1
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Zhu X, Xia Y, Wang H, Shi L, Yin H, Gu M, Yan F. PM 2.5 induced neurotoxicity through unbalancing vitamin B12 metabolism by gut microbiota disturbance. Gut Microbes 2023; 15:2267186. [PMID: 37842922 PMCID: PMC10580859 DOI: 10.1080/19490976.2023.2267186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
Fine particulate matter (PM2.5) in the atmosphere is easily accompanied by toxic and harmful substances, causing serious harm to human health, including cognitive impairment. Vitamin B12 (VitB12) is an essential micronutrient that is synthesized by bacteria and contributes to neurotransmitter synthesis as a nutrition and signaling molecule. However, the relationship between VitB12 attenuation of cognitive impairment and intestinal microbiota regulation in PM2.5 exposure has not been elucidated. In this study, we demonstrated that PM2.5 caused behavioral defects and neuronal damage in Caenorhabditis elegans (C. elegans), along with significant gene expression changes in neurotransmitter receptors and a decrease in VitB12 content, causing behavioral defects and neuronal damage in C. elegans. Methylcobalamin (MeCbl), a VitB12 analog, alleviated PM2.5-induced neurotoxicity in C. elegans. Moreover, using in vivo and in vitro models, we discovered that long-term exposure to PM2.5 led to changes in the structure of the gut microbiota, resulting in an imbalance of the VitB12-associated metabolic pathway followed by cognitive impairment. MeCbl supplementation could increase the diversity of the bacteria, reduce harmful substance contents, and restore the concentration of short-chain fatty acids (SCFAs) and neurotransmitters to the level of the control group to some degree. Here, a new target to mitigate the harm caused by PM2.5 was discovered, supplying MeCbl for relieving intestinal and intracellular neurotransmitter disorders. Our results also provide a reference for the use of VitB12 to target the adjustment of the human intestinal microbiota to improve metabolic disorders in people exposed to PM2.5.
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Affiliation(s)
- Xuan Zhu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People’s Republic of China
- Zhejiang Provincial Key Laboratory of Food Safety, Zhejiang Gongshang University, Hangzhou, China
| | - Yanting Xia
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People’s Republic of China
| | - Huanhuan Wang
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Laboratory animal center, Hangzhou Normal University, Hangzhou, China
| | - Lihua Shi
- Weifang Elbe Health Food Co. Ltd, Weifang, China
| | - Hongping Yin
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Laboratory animal center, Hangzhou Normal University, Hangzhou, China
| | - Meier Gu
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Laboratory animal center, Hangzhou Normal University, Hangzhou, China
| | - Fujie Yan
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
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2
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Abstract
TonB-dependent transporters (TBDTs) are present in all gram-negative bacteria and mediate energy-dependent uptake of molecules that are too scarce or large to be taken up efficiently by outer membrane (OM) diffusion channels. This process requires energy that is derived from the proton motive force and delivered to TBDTs by the TonB-ExbBD motor complex in the inner membrane. Together with the need to preserve the OM permeability barrier, this has led to an extremely complex and fascinating transport mechanism for which the fundamentals, despite decades of research, are still unclear. In this review, we describe our current understanding of the transport mechanism of TBDTs, their potential role in the delivery of novel antibiotics, and the important contributions made by TBDT-associated (lipo)proteins.
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Affiliation(s)
- Augustinas Silale
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom; ,
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom; ,
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3
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Haysom SF, Machin J, Whitehouse JM, Horne JE, Fenn K, Ma Y, El Mkami H, Böhringer N, Schäberle TF, Ranson NA, Radford SE, Pliotas C. Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202218783. [PMID: 38515502 PMCID: PMC10952338 DOI: 10.1002/ange.202218783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Indexed: 03/23/2024]
Abstract
The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
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Affiliation(s)
- Samuel F. Haysom
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jonathan Machin
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - James M. Whitehouse
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jim E. Horne
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Katherine Fenn
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Yue Ma
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Hassane El Mkami
- School of Physics and AstronomyUniversity of St. AndrewsSt. AndrewsKY16 9SSUK
| | - Nils Böhringer
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
| | - Till F. Schäberle
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
- Natural Product DepartmentFraunhofer-Institute for Molecular Biology and Applied Ecology (IME)Ohlebergsweg 1235392GiessenGermany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
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4
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Haysom SF, Machin J, Whitehouse JM, Horne JE, Fenn K, Ma Y, El Mkami H, Böhringer N, Schäberle TF, Ranson NA, Radford SE, Pliotas C. Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. Angew Chem Int Ed Engl 2023; 62:e202218783. [PMID: 37162386 PMCID: PMC10952311 DOI: 10.1002/anie.202218783] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
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Affiliation(s)
- Samuel F. Haysom
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jonathan Machin
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - James M. Whitehouse
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jim E. Horne
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Katherine Fenn
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Yue Ma
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Hassane El Mkami
- School of Physics and AstronomyUniversity of St. AndrewsSt. AndrewsKY16 9SSUK
| | - Nils Böhringer
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
| | - Till F. Schäberle
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
- Natural Product DepartmentFraunhofer-Institute for Molecular Biology and Applied Ecology (IME)Ohlebergsweg 1235392GiessenGermany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
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5
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Wimalasiri VW, Jurczak KA, Wieliniec MK, Nilaweera TD, Nakamoto RK, Cafiso DS. A disulfide chaperone knockout facilitates spin labeling and pulse EPR spectroscopy of outer membrane transporters. Protein Sci 2023; 32:e4704. [PMID: 37312651 PMCID: PMC10288552 DOI: 10.1002/pro.4704] [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: 02/17/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Pulse EPR measurements provide information on distances and distance distributions in proteins but require the incorporation of pairs of spin labels that are usually attached to engineered cysteine residues. In previous work, we demonstrated that efficient in vivo labeling of the Escherichia coli outer membrane vitamin B12 transporter, BtuB, could only be achieved using strains defective in the periplasmic disulfide bond formation (Dsb) system. Here, we extend these in vivo measurements to FecA, the E. coli ferric citrate transporter. As seen for BtuB, pairs of cysteines cannot be labeled when the protein is present in a standard expression strain. However, incorporating plasmids that permit an arabinose induced expression of FecA into a strain defective in the thiol disulfide oxidoreductase, DsbA, enables efficient spin-labeling and pulse EPR of FecA in cells. A comparison of the measurements made on FecA in cells with measurements made in reconstituted phospholipid bilayers suggests that the cellular environment alters the behavior of the extracellular loops of FecA. In addition to these in situ EPR measurements, the use of a DsbA minus strain for the expression of BtuB improves the EPR signals and pulse EPR data obtained in vitro from BtuB that is labeled, purified, and reconstituted into phospholipid bilayers. The in vitro data also indicate the presence of intermolecular BtuB-BtuB interactions, which had not previously been observed in a reconstituted bilayer system. This result suggests that in vitro EPR measurements on other outer membrane proteins would benefit from protein expression in a DsbA minus strain.
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Affiliation(s)
- Viranga W. Wimalasiri
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Kinga A. Jurczak
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Monika K. Wieliniec
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Thushani D. Nilaweera
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
- Present address:
Genetics and Biochemistry BranchNational Institute of Diabetes and Digestive and Kidney DiseasesBethesdaMarylandUSA
| | - Robert K. Nakamoto
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - David S. Cafiso
- Department of Chemistry and Center for Membrane BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
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6
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White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Baslé A, Trost M, Bolam DN, van den Berg B, Ranson NA. Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes. Nature 2023:10.1038/s41586-023-06146-w. [PMID: 37286596 DOI: 10.1038/s41586-023-06146-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023]
Abstract
Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut1. Glycan uptake across the bacterial outer membrane of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, which is thought to open and close to facilitate substrate binding and transport. However, surface-exposed glycan-binding proteins and glycoside hydrolases also play critical roles in the capture, processing and transport of large glycan chains. The interactions between these components in the outer membrane are poorly understood, despite being crucial for nutrient acquisition by our colonic microbiota. Here we show that for both the levan and dextran utilization systems of Bacteroides thetaiotaomicron, the additional outer membrane components assemble on the core SusCD transporter, forming stable glycan-utilizing machines that we term utilisomes. Single-particle cryogenic electron microscopy structures in the absence and presence of substrate reveal concerted conformational changes that demonstrate the mechanism of substrate capture, and rationalize the role of each component in the utilisome.
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Affiliation(s)
- Joshua B R White
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Augustinas Silale
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew Feasey
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Tiaan Heunis
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Yiling Zhu
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Hong Zheng
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Akshada Gajbhiye
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Susan Firbank
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Arnaud Baslé
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Matthias Trost
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - David N Bolam
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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7
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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8
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Ketter S, Joseph B. Gd 3+-Trityl-Nitroxide Triple Labeling and Distance Measurements in the Heterooligomeric Cobalamin Transport Complex in the Native Lipid Bilayers. J Am Chem Soc 2023; 145:960-966. [PMID: 36599418 PMCID: PMC9853854 DOI: 10.1021/jacs.2c10080] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Increased efforts are being made for observing proteins in their native environments. Pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) is a powerful tool for this purpose. Conventionally, PELDOR employs an identical spin pair, which limits the output to a single distance for monomeric samples. Here, we show that the Gd3+-trityl-nitroxide (NO) three-spin system is a versatile tool to study heterooligomeric membrane protein complexes, even within their native membrane. This allowed for an independent determination of four different distances (Gd3+-trityl, Gd3+-NO, trityl-NO, and Gd3+-Gd3+) within the same sample. We demonstrate the feasibility of this approach by observing sequential ligand binding and the dynamics of complex formation in the cobalamin transport system involving four components (cobalamin, BtuB, TonB, and BtuF). Our results reveal that TonB binding alone is sufficient to release cobalamin from BtuB in the native asymmetric bilayers. This approach provides a potential tool for the structural and quantitative analysis of dynamic protein-protein interactions in oligomeric complexes, even within their native surroundings.
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9
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Pierro A, Bonucci A, Normanno D, Ansaldi M, Pilet E, Ouari O, Guigliarelli B, Etienne E, Gerbaud G, Magalon A, Belle V, Mileo E. Probing the Structural Dynamics of a Bacterial Chaperone in Its Native Environment by Nitroxide‐Based EPR Spectroscopy. Chemistry 2022; 28:e202202249. [DOI: 10.1002/chem.202202249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
- Department of Chemistry University of Konstanz, and Konstanz Research School Chemical Biology 78457 Konstanz Germany
| | - Alessio Bonucci
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Davide Normanno
- Aix Marseille Univ CNRS, Inserm Institut Paoli-Calmettes, CRCM Centre de Recherche en Cancérologie de Marseille 13273 Marseille France
- Univ Montpellier CNRS, IGH Institut de Génétique Humaine 34396 Montpellier France
| | - Mireille Ansaldi
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Eric Pilet
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Olivier Ouari
- Aix Marseille Univ CNRS, ICR Institut de Chimie Radicalaire 13397 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Emilien Etienne
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Axel Magalon
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
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10
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Lin X, Zmyslowski AM, Gagnon IA, Nakamoto RK, Sosnick TR. Development of in vivo
HDX‐MS
with applications to a
TonB
‐dependent transporter and other proteins. Protein Sci 2022; 31:e4402. [PMID: 36040258 PMCID: PMC9382693 DOI: 10.1002/pro.4402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022]
Abstract
Hydrogen‐deuterium exchange mass spectrometry (HDX‐MS) is a powerful tool that monitors protein dynamics in solution. However, the reversible nature of HDX labels has largely limited the application to in vitro systems. Here, we describe a protocol for measuring HDX‐MS in living Escherichia coli cells applied to BtuB, a TonB‐dependent transporter found in outer membranes (OMs). BtuB is a convenient and biologically interesting system for testing in vivo HDX‐MS due to its controllable HDX behavior and large structural rearrangements that occur during the B12 transport cycle. Our previous HDX‐MS study in native OMs provided evidence for B12 binding and breaking of a salt bridge termed the Ionic Lock, an event that leads to the unfolding of the amino terminus. Although purified OMs provide a more native‐like environment than reconstituted systems, disruption of the cell envelope during lysis perturbs the linkage between BtuB and the TonB complex that drives B12 transport. The in vivo HDX response of BtuB's plug domain (BtuBp) to B12 binding corroborates our previous in vitro findings that B12 alone is sufficient to break the Ionic Lock. In addition, we still find no evidence of B12 binding‐induced unfolding in other regions of BtuBp that could enable B12 passage. Our protocol was successful in reporting on the HDX of several endogenous E. coli proteins measured in the same measurement. Our success in performing HDX in live cells opens the possibility for future HDX‐MS studies in a native cellular environment.
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Affiliation(s)
- Xiaoxuan Lin
- Department of Biochemistry and Molecular Biology The University of Chicago Chicago Illinois USA
| | - Adam M. Zmyslowski
- Department of Biochemistry and Molecular Biology The University of Chicago Chicago Illinois USA
| | - Isabelle A. Gagnon
- Department of Biochemistry and Molecular Biology The University of Chicago Chicago Illinois USA
| | - Robert K. Nakamoto
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia USA
| | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology The University of Chicago Chicago Illinois USA
- Prizker School for Molecular Engineering The University of Chicago Chicago Illinois USA
- Institute for Biophysical Dynamics The University of Chicago Chicago Illinois USA
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11
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Zmyslowski AM, Baxa MC, Gagnon IA, Sosnick TR. HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain's allostery and unfolding upon B12 and TonB binding. Proc Natl Acad Sci U S A 2022; 119:e2119436119. [PMID: 35549554 PMCID: PMC9171809 DOI: 10.1073/pnas.2119436119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 04/09/2022] [Indexed: 11/18/2022] Open
Abstract
To import large metabolites across the outer membrane of gram-negative bacteria, TonB-dependent transporters (TBDTs) undergo significant conformational change. After substrate binding in BtuB, the Escherichia coli vitamin B12 TBDT, TonB binds and couples BtuB to the inner-membrane proton motive force that powers transport [N. Noinaj, M. Guillier, T. J. Barnard, S. K. Buchanan, Annu. Rev. Microbiol. 64, 43–60 (2010)]. However, the role of TonB in rearranging the plug domain of BtuB to form a putative pore remains enigmatic. Some studies focus on force-mediated unfolding [S. J. Hickman, R. E. M. Cooper, L. Bellucci, E. Paci, D. J. Brockwell, Nat. Commun. 8, 14804 (2017)], while others propose force-independent pore formation by TonB binding [T. D. Nilaweera, D. A. Nyenhuis, D. S. Cafiso, eLife 10, e68548 (2021)], leading to breakage of a salt bridge termed the “Ionic Lock.” Our hydrogen–deuterium exchange/mass spectrometry (HDX-MS) measurements in E. coli outer membranes find that the region surrounding the Ionic Lock, far from the B12 site, is fully destabilized upon substrate binding. A comparison of the exchange between the B12-bound and the B12+TonB–bound complexes indicates that B12 binding is sufficient to unfold the Ionic Lock region, with the subsequent binding of a TonB fragment having much weaker effects. TonB binding accelerates exchange in the third substrate-binding loop, but pore formation does not obviously occur in this or any region. This study provides a detailed structural and energetic description of the early stages of B12 passage that provides support both for and against current models of the transport process.
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Affiliation(s)
- Adam M. Zmyslowski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Michael C. Baxa
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Isabelle A. Gagnon
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- Prizker School for Molecular Engineering, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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