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Nissley DA, Jiang Y, Trovato F, Sitarik I, Narayan KB, To P, Xia Y, Fried SD, O'Brien EP. Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional. Nat Commun 2022; 13:3081. [PMID: 35654797 PMCID: PMC9163053 DOI: 10.1038/s41467-022-30548-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/05/2022] [Indexed: 01/12/2023] Open
Abstract
Some misfolded protein conformations can bypass proteostasis machinery and remain soluble in vivo. This is an unexpected observation, as cellular quality control mechanisms should remove misfolded proteins. Three questions, then, are: how do long-lived, soluble, misfolded proteins bypass proteostasis? How widespread are such misfolded states? And how long do they persist? We address these questions using coarse-grain molecular dynamics simulations of the synthesis, termination, and post-translational dynamics of a representative set of cytosolic E. coli proteins. We predict that half of proteins exhibit misfolded subpopulations that bypass molecular chaperones, avoid aggregation, and will not be rapidly degraded, with some misfolded states persisting for months or longer. The surface properties of these misfolded states are native-like, suggesting they will remain soluble, while self-entanglements make them long-lived kinetic traps. In terms of function, we predict that one-third of proteins can misfold into soluble less-functional states. For the heavily entangled protein glycerol-3-phosphate dehydrogenase, limited-proteolysis mass spectrometry experiments interrogating misfolded conformations of the protein are consistent with the structural changes predicted by our simulations. These results therefore provide an explanation for how proteins can misfold into soluble conformations with reduced functionality that can bypass proteostasis, and indicate, unexpectedly, this may be a wide-spread phenomenon.
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Affiliation(s)
- Daniel A Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Fabio Trovato
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Karthik B Narayan
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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Roch M, Lelong E, Panasenko OO, Sierra R, Renzoni A, Kelley WL. Thermosensitive PBP2a requires extracellular folding factors PrsA and HtrA1 for Staphylococcus aureus MRSA β-lactam resistance. Commun Biol 2019; 2:417. [PMID: 31754647 PMCID: PMC6858329 DOI: 10.1038/s42003-019-0667-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/25/2019] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen and represents a clinical challenge because of widespread antibiotic resistance. Methicillin resistant Staphylococcus aureus (MRSA) is particularly problematic and originates by the horizontal acquisition of mecA encoding PBP2a, an extracellular membrane anchored transpeptidase, which confers resistance to β-lactam antibiotics by allosteric gating of its active site channel. Herein, we show that dual disruption of PrsA, a lipoprotein chaperone displaying anti-aggregation activity, together with HtrA1, a membrane anchored chaperone/serine protease, resulted in severe and synergistic attenuation of PBP2a folding that restores sensitivity to β-lactams such as oxacillin. Purified PBP2a has a pronounced unfolding transition initiating at physiological temperatures that leads to irreversible precipitation and complete loss of activity. The concordance of genetic and biochemical data highlights the necessity for extracellular protein folding factors governing MRSA β-lactam resistance. Targeting the PBP2a folding pathway represents a particularly attractive adjuvant strategy to combat antibiotic resistance.
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Affiliation(s)
- Mélanie Roch
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
| | - Emmanuelle Lelong
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - Olesya O. Panasenko
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - Roberto Sierra
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
| | - Adriana Renzoni
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - William L. Kelley
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
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Deuerling E, Gamerdinger M, Kreft SG. Chaperone Interactions at the Ribosome. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a033977. [PMID: 30833456 DOI: 10.1101/cshperspect.a033977] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The continuous refreshment of the proteome is critical to maintain protein homeostasis and to adapt cells to changing conditions. Thus, de novo protein biogenesis by ribosomes is vitally important to every cellular system. This process is delicate and error-prone and requires, besides cytosolic chaperones, the guidance by a specialized set of molecular chaperones that bind transiently to the translation machinery and the nascent protein to support early folding events and to regulate cotranslational protein transport. These chaperones include the bacterial trigger factor (TF), the archaeal and eukaryotic nascent polypeptide-associated complex (NAC), and the eukaryotic ribosome-associated complex (RAC). This review focuses on the structures, functions, and substrates of these ribosome-associated chaperones and highlights the most recent findings about their potential mechanisms of action.
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Affiliation(s)
- Elke Deuerling
- Molecular Microbiology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Martin Gamerdinger
- Molecular Microbiology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Stefan G Kreft
- Molecular Microbiology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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Can MT, Kurkcuoglu Z, Ezeroglu G, Uyar A, Kurkcuoglu O, Doruker P. Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states. PLoS One 2017; 12:e0176262. [PMID: 28437479 PMCID: PMC5402958 DOI: 10.1371/journal.pone.0176262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/07/2017] [Indexed: 11/30/2022] Open
Abstract
The chaperone trigger factor (TF) binds to the ribosome exit tunnel and helps cotranslational folding of nascent chains (NC) in bacterial cells and chloroplasts. In this study, we aim to investigate the functional dynamics of fully-atomistic apo TF and its complex with 50S. As TF accomodates a high percentage of charged residues on its surface, the effect of ionic strength on TF dynamics is assessed here by performing five independent molecular dynamics (MD) simulations (total of 1.3 micro-second duration) at 29 mM and 150 mM ionic strengths. At both concentrations, TF exhibits high inter- and intra-domain flexibility related to its binding (BD), core (CD), and head (HD) domains. Even though large oscillations in gyration radius exist during each run, we do not detect the so-called ‘fully collapsed’ state with both HD and BD collapsed upon the core. In fact, the extended conformers with relatively open HD and BD are highly populated at the physiological concentration of 150 mM. More importantly, extended TF snapshots stand out in terms of favorable docking onto the 50S subunit. Elastic network modeling (ENM) indicates significant changes in TF’s functional dynamics and domain decomposition depending on its conformation and positioning on the 50S. The most dominant slow motions are the lateral sweeping and vertical opening/closing of HD relative to 50S. Finally, our ENM-based efficient technique -ClustENM- is used to sample atomistic conformers starting with an extended TF-50S complex. Specifically, BD and CD motions are restricted near the tunnel exit, while HD is highly mobile. The atomistic conformers generated without an NC are in agreement with the cryo-EM maps available for TF-ribosome-NC complex.
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Affiliation(s)
- Mehmet Tarik Can
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
| | - Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
| | - Gokce Ezeroglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
| | - Arzu Uyar
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
- * E-mail:
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Sun J, Zhou J, Wang Z, He W, Zhang D, Tong Q, Su X. Multi-omics based changes in response to cadmium toxicity in Bacillus licheniformis A. RSC Adv 2015. [DOI: 10.1039/c4ra15280h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cadmium (Cd), a widespread substance with high toxicity and persistence, is known to cause a broad range of adverse effects in all living organisms.
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Affiliation(s)
- Jing Sun
- School of Marine Sciences
- Ningbo University
- Ningbo 315211
- China
- College of Food Science and Technology
| | - Jun Zhou
- School of Marine Sciences
- Ningbo University
- Ningbo 315211
- China
| | - Zhonghua Wang
- School of Marine Sciences
- Ningbo University
- Ningbo 315211
- China
| | - Weina He
- School of Marine Sciences
- Ningbo University
- Ningbo 315211
- China
| | - Dijun Zhang
- School of Marine Sciences
- Ningbo University
- Ningbo 315211
- China
| | - Qianqian Tong
- School of Marine Sciences
- Ningbo University
- Ningbo 315211
- China
| | - Xiurong Su
- School of Marine Sciences
- Ningbo University
- Ningbo 315211
- China
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