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PreprintCited by 25Heat shock proteins researchMitochondrial Function and PathologyProtein Structure and Dynamics

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Unique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3

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Cupo, Ryan R., Rizo, Alexandrea N., Braun, Gabriel A., Tse, Eric, Chuang, Edward, Southworth, Daniel R., Shorter, James·2022·Cell Reports
DOI 10.1101/2022.02.17.480866PMC PMC9584538

Preprint — published as 10.1016/j.celrep.2022.111408 · Paper page

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Abstract

Summary: The AAA+ protein, Skd3 (human CLPB ), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with impaired protein-disaggregase activity cause severe congenital neutropenia (SCN) and 3-methylglutaconic aciduria type 7 (MGCA7). Yet how Skd3 disaggregates proteins remains poorly understood. Here, we report a high-resolution structure of a Skd3-substrate complex. Skd3 adopts a spiral hexameric arrangement that engages substrate via pore-loop interactions in the nucleotide-binding domain (NBD). Unexpectedly, substrate-bound Skd3 hexamers stack head-to-head via unique, adaptable ankyrin-repeat domain (ANK)-mediated interactions to form dodecamers. Deleting the ANK-linker region reduces dodecamerization and disaggregase activity. We elucidate apomorphic features of the Skd3 NBD and C-terminal domain that regulate disaggregase activity. We also define how Skd3 subunits collaborate to disaggregate proteins. Importantly, SCN-linked subunits sharply inhibit disaggregase activity, whereas MGCA7-linked subunits do not. Our findings illuminate Skd3 structure and mechanism, explain SCN and MGCA7 inheritance patterns, and suggest therapeutic strategies.

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Research works printed but not linked: 92

  1. 2019, AVXS-101 (Onasemnogene Abeparvovec) for SMA1: Comparative Study with a Prospective Natural History Cohort, J Neuromuscul Dis, 6, 307, 10.3233/JND-190403 · DOI · Paper page
  2. 2018, Gene Therapy for Retinal Degeneration, Cell, 173, 5, 10.1016/j.cell.2018.03.021 · DOI
  3. 10.1136/jmedgenet-2014-102952 · DOI
  4. 10.1158/2159-8290.CD-19-0117 · DOI
  5. 10.1107/S2059798318002425 · DOI
  6. 2021, Antisense technology: an overview and prospectus, Nat Rev Drug Discov, 20, 427, 10.1038/s41573-021-00162-z · DOI · Paper page
  7. 2020, Expression and Purification of Recombinant Skd3 (Human ClpB) Protein and Tobacco Etch Virus (TEV) Protease from Escherichia coli, Bio Protoc, 10, e3858
  8. Cupo, R.R. , and Shorter, J . (2020b). Skd3 (human ClpB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations. Elife 9. · DOI
  9. 10.1371/journal.pgen.1003781 · DOI
  10. 2021, Combating deleterious phase transitions in neurodegenerative disease, Biochim Biophys Acta Mol Cell Res, 1868, 118984, 10.1016/j.bbamcr.2021.118984 · DOI
  11. 10.1016/j.molcel.2006.03.036 · DOI
  12. 10.1016/j.cell.2012.09.038 · DOI
  13. 10.1074/jbc.M113.520759 · DOI
  14. 10.1038/nsmb1198 · DOI
  15. 10.1016/j.bpj.2019.03.035 · DOI
  16. 10.1038/nrd4593 · DOI
  17. Erives, A. , and Fassler, J . (2015). Metabolic and chaperone gene loss marks the origin of animals: evidence for hsp104 and hsp78 chaperones sharing mitochondrial enzymes as clients. PLoS One 10. · DOI
  18. 10.1146/annurev.biophys.35.040405.101933 · DOI
  19. Fare, C.M. , and Shorter, J . (2021). (Dis)Solving the problem of aberrant protein states. Dis Model Mech 14. · DOI
  20. Fei, X. , Bell, T.A. , Jenni, S. , Stinson, B.M. , Baker, T.A. , Harrison, S.C. , and Sauer, R.T . (2020). Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate. Elife 9. · DOI
  21. 2021, CRISPR-Cas9 Gene Editing for Sickle Cell Disease and beta-Thalassemia, N Engl J Med, 384, 252, 10.1056/NEJMoa2031054 · DOI · Paper page
  22. 10.1126/science.aan1052 · DOI
  23. 2002, The quantitation of ADP diffusion gradients across the outer membrane of heart mitochondria in the presence of macromolecules, Biochim Biophys Acta, 1554, 48, 10.1016/S0005-2728(02)00212-8 · DOI
  24. 10.1016/S0092-8674(00)81223-4 · DOI
  25. 10.1016/j.jmb.2008.09.066 · DOI
  26. 10.1074/jbc.M312403200 · DOI
  27. 10.1016/j.cell.2018.03.002 · DOI
  28. 10.1038/nrm1684 · DOI
  29. 10.1093/emboj/21.1.12 · DOI
  30. 1972, Differences between the ATP-ADP ratios in the mitochondrial matrix and in the extramitochondrial space, Eur J Biochem, 30, 434, 10.1111/j.1432-1033.1972.tb02115.x · DOI
  31. 2020, Functional analysis of proposed substrate-binding residues of Hsp104, PLoS One, 15, e0230198, 10.1371/journal.pone.0230198 · DOI
  32. 2021, DAXX represents a new type of protein-folding enabler, Nature, 597, 132, 10.1038/s41586-021-03824-5 · DOI
  33. 10.1073/pnas.0904764106 · DOI
  34. 10.1074/jbc.M113.462861 · DOI
  35. 10.1038/nsmb.1836 · DOI
  36. 2015, Bi-allelic CLPB mutations cause cataract, renal cysts, nephrocalcinosis and 3-methylglutaconic aciduria, a novel disorder of mitochondrial protein disaggregation, J Inherit Metab Dis, 38, 211, 10.1007/s10545-015-9813-0 · DOI
  37. 10.1038/s41586-020-2308-7 · DOI · Paper page
  38. 10.1016/j.clim.2016.02.008 · DOI
  39. Klosowska, A. , Chamera, T. , and Liberek, K . (2016). Adenosine diphosphate restricts the protein remodeling activity of the Hsp104 chaperone to Hsp70 assisted disaggregation. Elife 5. · DOI
  40. 10.1073/pnas.0337680100 · DOI
  41. 10.1038/d41573-021-00017-7 · DOI · Paper page
  42. 10.1016/S0092-8674(03)00807-9 · DOI
  43. 10.1172/JCI35781 · DOI
  44. 10.1038/s41594-020-0409-5 · DOI
  45. 10.1021/bi701714s · DOI
  46. 10.1093/nar/gkz268 · DOI · Paper page
  47. 2021, Treatment by CRISPR-Cas9 Gene Editing -A Proof of Principle, N Engl J Med, 384, 286, 10.1056/NEJMe2034624 · DOI
  48. 10.1038/nsmb974 · DOI
  49. 10.1056/NEJMoa1706198 · DOI · Paper page
  50. 10.1016/j.str.2018.11.001 · DOI
  51. 10.1016/j.molcel.2007.08.013 · DOI
  52. 10.1110/ps.03554604 · DOI
  53. 10.1073/pnas.252537899 · DOI
  54. 2020, CLPB (caseinolytic peptidase B homolog), the first mitochondrial protein refoldase associated with human disease, Biochim Biophys Acta Gen Subj, 1864, 129512, 10.1016/j.bbagen.2020.129512 · DOI
  55. 10.1371/journal.pcbi.1004659 · DOI
  56. 10.1016/0378-1119(94)00697-Q · DOI
  57. 10.1002/jcc.20084 · DOI
  58. 10.1002/PRO.3943 · DOI
  59. 10.1007/s10545-017-0057-z · DOI
  60. Puchades, C. , Rampello, A.J. , Shin, M. , Giuliano, C.J. , Wiseman, R.L. , Glynn, S.E. , and Lander, G.C . (2017). Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing. Science 358. · DOI
  61. 10.1038/s41580-019-0183-6 · DOI
  62. 2020, Gene Expression Changes and Associated Pathways Involved in the Progression of Prostate Cancer Advanced Stages, Front Genet, 11, 613162
  63. 10.1038/nmeth.4169 · DOI · Paper page
  64. 10.1038/s41467-019-10150-y · DOI
  65. 10.1038/ncb3488 · DOI
  66. 2015, CLPB variants associated with autosomal-recessive mitochondrial disorder with cataract, neutropenia, epilepsy, and methylglutaconic aciduria, Am J Hum Genet, 96, 258, 10.1016/j.ajhg.2014.12.020 · DOI
  67. 10.1074/jbc.273.25.15546 · DOI
  68. 10.1016/j.cub.2020.01.044 · DOI
  69. 10.1073/pnas.1914245116 · DOI
  70. 10.1016/j.gde.2017.01.008 · DOI
  71. 10.1126/science.1098007 · DOI
  72. 10.1016/j.molcel.2006.05.042 · DOI
  73. Shorter, J. , and Southworth, D.R . (2019). Spiraling in Control: Structures and Mechanisms of the Hsp104 Disaggregase. Cold Spring Harb Perspect Biol 11. · DOI
  74. 2017, Severe congenital neutropenias, Nat Rev Dis Primers, 3, 17032, 10.1038/nrdp.2017.32 · DOI
  75. 10.1016/j.molcel.2014.12.021 · DOI
  76. 10.1016/j.jmb.2015.11.016 · DOI
  77. 10.1074/jbc.RA119.011577 · DOI
  78. 10.1093/nar/gkaa1100 · DOI · Paper page
  79. 10.1074/jbc.M115.707976 · DOI
  80. 10.1107/S2059798317002662 · DOI
  81. 2022, Heterozygous variants of CLPB are a cause of severe congenital neutropenia, Blood, 139, 779, 10.1182/blood.2021010762 · DOI
  82. 10.1093/nar/gky427 · DOI
  83. 10.1021/acs.biochem.7b00225 · DOI
  84. 10.1016/j.bbamcr.2011.06.014 · DOI
  85. 10.1016/j.jmb.2008.02.026 · DOI
  86. 2021, Neutropenia and intellectual disability are hallmarks of biallelic and de novo CLPB deficiency, Genet Med, 23, 1705, 10.1038/s41436-021-01194-x · DOI
  87. 2015, CLPB mutations cause 3-methylglutaconic aciduria, progressive brain atrophy, intellectual disability, congenital neutropenia, cataracts, movement disorder, Am J Hum Genet, 96, 245, 10.1016/j.ajhg.2014.12.013 · DOI
  88. 10.1038/nsmb.3277 · DOI
  89. Yoo, H. , Bard, J.A.M. , Pilipenko, E.V. , and Drummond, D.A . (2022). Chaperones directly and efficiently disperse stress-triggered biomolecular condensates. Mol Cell. · DOI
  90. 2020, [Clinical and genetic analysis of an infant with 3-methylglutaconic aciduria type VII], Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 37, 423
  91. 10.1038/nmeth.4193 · DOI
  92. 2020, TRIM11 Prevents and Reverses Protein Aggregation and Rescues a Mouse Model of Parkinson’s Disease, Cell Rep, 33, 108418, 10.1016/j.celrep.2020.108418 · DOI

Metadata

Authors
Cupo, R. R., Rizo, A. N., Braun, G. A., Tse, E., Chuang, E., Southworth, D. R., & Shorter, J.
Affiliations
  • University of Pennsylvania (US)
  • University of California, San Francisco (US)
Corresponding author
  • Southworth, Daniel R.
  • Shorter, James
ORCID
Venue
Cell Reports
Publisher
openRxiv
Published
2022-02-17
Volume
40
Issue
13
Pages
111408-111408
ISSN
2211-1247 (ISSN-L)
DOI
10.1101/2022.02.17.480866
PMC
PMC9584538
OpenAlex
W4297373146
Cited by
25
References
1
Citations by year
2026: 4 · 2025: 5 · 2024: 6 · 2023: 7 · 2022: 3
FWCI
1.71
Type
journal article
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • Cell Reports (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion, cc-by-nc-nd)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
Funders
  • Johnson Foundation
  • Blavatnik Family Foundation
  • G. Harold and Leila Y. Mathers Foundation
  • National Institutes of Health
  • National Institute on Aging (F31AG060672, R21AG061784)
  • National Institute of General Medical Sciences (T32GM008275, R01GM138690, R01GM099836)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Heat shock proteins research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
ClpB, AAA+ ATPase, protein disaggregation, mitochondrial intermembrane space, congenital neutropenia, nucleotide-binding domain, ankyrin repeat domain, disease inheritance, treatment options
MeSH terms
Adenosine Triphosphate, Heat-Shock Proteins, Humans, Models, Molecular, Nucleotides, Ankyrins, Protein Transport

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