1
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Egner JM, Nolden KA, Harwig MC, Bonate RP, De Anda J, Tessmer MH, Noey EL, Ihenacho UK, Liu Z, Peterson FC, Wong GCL, Widlansky ME, Hill RB. Structural studies of human fission protein FIS1 reveal a dynamic region important for GTPase DRP1 recruitment and mitochondrial fission. J Biol Chem 2022; 298:102620. [PMID: 36272645 PMCID: PMC9747602 DOI: 10.1016/j.jbc.2022.102620] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Fission protein 1 (FIS1) and dynamin-related protein 1 (DRP1) were initially described as being evolutionarily conserved for mitochondrial fission, yet in humans the role of FIS1 in this process is unclear and disputed by many. In budding yeast where Fis1p helps to recruit the DRP1 ortholog from the cytoplasm to mitochondria for fission, an N-terminal "arm" of Fis1p is required for function. The yeast Fis1p arm interacts intramolecularly with a conserved tetratricopeptide repeat core and governs in vitro interactions with yeast DRP1. In human FIS1, NMR and X-ray structures show different arm conformations, but its importance for human DRP1 recruitment is unknown. Here, we use molecular dynamics simulations and comparisons to experimental NMR chemical shifts to show the human FIS1 arm can adopt an intramolecular conformation akin to that observed with yeast Fis1p. This finding is further supported through intrinsic tryptophan fluorescence and NMR experiments on human FIS1 with and without the arm. Using NMR, we observed the human FIS1 arm is also sensitive to environmental changes. We reveal the importance of these findings in cellular studies where removal of the FIS1 arm reduces DRP1 recruitment and mitochondrial fission similar to the yeast system. Moreover, we determined that expression of mitophagy adapter TBC1D15 can partially rescue arm-less FIS1 in a manner reminiscent of expression of the adapter Mdv1p in yeast. These findings point to conserved features of FIS1 important for its activity in mitochondrial morphology. More generally, other tetratricopeptide repeat-containing proteins are flanked by disordered arms/tails, suggesting possible common regulatory mechanisms.
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Affiliation(s)
- John M Egner
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kelsey A Nolden
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Megan Cleland Harwig
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Ryan P Bonate
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jaime De Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
| | - Maxx H Tessmer
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Elizabeth L Noey
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Ugochukwu K Ihenacho
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Ziwen Liu
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
| | - Michael E Widlansky
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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2
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Lee M, Lee EY, Lai GH, Kennedy NW, Posey AE, Xian W, Ferguson AL, Hill RB, Wong GCL. Molecular Motor Dnm1 Synergistically Induces Membrane Curvature To Facilitate Mitochondrial Fission. ACS CENTRAL SCIENCE 2017; 3:1156-1167. [PMID: 29202017 PMCID: PMC5704292 DOI: 10.1021/acscentsci.7b00338] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Indexed: 05/30/2023]
Abstract
Dnm1 and Fis1 are prototypical proteins that regulate yeast mitochondrial morphology by controlling fission, the dysregulation of which can result in developmental disorders and neurodegenerative diseases in humans. Loss of Dnm1 blocks the formation of fission complexes and leads to elongated mitochondria in the form of interconnected networks, while overproduction of Dnm1 results in excessive mitochondrial fragmentation. In the current model, Dnm1 is essentially a GTP hydrolysis-driven molecular motor that self-assembles into ring-like oligomeric structures that encircle and pinch the outer mitochondrial membrane at sites of fission. In this work, we use machine learning and synchrotron small-angle X-ray scattering (SAXS) to investigate whether the motor Dnm1 can synergistically facilitate mitochondrial fission by membrane remodeling. A support vector machine (SVM)-based classifier trained to detect sequences with membrane-restructuring activity identifies a helical Dnm1 domain capable of generating negative Gaussian curvature (NGC), the type of saddle-shaped local surface curvature found on scission necks during fission events. Furthermore, this domain is highly conserved in Dnm1 homologues with fission activity. Synchrotron SAXS measurements reveal that Dnm1 restructures membranes into phases rich in NGC, and is capable of inducing a fission neck with a diameter of 12.6 nm. Through in silico mutational analysis, we find that the helical Dnm1 domain is locally optimized for membrane curvature generation, and phylogenetic analysis suggests that dynamin superfamily proteins that are close relatives of human dynamin Dyn1 have evolved the capacity to restructure membranes via the induction of curvature mitochondrial fission. In addition, we observe that Fis1, an adaptor protein, is able to inhibit the pro-fission membrane activity of Dnm1, which points to the antagonistic roles of the two proteins in the regulation of mitochondrial fission.
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Affiliation(s)
- Michelle
W. Lee
- Department
of Bioengineering, Department of Chemistry & Biochemistry, and California NanoSystems
Institute, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Ernest Y. Lee
- Department
of Bioengineering, Department of Chemistry & Biochemistry, and California NanoSystems
Institute, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Ghee Hwee Lai
- Department
of Bioengineering, Department of Chemistry & Biochemistry, and California NanoSystems
Institute, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Nolan W. Kennedy
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Ammon E. Posey
- Department
of Biomedical Engineering, Washington University
in St. Louis, St. Louis, Missouri 63130, United
States
| | - Wujing Xian
- Department
of Bioengineering, Department of Chemistry & Biochemistry, and California NanoSystems
Institute, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Andrew L. Ferguson
- Department of Materials Science
and Engineering and Department of Chemical and Biomolecular
Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - R. Blake Hill
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Gerard C. L. Wong
- Department
of Bioengineering, Department of Chemistry & Biochemistry, and California NanoSystems
Institute, University of California, Los
Angeles, Los Angeles, California 90095, United States
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3
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Koppenol-Raab M, Harwig MC, Posey AE, Egner JM, MacKenzie KR, Hill RB. A Targeted Mutation Identified through pKa Measurements Indicates a Postrecruitment Role for Fis1 in Yeast Mitochondrial Fission. J Biol Chem 2016; 291:20329-44. [PMID: 27496949 DOI: 10.1074/jbc.m116.724005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Indexed: 12/25/2022] Open
Abstract
The tail-anchored protein Fis1 is implicated as a passive tether in yeast mitochondrial fission. We probed the functional role of Fis1 Glu-78, whose elevated side chain pKa suggests participation in protein interactions. Fis1 binds partners Mdv1 or Dnm1 tightly, but mutation E78A weakens Fis1 interaction with Mdv1, alters mitochondrial morphology, and abolishes fission in a growth assay. In fis1Δ rescue experiments, Fis1-E78A causes a novel localization pattern in which Dnm1 uniformly coats the mitochondria. By contrast, Fis1-E78A at lower expression levels recruits Dnm1 into mitochondrial punctate structures but fails to support normal fission. Thus, Fis1 makes multiple interactions that support Dnm1 puncta formation and may be essential after this step, supporting a revised model for assembly of the mitochondrial fission machinery. The insights gained by mutating a residue with a perturbed pKa suggest that side chain pKa values inferred from routine NMR sample pH optimization could provide useful leads for functional investigations.
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Affiliation(s)
| | - Megan Cleland Harwig
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
| | - Ammon E Posey
- From the Department of Biology and the Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218
| | - John M Egner
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
| | - Kevin R MacKenzie
- the Department of Pathology, Baylor College of Medicine, Houston, Texas 77030
| | - R Blake Hill
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
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4
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Hill RB, MacKenzie KR, Harwig MC. The Tail-End Is Only the Beginning: NMR Study Reveals a Membrane-Bound State of BCL-XL. J Mol Biol 2015; 427:2257-61. [PMID: 25896456 DOI: 10.1016/j.jmb.2015.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kevin R MacKenzie
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Megan Cleland Harwig
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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5
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Cheong FKY, Feng L, Sarkeshik A, Yates JR, Schroer TA. Dynactin integrity depends upon direct binding of dynamitin to Arp1. Mol Biol Cell 2014; 25:2171-80. [PMID: 24829381 PMCID: PMC4091830 DOI: 10.1091/mbc.e14-03-0842] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Dynactin is an adaptor complex that binds cytoplasmic dynein to cellular cargoes. Its dynamitin (p50) component plays a key role in dynactin stability. Affinity chromatography, direct binding assays, and RNAi demonstrate that the unstructured dynamitin N-terminus binds the dynactin component Arp1 directly. Dynactin is a multiprotein complex that works with cytoplasmic dynein and other motors to support a wide range of cell functions. It serves as an adaptor that binds both dynein and cargoes and enhances single-motor processivity. The dynactin subunit dynamitin (also known as p50) is believed to be integral to dynactin structure because free dynamitin displaces the dynein-binding p150Glued subunit from the cargo-binding Arp1 filament. We show here that the intrinsically disordered dynamitin N-terminus binds to Arp1 directly. When expressed in cells, dynamitin amino acids (AA) 1–87 causes complete release of endogenous dynamitin, p150, and p24 from dynactin, leaving behind Arp1 filaments carrying the remaining dynactin subunits (CapZ, p62, Arp11, p27, and p25). Tandem-affinity purification–tagged dynamitin AA 1–87 binds the Arp filament specifically, and binding studies with purified native Arp1 reveal that this fragment binds Arp1 directly. Neither CapZ nor the p27/p25 dimer contributes to interactions between dynamitin and the Arp filament. This work demonstrates for the first time that Arp1 can directly bind any protein besides another Arp and provides important new insight into the underpinnings of dynactin structure.
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Affiliation(s)
| | - Lijuan Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Ali Sarkeshik
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - Trina A Schroer
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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6
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Lees JPB, Manlandro CM, Picton LK, Tan AZE, Casares S, Flanagan JM, Fleming KG, Hill RB. A designed point mutant in Fis1 disrupts dimerization and mitochondrial fission. J Mol Biol 2012; 423:143-58. [PMID: 22789569 DOI: 10.1016/j.jmb.2012.06.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/21/2012] [Accepted: 06/24/2012] [Indexed: 01/06/2023]
Abstract
Mitochondrial and peroxisomal fission are essential processes with defects resulting in cardiomyopathy and neonatal lethality. Central to organelle fission is Fis1, a monomeric tetratricopeptide repeat (TPR)-like protein whose role in assembly of the fission machinery remains obscure. Two nonfunctional, Saccharomyces cerevisiae Fis1 mutants (L80P or E78D/I85T/Y88H) were previously identified in genetic screens. Here, we find that these two variants in the cytosolic domain of Fis1 (Fis1ΔTM) are unexpectedly dimeric. A truncation variant of Fis1ΔTM that lacks an N-terminal regulatory domain is also found to be dimeric. The ability to dimerize is a property innate to the native Fis1ΔTM amino acid sequence as we find this domain is dimeric after transient exposure to elevated temperature or chemical denaturants and is kinetically trapped at room temperature. This is the first demonstration of a specific self-association in solution for the Fis1 cytoplasmic domain. We propose a three-dimensional domain-swapped model for dimerization that is validated by a designed mutation, A72P, which potently disrupts dimerization of wild-type Fis1. A72P also disrupts dimerization of nonfunctional variants, indicating a common structural basis for dimerization. The obligate monomer variant A72P, like the dimer-promoting variants, is nonfunctional in fission, consistent with a model in which Fis1 activity depends on its ability to interconvert between monomer and dimer species. These studies suggest a new functionally important manner in which TPR-containing proteins may reversibly self-associate.
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Affiliation(s)
- Jonathan P B Lees
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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7
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Tooley JE, Khangulov V, Lees JPB, Schlessman JL, Bewley MC, Heroux A, Bosch J, Hill RB. The 1.75 Å resolution structure of fission protein Fis1 from Saccharomyces cerevisiae reveals elusive interactions of the autoinhibitory domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1310-5. [PMID: 22102223 DOI: 10.1107/s1744309111029368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/20/2011] [Indexed: 11/10/2022]
Abstract
Fis1 mediates mitochondrial and peroxisomal fission. It is tail-anchored to these organelles by a transmembrane domain, exposing a soluble cytoplasmic domain. Previous studies suggested that Fis1 is autoinhibited by its N-terminal region. Here, a 1.75 Å resolution crystal structure of the Fis1 cytoplasmic domain from Saccharomyces cerevisiae is reported which adopts a tetratricopeptide-repeat fold. It is observed that this fold creates a concave surface important for fission, but is sterically occluded by its N-terminal region. Thus, this structure provides a physical basis for autoinhibition and allows a detailed examination of the interactions that stabilize the inhibited state of this molecule.
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Affiliation(s)
- James E Tooley
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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8
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Wells RC, Hill RB. The cytosolic domain of Fis1 binds and reversibly clusters lipid vesicles. PLoS One 2011; 6:e21384. [PMID: 21738650 PMCID: PMC3125187 DOI: 10.1371/journal.pone.0021384] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/27/2011] [Indexed: 11/18/2022] Open
Abstract
Every lipid membrane fission event involves the association of two apposing bilayers, mediated by proteins that can promote membrane curvature, fusion and fission. We tested the hypothesis that Fis1, a tail-anchored protein involved in mitochondrial and peroxisomal fission, promotes changes in membrane structure. We found that the cytosolic domain of Fis1 alone binds lipid vesicles, which is enhanced upon protonation and increasing concentrations of anionic phospholipids. Fluorescence and circular dichroism data indicate that the cytosolic domain undergoes a membrane-induced conformational change that buries two tryptophan side chains upon membrane binding. Light scattering and electron microscopy data show that membrane binding promotes lipid vesicle clustering. Remarkably, this vesicle clustering is reversible and vesicles largely retain their original shape and size. This raises the possibility that the Fis1 cytosolic domain might act in membrane fission by promoting a reversible membrane association, a necessary step in membrane fission.
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Affiliation(s)
- Robert C. Wells
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - R. Blake Hill
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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9
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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10
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Hofmann L, Saunier R, Cossard R, Esposito M, Rinaldi T, Delahodde A. A nonproteolytic proteasome activity controls organelle fission in yeast. J Cell Sci 2009; 122:3673-83. [PMID: 19773362 DOI: 10.1242/jcs.050229] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To understand the processes underlying organelle function, dynamics and inheritance, it is necessary to identify and characterize the regulatory components involved. Recently in yeast and mammals, proteins of the membrane fission machinery (Dnm1-Mdv1-Caf4-Fis1 in yeast and DLP1-FIS1 in human) have been shown to have a dual localization on mitochondria and peroxisomes, where they control mitochondrial fission and peroxisome division. Here, we show that whereas vacuole fusion is regulated by the proteasome degradation function, mitochondrial fission and peroxisomal division are not controlled by the proteasome activity but rather depend on a new function of the proteasomal lid subunit Rpn11. Rpn11 was found to regulate the Fis1-dependent fission machinery of both organelles. These findings indicate a unique role of the Rpn11 protein in mitochondrial fission and peroxisomal proliferation that is independent of its role in proteasome-associated deubiquitylation.
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Affiliation(s)
- Line Hofmann
- University of Paris-Sud, CNRS, UMR 8621, Institute of Genetics and Microbiology, Orsay 91405, France
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