Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain

Cho, N. H. et al. OpenCell: endogenous tagging for the cartography of human cellular organization. Science. 375, eabi6983 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu, L. Z. et al. EPIC: software toolkit for elution profile-based inference of protein complexes. Nat. Methods 16, 737–742 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gupta, R., Karczewski, K. J., Howrigan, D., Neale, B. M. & Mootha, V. K. Human genetic analyses of organelles highlight the nucleus in age-related trait heritability. eLife 10, e68610 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Uher, R. The role of genetic variation in the causation of mental illness: an evolution-informed framework. Mol. Psychiatry 14, 1072–1082 (2009).

Article  CAS  PubMed  Google Scholar 

Pang, S. Y. et al. The interplay of aging, genetics and environmental factors in the pathogenesis of Parkinson’s disease. Transl. Neurodegener. 8, 23 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Kuzmanov, U. & Emili, A. Protein–protein interaction networks: probing disease mechanisms using model systems. Genome Med. 5, 37 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. From molecular to modular cell biology. Nature 402, C47–C52 (1999).

Article  CAS  PubMed  Google Scholar 

Walhout, A. J. & Vidal, M. Protein interaction maps for model organisms. Nat. Rev. Mol. Cell Biol. 2, 55–62 (2001).

Article  CAS  PubMed  Google Scholar 

Malty, R. H. et al. A map of human mitochondrial protein interactions linked to neurodegeneration reveals new mechanisms of redox homeostasis and NF-kappaB signaling. Cell Syst. 5, 1–14 (2017).

Google Scholar 

Pourhaghighi, R. et al. BraInMap elucidates the macromolecular connectivity landscape of mammalian brain. Cell Syst. 10, 333–350.e14 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Barabasi, A. L., Gulbahce, N. & Loscalzo, J. Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 12, 56–68 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Babu, M. et al. Global landscape of cell envelope protein complexes in Escherichia coli. Nat. Biotechnol. 36, 103–112 (2018).

Article  CAS  PubMed  Google Scholar 

Babu, M. et al. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature 489, 585–589 (2012).

Article  CAS  PubMed  Google Scholar 

Krogan, N. J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643 (2006).

Article  CAS  PubMed  Google Scholar 

Malovannaya, A. et al. Analysis of the human endogenous coregulator complexome. Cell 145, 787–799 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huttlin, E. L. et al. Architecture of the human interactome defines protein communities and disease networks. Nature. 545, 505–509 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huttlin, E. L. et al. The BioPlex network: a systematic exploration of the human interactome. Cell 162, 425–440 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huttlin, E. L. et al. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 184, 3022–3040 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guruharsha, K. G. et al. A protein complex network of Drosophila melanogaster. Cell 147, 690–703 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cho, K. F. et al. Proximity labeling in mammalian cells with TurboID and split-TurboID. Nat. Protoc. 15, 3971–3999 (2020).

Article  CAS  PubMed  Google Scholar 

Havugimana, P. C. et al. A census of human soluble protein complexes. Cell 150, 1068–1081 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bludau, I. et al. Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. Nat. Protoc. 15, 2341–2386 (2020).

Article  CAS  PubMed  Google Scholar 

Liu, X. et al. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat. Commun. 9, 1188 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Hung, V. et al. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol. Cell 55, 332–341 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Branon, T. C. et al. Efficient proximity labeling in living cells and organisms with TurboID. Nat. Biotechnol. 36, 880–887 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Go, C. D. et al. A proximity-dependent biotinylation map of a human cell. Nature 595, 120–124 (2021).

Article  CAS  PubMed  Google Scholar 

Samavarchi-Tehrani, P., Samson, R. & Gingras, A. C. Proximity dependent biotinylation: key enzymes and adaptation to proteomics approaches. Mol. Cell Proteomics 19, 757–773 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wan, C. et al. Panorama of ancient metazoan macromolecular complexes. Nature 525, 339–344 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Skinnider, M. A. et al. An atlas of protein–protein interactions across mouse tissues. Cell 184, 4073–4089.e17 (2021).

Article  CAS  PubMed  Google Scholar 

Skinnider, M. A. & Foster, L. J. Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments. Nat. Methods 18, 806–815 (2021).

Article  CAS  PubMed  Google Scholar 

Magistretti, P. J. & Allaman, I. A cellular perspective on brain energy metabolism and functional imaging. Neuron 86, 883–901 (2015).

Article  CAS  PubMed  Google Scholar 

Picard, M. & McEwen, B. S. Mitochondria impact brain function and cognition. Proc. Natl Acad. Sci. USA 111, 7–8 (2014).

Article  CAS  PubMed  Google Scholar 

Aly, K. A., Moutaoufik, M. T., Phanse, S., Zhang, Q. & Babu, M. From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. iScience 24, 102030 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Norat, P. et al. Mitochondrial dysfunction in neurological disorders: exploring mitochondrial transplantation. NPJ Regen. Med. 5, 22 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Zilocchi, M., Broderick, K., Phanse, S., Aly, K. A. & Babu, M. Mitochondria under the spotlight: on the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. Comput. Struct. Biotechnol. J 18, 2535–2546 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

DiMauro, S. & Schon, E. A. Mitochondrial disorders in the nervous system. Annu. Rev. Neurosci. 31, 91–123 (2008).

Article  CAS  PubMed  Google Scholar 

Floyd, B. J. et al. Mitochondrial protein interaction mapping identifies regulators of respiratory chain function. Mol. Cell 63, 621–632 (2016).

Article 

Comments (0)

No login
gif