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Marszalek J, Craig EA, Pitek M, Dutkiewicz R. Chaperone function in Fe-S protein biogenesis: Three possible scenarios. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119717. [PMID: 38574821 DOI: 10.1016/j.bbamcr.2024.119717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/22/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Among the six known iron‑sulfur (FeS) cluster biogenesis machineries that function across all domains of life only one involves a molecular chaperone system. This machinery, called ISC for 'iron sulfur cluster', functions in bacteria and in mitochondria of eukaryotes including humans. The chaperone system - a dedicated J-domain protein co-chaperone termed Hsc20 and its Hsp70 partner - is essential for proper ISC machinery function, interacting with the scaffold protein IscU which serves as a platform for cluster assembly and subsequent transfer onto recipient apo-proteins. Despite many years of research, surprisingly little is known about the specific role(s) that the chaperones play in the ISC machinery. Here we review three non-exclusive scenarios that range from involvement of the chaperones in the cluster transfer to regulation of the cellular levels of IscU itself.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States of America.
| | - Marcin Pitek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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2
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Morizono MA, McGuire KL, Birouty NI, Herzik MA. Structural insights into GrpEL1-mediated nucleotide and substrate release of human mitochondrial Hsp70. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593630. [PMID: 38798347 PMCID: PMC11118385 DOI: 10.1101/2024.05.10.593630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Maintenance of protein homeostasis is necessary for cell viability and depends on a complex network of chaperones and co-chaperones, including the heat-shock protein 70 (Hsp70) system. In human mitochondria, mitochondrial Hsp70 (mortalin) and the nucleotide exchange factor (GrpEL1) work synergistically to stabilize proteins, assemble protein complexes, and facilitate protein import. However, our understanding of the molecular mechanisms guiding these processes is hampered by limited structural information. To elucidate these mechanistic details, we used cryoEM to determine the first structures of full-length human mortalin-GrpEL1 complexes in previously unobserved states. Our structures and molecular dynamics simulations allow us to delineate specific roles for mortalin-GrpEL1 interfaces and to identify steps in GrpEL1-mediated nucleotide and substrate release by mortalin. Subsequent analyses reveal conserved mechanisms across bacteria and mammals and facilitate a complete understanding of sequential nucleotide and substrate release for the Hsp70 chaperone system.
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Affiliation(s)
- Marc A. Morizono
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Kelly L. McGuire
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Natalie I. Birouty
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Mark A. Herzik
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
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3
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Buchner J, Alasady MJ, Backe SJ, Blagg BSJ, Carpenter RL, Colombo G, Gelis I, Gewirth DT, Gierasch LM, Houry WA, Johnson JL, Kang BH, Kao AW, LaPointe P, Mattoo S, McClellan AJ, Neckers LM, Prodromou C, Rasola A, Sager RA, Theodoraki MA, Truman AW, Truttman MC, Zachara NE, Bourboulia D, Mollapour M, Woodford MR. Second international symposium on the chaperone code, 2023. Cell Stress Chaperones 2024; 29:88-96. [PMID: 38316354 PMCID: PMC10939070 DOI: 10.1016/j.cstres.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Affiliation(s)
- Johannes Buchner
- Department of Bioscience, Technical University of Munich, D85748, Garching, Germany.
| | - Milad J Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Brian S J Blagg
- Department of Chemistry and Biochemistry, Warren Family Research Center for Drug Discovery and Development, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Richard L Carpenter
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Bloomington, IN, 47405, USA; Medical Sciences, Indiana University School of Medicine, Bloomington, IN, 47405, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 47405, USA
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Ioannis Gelis
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Daniel T Gewirth
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Lila M Gierasch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA; Hauptman-Woodward Medical Research Institute, Buffalo, NY, 14203, USA
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| | - Jill L Johnson
- Department of Biological Sciences and the Center for Reproductive Biology, University of Idaho, Moscow, ID, 83844, USA
| | - Byoung Heon Kang
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Aimee W Kao
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Paul LaPointe
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Seema Mattoo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Amie J McClellan
- Division of Science and Mathematics, Bennington College, Bennington, VT, 05201, USA
| | - Leonard M Neckers
- Center for Cancer Research, National Cancer Institute, Rockville, MD, 20892, USA
| | | | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | | | - Andrew W Truman
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Matthias C Truttman
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA; Geriatrics Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Natasha E Zachara
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
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4
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Apostolidou D, Zhang P, Pandya D, Bock K, Liu Q, Yang W, Marszalek PE. Tandem repeats of highly bioluminescent NanoLuc are refolded noncanonically by the Hsp70 machinery. Protein Sci 2024; 33:e4895. [PMID: 38284490 PMCID: PMC10804678 DOI: 10.1002/pro.4895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
Chaperones are a large family of proteins crucial for maintaining cellular protein homeostasis. One such chaperone is the 70 kDa heat shock protein (Hsp70), which plays a crucial role in protein (re)folding, stability, functionality, and translocation. While the key events in the Hsp70 chaperone cycle are well established, a relatively small number of distinct substrates were repetitively investigated. This is despite Hsp70 engaging with a plethora of cellular proteins of various structural properties and folding pathways. Here we analyzed novel Hsp70 substrates, based on tandem repeats of NanoLuc (Nluc), a small and highly bioluminescent protein with unique structural characteristics. In previous mechanical unfolding and refolding studies, we have identified interesting misfolding propensities of these Nluc-based tandem repeats. In this study, we further investigate these properties through in vitro bulk experiments. Similar to monomeric Nluc, engineered Nluc dyads and triads proved to be highly bioluminescent. Using the bioluminescence signal as the proxy for their structural integrity, we determined that heat-denatured Nluc dyads and triads can be efficiently refolded by the E. coli Hsp70 chaperone system, which comprises DnaK, DnaJ, and GrpE. In contrast to previous studies with other substrates, we observed that Nluc repeats can be efficiently refolded by DnaK and DnaJ, even in the absence of GrpE co-chaperone. Taken together, our study offers a new powerful substrate for chaperone research and raises intriguing questions about the Hsp70 mechanisms, particularly in the context of structurally diverse proteins.
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Affiliation(s)
- Dimitra Apostolidou
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth CarolinaUnited States
| | - Pan Zhang
- Department of ChemistryDuke UniversityDurhamNorth CarolinaUnited States
| | - Devanshi Pandya
- Department of Electrical and Computer EngineeringDuke UniversityDurhamNorth CarolinaUnited States
| | - Kaden Bock
- Department of Biomedical EngineeringDuke UniversityDurhamNorth CarolinaUnited States
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUnited States
| | - Weitao Yang
- Department of ChemistryDuke UniversityDurhamNorth CarolinaUnited States
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth CarolinaUnited States
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5
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Ciesielski SJ, Young C, Ciesielska EJ, Ciesielski GL. The Hsp70 and JDP proteins: Structure-function perspective on molecular chaperone activity. Enzymes 2023; 54:221-245. [PMID: 37945173 DOI: 10.1016/bs.enz.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Proteins are the most structurally diverse cellular biomolecules that act as molecular machines driving essential activities of all living organisms. To be functional, most of the proteins need to fold into a specific three-dimensional structure, which on one hand should be stable enough to oppose disruptive conditions and on the other hand flexible enough to allow conformational dynamics necessary for their biological functions. This compromise between stability and dynamics makes proteins susceptible to stress-induced misfolding and aggregation. Moreover, the folding process itself is intrinsically prone to conformational errors. Molecular chaperones are proteins that mitigate folding defects and maintain the structural integrity of the cellular proteome. Promiscuous Hsp70 chaperones are central to these processes and their activity depends on the interaction with obligatory J-domain protein (JDP) partners. In this review, we discuss structural aspects of Hsp70s, JDPs, and their interaction in the context of biological activities.
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Affiliation(s)
- Szymon J Ciesielski
- Department of Chemistry and Biochemistry, University of North Florida, Jacksonville, FL, United States.
| | - Cameron Young
- Department of Chemistry and Biochemistry, University of North Florida, Jacksonville, FL, United States
| | - Elena J Ciesielska
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States; Department of Biology, University of North Florida, Jacksonville, FL, United States
| | - Grzegorz L Ciesielski
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States; Department of Biology, University of North Florida, Jacksonville, FL, United States
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6
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Zhu Y, Dou Q, Du L, Wang Y. QseB/QseC: a two-component system globally regulating bacterial behaviors. Trends Microbiol 2023:S0966-842X(23)00046-X. [PMID: 36849330 DOI: 10.1016/j.tim.2023.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
QseB/QseC is a two-component system that is involved in the regulation of multiple bacterial behaviors by regulating quorum sensing, bacterial pathogenicity, and antibiotic resistance. Thus, QseB/QseC could provide a target for new antibiotic development. Recently, QseB/QseC has been found to confer survival advantages to environmental bacteria under stress conditions. The molecular mechanistic understanding of QseB/QseC has become an active area of research and revealed some emerging themes, including a deeper understanding of QseB/QseC regulation in different pathogens and environmental bacteria, the functional difference of QseB/QseC among species, and the possibility of analyzing QseB/QseC evolution. Here, we discuss the progression of QseB/QseC studies and describe several unresolved issues and future directions. Resolving these issues is among the challenges of future QseB/QseC studies.
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Affiliation(s)
- Yuxiang Zhu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qin Dou
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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7
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Johansson KE, Mashahreh B, Hartmann-Petersen R, Ravid T, Lindorff-Larsen K. Prediction of Quality-control Degradation Signals in Yeast Proteins. J Mol Biol 2023; 435:167915. [PMID: 36495918 DOI: 10.1016/j.jmb.2022.167915] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Effective proteome homeostasis is key to cellular and organismal survival, and cells therefore contain efficient quality control systems to monitor and remove potentially toxic misfolded proteins. Such general protein quality control to a large extent relies on the efficient and robust delivery of misfolded or unfolded proteins to the ubiquitin-proteasome system. This is achieved via recognition of so-called degradation motifs-degrons-that are assumed to become exposed as a result of protein misfolding. Despite their importance, the nature and sequence properties of quality-control degrons remain elusive. Here, we have used data from a yeast-based screen of 23,600 17-residue peptides to build a predictor of quality-control degrons. The resulting model, QCDPred (Quality Control Degron Prediction), achieves good accuracy using only the sequence composition of the peptides as input. Our analysis reveals that strong degrons are enriched in hydrophobic amino acids and depleted in negatively charged amino acids, in line with the expectation that they are buried in natively folded proteins. We applied QCDPred to the yeast proteome, enabling us to analyse more widely the potential effects of degrons. As an example, we show a correlation between cellular abundance and degron potential in disordered regions of proteins. Together with recent results on membrane proteins, our work suggest that the recognition of exposed hydrophobic residues is a key and generic mechanism for proteome homeostasis. QCDPred is freely available as open source code and via a web interface.
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Affiliation(s)
- Kristoffer E Johansson
- Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Copenhagen, Denmark. https://twitter.com/kristofferenoee
| | - Bayan Mashahreh
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rasmus Hartmann-Petersen
- Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Copenhagen, Denmark. https://twitter.com/rasmushartmannp
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Copenhagen, Denmark.
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8
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Abildgaard AB, Voutsinos V, Petersen SD, Larsen FB, Kampmeyer C, Johansson KE, Stein A, Ravid T, Andréasson C, Jensen MK, Lindorff-Larsen K, Hartmann-Petersen R. HSP70-binding motifs function as protein quality control degrons. Cell Mol Life Sci 2023; 80:32. [PMID: 36609589 PMCID: PMC11072582 DOI: 10.1007/s00018-022-04679-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023]
Abstract
Protein quality control (PQC) degrons are short protein segments that target misfolded proteins for proteasomal degradation, and thus protect cells against the accumulation of potentially toxic non-native proteins. Studies have shown that PQC degrons are hydrophobic and rarely contain negatively charged residues, features which are shared with chaperone-binding regions. Here we explore the notion that chaperone-binding regions may function as PQC degrons. When directly tested, we found that a canonical Hsp70-binding motif (the APPY peptide) functioned as a dose-dependent PQC degron both in yeast and in human cells. In yeast, Hsp70, Hsp110, Fes1, and the E3 Ubr1 target the APPY degron. Screening revealed that the sequence space within the chaperone-binding region of APPY that is compatible with degron function is vast. We find that the number of exposed Hsp70-binding sites in the yeast proteome correlates with a reduced protein abundance and half-life. Our results suggest that when protein folding fails, chaperone-binding sites may operate as PQC degrons, and that the sequence properties leading to PQC-linked degradation therefore overlap with those of chaperone binding.
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Affiliation(s)
- Amanda B Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Vasileios Voutsinos
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Søren D Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fia B Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Kampmeyer
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Stein
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
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9
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Shan SO. Role of Hsp70 in Post-Translational Protein Targeting: Tail-Anchored Membrane Proteins and Beyond. Int J Mol Sci 2023; 24:1170. [PMID: 36674686 PMCID: PMC9866221 DOI: 10.3390/ijms24021170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The Hsp70 family of molecular chaperones acts as a central 'hub' in the cell that interacts with numerous newly synthesized proteins to assist in their biogenesis. Apart from its central and well-established role in facilitating protein folding, Hsp70s also act as key decision points in the cellular chaperone network that direct client proteins to distinct biogenesis and quality control pathways. In this paper, we review accumulating data that illustrate a new branch in the Hsp70 network: the post-translational targeting of nascent membrane and organellar proteins to diverse cellular organelles. Work in multiple pathways suggests that Hsp70, via its ability to interact with components of protein targeting and translocation machineries, can initiate elaborate substrate relays in a sophisticated cascade of chaperones, cochaperones, and receptor proteins, and thus provide a mechanism to safeguard and deliver nascent membrane proteins to the correct cellular membrane. We discuss the mechanistic principles gleaned from better-studied Hsp70-dependent targeting pathways and outline the observations and outstanding questions in less well-studied systems.
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Affiliation(s)
- Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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10
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Marszalek J, Craig EA, Tomiczek B. J-Domain Proteins Orchestrate the Multifunctionality of Hsp70s in Mitochondria: Insights from Mechanistic and Evolutionary Analyses. Subcell Biochem 2023; 101:293-318. [PMID: 36520311 DOI: 10.1007/978-3-031-14740-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mitochondrial J-domain protein (JDP) co-chaperones orchestrate the function of their Hsp70 chaperone partner(s) in critical organellar processes that are essential for cell function. These include folding, refolding, and import of mitochondrial proteins, maintenance of mitochondrial DNA, and biogenesis of iron-sulfur cluster(s) (FeS), prosthetic groups needed for function of mitochondrial and cytosolic proteins. Consistent with the organelle's endosymbiotic origin, mitochondrial Hsp70 and the JDPs' functioning in protein folding and FeS biogenesis clearly descended from bacteria, while the origin of the JDP involved in protein import is less evident. Regardless of their origin, all mitochondrial JDP/Hsp70 systems evolved unique features that allowed them to perform mitochondria-specific functions. Their modes of functional diversification and specialization illustrate the versatility of JDP/Hsp70 systems and inform our understanding of system functioning in other cellular compartments.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bartlomiej Tomiczek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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11
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Conformational dynamics of the Hsp70 chaperone throughout key steps of its ATPase cycle. Proc Natl Acad Sci U S A 2022; 119:e2123238119. [PMID: 36409905 PMCID: PMC9889847 DOI: 10.1073/pnas.2123238119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The 70 kDa heat shock proteins (Hsp70s) are highly versatile molecular chaperones that assist in a wide variety of protein-folding processes. They exert their functions by continuously cycling between states of low and high affinity for client polypeptides, driven by ATP-binding and hydrolysis. This cycling is tuned by cochaperones and clients. Although structures for the high and low client affinity conformations of Hsp70 and Hsp70 domains in complex with various cochaperones and peptide clients are available, it is unclear how structural rearrangements in the presence of cochaperones and clients are orchestrated in space and time. Here, we report insights into the conformational dynamics of the prokaryotic model Hsp70 DnaK throughout its adenosine-5'-triphosphate hydrolysis (ATPase) cycle using proximity-induced fluorescence quenching. Our data suggest that ATP and cochaperone-induced structural rearrangements in DnaK occur in a sequential manner and resolve hitherto unpredicted cochaperone and client-induced structural rearrangements. Peptides induce large conformational changes in DnaK·ATP prior to ATP hydrolysis, whereas a protein client induces significantly smaller changes but is much more effective in stimulating ATP hydrolysis. Analysis of the enthalpies of activation for the ATP-induced opening of the DnaK lid in the presence of clients indicates that the lid does not exert an enthalpic pulling force onto bound clients, suggesting entropic pulling as a major mechanism for client unfolding. Our data reveal important insights into the mechanics, allostery, and dynamics of Hsp70 chaperones. We established a methodology for understanding the link between dynamics and function, Hsp70 diversity, and activity modulation.
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12
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Marszalek J, Craig EA. Interaction of client—the scaffold on which FeS clusters are build—with J-domain protein Hsc20 and its evolving Hsp70 partners. Front Mol Biosci 2022; 9:1034453. [PMID: 36310602 PMCID: PMC9596805 DOI: 10.3389/fmolb.2022.1034453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
In cells molecular chaperone systems consisting of Hsp70 and its obligatory J-domain protein (JDP) co-chaperones transiently interact with a myriad of client proteins—with JDPs typically recruiting their partner Hsp70 to interact with particular clients. The fundamentals of this cyclical interactions between JDP/Hsp70 systems and clients are well established. Much less is known about other aspects of JDP/Hsp70 system function, including how such systems evolved over time. Here we discuss the JDP/Hsp70 system involved in the biogenesis of iron-sulfur (FeS) clusters. Interaction between the client protein, the scaffold on which clusters are built, and its specialized JDP Hsc20 has stayed constant. However, the system’s Hsp70 has changed at least twice. In some species Hsc20’s Hsp70 partner interacts only with the scaffold, in others it has many JDP partners in addition to Hsc20 and interacts with many client proteins. Analysis of this switching of Hsp70 partners has provided insight into the insulation of JDP/Hsp70 systems from one another that can occur when more than one Hsp70 is present in a cellular compartment, as well as how competition among JDPs is balanced when an Hsp70 partner is shared amongst a number of JDPs. Of particularly broad relevance, even though the scaffold’s interactions with Hsc20 and Hsp70 are functionally critical for the biogenesis of FeS cluster-containing proteins, it is the modulation of the Hsc20-Hsp70 interaction per se that allows Hsc20 to function with such different Hsp70 partners.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
- *Correspondence: Jaroslaw Marszalek, ; Elizabeth A. Craig,
| | - Elizabeth A. Craig
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI, United States
- *Correspondence: Jaroslaw Marszalek, ; Elizabeth A. Craig,
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Nordquist EB, Clerico EM, Chen J, Gierasch LM. Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future. J Phys Chem B 2022; 126:6780-6791. [PMID: 36040440 PMCID: PMC10309085 DOI: 10.1021/acs.jpcb.2c03806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hsp70 molecular chaperones play central roles in maintaining a healthy cellular proteome. Hsp70s function by binding to short peptide sequences in incompletely folded client proteins, thus preventing them from misfolding and/or aggregating, and in many cases holding them in a state that is competent for subsequent processes like translocation across membranes. There is considerable interest in predicting the sites where Hsp70s may bind their clients, as the ability to do so sheds light on the cellular functions of the chaperone. In addition, the capacity of the Hsp70 chaperone family to bind to a broad array of clients and to identify accessible sequences that enable discrimination of those that are folded from those that are not fully folded, which is essential to their cellular roles, is a fascinating puzzle in molecular recognition. In this article we discuss efforts to harness computational modeling with input from experimental data to develop a predictive understanding of the promiscuous yet selective binding of Hsp70 molecular chaperones to accessible sequences within their client proteins. We trace how an increasing understanding of the complexities of Hsp70-client interactions has led computational modeling to new underlying assumptions and design features. We describe the trend from purely data-driven analysis toward increased reliance on physics-based modeling that deeply integrates structural information and sequence-based functional data with physics-based binding energies. Notably, new experimental insights are adding to our understanding of the molecular origins of "selective promiscuity" in substrate binding by Hsp70 chaperones and challenging the underlying assumptions and design used in earlier predictive models. Taking the new experimental findings together with exciting progress in computational modeling of protein structures leads us to foresee a bright future for a predictive understanding of selective-yet-promiscuous binding exploited by Hsp70 molecular chaperones; the resulting new insights will also apply to substrate binding by other chaperones and by signaling proteins.
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Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Eugenia M. Clerico
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Lila M. Gierasch
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
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14
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François-Moutal L, Scott DD, Ambrose AJ, Zerio CJ, Rodriguez-Sanchez M, Dissanayake K, May DG, Carlson JM, Barbieri E, Moutal A, Roux KJ, Shorter J, Khanna R, Barmada SJ, McGurk L, Khanna M. Heat shock protein Grp78/BiP/HspA5 binds directly to TDP-43 and mitigates toxicity associated with disease pathology. Sci Rep 2022; 12:8140. [PMID: 35581326 PMCID: PMC9114370 DOI: 10.1038/s41598-022-12191-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/04/2022] [Indexed: 11/09/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no cure or effective treatment in which TAR DNA Binding Protein of 43 kDa (TDP-43) abnormally accumulates into misfolded protein aggregates in affected neurons. It is widely accepted that protein misfolding and aggregation promotes proteotoxic stress. The molecular chaperones are a primary line of defense against proteotoxic stress, and there has been long-standing interest in understanding the relationship between chaperones and aggregated protein in ALS. Of particular interest are the heat shock protein of 70 kDa (Hsp70) family of chaperones. However, defining which of the 13 human Hsp70 isoforms is critical for ALS has presented many challenges. To gain insight into the specific Hsp70 that modulates TDP-43, we investigated the relationship between TDP-43 and the Hsp70s using proximity-dependent biotin identification (BioID) and discovered several Hsp70 isoforms associated with TDP-43 in the nucleus, raising the possibility of an interaction with native TDP-43. We further found that HspA5 bound specifically to the RNA-binding domain of TDP-43 using recombinantly expressed proteins. Moreover, in a Drosophila strain that mimics ALS upon TDP-43 expression, the mRNA levels of the HspA5 homologue (Hsc70.3) were significantly increased. Similarly we observed upregulation of HspA5 in prefrontal cortex neurons from human ALS patients. Finally, overexpression of HspA5 in Drosophila rescued TDP-43-induced toxicity, suggesting that upregulation of HspA5 may have a compensatory role in ALS pathobiology.
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Affiliation(s)
- Liberty François-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - David Donald Scott
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Andrew J Ambrose
- Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ, 85724, USA
| | - Christopher J Zerio
- Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ, 85724, USA
| | | | - Kumara Dissanayake
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Danielle G May
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Jacob M Carlson
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Edward Barbieri
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Aubin Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Kyle J Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA.,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - James Shorter
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - Rajesh Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Leeanne McGurk
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA. .,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA. .,Department of Molecular Pathobiology, NYU, New York, NY, USA. .,Department of Molecular Pathobiology, College of Dentistry, NYU, 433 1st Ave, New York, NY, 10010, USA.
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Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding. Int J Mol Sci 2022; 23:ijms23052485. [PMID: 35269628 PMCID: PMC8910466 DOI: 10.3390/ijms23052485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/10/2022] Open
Abstract
Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics-activity relationships to explain the mechanism of functional diversity of molecular chaperones.
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