced putative kinase 1 (PINK1) cause autosomal recessive early onset Parkinson disease (PD). PINK1 is a Ser/Thr kinase that regulates mitochondrial quality control by triggering mitophagy mediated by the ubiquitin ligase Parkin. Upon mitochondrial damage, PINK1 accumulates on the outer mitochondrial membrane (OMM) forming a high molecular weight complex with the translocase of the outer membrane (TOM). PINK1 then phosphorylates ubiquitin, which enables recruitment and activation of Parkin followed by autophagic clearance of the damaged mitochondrion. Thus, Parkin-dependent mitophagy hinges on the stable accumulation of PINK1 on the TOM complex. Yet, the mechanism linking mitochondrial stressors to PINK1 accumulation and whether the translocases of the inner membrane (TIMs) are also involved, remain unclear. Herein, we demonstrate that mitochondrial stress induces the formation of a PINK1-TOM-TIM23 supercomplex in human cultured cell lines, dopamine neurons, and midbrain organoids. Moreover, we show that PINK1 is required to stably tether the TOM to TIM23 complexes in response to stress, such that the supercomplex fails to accumulate in cells lacking PINK1. This tethering is dependent on an interaction between the PINK1 NT-CTE module and the cytosolic domain of the Tom20 subunit of the TOM complex, the disruption of which, by either designer or PD-associated PINK1 mutations, inhibits downstream mitophagy. Together, the findings provide key insight into how PINK1 interfaces with the mitochondrial import machinery, with important implications for the mechanisms of mitochondrial quality control and PD pathogenesis.

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Project description:Protein import and genome replication are essential processes for mitochondrial biogenesis and propagation. The J-domain proteins Pam16 and Pam18 regulate the presequence translocase of the mitochondrial inner membrane. In the protozoan Trypanosoma brucei, their counterparts are TbPam16 and TbPam18, which are essential for the procyclic form of the parasite, though not involved in mitochondrial protein import. Here, we show that during evolution, the two proteins have been repurposed to regulate the replication of maxicircles within the intricate kDNA network, the most complex mitochondrial genome known. TbPam18 and TbPam16 have inactive J-domains suggesting a function independent of heat shock proteins. However, their single transmembrane domain is essential for function. Pulldown of TbPam16 identifies a putative client protein, termed MaRF11, the depletion of which causes the selective loss of maxicircles, akin to the effects observed for TbPam18 and TbPam16. The level of MaRF11 is controlled by the mitochondrial proteasome. Thus, we propose a model for a membrane-bound regulatory circuit that controls maxicircle replication in response to an unknown nuclear signal. This model posits that MaRF11 directly mediates maxicircle replication, that its activity is regulated by the mitochondrial proteasome that its level is controlled by proteasomal digested that it is protected from degradation by binding to the TbPam18/TbPam16 dimer.

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Silencing mitochondrial gene expression in living cells – FLAG IPs

Project description:Mitochondria fullfill central functions in cellular metabolism and energy supply. They express their own genome, which encodes key subunits of the oxidative phosphorylation system. However, central mechanisms underlying mitochondrial gene expression remain enigmatic. A lack of suitable technologies to target mitochondrial protein synthesis in living cells has limited experimental access. Here, we silence the translation of specific mitochondrial mRNAs in living cells by delivering synthetic peptide-morpholino chimeras. This approach allows comprehensive temporal monitoring of cellular responses. Our study provides insights into mitochondrial translation, its integration into cellular physiology, and represents an innovative strategy to address mitochondrial gene expression in living cells. The tools that we present can readily be applied to analyze the mechanisms and pathophysiology of mitochondrial gene expression in a broad range of cellular model systems.

2025-04-17 | PXD061877 | Pride

A hybrid TIM complex mediates protein import into hydrogenosomes of Trichomonas vaginalis

Project description:Hydrogenosomes are a specific type of mitochondria that have adapted for life under anaerobiosis. Limited availability of oxygen has resulted in the loss of the membrane- associated respiratory chain, and consequently in the generation of minimal inner membrane potential (), and inefficient ATP synthesis via substrate-level phosphorylation. The changes in energy metabolism are directly linked with the organelle biogenesis. In mitochondria, proteins are imported across the outer membrane via the Translocase of the Outer Membrane (TOM complex), while two Translocases of the Inner Membrane, TIM22, and TIM23, facilitate import to the inner membrane and matrix. TIM23-mediated steps are entirely dependent on and ATP hydrolysis, while TIM22 requires only . The character of the hydrogenosomal inner membrane translocase and the mechanism of translocation is currently unknown.

2024-06-16 | PXD047649 | Pride

Effect of LINC00899 depletion on histone mark enrichment in HeLa cells

Project description:LncRNAs represent a major transcriptional output of the human genome, but the function of many of these elements is unknown. In this experiment, we have used the ‘CUT&RUN’ technique to quantify the changes in histone mark enrichment across the genome upon depletion of the lncRNA LINC00899 in HeLa cells. LINC00899 is of interest as its depletion results in mitotic delay, suggesting a role in mitotic progression. The CUT&RUN procedure uses antibodies to target a nuclease to the relevant protein binding site, cleaving the surrounding DNA for sequencing and yielding output equivalent to that of ChIP-seq. This experiment contains 2 replicate batches where each batch contains a sample with LINC00899 knocked down by RNA interference (RNAi); a RNAi negative control; a sample with LINC00899 knocked down with locked nucleic acid antisense oligonucleotides (LNA); and a LNA negative control. This was performed using antibodies against H3K4me3, H3K27ac, H3K36me3 and H3K27me3, as well as an IgG (goat-derived anti-rabbit) control. All samples in each batch were generated at the same time. Within each batch, all CUT&RUN experiments with the same knockdown were performed on nuclei obtained from the same cell culture. Independent cell cultures were used for experiments with different knockdown or in different batches.

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2023-01-11 | E-MTAB-12512 | biostudies-arrayexpress

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