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Yuan Z, van Delft MF, Li MX, Sumardy F, Smith BJ, Huang DCS, Lessene G, Khakam Y, Jin R, He S, Smith NA, Birkinshaw RW, Czabotar PE, Dewson G. Key residues in the VDAC2-BAK complex can be targeted to modulate apoptosis. PLoS Biol 2024; 22:e3002617. [PMID: 38696533 PMCID: PMC11098506 DOI: 10.1371/journal.pbio.3002617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/16/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
BAK and BAX execute intrinsic apoptosis by permeabilising the mitochondrial outer membrane. Their activity is regulated through interactions with pro-survival BCL-2 family proteins and with non-BCL-2 proteins including the mitochondrial channel protein VDAC2. VDAC2 is important for bringing both BAK and BAX to mitochondria where they execute their apoptotic function. Despite this important function in apoptosis, while interactions with pro-survival family members are well characterised and have culminated in the development of drugs that target these interfaces to induce cancer cell apoptosis, the interaction between BAK and VDAC2 remains largely undefined. Deep scanning mutagenesis coupled with cysteine linkage identified key residues in the interaction between BAK and VDAC2. Obstructive labelling of specific residues in the BH3 domain or hydrophobic groove of BAK disrupted this interaction. Conversely, mutating specific residues in a cytosol-exposed region of VDAC2 stabilised the interaction with BAK and inhibited BAK apoptotic activity. Thus, this VDAC2-BAK interaction site can potentially be targeted to either inhibit BAK-mediated apoptosis in scenarios where excessive apoptosis contributes to disease or to promote BAK-mediated apoptosis for cancer therapy.
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Affiliation(s)
- Zheng Yuan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Mark F. van Delft
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Mark Xiang Li
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Australia
| | - Fransisca Sumardy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Brian J. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - David C. S. Huang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Guillaume Lessene
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Melbourne, Australia
| | - Yelena Khakam
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Ruitao Jin
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
- Research School of Biology, Australian National University, Canberra, Australia
| | - Sitong He
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Nicholas A. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Richard W. Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Peter E. Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Grant Dewson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
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Gan ZY, Callegari S, Nguyen TN, Kirk NS, Leis A, Lazarou M, Dewson G, Komander D. Interaction of PINK1 with nucleotides and kinetin. Sci Adv 2024; 10:eadj7408. [PMID: 38241364 PMCID: PMC10798554 DOI: 10.1126/sciadv.adj7408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
The ubiquitin kinase PINK1 accumulates on damaged mitochondria to trigger mitophagy, and PINK1 loss-of-function mutations cause early onset Parkinson's disease. Nucleotide analogs such as kinetin triphosphate (KTP) were reported to enhance PINK1 activity and may represent a therapeutic strategy for the treatment of Parkinson's disease. Here, we investigate the interaction of PINK1 with nucleotides, including KTP. We establish a cryo-EM platform exploiting the dodecamer assembly of Pediculus humanus corporis (Ph) PINK1 and determine PINK1 structures bound to AMP-PNP and ADP, revealing conformational changes in the kinase N-lobe that help establish PINK1's ubiquitin binding site. Notably, we find that KTP is unable to bind PhPINK1 or human (Hs) PINK1 due to a steric clash with the kinase "gatekeeper" methionine residue, and mutation to Ala or Gly is required for PINK1 to bind and use KTP as a phosphate donor in ubiquitin phosphorylation and mitophagy. HsPINK1 M318G can be used to conditionally uncouple PINK1 stabilization and activity on mitochondria.
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Affiliation(s)
- Zhong Yan Gan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sylvie Callegari
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Thanh N. Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Nicholas S. Kirk
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Leis
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Grant Dewson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - David Komander
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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Frank D, Bergamasco M, Mlodzianoski MJ, Kueh A, Tsui E, Hall C, Kastrappis G, Voss AK, McLean C, Faux M, Rogers KL, Tran B, Vincan E, Komander D, Dewson G, Tran H. Trabid patient mutations impede the axonal trafficking of adenomatous polyposis coli to disrupt neurite growth. eLife 2023; 12:RP90796. [PMID: 38099646 PMCID: PMC10723793 DOI: 10.7554/elife.90796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
ZRANB1 (human Trabid) missense mutations have been identified in children diagnosed with a range of congenital disorders including reduced brain size, but how Trabid regulates neurodevelopment is not understood. We have characterized these patient mutations in cells and mice to identify a key role for Trabid in the regulation of neurite growth. One of the patient mutations flanked the catalytic cysteine of Trabid and its deubiquitylating (DUB) activity was abrogated. The second variant retained DUB activity, but failed to bind STRIPAK, a large multiprotein assembly implicated in cytoskeleton organization and neural development. Zranb1 knock-in mice harboring either of these patient mutations exhibited reduced neuronal and glial cell densities in the brain and a motor deficit consistent with fewer dopaminergic neurons and projections. Mechanistically, both DUB-impaired and STRIPAK-binding-deficient Trabid variants impeded the trafficking of adenomatous polyposis coli (APC) to microtubule plus-ends. Consequently, the formation of neuronal growth cones and the trajectory of neurite outgrowth from mutant midbrain progenitors were severely compromised. We propose that STRIPAK recruits Trabid to deubiquitylate APC, and that in cells with mutant Trabid, APC becomes hyperubiquitylated and mislocalized causing impaired organization of the cytoskeleton that underlie the neuronal and developmental phenotypes.
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Affiliation(s)
- Daniel Frank
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Maria Bergamasco
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Michael J Mlodzianoski
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Centre for Dynamic Imaging, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Andrew Kueh
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Melbourne Advanced Genome Editing Centre, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, Australia
| | - Ellen Tsui
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Histology Facility, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Cathrine Hall
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Georgios Kastrappis
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anne Kathrin Voss
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Catriona McLean
- Department of Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Maree Faux
- Neuro-Oncology Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Kelly L Rogers
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Centre for Dynamic Imaging, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Bang Tran
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Elizabeth Vincan
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- The Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David Komander
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Grant Dewson
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Hoanh Tran
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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