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Mellouk A, Jaouen P, Ruel LJ, Lê M, Martini C, Moraes TF, El Bakkouri M, Lagüe P, Boisselier E, Calmettes C. POTRA domains of the TamA insertase interact with the outer membrane and modulate membrane properties. Proc Natl Acad Sci U S A 2024; 121:e2402543121. [PMID: 38959031 PMCID: PMC11252910 DOI: 10.1073/pnas.2402543121] [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: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 07/04/2024] Open
Abstract
The outer membrane (OM) of gram-negative bacteria serves as a vital organelle that is densely populated with OM proteins (OMPs) and plays pivotal roles in cellular functions and virulence. The assembly and insertion of these OMPs into the OM represent a fundamental process requiring specialized molecular chaperones. One example is the translocation and assembly module (TAM), which functions as a transenvelope chaperone promoting the folding of specific autotransporters, adhesins, and secretion systems. The catalytic unit of TAM, TamA, comprises a catalytic β-barrel domain anchored within the OM and three periplasmic polypeptide-transport-associated (POTRA) domains that recruit the TamB subunit. The latter acts as a periplasmic ladder that facilitates the transport of unfolded OMPs across the periplasm. In addition to their role in recruiting the auxiliary protein TamB, our data demonstrate that the POTRA domains mediate interactions with the inner surface of the OM, ultimately modulating the membrane properties. Through the integration of X-ray crystallography, molecular dynamic simulations, and biomolecular interaction methodologies, we located the membrane-binding site on the first and second POTRA domains. Our data highlight a binding preference for phosphatidylglycerol, a minor lipid constituent present in the OM, which has been previously reported to facilitate OMP assembly. In the context of the densely OMP-populated membrane, this association may serve as a mechanism to secure lipid accessibility for nascent OMPs through steric interactions with existing OMPs, in addition to creating favorable conditions for OMP biogenesis.
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Affiliation(s)
- Abdelkader Mellouk
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Paul Jaouen
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, centre hospitalier universitaire de Québec, Université Laval, Québec City, QCG1S 4L8, Canada
| | - Louis-Jacques Ruel
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec City, QCG1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QCG1V 0A6, Canada
| | - Michel Lê
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Cyrielle Martini
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, ONM5G 1M1, Canada
| | - Majida El Bakkouri
- National Research Council Canada, Human Health Therapeutics, Montréal, QCH4P 2R2, Canada
| | - Patrick Lagüe
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec City, QCG1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QCG1V 0A6, Canada
| | - Elodie Boisselier
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, centre hospitalier universitaire de Québec, Université Laval, Québec City, QCG1S 4L8, Canada
| | - Charles Calmettes
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
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2
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Wang Z, Chu Y, Li Q, Han X, Zhao L, Zhang H, Cai K, Zhang X, Wang X, Qin Y, Fan E. A minimum functional form of the Escherichia coli BAM complex constituted by BamADE assembles outer membrane proteins in vitro. J Biol Chem 2024; 300:107324. [PMID: 38677515 PMCID: PMC11130730 DOI: 10.1016/j.jbc.2024.107324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
The biogenesis of outer membrane proteins is mediated by the β-barrel assembly machinery (BAM), which is a heteropentomeric complex composed of five proteins named BamA-E in Escherichia coli. Despite great progress in the BAM structural analysis, the molecular details of BAM-mediated processes as well as the exact function of each BAM component during OMP assembly are still not fully understood. To enable a distinguishment of the function of each BAM component, it is the aim of the present work to examine and identify the effective minimum form of the E. coli BAM complex by use of a well-defined reconstitution strategy based on a previously developed versatile assay. Our data demonstrate that BamADE is the core BAM component and constitutes a minimum functional form for OMP assembly in E. coli, which can be stimulated by BamB and BamC. While BamB and BamC have a redundant function based on the minimum form, both together seem to cooperate with each other to substitute for the function of the missing BamD or BamE. Moreover, the BamAE470K mutant also requires the function of BamD and BamE to assemble OMPs in vitro, which vice verse suggests that BamADE are the effective minimum functional form of the E. coli BAM complex.
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Affiliation(s)
- Zhe Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yindi Chu
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Qingrong Li
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xiaochen Han
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Leyi Zhao
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Hanqing Zhang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Kun Cai
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xuyan Zhang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xingyuan Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Youcai Qin
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Enguo Fan
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China; School of Medicine, Linyi University, Linyi, China.
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3
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Woodard AM, Peccati F, Navo CD, Jiménez-Osés G, Mitchell DA. Darobactin Substrate Engineering and Computation Show Radical Stability Governs Ether versus C-C Bond Formation. J Am Chem Soc 2024; 146:14328-14340. [PMID: 38728535 PMCID: PMC11225102 DOI: 10.1021/jacs.4c03994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
The Gram-negative selective antibiotic darobactin A has attracted interest owing to its intriguing fused bicyclic structure and unique targeting of the outer membrane protein BamA. Darobactin, a ribosomally synthesized and post-translationally modified peptide (RiPP), is produced by a radical S-adenosyl methionine (rSAM)-dependent enzyme (DarE) and contains one ether and one C-C cross-link. Herein, we analyze the substrate tolerance of DarE and describe an underlying catalytic principle of the enzyme. These efforts produced 51 enzymatically modified darobactin variants, revealing that DarE can install the ether and C-C cross-links independently and in different locations on the substrate. Notable variants with fused bicyclic structures were characterized, including darobactin W3Y, with a non-Trp residue at the twice-modified central position, and darobactin K5F, which displays a fused diether ring pattern. While lacking antibiotic activity, quantum mechanical modeling of darobactins W3Y and K5F aided in the elucidation of the requisite features for high-affinity BamA engagement. We also provide experimental evidence for β-oxo modification, which adds support for a proposed DarE mechanism. Based on these results, ether and C-C cross-link formation was investigated computationally, and it was determined that more stable and longer-lived aromatic Cβ radicals correlated with ether formation. Further, molecular docking and transition state structures based on high-level quantum mechanical calculations support the different indole connectivity observed for ether (Trp-C7) and C-C (Trp-C6) cross-links. Finally, mutational analysis and protein structural predictions identified substrate residues that govern engagement to DarE. Our work informs on darobactin scaffold engineering and further unveils the underlying principles of rSAM catalysis.
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Affiliation(s)
- Austin M Woodard
- Department of Chemistry, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
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4
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Hartojo A, Doyle MT. β-barrel membrane proteins fold via hybrid-barrel intermediate states. Curr Opin Struct Biol 2024; 87:102830. [PMID: 38728831 DOI: 10.1016/j.sbi.2024.102830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/15/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]
Abstract
Gram-negative bacteria and eukaryotic organelles of bacterial origin contain outer membrane proteins that possess a transmembrane "β-barrel" domain. The conserved β-barrel assembly machine (BAM) and the sorting and assembly machine (SAM) are required for the folding and membrane insertion of β-barrels in Gram-negative bacteria and mitochondria, respectively. Although the mechanisms by which β-barrels are folded are incompletely understood, advances in cryo-electron microscopy (cryo-EM) have recently yielded unprecedented insights into their folding process. Here we highlight recent studies that show that both bacterial and mitochondrial β-barrels fold via the formation of remarkable "hybrid-barrel" intermediate states during their interaction with the folding machinery. We discuss how these results align with a general model of β-barrel folding.
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Affiliation(s)
- Alfred Hartojo
- Sydney Infectious Diseases Institute, The University of Sydney, Darlington, New South Wales, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, New South Wales, Australia. https://twitter.com/AlfredHartojo29
| | - Matthew Thomas Doyle
- Sydney Infectious Diseases Institute, The University of Sydney, Darlington, New South Wales, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, New South Wales, Australia.
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5
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Goh KJ, Stubenrauch CJ, Lithgow T. The TAM, a Translocation and Assembly Module for protein assembly and potential conduit for phospholipid transfer. EMBO Rep 2024; 25:1711-1720. [PMID: 38467907 PMCID: PMC11014939 DOI: 10.1038/s44319-024-00111-y] [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: 09/18/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The assembly of β-barrel proteins into the bacterial outer membrane is an essential process enabling the colonization of new environmental niches. The TAM was discovered as a module of the β-barrel protein assembly machinery; it is a heterodimeric complex composed of an outer membrane protein (TamA) bound to an inner membrane protein (TamB). The TAM spans the periplasm, providing a scaffold through the peptidoglycan layer and catalyzing the translocation and assembly of β-barrel proteins into the outer membrane. Recently, studies on another membrane protein (YhdP) have suggested that TamB might play a role in phospholipid transport to the outer membrane. Here we review and re-evaluate the literature covering the experimental studies on the TAM over the past decade, to reconcile what appear to be conflicting claims on the function of the TAM.
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Affiliation(s)
- Kwok Jian Goh
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christopher J Stubenrauch
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia.
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
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6
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Christoffer C, Harini K, Archit G, Kihara D. Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints. J Mol Biol 2024; 436:168486. [PMID: 38336197 PMCID: PMC10942765 DOI: 10.1016/j.jmb.2024.168486] [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: 11/08/2023] [Revised: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Membrane proteins play crucial roles in various cellular processes, and their interactions with other proteins in and on the membrane are essential for their proper functioning. While an increasing number of structures of more membrane proteins are being determined, the available structure data is still sparse. To gain insights into the mechanisms of membrane protein complexes, computational docking methods are necessary due to the challenge of experimental determination. Here, we introduce Mem-LZerD, a rigid-body membrane docking algorithm designed to take advantage of modern membrane modeling and protein docking techniques to facilitate the docking of membrane protein complexes. Mem-LZerD is based on the LZerD protein docking algorithm, which has been constantly among the top servers in many rounds of CAPRI protein docking assessment. By employing a combination of geometric hashing, newly constrained by the predicted membrane height and tilt angle, and model scoring accounting for the energy of membrane insertion, we demonstrate the capability of Mem-LZerD to model diverse membrane protein-protein complexes. Mem-LZerD successfully performed unbound docking on 13 of 21 (61.9%) transmembrane complexes in an established benchmark, more than shown by previous approaches. It was additionally tested on new datasets of 44 transmembrane complexes and 92 peripheral membrane protein complexes, of which it successfully modeled 35 (79.5%) and 15 (16.3%) complexes respectively. When non-blind orientations of peripheral targets were included, the number of successes increased to 54 (58.7%). We further demonstrate that Mem-LZerD produces complex models which are suitable for molecular dynamics simulation. Mem-LZerD is made available at https://lzerd.kiharalab.org.
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Affiliation(s)
- Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Kannan Harini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Gupta Archit
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur 603203, India
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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7
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George A, Patil AG, Mahalakshmi R. ATP-independent assembly machinery of bacterial outer membranes: BAM complex structure and function set the stage for next-generation therapeutics. Protein Sci 2024; 33:e4896. [PMID: 38284489 PMCID: PMC10804688 DOI: 10.1002/pro.4896] [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: 09/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/30/2024]
Abstract
Diderm bacteria employ β-barrel outer membrane proteins (OMPs) as their first line of communication with their environment. These OMPs are assembled efficiently in the asymmetric outer membrane by the β-Barrel Assembly Machinery (BAM). The multi-subunit BAM complex comprises the transmembrane OMP BamA as its functional subunit, with associated lipoproteins (e.g., BamB/C/D/E/F, RmpM) varying across phyla and performing different regulatory roles. The ability of BAM complex to recognize and fold OM β-barrels of diverse sizes, and reproducibly execute their membrane insertion, is independent of electrochemical energy. Recent atomic structures, which captured BAM-substrate complexes, show the assembly function of BamA can be tailored, with different substrate types exhibiting different folding mechanisms. Here, we highlight common and unique features of its interactome. We discuss how this conserved protein complex has evolved the ability to effectively achieve the directed assembly of diverse OMPs of wide-ranging sizes (8-36 β-stranded monomers). Additionally, we discuss how darobactin-the first natural membrane protein inhibitor of Gram-negative bacteria identified in over five decades-selectively targets and specifically inhibits BamA. We conclude by deliberating how a detailed deduction of BAM complex-associated regulation of OMP biogenesis and OM remodeling will open avenues for the identification and development of effective next-generation therapeutics against Gram-negative pathogens.
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Affiliation(s)
- Anjana George
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
| | - Akanksha Gajanan Patil
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
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8
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Gopinath A, Rath T, Morgner N, Joseph B. Lateral gating mechanism and plasticity of the β-barrel assembly machinery complex in micelles and Escherichia coli. PNAS NEXUS 2024; 3:pgae019. [PMID: 38312222 PMCID: PMC10833450 DOI: 10.1093/pnasnexus/pgae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024]
Abstract
The β-barrel assembly machinery (BAM) mediates the folding and insertion of the majority of outer membrane proteins (OMPs) in gram-negative bacteria. BAM is a penta-heterooligomeric complex consisting of the central β-barrel BamA and four interacting lipoproteins BamB, C, D, and E. The conformational switching of BamA between inward-open (IO) and lateral-open (LO) conformations is required for substrate recognition and folding. However, the mechanism for the lateral gating or how the structural details observed in vitro correspond with the cellular environment remains elusive. In this study, we addressed these questions by characterizing the conformational heterogeneity of BamAB, BamACDE, and BamABCDE complexes in detergent micelles and/or Escherichia coli using pulsed dipolar electron spin resonance spectroscopy (PDS). We show that the binding of BamB does not induce any visible changes in BamA, and the BamAB complex exists in the IO conformation. The BamCDE complex induces an IO to LO transition through a coordinated movement along the BamA barrel. However, the extracellular loop 6 (L6) is unaffected by the presence of lipoproteins and exhibits large segmental dynamics extending to the exit pore. PDS experiments with the BamABCDE complex in intact E. coli confirmed the dynamic behavior of both the lateral gate and the L6 in the native environment. Our results demonstrate that the BamCDE complex plays a key role in the function by regulating lateral gating in BamA.
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Affiliation(s)
- Aathira Gopinath
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
- Institute of Biophysics, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Tobias Rath
- Institute of Physical and Theoretical Chemistry, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
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9
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Germany EM, Thewasano N, Imai K, Maruno Y, Bamert RS, Stubenrauch CJ, Dunstan RA, Ding Y, Nakajima Y, Lai X, Webb CT, Hidaka K, Tan KS, Shen H, Lithgow T, Shiota T. Dual recognition of multiple signals in bacterial outer membrane proteins enhances assembly and maintains membrane integrity. eLife 2024; 12:RP90274. [PMID: 38226797 PMCID: PMC10945584 DOI: 10.7554/elife.90274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
Outer membrane proteins (OMPs) are essential components of the outer membrane of Gram-negative bacteria. In terms of protein targeting and assembly, the current dogma holds that a 'β-signal' imprinted in the final β-strand of the OMP engages the β-barrel assembly machinery (BAM) complex to initiate membrane insertion and assembly of the OMP into the outer membrane. Here, we revealed an additional rule that signals equivalent to the β-signal are repeated in other, internal β-strands within bacterial OMPs, by peptidomimetic and mutational analysis. The internal signal is needed to promote the efficiency of the assembly reaction of these OMPs. BamD, an essential subunit of the BAM complex, recognizes the internal signal and the β-signal, arranging several β-strands and partial folding for rapid OMP assembly. The internal signal-BamD ordering system is not essential for bacterial viability but is necessary to retain the integrity of the outer membrane against antibiotics and other environmental insults.
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Affiliation(s)
- Edward M Germany
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - Nakajohn Thewasano
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Yuki Maruno
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - Rebecca S Bamert
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Christopher J Stubenrauch
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Rhys A Dunstan
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Yue Ding
- Department of Materials Science and Engineering, Monash UniversityClaytonAustralia
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash UniversityClaytonAustralia
| | - Yukari Nakajima
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - XiangFeng Lai
- Department of Materials Science and Engineering, Monash UniversityClaytonAustralia
| | - Chaille T Webb
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Kentaro Hidaka
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - Kher Shing Tan
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Hsinhui Shen
- Department of Materials Science and Engineering, Monash UniversityClaytonAustralia
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash UniversityClaytonAustralia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Takuya Shiota
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
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10
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Woodard AM, Peccati F, Navo CD, Jiménez-Osés G, Mitchell DA. Benzylic Radical Stabilization Permits Ether Formation During Darobactin Biosynthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569256. [PMID: 38076856 PMCID: PMC10705402 DOI: 10.1101/2023.11.29.569256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The Gram-negative selective antibiotic darobactin A has attracted interest owing to its intriguing fused bicyclic structure and unique mode of action. Biosynthetic studies have revealed that darobactin is a ribosomally synthesized and post-translationally modified peptide (RiPP). During maturation, the darobactin precursor peptide (DarA) is modified by a radical S-adenosyl methionine (rSAM)-dependent enzyme (DarE) to contain ether and C-C crosslinks. In this work, we describe the enzymatic tolerance of DarE using a panel of DarA variants, revealing that DarE can install the ether and C-C crosslinks independently and in different locations on DarA. These efforts produced 57 darobactin variants, 50 of which were enzymatically modified. Several new variants with fused bicyclic structures were characterized, including darobactin W3Y, which replaces tryptophan with tyrosine at the twice-modified central position, and darobactin K5F, which displays a fused diether ring pattern. Three additional darobactin variants contained fused diether macrocycles, leading us to investigate the origin of ether versus C-C crosslink formation. Computational analyses found that more stable and long-lived Cβ radicals found on aromatic amino acids correlated with ether formation. Further, molecular docking and calculated transition state structures provide support for the different indole connectivity observed for ether (Trp-C7) and C-C (Trp-C6) crosslink formation. We also provide experimental evidence for a β-oxotryptophan modification, a proposed intermediate during ether crosslink formation. Finally, mutational analysis of the DarA leader region and protein structural predictions identified which residues were dispensable for processing and others that govern substrate engagement by DarE. Our work informs on darobactin scaffold engineering and sheds additional light on the underlying principles of rSAM catalysis.
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Affiliation(s)
- Austin M. Woodard
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Claudio D. Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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11
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Christoffer C, Harini K, Archit G, Kihara D. Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563303. [PMID: 37961264 PMCID: PMC10634698 DOI: 10.1101/2023.10.20.563303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Membrane proteins play crucial roles in various cellular processes, and their interactions with other proteins in and on the membrane are essential for their proper functioning. While an increasing number of structures of more membrane proteins are being determined, the available structure data is still sparse. To gain insights into the mechanisms of membrane protein complexes, computational docking methods are necessary due to the challenge of experimental determination. Here, we introduce Mem-LZerD, a rigid-body membrane docking algorithm designed to take advantage of modern membrane modeling and protein docking techniques to facilitate the docking of membrane protein complexes. Mem-LZerD is based on the LZerD protein docking algorithm, which has been constantly among the top servers in many rounds of CAPRI protein docking assessment. By employing a combination of geometric hashing, newly constrained by the predicted membrane height and tilt angle, and model scoring accounting for the energy of membrane insertion, we demonstrate the capability of Mem-LZerD to model diverse membrane protein-protein complexes. Mem-LZerD successfully performed unbound docking on 13 of 21 (61.9%) transmembrane complexes in an established benchmark, more than shown by previous approaches. It was additionally tested on new datasets of 44 transmembrane complexes and 92 peripheral membrane protein complexes, of which it successfully modeled 35 (79.5%) and 15 (16.3%) complexes respectively. When non-blind orientations of peripheral targets were included, the number of successes increased to 54 (58.7%). We further demonstrate that Mem-LZerD produces complex models which are suitable for molecular dynamics simulation. Mem-LZerD is made available at https://lzerd.kiharalab.org.
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Affiliation(s)
- Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Kannan Harini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Gupta Archit
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur 603203, India
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
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12
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Kumar S, Konovalova A. BamE directly interacts with BamA and BamD coordinating their functions. Mol Microbiol 2023; 120:397-407. [PMID: 37455652 PMCID: PMC10528117 DOI: 10.1111/mmi.15127] [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: 05/21/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
The β-barrel assembly machinery (Bam) complex facilitates the assembly of outer membrane proteins (OMPs) in gram-negative bacteria. The Bam complex is conserved and essential for bacterial viability and consists of five subunits, BamA-E. BamA is the transmembrane component, and its β-barrel domain opens laterally to allow folding and insertion of incoming OMPs. The remaining components are regulatory, among which only BamD is essential. Previous studies suggested that BamB regulates BamA directly, while BamE and BamC serve as BamD regulators. However, specific molecular details of their functions remain unknown. Our previous research demonstrated that BamE plays a specialized role in assembling the complex between the lipoprotein RcsF and its OMP partners, required for the Regulator of Capsule Synthesis (Rcs) stress response. Here, we used RcsF/OmpA as a model substrate to investigate BamE function. Our results challenge the current view that BamE only serves as a BamD regulator. We show that BamE also directly interacts with BamA. BamE interaction with both BamA and BamD is important for function. Our genetic and biochemical analysis shows that BamE stabilizes the Bam complex and promotes bidirectional signaling interaction between BamA and BamD. This BamE function becomes essential when direct BamA/BamD communication is impeded.
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Affiliation(s)
- Santosh Kumar
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
| | - Anna Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
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13
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Kuo K, Liu J, Pavlova A, Gumbart JC. Drug Binding to BamA Targets Its Lateral Gate. J Phys Chem B 2023; 127:7509-7517. [PMID: 37587651 PMCID: PMC10476194 DOI: 10.1021/acs.jpcb.3c04501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/30/2023] [Indexed: 08/18/2023]
Abstract
BamA, the core component of the β-barrel assembly machinery (BAM) complex, is an outer-membrane protein (OMP) in Gram-negative bacteria. Its function is to insert and fold substrate OMPs into the outer membrane (OM). Evidence suggests that BamA follows the asymmetric hybrid-barrel model where the first and last strands of BamA separate, a process known as lateral gate opening, to allow nascent substrate OMP β-strands to sequentially insert and fold through β-augmentation. Recently, multiple lead compounds that interfere with BamA's function have been identified. We modeled and then docked one of these compounds into either the extracellular loops of BamA or the open lateral gate. With the compound docked in the loops, we found that the lateral gate remains closed during 5 μs molecular dynamics simulations. The same compound when docked in the open lateral gate stays bound to the β16 strand of BamA during the simulation, which would prevent substrate OMP folding. In addition, we simulated mutants of BamA that are resistant to one or more of the identified lead compounds. In these simulations, we observed a differing degree and/or frequency of opening of BamA's lateral gate compared to BamA-apo, suggesting that the mutations grant resistance by altering the dynamics at the gate. We conclude that the compounds act by inhibiting BamA lateral gate opening and/or binding of substrate, thus preventing subsequent OMP folding and insertion.
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Affiliation(s)
- Katie
M. Kuo
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jinchan Liu
- Department
of Molecular Biophysics and Biochemistry (MB&B), Yale University, New Haven, Connecticut 06510, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C. Gumbart
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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14
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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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15
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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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16
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Pang YT, Hazel AJ, Gumbart JC. Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding. Biophys J 2023; 122:2988-2995. [PMID: 36960532 PMCID: PMC10398254 DOI: 10.1016/j.bpj.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023] Open
Abstract
Autotransporters are a large family of virulence factors found in Gram-negative bacteria that play important roles in their pathogenesis. The passenger domain of autotransporters is almost always composed of a large β-helix, with only a small portion of it being relevant to its virulence function. This has led to the hypothesis that the folding of the β-helical structure aids the secretion of the passenger domain across the Gram-negative outer membrane. In this study, we used molecular dynamics simulations and enhanced sampling methods to investigate the stability and folding of the passenger domain of pertactin, an autotransporter from Bordetella pertussis. Specifically, we employed steered molecular dynamics to simulate the unfolding of the entire passenger domain as well as self-learning adaptive umbrella sampling to compare the energetics of folding rungs of the β-helix independently ("isolated folding") versus folding rungs on top of a previously folded rung ("vectorial folding"). Our results showed that vectorial folding is highly favorable compared with isolated folding; moreover, our simulations showed that the C-terminal rung of the β-helix is the most resistant to unfolding, in agreement with previous studies that found the C-terminal half of the passenger domain to be more stable than the N-terminal one. Overall, this study provides new insights into the folding process of an autotransporter passenger domain and its potential role in secretion across the outer membrane.
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Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, GA
| | - Anthony J Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, GA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA.
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17
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Shen C, Chang S, Luo Q, Chan KC, Zhang Z, Luo B, Xie T, Lu G, Zhu X, Wei X, Dong C, Zhou R, Zhang X, Tang X, Dong H. Structural basis of BAM-mediated outer membrane β-barrel protein assembly. Nature 2023; 617:185-193. [PMID: 37100902 DOI: 10.1038/s41586-023-05988-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/21/2023] [Indexed: 04/28/2023]
Abstract
The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of materials1-3. All known OMPs share the antiparallel β-strand topology4, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial β-barrel assembly machinery (BAM) to initiate OMP folding5,6; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly.
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Affiliation(s)
- Chongrong Shen
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shenghai Chang
- Department of Biophysics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qinghua Luo
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Kevin Chun Chan
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
| | - Zhibo Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Bingnan Luo
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Teng Xie
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guangwen Lu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Xiaofeng Zhu
- College of Life Science, Sichuan University, Chengdu, China
| | - Xiawei Wei
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Changjiang Dong
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China.
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - Xing Zhang
- Department of Biophysics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Xiaodi Tang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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18
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Overly Cottom C, Stephenson R, Wilson L, Noinaj N. Targeting BAM for Novel Therapeutics against Pathogenic Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:679. [PMID: 37107041 PMCID: PMC10135246 DOI: 10.3390/antibiotics12040679] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 04/29/2023] Open
Abstract
The growing emergence of multidrug resistance in bacterial pathogens is an immediate threat to human health worldwide. Unfortunately, there has not been a matching increase in the discovery of new antibiotics to combat this alarming trend. Novel contemporary approaches aimed at antibiotic discovery against Gram-negative bacterial pathogens have expanded focus to also include essential surface-exposed receptors and protein complexes, which have classically been targeted for vaccine development. One surface-exposed protein complex that has gained recent attention is the β-barrel assembly machinery (BAM), which is conserved and essential across all Gram-negative bacteria. BAM is responsible for the biogenesis of β-barrel outer membrane proteins (β-OMPs) into the outer membrane. These β-OMPs serve essential roles for the cell including nutrient uptake, signaling, and adhesion, but can also serve as virulence factors mediating pathogenesis. The mechanism for how BAM mediates β-OMP biogenesis is known to be dynamic and complex, offering multiple modes for inhibition by small molecules and targeting by larger biologics. In this review, we introduce BAM and establish why it is a promising and exciting new therapeutic target and present recent studies reporting novel compounds and vaccines targeting BAM across various bacteria. These reports have fueled ongoing and future research on BAM and have boosted interest in BAM for its therapeutic promise in combatting multidrug resistance in Gram-negative bacterial pathogens.
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Affiliation(s)
- Claire Overly Cottom
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Robert Stephenson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Lindsey Wilson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
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19
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Surveying membrane landscapes: a new look at the bacterial cell surface. Nat Rev Microbiol 2023:10.1038/s41579-023-00862-w. [PMID: 36828896 DOI: 10.1038/s41579-023-00862-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 02/26/2023]
Abstract
Recent studies applying advanced imaging techniques are changing the way we understand bacterial cell surfaces, bringing new knowledge on everything from single-cell heterogeneity in bacterial populations to their drug sensitivity and mechanisms of antimicrobial resistance. In both Gram-positive and Gram-negative bacteria, the outermost surface of the bacterial cell is being imaged at nanoscale; as a result, topographical maps of bacterial cell surfaces can be constructed, revealing distinct zones and specific features that might uniquely identify each cell in a population. Functionally defined assembly precincts for protein insertion into the membrane have been mapped at nanoscale, and equivalent lipid-assembly precincts are suggested from discrete lipopolysaccharide patches. As we review here, particularly for Gram-negative bacteria, the applications of various modalities of nanoscale imaging are reawakening our curiosity about what is conceptually a 3D cell surface landscape: what it looks like, how it is made and how it provides resilience to respond to environmental impacts.
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20
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Guest RL, Silhavy TJ. Cracking outer membrane biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119405. [PMID: 36455781 PMCID: PMC9878550 DOI: 10.1016/j.bbamcr.2022.119405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022]
Abstract
The outer membrane is a distinguishing feature of the Gram-negative envelope. It lies on the external face of the peptidoglycan sacculus and forms a robust permeability barrier that protects extracytoplasmic structures from environmental insults. Overcoming the barrier imposed by the outer membrane presents a significant hurdle towards developing novel antibiotics that are effective against Gram-negative bacteria. As the outer membrane is an essential component of the cell, proteins involved in its biogenesis are themselves promising antibiotic targets. Here, we summarize key findings that have built our understanding of the outer membrane. Foundational studies describing the discovery and composition of the outer membrane as well as the pathways involved in its construction are discussed.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, United States of America
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, United States of America.
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21
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Takeda H, Busto JV, Lindau C, Tsutsumi A, Tomii K, Imai K, Yamamori Y, Hirokawa T, Motono C, Ganesan I, Wenz LS, Becker T, Kikkawa M, Pfanner N, Wiedemann N, Endo T. A multipoint guidance mechanism for β-barrel folding on the SAM complex. Nat Struct Mol Biol 2023; 30:176-187. [PMID: 36604501 DOI: 10.1038/s41594-022-00897-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/11/2022] [Indexed: 01/07/2023]
Abstract
Mitochondrial β-barrel proteins are essential for the transport of metabolites, ions and proteins. The sorting and assembly machinery (SAM) mediates their folding and membrane insertion. We report the cryo-electron microscopy structure of the yeast SAM complex carrying an early eukaryotic β-barrel folding intermediate. The lateral gate of Sam50 is wide open and pairs with the last β-strand (β-signal) of the substrate-the 19-β-stranded Tom40 precursor-to form a hybrid barrel in the membrane plane. The Tom40 barrel grows and curves, guided by an extended bridge with Sam50. Tom40's first β-segment (β1) penetrates into the nascent barrel, interacting with its inner wall. The Tom40 amino-terminal segment then displaces β1 to promote its pairing with Tom40's last β-strand to complete barrel formation with the assistance of Sam37's dynamic α-protrusion. Our study thus reveals a multipoint guidance mechanism for mitochondrial β-barrel folding.
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Affiliation(s)
- Hironori Takeda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Nara Institute of Science and Technology, Ikoma, Japan
| | - Jon V Busto
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
| | - Chie Motono
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.,Computational Bio Big-Data Open Innovation Laboratory, AIST, Waseda University, Tokyo, Japan
| | - Iniyan Ganesan
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lena-Sophie Wenz
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan. .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.
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22
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Factors That Control the Force Needed to Unfold a Membrane Protein in Silico Depend on the Mode of Denaturation. Int J Mol Sci 2023; 24:ijms24032654. [PMID: 36768981 PMCID: PMC9917119 DOI: 10.3390/ijms24032654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Single-molecule force spectroscopy methods, such as AFM and magnetic tweezers, have proved extremely beneficial in elucidating folding pathways for soluble and membrane proteins. To identify factors that determine the force rupture levels in force-induced membrane protein unfolding, we applied our near-atomic-level Upside molecular dynamics package to study the vertical and lateral pulling of bacteriorhodopsin (bR) and GlpG, respectively. With our algorithm, we were able to selectively alter the magnitudes of individual interaction terms and identify that, for vertical pulling, hydrogen bond strength had the strongest effect, whereas other non-bonded protein and membrane-protein interactions had only moderate influences, except for the extraction of the last helix where the membrane-protein interactions had a stronger influence. The up-down topology of the transmembrane helices caused helices to be pulled out as pairs. The rate-limiting rupture event often was the loss of H-bonds and the ejection of the first helix, which then propagated tension to the second helix, which rapidly exited the bilayer. The pulling of the charged linkers across the membrane had minimal influence, as did changing the bilayer thickness. For the lateral pulling of GlpG, the rate-limiting rupture corresponded to the separation of the helices within the membrane, with the H-bonds generally being broken only afterward. Beyond providing a detailed picture of the rupture events, our study emphasizes that the pulling mode greatly affects the factors that determine the forces needed to unfold a membrane protein.
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23
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Kuo KM, Ryoo D, Lundquist K, Gumbart JC. Modeling intermediates of BamA folding an outer membrane protein. Biophys J 2022; 121:3242-3252. [PMID: 35927955 PMCID: PMC9463690 DOI: 10.1016/j.bpj.2022.07.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/03/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
BamA, the core component of the β-barrel assembly machinery complex, is an integral outer-membrane protein (OMP) in Gram-negative bacteria that catalyzes the folding and insertion of OMPs. A key feature of BamA relevant to its function is a lateral gate between its first and last β-strands. Opening of this lateral gate is one of the first steps in the asymmetric-hybrid-barrel model of BamA function. In this study, multiple hybrid-barrel folding intermediates of BamA and a substrate OMP, EspP, were constructed and simulated to better understand the model's physical consequences. The hybrid-barrel intermediates consisted of the BamA β-barrel and its POTRA5 domain and either one, two, three, four, five, or six β-hairpins of EspP. The simulation results support an asymmetric-hybrid-barrel model in which the BamA N-terminal β-strand forms stronger interactions with the substrate OMP than the C-terminal β-strand. A consistent "B"-shaped conformation of the final folding intermediate was observed, and the shape of the substrate β-barrel within the hybrid matched the shape of the fully folded substrate. Upon further investigation, inward-facing glycines were found at sharp bends within the hybrid and fully folded β-barrels. Together, the data suggest an influence of sequence on shape of the substrate barrel throughout the OMP folding process and of the fully folded OMP.
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Affiliation(s)
- Katie M Kuo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - David Ryoo
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia
| | - Karl Lundquist
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia; School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
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24
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Xiang S, Pinto C, Baldus M. Divide and Conquer: A Tailored Solid‐state NMR Approach to Study Large Membrane Protein Complexes. Angew Chem Int Ed Engl 2022; 61:e202203319. [PMID: 35712982 PMCID: PMC9540533 DOI: 10.1002/anie.202203319] [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: 03/03/2022] [Indexed: 11/18/2022]
Abstract
Membrane proteins are known to exert many essential biological functions by forming complexes in cell membranes. An example refers to the β‐barrel assembly machinery (BAM), a 200 kDa pentameric complex containing BAM proteins A–E that catalyzes the essential process of protein insertion into the outer membrane of gram‐negative bacteria. While progress has been made in capturing three‐dimensional structural snapshots of the BAM complex, the role of the lipoprotein BamC in the complex assembly in functional lipid bilayers has remained unclear. We have devised a component‐selective preparation scheme to directly study BamC as part of the entire BAM complex in lipid bilayers. Combination with proton‐detected solid‐state NMR methods allowed us to probe the structure, dynamics, and supramolecular topology of full‐length BamC embedded in the entire complex in lipid bilayers. Our approach may help decipher how individual proteins contribute to the dynamic formation and functioning of membrane protein complexes in membranes.
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Affiliation(s)
- ShengQi Xiang
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- MOE Key Lab for Cellular Dynamics School of Life Sciences University of Science and Technology of China 96 Jinzhai Road Hefei 230026 Anhui China
| | - Cecilia Pinto
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- Current address: Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Van der Maasweg 9 2629 H. Z. Delft The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
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25
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Sicoli G, Konijnenberg A, Guérin J, Hessmann S, Del Nero E, Hernandez-Alba O, Lecher S, Rouaut G, Müggenburg L, Vezin H, Cianférani S, Sobott F, Schneider R, Jacob-Dubuisson F. Large-Scale Conformational Changes of FhaC Provide Insights Into the Two-Partner Secretion Mechanism. Front Mol Biosci 2022; 9:950871. [PMID: 35936790 PMCID: PMC9355242 DOI: 10.3389/fmolb.2022.950871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
The Two-Partner secretion pathway mediates protein transport across the outer membrane of Gram-negative bacteria. TpsB transporters belong to the Omp85 superfamily, whose members catalyze protein insertion into, or translocation across membranes without external energy sources. They are composed of a transmembrane β barrel preceded by two periplasmic POTRA domains that bind the incoming protein substrate. Here we used an integrative approach combining in vivo assays, mass spectrometry, nuclear magnetic resonance and electron paramagnetic resonance techniques suitable to detect minor states in heterogeneous populations, to explore transient conformers of the TpsB transporter FhaC. This revealed substantial, spontaneous conformational changes on a slow time scale, with parts of the POTRA2 domain approaching the lipid bilayer and the protein’s surface loops. Specifically, our data indicate that an amphipathic POTRA2 β hairpin can insert into the β barrel. We propose that these motions enlarge the channel and initiate substrate secretion. Our data propose a solution to the conundrum how TpsB transporters mediate protein secretion without the need for cofactors, by utilizing intrinsic protein dynamics.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Lille, France
| | | | - Jérémy Guérin
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Elise Del Nero
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Sophie Lecher
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Guillaume Rouaut
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Linn Müggenburg
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Hervé Vezin
- Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Lille, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Frank Sobott
- BAMS Research Group, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Robert Schneider
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
- *Correspondence: Robert Schneider, ; Françoise Jacob-Dubuisson,
| | - Françoise Jacob-Dubuisson
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
- *Correspondence: Robert Schneider, ; Françoise Jacob-Dubuisson,
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26
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Xiang S, Pinto C, Baldus M. Divide and Conquer: A Tailored Solid‐state NMR Approach to Study Large Membrane Protein Complexes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- ShengQi Xiang
- University of Science and Technology of China, Anhui, MOE Key lab for Cellular Dynamics CHINA
| | - Cecilia Pinto
- Delft University of Technology: Technische Universiteit Delft Department of Bionanoscience NETHERLANDS
| | - Marc Baldus
- Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 Utrecht NETHERLANDS
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27
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Dynamic interplay between the periplasmic chaperone SurA and the BAM complex in outer membrane protein folding. Commun Biol 2022; 5:560. [PMID: 35676411 PMCID: PMC9177699 DOI: 10.1038/s42003-022-03502-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/18/2022] [Indexed: 12/12/2022] Open
Abstract
Correct folding of outer membrane proteins (OMPs) into the outer membrane of Gram-negative bacteria depends on delivery of unfolded OMPs to the β-barrel assembly machinery (BAM). How unfolded substrates are presented to BAM remains elusive, but the major OMP chaperone SurA is proposed to play a key role. Here, we have used hydrogen deuterium exchange mass spectrometry (HDX-MS), crosslinking, in vitro folding and binding assays and computational modelling to show that the core domain of SurA and one of its two PPIase domains are key to the SurA-BAM interaction and are required for maximal catalysis of OMP folding. We reveal that binding causes changes in BAM and SurA conformation and/or dynamics distal to the sites of binding, including at the BamA β1-β16 seam. We propose a model for OMP biogenesis in which SurA plays a crucial role in OMP delivery and primes BAM to accept substrates for folding. Interaction of the outer membrane protein (OMP) chaperone SurA and the OMP folding catalyst BAM results in changes in the conformational ensembles of both species, suggesting a mechanism for delivery of OMPs to BAM in Gram-negative bacteria.
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28
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Doyle MT, Jimah JR, Dowdy T, Ohlemacher SI, Larion M, Hinshaw JE, Bernstein HD. Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding. Cell 2022; 185:1143-1156.e13. [PMID: 35294859 DOI: 10.1016/j.cell.2022.02.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/01/2021] [Accepted: 02/13/2022] [Indexed: 02/08/2023]
Abstract
Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle cryo-EM to visualize the folding dynamics of a model β barrel protein (EspP) by BAM. We found that BAM binds the highly conserved "β signal" motif of EspP to correctly orient β strands in the OM during folding. We also found that the folding of EspP proceeds via "hybrid-barrel" intermediates in which membrane integrated β sheets are attached to the essential BAM subunit, BamA. The structures show an unprecedented deflection of the membrane surrounding the EspP intermediates and suggest that β sheets progressively fold toward BamA to form a β barrel. Along with in vivo experiments that tracked β barrel folding while the OM tension was modified, our results support a model in which BAM harnesses OM elasticity to accelerate β barrel folding.
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Affiliation(s)
- Matthew Thomas Doyle
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Jimah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyrone Dowdy
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shannon I Ohlemacher
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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29
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Horne JE, Radford SE. Roll out the barrel! Outer membrane tension resolves an unexpected folding intermediate. Cell 2022; 185:1107-1109. [DOI: 10.1016/j.cell.2022.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 12/01/2022]
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