A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling

Malty, Ramy H.; Aoki, Hiroyuki; Kumar, Ashwani; Phanse, Sadhna; Amin, Shahreen; Zhang, Qingzhou; Minić, Zoran; Goebels, Florian; Musso, Gabriel; Wu, Zhuoran; Abou-tok, Hosam; Meyer, Michael J.; Deineko, Viktor; Kassir, Sandy; Sidhu, Vishaldeep; Jessulat, Matthew; Scott, Nichollas E.; Xiong, Xuejian; Vlasblom, James; Prasad, Bhanu; Foster, Leonard J.; Alberio, Tiziana; Garavaglia, Barbara; Yu, Haiyuan; Bader, Gary D.; Nakamura, Ken; Parkinson, John; Babu, Mohan

doi:10.1016/j.cels.2017.10.010

Cited by 47 publications

(38 citation statements)

References 47 publications

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“…We have detected differentially interacting proteins by comparing data sets from the hippocampus and the CA3 subfield of the hippocampus. All the CA3 (PSD95-cTAP; Grik4 Cre) enriched proteins (Abr, Actn4, Bai3, Cacng8, Grik2, Hist1h2al, Mbp, Nlgn3 and Prdx5) have been reported to have important functions in brain that include roles in synapse formation, synaptic plasticity and psychiatric disorders (Duman, Tu, & Tolias, 2016;Ge et al, 2016;Kalinowska et al, 2015;Lanoue et al, 2013;Malty et al, 2017;Martinelli et al, 2016;Oh et al, 2010;Park et al, 2017;Sigoillot et al, 2015;Walikonis et al, 2001;Yamagata et al, 2017). This might indicate that different types of PSD95 complexes exist in different brain regions with distinct functions.…”

Section: Discussionmentioning

confidence: 99%

Cell‐type‐specific visualisation and biochemical isolation of endogenous synaptic proteins in mice

Zhu

Collins

Harmse

et al. 2019

Eur J of Neuroscience

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In recent years, the remarkable molecular complexity of synapses has been revealed, with over 1,000 proteins identified in the synapse proteome. Although it is known that different receptors and other synaptic proteins are present in different types of neurons, the extent of synapse diversity across the brain is largely unknown. This is mainly due to the limitations of current techniques. Here, we report an efficient method for the purification of synaptic protein complexes, fusing a high‐affinity tag to endogenous PSD95 in specific cell types. We also developed a strategy, which enables the visualisation of endogenous PSD95 with fluorescent‐protein tag in Cre‐recombinase‐expressing cells. We demonstrate the feasibility of proteomic analysis of synaptic protein complexes and visualisation of these in specific cell types. We find that the composition of PSD95 complexes purified from specific cell types differs from those extracted from tissues with diverse cellular composition. The results suggest that there might be differential interactions in the PSD95 complexes in different brain regions. We have detected differentially interacting proteins by comparing data sets from the whole hippocampus and the CA3 subfield of the hippocampus. Therefore, these novel conditional PSD95 tagging lines will not only serve as powerful tools for precisely dissecting synapse diversity in specific brain regions and subsets of neuronal cells, but also provide an opportunity to better understand brain region‐ and cell‐type‐specific alterations associated with various psychiatric/neurological diseases. These newly developed conditional gene tagging methods can be applied to many different synaptic proteins and will facilitate research on the molecular complexity of synapses.

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Section: Discussionmentioning

confidence: 99%

Cell‐type‐specific visualisation and biochemical isolation of endogenous synaptic proteins in mice

Zhu

Collins

Harmse

et al. 2019

Eur J of Neuroscience

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“…Our group (Antonicka et al, 2017;Antonicka and Shoubridge, 2015;Janer et al, 2016) and others (Floyd et al, 2016) have defined, for mitochondrial proteins of interest, their interacting protein partners using affinity purification (or affinity enrichment)-mass spectrometry approaches. Large-scale investigations of protein-protein interactions have also been carried out by affinity purification followed by mass spectrometry using tagged, overexpressed baits (Huttlin et al, 2017;Malty et al, 2017). While these data are generally very useful in identifying soluble protein complexes, they are performed under conditions that may be sub-optimal for membrane proteins in organelles, and the analyses are carried out after cell lysis, which does not always represent the in vivo situation.…”

Section: Introductionmentioning

confidence: 99%

A high-density human mitochondrial proximity interaction network

Antonická

Lin

Janer

et al. 2020

Preprint

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We used BioID, a proximity-dependent biotinylation assay, to interrogate 100 mitochondrial baits from all mitochondrial sub-compartments to create a high resolution human mitochondrial proximity interaction network. We identified 1465 proteins, producing 15626 unique high confidence proximity interactions. Of these, 528 proteins were previously annotated as mitochondrial, nearly half of the mitochondrial proteome defined by Mitocarta 2.0. Bait-bait analysis showed a clear separation of mitochondrial compartments, and correlation analysis among preys across all baits allowed us to identify functional clusters involved in diverse mitochondrial functions, and to assign uncharacterized proteins to specific modules. We demonstrate that this analysis can assign isoforms of the same mitochondrial protein to different mitochondrial sub-compartments, and show that some proteins may have multiple cellular locations. Outer membrane baits showed specific proximity interactions with cytosolic proteins and proteins in other organellar membranes, suggesting specialization of proteins responsible for contact site formation between mitochondria and individual organelles. This proximity network will be a valuable resource for exploring the biology of uncharacterized mitochondrial proteins, the interactions of mitochondria with other cellular organelles, and will provide a framework to interpret alterations in sub-mitochondrial environments associated with mitochondrial disease. Bullet points• We created a high resolution human mitochondrial protein proximity map using BioID• Bait-bait analysis showed that the map has sub-compartment resolution and correlation analysis of preys identified functional clusters and assigned proteins to specific modules• We identified isoforms of matrix and IMS proteins with multiple cellular localizations and an endonuclease that localizes to both the matrix and the OMM • OMM baits showed specific interactions with non-mitochondrial proteins reflecting organellar contact sites and protein dual localization 2013). Mitochondrial diseases due to deficiencies in the oxidative phosphorylation machinery are amongst the most common inherited metabolic disorders (Frazier et al., 2019;Nunnari and Suomalainen, 2012). While nearly 300 causal genes have now been identified, the molecular basis for the extraordinary tissue specificity associated with these diseases remains an enduring mystery.Mitochondria are double-membraned organelles, whose ultrastructure has been investigated for decades. The outer membrane (OMM), which serves as a platform for molecules involved in the regulation of innate immunity and for regulation of apoptosis, is permeable to metabolites and small proteins, and it forms close contacts with the endoplasmic reticulum (ER) for the exchange of lipids and calcium (Csordas et al., 2018). The impermeable inner membrane (IMM) is composed of invaginations called cristae that contain the complexes of the oxidative phosphorylation system. The intermembrane space (IMS) comprises both the space formed...

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“…have been reported to have important functions in brain that include roles for synapse formation, synaptic plasticity and psychiatric disorder (Walikonis et al, 2001;Oh et al, 2010;Lanoue et al, 2013;Kalinowska et al, 2015;Sigoillot et al, 2015;Duman et al, 2016;Ge et al, 2016;Martinelli et al, 2016;Malty et al, 2017;Park et al, 2017;Yamagata et al, 2017). This might implicate that different types of PSD95 complexes exist in different brain regions with distinct functions.…”

Section: Discussionmentioning

confidence: 99%

Cell-type specific visualization and biochemical isolation of endogenous synaptic proteins in mice

Zhu

Collins

Harmse

et al. 2018

Preprint

View full text Add to dashboard Cite

In recent years, the remarkable molecular complexity of synapses has been revealed, with over 1000 proteins identified in the synapse proteome. Although it is known that different receptors and other synaptic proteins are present in different types of neurons and synapses, the extent of synapse diversity across the brain is largely unknown, mainly owing to technical limitations. Combining mouse genetics and proteomics we have previously reported highly efficient methods for purification of synaptic protein complexes under native conditions. In that approach, tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD95 using gene targeting in mice. Here we report an approach that restricts tagging of endogenous PSD95 to cells expressing Cre recombinase. In addition, we developed a labelling strategy enabling visualization of endogenous PSD95 tagged by fluorescent proteins in Cre-expressing cells. We demonstrate the feasibility of proteomic characterisation of synapse proteomes and visualization of synapse proteins in specific cell types. We find that composition of PSD95 complexes purified from specific cell types differs from those extracted from tissues with diverse cellular composition. Therefore, these novel conditional PSD95 tagging lines will not only serve as powerful tools for precisely dissecting synapse diversity in specific subsets of regions/neuronal cells, but also provide an opportunity to better understand brain region-specific alterations associated with various psychiatric/neurological diseases. The newly developed conditional gene tagging methods can be applied to many different synaptic proteins and will thus facilitate research on the molecular complexity of synapses.

show abstract

A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling

Cited by 47 publications

References 47 publications

Cell‐type‐specific visualisation and biochemical isolation of endogenous synaptic proteins in mice

Cell‐type‐specific visualisation and biochemical isolation of endogenous synaptic proteins in mice

A high-density human mitochondrial proximity interaction network

Cell-type specific visualization and biochemical isolation of endogenous synaptic proteins in mice

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