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Piñeyro MD, Chiribao ML, Arias DG, Robello C, Parodi-Talice A. Overoxidation and Oligomerization of Trypanosoma cruzi Cytosolic and Mitochondrial Peroxiredoxins. Pathogens 2023; 12:1273. [PMID: 37887789 PMCID: PMC10610341 DOI: 10.3390/pathogens12101273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Peroxiredoxins (Prxs) have been shown to be important enzymes for trypanosomatids, counteracting oxidative stress and promoting cell infection and intracellular survival. In this work, we investigate the in vitro sensitivity to overoxidation and the overoxidation dynamics of Trypanosoma cruzi Prxs in parasites in culture and in the infection context. We showed that recombinant m-TXNPx, in contrast to what was observed for c-TXNPx, exists as low molecular mass forms in the overoxidized state. We observed that T. cruzi Prxs were overoxidized in epimastigotes treated with oxidants, and a significant proportion of the overoxidized forms were still present at least 24 h after treatment suggesting that these forms are not actively reversed. In in vitro infection experiments, we observed that Prxs are overoxidized in amastigotes residing in infected macrophages, demonstrating that inactivation of at least part of the Prxs by overoxidation occurs in a physiological context. We have shown that m-TXNPx has a redox-state-dependent chaperone activity. This function may be related to the increased thermotolerance observed in m-TXNPx-overexpressing parasites. This study suggests that despite the similarity between protozoan and mammalian Prxs, T. cruzi Prxs have different oligomerization dynamics and sensitivities to overoxidation, which may have implications for their function in the parasite life cycle and infection process.
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Affiliation(s)
- María Dolores Piñeyro
- Laboratorio de Interacciones Hospedero Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (M.D.P.); (M.L.C.); (C.R.)
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - María Laura Chiribao
- Laboratorio de Interacciones Hospedero Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (M.D.P.); (M.L.C.); (C.R.)
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - Diego G. Arias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral, UNL-CONICET, Santa Fe 3000, Argentina;
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (M.D.P.); (M.L.C.); (C.R.)
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - Adriana Parodi-Talice
- Laboratorio de Interacciones Hospedero Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (M.D.P.); (M.L.C.); (C.R.)
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
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2
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Zhang Y, Fu H, Chen J, Xu L, An Y, Ma R, Zhu C, Liu Y, Ma F, Shi L. Holdase/Foldase Mimetic Nanochaperone Improves Antibody-Based Cancer Immunotherapy. SMALL METHODS 2023; 7:e2201051. [PMID: 36228110 DOI: 10.1002/smtd.202201051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/30/2022] [Indexed: 05/17/2023]
Abstract
Despite unprecedented successes of antibody-based cancer immunotherapy, the serious side effects and rapid clearance following systemic administration remain big challenges to realize its full potential. At the same time, combination immunotherapy using multiple antibodies has shown particularly promising in cancer treatment. It is noticed that the working mechanisms of natural holdase and foldase chaperone are desirable to overcome the limitations of therapeutic antibodies. Holdase chaperone stabilizes unfolded client and prevents it from activation and degradation, while foldase chaperone assists unfolded client to its native state to function. Here a holdase/foldase mimetic nanochaperone (H/F-nChap) to co-delivery two types of monoclonal antibodies (mAbs), αCD16 and αPDL1, and resiquimod (R848) is developed, which significantly improves cancer immunotherapy. The H/F-nChap presents holdase activity in blood and normal tissues that hides and protects mAbs from unnecessary targeted activation and degradation, thereby prolonging blood circulation and reducing immunotoxicity in vivo. Furthermore, H/F-nChap switches to foldase activity in the tumor microenvironment that exposes mAbs and releases R848 to enhance the engagement between NK cells and tumor cells and promote immune activation, respectively. The H/F-nChap represents a strategy for safe and spatiotemporal delivery of multiple mAbs, providing a promising platform for improved cancer immunotherapy.
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Affiliation(s)
- Yongxin Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Hao Fu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Jiajing Chen
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Linlin Xu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yingli An
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Rujiang Ma
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Chunlei Zhu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yang Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Feihe Ma
- State Key Laboratory of Separation Membranes and Membrane Processes and School of Materials Science and Engineering, Tiangong University, Tianjin, 300387, P. R. China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, P. R. China
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3
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Gadkari VV, Juliano BR, Mallis CS, May JC, Kurulugama RT, Fjeldsted JC, McLean JA, Russell DH, Ruotolo BT. Performance evaluation of in-source ion activation hardware for collision-induced unfolding of proteins and protein complexes on a drift tube ion mobility-mass spectrometer. Analyst 2023; 148:391-401. [PMID: 36537590 PMCID: PMC10103148 DOI: 10.1039/d2an01452a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) has emerged as an information-rich technique for gas phase protein structure characterization; however, IM resolution is currently insufficient for the detection of subtle structural differences in large biomolecules. This challenge has spurred the development of collision-induced unfolding (CIU) which utilizes incremental gas phase activation to unfold a protein in order to expand the number of measurable descriptors available for native protein ions. Although CIU is now routinely used in native mass spectrometry studies, the interlaboratory reproducibility of CIU has not been established. Here we evaluate the reproducibility of the CIU data produced across three laboratories (University of Michigan, Texas A&M University, and Vanderbilt University). CIU data were collected for a variety of protein ions ranging from 8.6-66 kDa. Within the same laboratory, the CIU fingerprints were found to be repeatable with root mean square deviation (RMSD) values of less than 5%. Collision cross section (CCS) values of the CIU intermediates were consistent across the laboratories, with most features exhibiting an interlaboratory reproducibility of better than 1%. In contrast, the activation potentials required to induce protein CIU transitions varied between the three laboratories. To address these differences, three source assemblies were constructed with an updated ion activation hardware design utilizing higher mechanical tolerance specifications. The production-grade assemblies were found to produce highly consistent CIU data for intact antibodies, exhibiting high precision ion CCS and CIU transition values, thus opening the door to establishing databases of CIU fingerprints to support future biomolecular classification efforts.
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Affiliation(s)
- Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Jody C May
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | | | | | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
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4
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Wang SM, Wu HE, Yasui Y, Geva M, Hayden M, Maurice T, Cozzolino M, Su TP. Nucleoporin POM121 signals TFEB-mediated autophagy via activation of SIGMAR1/sigma-1 receptor chaperone by pridopidine. Autophagy 2023; 19:126-151. [PMID: 35507432 PMCID: PMC9809944 DOI: 10.1080/15548627.2022.2063003] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 01/09/2023] Open
Abstract
Macroautophagy/autophagy is an essential process for cellular survival and is implicated in many diseases. A critical step in autophagy is the transport of the transcription factor TFEB from the cytosol into the nucleus, through the nuclear pore (NP) by KPNB1/importinβ1. In the C9orf72 subtype of amyotrophic lateral sclerosis-frontotemporal lobar degeneration (ALS-FTD), the hexanucleotide (G4C2)RNA expansion (HRE) disrupts the nucleocytoplasmic transport of TFEB, compromising autophagy. Here we show that a molecular chaperone, the SIGMAR1/Sigma-1 receptor (sigma non-opioid intracellular receptor 1), facilitates TFEB transport into the nucleus by chaperoning the NP protein (i.e., nucleoporin) POM121 which recruits KPNB1. In NSC34 cells, HRE reduces TFEB transport by interfering with the association between SIGMAR1 and POM121, resulting in reduced nuclear levels of TFEB, KPNB1, and the autophagy marker LC3-II. Overexpression of SIGMAR1 or POM121, or treatment with the highly selective and potent SIGMAR1 agonist pridopidine, currently in phase 2/3 clinical trials for ALS and Huntington disease, rescues all of these deficits. Our results implicate nucleoporin POM121 not merely as a structural nucleoporin, but also as a chaperone-operated signaling molecule enabling TFEB-mediated autophagy. Our data suggest the use of SIGMAR1 agonists, such as pridopidine, for therapeutic development of diseases in which autophagy is impaired.Abbreviations: ALS-FTD, amyotrophic lateral sclerosis-frontotemporal dementiaC9ALS-FTD, C9orf72 subtype of amyotrophic lateral sclerosis-frontotemporal dementiaCS, citrate synthaseER, endoplasmic reticulumGSS, glutathione synthetaseHRE, hexanucleotide repeat expansionHSPA5/BiP, heat shock protein 5LAMP1, lysosomal-associated membrane protein 1MAM, mitochondria-associated endoplasmic reticulum membraneMAP1LC3/LC3, microtubule-associated protein 1 light chain 3NP, nuclear poreNSC34, mouse motor neuron-like hybrid cell lineNUPs, nucleoporinsPOM121, nuclear pore membrane protein 121SIGMAR1/Sigma-1R, sigma non-opioid intracellular receptor 1TFEB, transcription factor EBTMEM97/Sigma-2R, transmembrane protein 97.
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Affiliation(s)
- Shao-Ming Wang
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, DHHS, 333 Cassell Drive, Baltimore, Maryland21224, USA
- China Medical University, Graduate Institute of Biomedical Sciences, Taiwan
- Neuroscience and Brain Disease Center, China Medical University, No.91, Hsueh-Shih Road, Taichung city, 404333, Taiwan
- Department of Neurology, China Medical University Hospital, No.2, Yude Road, North District, Taichung city, 404333, Taiwan
| | - Hsiang-En Wu
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, DHHS, 333 Cassell Drive, Baltimore, Maryland21224, USA
| | - Yuko Yasui
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, DHHS, 333 Cassell Drive, Baltimore, Maryland21224, USA
| | - Michal Geva
- Prilenia Therapeutics Development Ltd, Herzliya, Israel
| | - Michael Hayden
- Prilenia Therapeutics Development Ltd, Herzliya, Israel
- The Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tangui Maurice
- MMDN, University of Montpellier, EPHE, INSERM, Montpellier, France
| | - Mauro Cozzolino
- Institute of Translational Pharmacology, CNR, Via del Fosso del Cavaliere 100, 00133, Rome, Italy
| | - Tsung-Ping Su
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, DHHS, 333 Cassell Drive, Baltimore, Maryland21224, USA
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5
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Klanschnig M, Cserjan-Puschmann M, Striedner G, Grabherr R. CRISPRactivation-SMS, a message for PAM sequence independent gene up-regulation in Escherichia coli. Nucleic Acids Res 2022; 50:10772-10784. [PMID: 36134715 PMCID: PMC9561276 DOI: 10.1093/nar/gkac804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/10/2022] [Accepted: 09/08/2022] [Indexed: 12/26/2022] Open
Abstract
Governance of the endogenous gene regulatory network enables the navigation of cells towards beneficial traits for recombinant protein production. CRISPRactivation and interference provides the basis for gene expression modulation but is primarily applied in eukaryotes. Particularly the lack of wide-ranging prokaryotic CRISPRa studies might be attributed to intrinsic limitations of bacterial activators and Cas9 proteins. While bacterial activators need accurate spatial orientation and distancing towards the target promoter to be functional, Cas9-based CRISPR tools only bind sites adjacent to NGG PAM sequences. These circumstances hampered Cas9-guided activators from mediating the up-regulation of endogenous genes at precise positions in bacteria. We could overcome this limitation by combining the PAM independent Cas9 variant SpRY and a CRISPRa construct using phage protein MCP fused to transcriptional activator SoxS. This CRISPRa construct, referred to as SMS, was compared with previously reported CRISPRa constructs and showed up-regulation of a reporter gene library independent of its PAM sequence in Escherichia coli. We also demonstrated down-regulation and multi-gene expression control with SMS at non-NGG PAM sites. Furthermore, we successfully applied SMS to up-regulate endogenous genes, and transgenes at non-NGG PAM sites, which was impossible with the previous CRISPRa construct.
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Affiliation(s)
- Marco Klanschnig
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Reingard Grabherr
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
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6
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Wang Y, Yuan W, Guo S, Li Q, Chen X, Li C, Liu Q, Sun L, Chen Z, Yuan Z, Luo C, Chen S, Tong S, Nassal M, Wen YM, Wang YX. A 33-residue peptide tag increases solubility and stability of Escherichia coli produced single-chain antibody fragments. Nat Commun 2022; 13:4614. [PMID: 35941164 PMCID: PMC9359998 DOI: 10.1038/s41467-022-32423-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
Single-chain variable fragments (scFvs), composed of variable domains of heavy and light chains of an antibody joined by a linker, share antigen binding capacity with their parental antibody. Due to intrinsically low solubility and stability, only two Escherichia coli-produced scFvs have been approved for therapy. Here we report that a 33-residue peptide, termed P17 tag, increases the solubility of multiple scFvs produced in Escherichia coli SHuffle strain by up to 11.6 fold. Hydrophilic sequence, especially charged residues, but not the predicted α-helical secondary structure of P17 tag, contribute to the solubility enhancement. Notably, the P17 tag elevates the thermostability of scFv as efficiently as intra-domain disulfide bonds. Moreover, a P17-tagged scFv targeting hepatitis B virus surface proteins shows over two-fold higher antigen-binding affinity and virus-neutralizing activity than the untagged version. These data strongly suggest a type I intramolecular chaperone-like activity of the P17 tag. Hence, the P17 tag could benefit the research, production, and application of scFv. Low solubility and stability of Escherichia coli produced single chain variable fragments (scFvs) restrict their applications. Here the authors report a 33-residue peptide tag which simultaneously increases the solubility and thermostability of multiple scFvs produced in Escherichia coli SHuffle strain.
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Affiliation(s)
- Yang Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenjie Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Siqi Guo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, Nanchang University, Nanchang, China
| | - Qiqi Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaomei Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qianying Liu
- Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Lei Sun
- Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Zhenguo Chen
- Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Shijie Chen
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Shuping Tong
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Yu-Mei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yong-Xiang Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
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7
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Wu K, Minshull TC, Radford SE, Calabrese AN, Bardwell JCA. Trigger factor both holds and folds its client proteins. Nat Commun 2022; 13:4126. [PMID: 35840586 PMCID: PMC9287376 DOI: 10.1038/s41467-022-31767-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/15/2022] [Indexed: 12/12/2022] Open
Abstract
ATP-independent chaperones like trigger factor are generally assumed to play passive roles in protein folding by acting as holding chaperones. Here we show that trigger factor plays a more active role. Consistent with a role as an aggregation inhibiting chaperone, we find that trigger factor rapidly binds to partially folded glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and prevents it from non-productive self-association by shielding oligomeric interfaces. In the traditional view of holding chaperone action, trigger factor would then be expected to transfer its client to a chaperone foldase system for complete folding. Unexpectedly, we noticed that GAPDH folds into a monomeric but otherwise rather native-like intermediate state while trigger factor-bound. Upon release from trigger factor, the mostly folded monomeric GAPDH rapidly self-associates into its native tetramer and acquires enzymatic activity without needing additional folding factors. The mechanism we propose here for trigger factor bridges the holding and folding activities of chaperone function.
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Affiliation(s)
- Kevin Wu
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Thomas C Minshull
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
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8
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He W, Li X, Xue H, Yang Y, Mencius J, Bai L, Zhang J, Xu J, Wu B, Xue Y, Quan S. Insights into the client protein release mechanism of the ATP-independent chaperone Spy. Nat Commun 2022; 13:2818. [PMID: 35595811 PMCID: PMC9122904 DOI: 10.1038/s41467-022-30499-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Molecular chaperones play a central role in regulating protein homeostasis, and their active forms often contain intrinsically disordered regions (IDRs). However, how IDRs impact chaperone action remains poorly understood. Here, we discover that the disordered N terminus of the prototype chaperone Spy facilitates client release. With NMR spectroscopy and molecular dynamics simulations, we find that the N terminus can bind transiently to the client-binding cavity of Spy primarily through electrostatic interactions mediated by the N-terminal D26 residue. This intramolecular interaction results in a dynamic competition of the N terminus with the client for binding to Spy, which promotes client discharge. Our results reveal the mechanism by which Spy releases clients independent of energy input, thus enriching the current knowledge on how ATP-independent chaperones release their clients and highlighting the importance of synergy between IDRs and structural domains in regulating protein function.
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Affiliation(s)
- Wei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Xinming Li
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yuanyuan Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Ling Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jiayin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jianhe Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Yi Xue
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China.
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China. .,Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
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9
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Abstract
The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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10
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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11
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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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12
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A Critical Review on the Economically Feasible and Sustainable Poly(3-Hydroxybutyrate- co-3-hydroxyvalerate) Production from Alkyl Alcohols. Polymers (Basel) 2022; 14:polym14040670. [PMID: 35215584 PMCID: PMC8876610 DOI: 10.3390/polym14040670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 01/14/2023] Open
Abstract
Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (P(3HB-co-3HV)) is the most studied short-chain-length polyhydroxyalkanoates (PHA) with high application importance in various fields. The domination of high-cost propionate and valerate over other 3-hydroxyvalerate (3HV) precursors owing to their wide preference among PHA-producing bacteria has hindered the development of diverse production processes. As alkyl alcohols are mainly produced from inexpensive starting materials through oxo synthesis, they contribute a cost-effective advantage over propionate and valerate. Moreover, alkyl alcohols can be biosynthesized from natural substrates and organic wastes. Despite their great potential, their toxicity to most PHA-producing bacteria has been the major drawback for their wide implementation as 3HV precursors for decades. Although the standard PHA-producing bacteria Cupriavidus necator showed promising alcohol tolerance, the 3HV yield was discouraging. Continuous discovery of alkyl alcohols-utilizing PHA-producing bacteria has enabled broader choices in 3HV precursor selection for diverse P(3HB-co-3HV) production processes with higher economic feasibility. Besides continuous effort in searching for promising wild-type strains, genetic engineering to construct promising recombinant strains based on the understanding of the mechanisms involved in alkyl alcohols toxicity and tolerance is an alternative approach. However, more studies are required for techno-economic assessment to analyze the economic performance of alkyl alcohol-based production compared to that of organic acids.
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13
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Sučec I, Bersch B, Schanda P. How do Chaperones Bind (Partly) Unfolded Client Proteins? Front Mol Biosci 2021; 8:762005. [PMID: 34760928 PMCID: PMC8573040 DOI: 10.3389/fmolb.2021.762005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/06/2021] [Indexed: 01/03/2023] Open
Abstract
Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.
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Affiliation(s)
- Iva Sučec
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France
| | - Beate Bersch
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France
| | - Paul Schanda
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France.,Institute of Science and Technology Austria, Klosterneuburg, Austria
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14
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Arhar T, Shkedi A, Nadel CM, Gestwicki JE. The interactions of molecular chaperones with client proteins: why are they so weak? J Biol Chem 2021; 297:101282. [PMID: 34624315 PMCID: PMC8567204 DOI: 10.1016/j.jbc.2021.101282] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/30/2022] Open
Abstract
The major classes of molecular chaperones have highly variable sequences, sizes, and shapes, yet they all bind to unfolded proteins, limit their aggregation, and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, "client" proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK, and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone-client interactions are readily outcompeted by stronger, intra- and intermolecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.
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Affiliation(s)
- Taylor Arhar
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Arielle Shkedi
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA.
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15
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Kim H, Wu K, Lee C. Stress-Responsive Periplasmic Chaperones in Bacteria. Front Mol Biosci 2021; 8:678697. [PMID: 34046432 PMCID: PMC8144458 DOI: 10.3389/fmolb.2021.678697] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/19/2021] [Indexed: 01/14/2023] Open
Abstract
Periplasmic proteins are involved in a wide range of bacterial functions, including motility, biofilm formation, sensing environmental cues, and small-molecule transport. In addition, a wide range of outer membrane proteins and proteins that are secreted into the media must travel through the periplasm to reach their final destinations. Since the porous outer membrane allows for the free diffusion of small molecules, periplasmic proteins and those that travel through this compartment are more vulnerable to external environmental changes, including those that result in protein unfolding, than cytoplasmic proteins are. To enable bacterial survival under various stress conditions, a robust protein quality control system is required in the periplasm. In this review, we focus on several periplasmic chaperones that are stress responsive, including Spy, which responds to envelope-stress, DegP, which responds to temperature to modulate chaperone/protease activity, HdeA and HdeB, which respond to acid stress, and UgpB, which functions as a bile-responsive chaperone.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, South Korea
- Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, United States
| | - Kevin Wu
- Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
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