1
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Giovannercole F, De Smet T, Vences-Guzmán MÁ, Lauber F, Dugauquier R, Dieu M, Lizen L, Dehairs J, Lima-Mendez G, Guan Z, Sohlenkamp C, Renzi F. TamL is a Key Player of the Outer Membrane Homeostasis in Bacteroidota. J Mol Biol 2025; 437:169063. [PMID: 40043834 PMCID: PMC12045153 DOI: 10.1016/j.jmb.2025.169063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 02/27/2025] [Accepted: 02/27/2025] [Indexed: 03/19/2025]
Abstract
In Proteobacteria, the outer membrane protein TamA and the inner membrane-anchored protein TamB form the Translocation and Assembly Module (TAM) complex, which facilitates the transport of autotransporters, virulence factors, and likely lipids across the two membranes. In Bacteroidota, TamA is replaced by TamL, a TamA-like lipoprotein with a lipid modification at its N-terminus that likely anchors it to the outer membrane. This structural difference suggests that TamL may have a distinct function compared to TamA. However, the role of TAM in bacterial phyla other than Proteobacteria remains unexplored. Our study aimed to elucidate the function of TamL in Flavobacterium johnsoniae, an environmental Bacteroidota. Unlike its homologs in Proteobacteria, we found that TamL and TamB are essential in F. johnsoniae. Through genetic, phenotypic, proteomic, and lipidomic analyses, we show that TamL depletion severely compromises outer membrane integrity, as evidenced by reduced cell viability, altered cell shape, increased susceptibility to membrane-disrupting agents, and elevated levels of outer membrane lipoproteins. Notably, we did not observe an overall decrease in the levels of β-barrel outer membrane proteins, nor substantial alterations in outer membrane lipid composition. By pull-down assays, we found TamL co-purifying with TamB in F. johnsoniae, suggesting an interaction. Furthermore, we found that while TamL and TamB monocistronic genes are conserved among Bacteroidota, only some species encode multiple TamL, TamB and TamA proteins. To our knowledge, this study is the first to provide functional insights into a TAM subunit beyond Proteobacteria.
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Affiliation(s)
- Fabio Giovannercole
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Tom De Smet
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Miguel Ángel Vences-Guzmán
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n Col. Chamilpa, C.P. 62210 Cuernavaca, Morelos, Mexico
| | - Frédéric Lauber
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Rémy Dugauquier
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Marc Dieu
- Technological Platform Mass Spectrometry Service (MaSUN), Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Laura Lizen
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gipsi Lima-Mendez
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Ziqiang Guan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n Col. Chamilpa, C.P. 62210 Cuernavaca, Morelos, Mexico
| | - Francesco Renzi
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for life Sciences (Narilis), University of Namur, Namur, Belgium.
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2
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Wang Y, Cheng Y, Li Y, Wang Y, Fu X. Rationally Designed Self-Derived Peptides Kill Escherichia coli by Targeting BamA and BamD Essential for Outer Membrane Protein Biogenesis. ACS Infect Dis 2025; 11:1092-1103. [PMID: 40265351 DOI: 10.1021/acsinfecdis.4c00812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2025]
Abstract
There is an urgent need to develop antibiotics with new mechanisms of action for combating antibiotic-resistant bacteria, particularly against Gram-negative pathogens that severely threaten human health. Here, we introduce the rational design and comprehensive characterization of self-derived antibacterial peptides that specifically target Escherichia coli BamA and BamD, vital components of the β-barrel assembly machine (BAM) for the folding and membrane integration of outer membrane proteins (OMPs) in Gram-negative bacteria. Among the three BamA-targeted peptides, BamA543-551, which corresponds to an extracellular loop of BamA, exhibits remarkable bactericidal activity against OM-permeabilizedE. coli cells. Similarly, among four BamD-targeted peptides, BamD163-187 corresponding to a BamA-interacting α-helix exhibits potent bactericidal activity. Notably, both BamA543-551 and BamD163-187 are able to kill other OM-permeabilized Gram-negative pathogens but not Gram-positive ones, and fusion with a cell membrane-penetrating peptide enabled them to directly kill intactE. coli cells. Further, both of them significantly change the cell membrane integrity ofE. coli, induce the accumulation of misfolded OmpF, and reduce the level of folded OmpF. In particular, in vivo photo-cross-linking analysis indicates that BamA543-551 disrupts the direct interaction between BamA and periplasmic chaperone SurA in livingE. coli cells, thus offering insights into their mode of action. Collectively, our findings confirm the potential of BamA and BamD as promising antibiotic targets and suggest that BamA- and BamD-derived peptides can be candidates for antibiotic development.
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Affiliation(s)
- Yuchan Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Yu Cheng
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Yinghong Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Yan Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
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3
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Walker ME, Zhu W, Peterson JH, Wang H, Patteson J, Soriano A, Zhang H, Mayhood T, Hou Y, Mesbahi-Vasey S, Gu M, Frost J, Lu J, Johnston J, Hipolito C, Lin S, Painter RE, Klein D, Walji A, Weinglass A, Kelly TM, Saldanha A, Schubert J, Bernstein HD, Walker SS. Antibacterial macrocyclic peptides reveal a distinct mode of BamA inhibition. Nat Commun 2025; 16:3395. [PMID: 40210867 PMCID: PMC11986105 DOI: 10.1038/s41467-025-58086-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 03/06/2025] [Indexed: 04/12/2025] Open
Abstract
Outer membrane proteins (OMPs) produced by Gram-negative bacteria contain a cylindrical amphipathic β-sheet ("β-barrel") that functions as a membrane spanning domain. The assembly (folding and membrane insertion) of OMPs is mediated by the heterooligomeric β-barrel assembly machine (BAM). The central BAM subunit (BamA) is an attractive antibacterial target because its structure and cell surface localization are conserved, it catalyzes an essential reaction, and potent bactericidal compounds that inhibit its activity have been described. Here we utilize mRNA display to discover cyclic peptides that bind to Escherichia coli BamA with high affinity. We describe three peptides that arrest the growth of BAM deficient E. coli strains, inhibit OMP assembly in live cells and in vitro, and bind to unique sites within the BamA β-barrel lumen. Remarkably, we find that if the peptides are added to cultures after a slowly assembling OMP mutant binds to BamA, they accelerate its biogenesis. The data strongly suggest that the peptides trap BamA in conformations that block the initiation of OMP assembly but favor a later assembly step. Molecular dynamics simulations provide further evidence that the peptides bind stably to BamA and function by a previously undescribed mechanism.
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Affiliation(s)
| | - Wei Zhu
- Merck & Co., Inc., Rahway, NJ, USA
| | - Janine H Peterson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hao Wang
- Merck & Co., Inc., West Point, PA, USA
| | | | | | - Han Zhang
- Merck & Co., Inc., West Point, PA, USA
| | | | - Yan Hou
- Merck & Co., Inc., Rahway, NJ, USA
| | | | - Meigang Gu
- Evotec Ltd., Abingdon, Oxfordshire, OX14 4RZ, UK
| | | | - Jun Lu
- Merck & Co., Inc., West Point, PA, 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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4
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Lehner PA, Degen M, Jakob RP, Modaresi SM, Callon M, Burmann BM, Maier T, Hiller S. Architecture and conformational dynamics of the BAM-SurA holo insertase complex. SCIENCE ADVANCES 2025; 11:eads6094. [PMID: 40184469 PMCID: PMC11970506 DOI: 10.1126/sciadv.ads6094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 02/28/2025] [Indexed: 04/06/2025]
Abstract
The proper folding of outer membrane proteins in Gram-negative bacteria relies on their delivery to the β-barrel assembly machinery (BAM) complex. The mechanism by which survival protein A (SurA), the major periplasmic chaperone, facilitates this process is not well understood. We determine the structure of the holo insertase complex, where SurA binds BAM for substrate delivery. High-resolution cryo-electron microscopy structures of four different states and a three-dimensional variability analysis show that the holo insertase complex has a large motional spectrum. SurA bound to BAM can undergo a large swinging motion between two states. This motion is uncoupled from the conformational flexibility of the BamA barrel, which can open and close without affecting SurA binding. Notably, we observed conformational coupling of the SurA swing state and the carboxyl-terminal helix grip domain of BamC. Substrate delivery by SurA to BAM appears to follow a concerted motion that encodes a gated delivery pathway through the BAM accessory proteins to the membrane entry site.
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Affiliation(s)
| | - Morris Degen
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | | | | | | | | | - Timm Maier
- Biozentrum, University of Basel, Basel, Switzerland
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5
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Peterson JH, Yang L, Gumbart JC, Bernstein HD. Conserved lipid-facing basic residues promote the insertion of the porin OmpC into the E. coli outer membrane. mBio 2025; 16:e0331924. [PMID: 39976443 PMCID: PMC11898585 DOI: 10.1128/mbio.03319-24] [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: 10/29/2024] [Accepted: 01/22/2025] [Indexed: 02/21/2025] Open
Abstract
Almost all integral membrane proteins that reside in the outer membrane (OM) of gram-negative bacteria contain a closed amphipathic β sheet ("β barrel") that serves as a membrane anchor. The membrane integration of β barrel structures is catalyzed by a highly conserved heterooligomer called the barrel assembly machine (BAM). Although charged residues that are exposed to the lipid bilayer are infrequently found in outer membrane protein β barrels, the β barrels of OmpC/OmpF-type trimeric porins produced by Enterobacterales contain multiple conserved lipid-facing basic residues located near the extracellular side of the OM. Here, we show that these residues are required for the efficient insertion of the Escherichia coli OmpC protein into the OM in vivo. We found that the mutation of multiple basic residues to glutamine or alanine slowed insertion and reduced insertion efficiency. Furthermore, molecular dynamics simulations provided evidence that the basic residues promote the formation of hydrogen bonds and salt bridges with lipopolysaccharide, a unique glycolipid located exclusively in the outer leaflet of the OM. Taken together, our results support a model in which hydrophilic interactions between OmpC and LPS help to anchor the protein in the OM when the local environment is perturbed by BAM during membrane insertion and suggest a surprising role for membrane lipids in the insertion reaction.IMPORTANCEThe assembly (folding and membrane insertion) of bacterial outer membrane proteins (OMPs) is an essential cellular process that is a potential target for novel antibiotics. A heterooligomer called the barrel assembly machine (BAM) plays a major role in catalyzing OMP assembly. Here, we show that a group of highly conserved lipid-facing basic residues in Escherichia coli OmpC, a member of a major family of abundant OMPs known as trimeric porins, is required for the efficient integration of the protein into the outer membrane (OM). Based on our work and previous studies, we propose that the basic residues form interactions with a unique OM lipid (lipopolysaccharide) that promotes the insertion reaction. Our results provide strong evidence that interactions between specific membrane lipids and at least a subset of OMPs are required to supplement the activity of BAM and facilitate the integration of the proteins into the membrane.
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Affiliation(s)
- Janine H. Peterson
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lixinhao Yang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - James C. Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Harris D. Bernstein
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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6
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Süssmuth RD, Kulike‐Koczula M, Gao P, Kosol S. Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research. Angew Chem Int Ed Engl 2025; 64:e202414325. [PMID: 39611429 PMCID: PMC11878372 DOI: 10.1002/anie.202414325] [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: 07/29/2024] [Revised: 10/15/2024] [Accepted: 10/15/2024] [Indexed: 11/30/2024]
Abstract
In the fight against bacterial infections, particularly those caused by multi-resistant pathogens known as "superbugs", the need for new antibacterials is undoubted in scientific communities and is by now also widely perceived by the general population. However, the antibacterial research landscape has changed considerably over the past years. With few exceptions, the majority of big pharma companies has left the field and thus, the decline in R&D on antibacterials severely impacts the drug pipeline. In recent years, antibacterial research has increasingly relied on smaller companies or academic research institutions, which mostly have only limited financial resources, to carry a drug discovery and development process from the beginning and through to the beginning of clinical phases. This review formulates the requirements for an antibacterial in regard of targeted pathogens, resistance mechanisms and drug discovery. Strategies are shown for the discovery of new antibacterial structures originating from natural sources, by chemical synthesis and more recently from artificial intelligence approaches. This is complemented by principles for the computer-aided design of antibacterials and the refinement of a lead structure. The second part of the article comprises a compilation of antibacterial molecules classified according to bacterial target structures, e.g. cell wall synthesis, protein synthesis, as well as more recently emerging target classes, e.g. fatty acid synthesis, proteases and membrane proteins. Aspects of the origin, the antibacterial spectrum, resistance and the current development status of the presented drug molecules are highlighted.
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Affiliation(s)
- Roderich D. Süssmuth
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 124, TC210629BerlinGermany
| | - Marcel Kulike‐Koczula
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 124, TC210629BerlinGermany
| | - Peng Gao
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 124, TC210629BerlinGermany
| | - Simone Kosol
- Medical School BerlinDepartment Human MedicineRüdesheimer Strasse 5014195BerlinGermany
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7
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Pang YT, Kuo KM, Yang L, Gumbart JC. DeepPath: Overcoming data scarcity for protein transition pathway prediction using physics-based deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.27.640693. [PMID: 40060558 PMCID: PMC11888466 DOI: 10.1101/2025.02.27.640693] [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: 03/15/2025]
Abstract
The structural dynamics of proteins play a crucial role in their function, yet most experimental and deep learning methods produce only static models. While molecular dynamics (MD) simulations provide atomistic insight into conformational transitions, they remain computationally prohibitive, particularly for large-scale motions. Here, we introduce DeepPath, a deep-learning-based framework that rapidly generates physically realistic transition pathways between known protein states. Unlike conventional supervised learning approaches, DeepPath employs active learning to iteratively refine its predictions, leveraging molecular mechanical force fields as an oracle to guide pathway generation. We validated DeepPath on three biologically relevant test cases: SHP2 activation, CdiB H1 secretion, and the BAM complex lateral gate opening. DeepPath accurately predicted the transition pathways for all test cases, reproducing key intermediate structures and transient interactions observed in previous studies. Notably, DeepPath also predicted an intermediate between the BAM inward- and outward-open states that closely aligns with an experimentally observed hybrid-barrel structure (TMscore = 0.91). Across all cases, DeepPath achieved accurate pathway predictions within hours, showcasing an efficient alternative to MD simulations for exploring protein conformational transitions.
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Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Katie M Kuo
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Lixinhao Yang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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8
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Ravi R, Routray D, Mahalakshmi R. Mitochondrial Sorting and Assembly Machinery: Chaperoning a Moonlighting Role? Biochemistry 2025; 64:312-328. [PMID: 39754567 DOI: 10.1021/acs.biochem.4c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2025]
Abstract
The mitochondrial outer membrane (OMM) β-barrel proteins link the mitochondrion with the cytosol, endoplasmic reticulum, and other cellular membranes, establishing cellular homeostasis. Their active insertion and assembly in the outer mitochondrial membrane is achieved in an energy-independent yet highly effective manner by the Sorting and Assembly Machinery (SAM) of the OMM. The core SAM constituent is the 16-stranded transmembrane β-barrel Sam50. For over two decades, the primary role of Sam50 has been linked to its function as a chaperone in the OMM, wherein it assembles all β-barrels through a lateral gating and β-barrel switching mechanism. Interestingly, recent studies have demonstrated that despite its low copy number, Sam50 performs various diverse functions beyond assembling β-barrels. This includes maintaining cristae morphology, bidirectional lipid shuttling between the ER and mitochondrial inner membrane, import of select proteins, regulation of PINK1-Parkin function, and timed trigger of cell death. Given these multifaceted critical regulatory functions of SAM across all eukaryotes, we now reason that SAM merely moonlights as the hub for β-barrel biogenesis and has indeed evolved a diverse array of primary roles in maintaining mitochondrial function and cellular homeostasis.
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Affiliation(s)
- Roshika Ravi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Deepsikha Routray
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
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9
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Kanaoka Y, Mori T, Nagaike W, Itaya S, Nonaka Y, Kohga H, Haruyama T, Sugano Y, Miyazaki R, Ichikawa M, Uchihashi T, Tsukazaki T. AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex. Nat Commun 2025; 16:225. [PMID: 39779699 PMCID: PMC11711467 DOI: 10.1038/s41467-024-54875-x] [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: 03/17/2024] [Accepted: 11/25/2024] [Indexed: 01/11/2025] Open
Abstract
Protein translocation across cellular membranes is an essential and nano-scale dynamic process. In the bacterial cytoplasmic membrane, the core proteins in this process are a membrane protein complex, SecYEG, corresponding to the eukaryotic Sec61 complex, and a cytoplasmic protein, SecA ATPase. Despite more than three decades of extensive research on Sec proteins, from genetic experiments to cutting-edge single-molecule analyses, no study has visually demonstrated protein translocation. Here, we visualize the translocation, via one unit of a SecYEG-SecA-embedded nanodisc, of an unfolded substrate protein by high-speed atomic force microscopy (HS-AFM). Additionally, the uniform unidirectional distribution of nanodiscs on a mica substrate enables the HS-AFM image data analysis, revealing dynamic structural changes in the polypeptide-crosslinking domain of SecA between wide-open and closed states depending on nucleotides. The nanodisc-AFM approach will allow us to execute detailed analyses of Sec proteins as well as visualize nano-scale events of other membrane proteins.
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Grants
- JPMJKP23H2 MEXT | Japan Science and Technology Agency (JST)
- JPMJPR20E1 MEXT | Japan Science and Technology Agency (JST)
- hp230209, hp240215, hp240277 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JPMXP1323015482 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 24ZR1403800 Natural Science Foundation of Shanghai (Natural Science Foundation of Shanghai Municipality)
- Naito Foundation
- Takeda Science Foundation
- JSPS/MEXT KAKENHI (Grant Nos. JP22H02567, JP22H02586, JP21H05155, JP21H05153, JP21K19226, JP21KK0125 to T.T.) The Chemo-Sero-Therapeutic Research Institute, the Institute for Fermentation (Osaka), and Yamada Science Foundation
- JSPS/MEXT KAKENHI (Grant Nos. JP21H05157, JP24K03035) MEXT as “Program for Promoting Researches on the Supercomputer Fugaku”(JPMXP1020230119)
- JSPS/MEXT KAKENHI (Grant No. JP23K14146 to H.K)
- JSPS/MEXT KAKENHI (Grant Nos. JP22K15061, JP22H05567 to R.M)
- JSPS/MEXT KAKENHI (Grant Nos. JP22K15075, JP20K15733)
- JSPS/MEXT KAKENHI (Grant Nos. JP21H000393, JP24K01309 to T.U.)
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Affiliation(s)
- Yui Kanaoka
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Takaharu Mori
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan.
| | - Wataru Nagaike
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Seira Itaya
- Nara Institute of Science and Technology, Nara, Japan
| | - Yuto Nonaka
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | | | | | | | | | - Muneyoshi Ichikawa
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Takayuki Uchihashi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan.
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Science, Okazaki, Aichi, Japan.
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan.
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10
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Beaud Benyahia B, Taib N, Beloin C, Gribaldo S. Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution. Nat Rev Microbiol 2025; 23:41-56. [PMID: 39198708 DOI: 10.1038/s41579-024-01088-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 09/01/2024]
Abstract
The bacterial envelope is one of the oldest and most essential cellular components and has been traditionally divided into Gram-positive (monoderm) and Gram-negative (diderm). Recent landmark studies have challenged a major paradigm in microbiology by inferring that the last bacterial common ancestor had a diderm envelope and that the outer membrane (OM) was lost repeatedly in evolution to give rise to monoderms. Intriguingly, OM losses appear to have occurred exclusively in the Terrabacteria, one of the two major clades of bacteria. In this Review, we present current knowledge about the Terrabacteria. We describe their diversity and phylogeny and then highlight the vast phenotypic diversity of the Terrabacteria cell envelopes, which display large deviations from the textbook examples of diderms and monoderms, challenging the classical Gram-positive-Gram-negative divide. We highlight the striking differences in the systems involved in OM biogenesis in Terrabacteria with respect to the classical diderm experimental models and how they provide novel insights into the diversity and biogenesis of the bacterial cell envelope. We also discuss the potential evolutionary steps that might have led to the multiple losses of the OM and speculate on how the very first OM might have emerged before the last bacterial common ancestor.
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Affiliation(s)
- Basile Beaud Benyahia
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Najwa Taib
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France.
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11
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Schreiber S, Jose J. Förster Resonance Energy Transfer Measurements in Living Bacteria for Interaction Studies of BamA with BamD and Inhibitor Identification. Cells 2024; 13:1858. [PMID: 39594607 PMCID: PMC11592675 DOI: 10.3390/cells13221858] [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: 10/16/2024] [Revised: 10/25/2024] [Accepted: 10/31/2024] [Indexed: 11/28/2024] Open
Abstract
The β-barrel assembly machinery (BAM) is a multimeric protein complex responsible for the folding of outer membrane proteins in gram-negative bacteria. It is essential for cell survival and outer membrane integrity. Therefore, it is of impact in the context of antibiotic resistance and can serve as a target for the development of new antibiotics. The interaction between two of its subunits, BamA and BamD, is essential for its function. Here, a FRET-based assay to quantify the affinity between these two proteins in living bacterial cells is presented. The method was applied to identify two interaction hotspots at the binding interface. BamDY184 was identified to significantly contribute to the binding between both proteins through hydrophobic interactions and hydrogen bonding. Additionally, two salt bridges formed between BamDR94, BamDR97, and BamAE127 contributed substantially to the binding of BamA to BamD as well. Two peptides (RFIRLN and VAEYYTER) that mimic the amino acid sequence of BamD around the identified hotspots were shown to inhibit the interaction between BamA and BamD in a dose-dependent manner in the upper micromolar range. These two peptides can potentially act as antibiotic enhancers. This shows that the BamA-BamD interaction site can be addressed for the design of protein-protein interaction inhibitors. Additionally, the method, as presented in this study, can be used for further functional studies on interactions within the BAM complex.
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Affiliation(s)
| | - Joachim Jose
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany;
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12
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Cottom CO, Stephenson R, Ricci D, Yang L, Gumbart JC, Noinaj N. Structural characterization of the POTRA domains from A. baumannii reveals new conformations in BamA. Structure 2024; 32:2038-2048.e3. [PMID: 39293443 PMCID: PMC11560574 DOI: 10.1016/j.str.2024.08.013] [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: 01/05/2024] [Revised: 07/17/2024] [Accepted: 08/22/2024] [Indexed: 09/20/2024]
Abstract
Recent studies have demonstrated BamA, the central component of the β-barrel assembly machinery (BAM), as an important therapeutic target to combat infections caused by Acinetobacter baumannii and other Gram-negative pathogens. Homology modeling indicates BamA in A. baumannii consists of five polypeptide transport-associated (POTRA) domains and a β-barrel membrane domain. We characterized the POTRA domains of BamA from A. baumannii in solution using size-exclusion chromatography small angle X-ray scattering (SEC-SAXS) analysis and determined crystal structures in two conformational states that are drastically different than those previously observed in BamA from other bacteria, indicating that the POTRA domains are even more conformationally dynamic than has been observed previously. Molecular dynamics simulations of the POTRA domains from A. baumannii and Escherichia coli allowed us to identify key structural features that contribute to the observed novel states. Together, these studies expand on our current understanding of the conformational plasticity within BamA across differing bacterial species.
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Affiliation(s)
| | - Robert Stephenson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Dante Ricci
- Achaogen, Inc., South San Francisco, CA, USA
| | - Lixinhao Yang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA; School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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13
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Tiu AKY, Conroy GC, Bobst CE, Hagan CL. Autoproteolytic mechanism of CdiA toxin release reconstituted in vitro. J Bacteriol 2024; 206:e0024924. [PMID: 39347575 PMCID: PMC11500576 DOI: 10.1128/jb.00249-24] [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: 06/17/2024] [Accepted: 08/28/2024] [Indexed: 10/01/2024] Open
Abstract
Contact-dependent inhibition (CDI) is a mechanism of interbacterial competition in Gram-negative bacteria. Bacteria that contain CDI systems produce a large, filamentous protein, CdiA, on their cell surfaces. CdiA contains a C-terminal toxin domain that is transported across the outer membranes (OMs) of neighboring bacteria. Once inside a target bacterium, the toxin is released from the CdiA protein via a proteolytic mechanism that has not been well characterized. We have developed an in vitro assay to monitor this toxin release process and have identified several conserved amino acids that play critical roles in the autocatalytic mechanism. Our results indicate that a hydrophobic, membrane-like environment is required for CdiA to fold, and the proteolysis occurs through an asparagine cyclization mechanism. Our in vitro assay thus provides a starting point for analyzing the conformational state of the CdiA protein when it is inserted into a target cell's OM and engaged in transporting the toxin across that membrane. IMPORTANCE It is challenging to develop new antibiotics capable of killing Gram-negative bacteria because their outer membranes are impermeable to many small molecules. Some Gram-negative bacteria, however, deliver much larger protein toxins through the outer membranes of competing bacteria in their environments using contact-dependent inhibition (CDI) systems. How these toxins traverse the outer membranes of their targets is not well understood. We have therefore developed a method to study the toxin delivery process in a highly simplified system using a fragment of a CDI protein. Our results indicate that the CDI protein assembles into a structure in the target membrane that catalyzes the release of the toxin. This CDI protein fragment enables further studies of the toxin delivery mechanism.
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Affiliation(s)
- Ana Katrina Y. Tiu
- Department of Chemistry, The College of the Holy Cross, Worcester, Massachusetts, USA
| | - Grace C. Conroy
- Department of Chemistry, The College of the Holy Cross, Worcester, Massachusetts, USA
| | - Cedric E. Bobst
- Mass Spectrometry Core Facility, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Christine L. Hagan
- Department of Chemistry, The College of the Holy Cross, Worcester, Massachusetts, USA
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14
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Schreiber S, Zaayenga A, Jose J. The Assembly of the Inverse Autotransporter Protein YeeJ is Driven by its C-terminal β-strand. J Mol Biol 2024; 436:168749. [PMID: 39173735 DOI: 10.1016/j.jmb.2024.168749] [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: 05/08/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 08/24/2024]
Abstract
Autotransporter proteins are bacterial outer membrane proteins that display passenger domains with various functions through a β-barrel shaped translocation domain. YeeJ is an autotransporter protein from E. coli MG1655. In contrast to most other autotransporter proteins, its passenger domain is located at the C-terminus of the translocation domain. Due to this inverted domain organization, YeeJ belongs to autotransporter proteins of type Ve. To investigate the assembly of YeeJ, the fluorescence of a heterologous mCherry passenger domain was measured to quantify its assembly. Based on AlphaFold2 models of 119 sequences similar to YeeJ, a sequence conservation logo for the β1- and the β12-strand of type Ve autotransporter proteins was generated. Then, the effect of mutations in these strands on the assembly of YeeJ were analyzed. Mutations of the N-terminal aromatic amino acid of the β1-strand did not affect the assembly of the translocation domain and the display of the passenger domain. Likewise, exchange of the β1-strand with the β3-strand did not impair the assembly of the autotransporter fusion protein. Mutation of the C-terminal aromatic amino acid of the β12-strand strongly impaired surface display of the mCherry passenger domain. This amino acid has been shown before as an essential feature of the β-signals of classical autotransporter proteins and outer membrane β-barrel proteins in general. We therefore propose that the β12-strand of YeeJ acts as its β-signal and that the assembly of the YeeJ β-barrel is driven by its C-terminal β-strand, like in most other autotransporter proteins, despite its inverted domain organization.
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Affiliation(s)
- Sebastian Schreiber
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstr. 48, 48149 Münster, Germany
| | - Annika Zaayenga
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstr. 48, 48149 Münster, Germany
| | - Joachim Jose
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstr. 48, 48149 Münster, Germany.
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15
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dos Santos TMA, Thomson BD, Marquez MD, Pan L, Monfared TH, Kahne DE. Native β-barrel substrates pass through two shared intermediates during folding on the BAM complex. Proc Natl Acad Sci U S A 2024; 121:e2409672121. [PMID: 39378083 PMCID: PMC11494362 DOI: 10.1073/pnas.2409672121] [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: 05/14/2024] [Accepted: 08/29/2024] [Indexed: 10/10/2024] Open
Abstract
The assembly of β-barrel proteins into membranes is mediated by the evolutionarily conserved β-barrel assembly machine (BAM) complex. In Escherichia coli, BAM folds numerous substrates which vary considerably in size and shape. How BAM is able to efficiently fold such a diverse array of β-barrel substrates is not clear. Here, we develop a disulfide crosslinking method to trap native substrates in vivo as they fold on BAM. By placing a cysteine within the luminal wall of the BamA barrel as well as in the substrate β-strands, we can compare the residence time of each substrate strand within the BamA lumen. We validated this method using two defective, slow-folding substrates. We used this method to characterize stable intermediates which occur during folding of two structurally different native substrates. Strikingly, these intermediates occur during identical stages of folding for both substrates: soon after folding has begun and just before folding is completed. We suggest that these intermediates arise due to barriers to folding that are common between β-barrel substrates, and that the BAM catalyst is able to fold so many different substrates because it addresses these common challenges.
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Affiliation(s)
| | - Benjamin D. Thomson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Melissa D. Marquez
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Lydia Pan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Tabasom H. Monfared
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Daniel E. Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
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16
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Sun D, Storek KM, Tegunov D, Yang Y, Arthur CP, Johnson M, Quinn JG, Liu W, Han G, Girgis HS, Alexander MK, Murchison AK, Shriver S, Tam C, Ijiri H, Inaba H, Sano T, Yanagida H, Nishikawa J, Heise CE, Fairbrother WJ, Tan MW, Skelton N, Sandoval W, Sellers BD, Ciferri C, Smith PA, Reid PC, Cunningham CN, Rutherford ST, Payandeh J. The discovery and structural basis of two distinct state-dependent inhibitors of BamA. Nat Commun 2024; 15:8718. [PMID: 39379361 PMCID: PMC11461620 DOI: 10.1038/s41467-024-52512-1] [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: 07/26/2023] [Accepted: 09/09/2024] [Indexed: 10/10/2024] Open
Abstract
BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of Gram-negative bacteria. Despite recent advances in our mechanistic and structural understanding of BamA, there are few potent and selective tool molecules that can bind to and modulate BamA activity. Here, we explored in vitro selection methods and different BamA/BAM protein formulations to discover peptide macrocycles that kill Escherichia coli by targeting extreme conformational states of BamA. Our studies show that Peptide Targeting BamA-1 (PTB1) targets an extracellular divalent cation-dependent binding site and locks BamA into a closed lateral gate conformation. By contrast, PTB2 targets a luminal binding site and traps BamA into an open lateral gate conformation. Our results will inform future antibiotic discovery efforts targeting BamA and provide a template to prospectively discover modulators of other dynamic integral membrane proteins.
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Affiliation(s)
- Dawei Sun
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Dimitry Tegunov
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Ying Yang
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Christopher P Arthur
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Matthew Johnson
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - John G Quinn
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Weijing Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Guanghui Han
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
- PTM Bio, Alameda, CA, USA
| | - Hany S Girgis
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Mary Kate Alexander
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Austin K Murchison
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Stephanie Shriver
- Department of BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Christine Tam
- Department of BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | | | - Christopher E Heise
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
- Septerna, South San Francisco, CA, USA
| | - Wayne J Fairbrother
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas Skelton
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin D Sellers
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
- Vilya, South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Peter A Smith
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
- Revagenix, San Mateo, CA, USA
| | | | - Christian N Cunningham
- Department of Peptide Therapeutics, Genentech Inc., South San Francisco, CA, USA.
- PeptiDream, Kawasaki, Japan.
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA.
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
- Exelixis, Alameda, CA, USA.
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17
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Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Protein interactions in human pathogens revealed through deep learning. Nat Microbiol 2024; 9:2642-2652. [PMID: 39294458 PMCID: PMC11445079 DOI: 10.1038/s41564-024-01791-x] [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: 04/28/2023] [Accepted: 07/23/2024] [Indexed: 09/20/2024]
Abstract
Identification of bacterial protein-protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer-membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
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Affiliation(s)
- Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Minkyung Baek
- Department of Biological Sciences, Seoul National University, Seoul, South Korea.
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Aditya Krishnakumar
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Catherine A Tower
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Blake A Jackson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Thulasi Warrier
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deborah T Hung
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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18
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Schiffrin B, Crossley JA, Walko M, Machin JM, Nasir Khan G, Manfield IW, Wilson AJ, Brockwell DJ, Fessl T, Calabrese AN, Radford SE, Zhuravleva A. Dual client binding sites in the ATP-independent chaperone SurA. Nat Commun 2024; 15:8071. [PMID: 39277579 PMCID: PMC11401910 DOI: 10.1038/s41467-024-52021-1] [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: 01/19/2024] [Accepted: 08/23/2024] [Indexed: 09/17/2024] Open
Abstract
The ATP-independent chaperone SurA protects unfolded outer membrane proteins (OMPs) from aggregation in the periplasm of Gram-negative bacteria, and delivers them to the β-barrel assembly machinery (BAM) for folding into the outer membrane (OM). Precisely how SurA recognises and binds its different OMP clients remains unclear. Escherichia coli SurA comprises three domains: a core and two PPIase domains (P1 and P2). Here, by combining methyl-TROSY NMR, single-molecule Förster resonance energy transfer (smFRET), and bioinformatics analyses we show that SurA client binding is mediated by two binding hotspots in the core and P1 domains. These interactions are driven by aromatic-rich motifs in the client proteins, leading to SurA core/P1 domain rearrangements and expansion of clients from collapsed, non-native states. We demonstrate that the core domain is key to OMP expansion by SurA, and uncover a role for SurA PPIase domains in limiting the extent of expansion. The results reveal insights into SurA-OMP recognition and the mechanism of activation for an ATP-independent chaperone, and suggest a route to targeting the functions of a chaperone key to bacterial virulence and OM integrity.
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Affiliation(s)
- Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joel A Crossley
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, UK
| | - Jonathan M Machin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, UK
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Anastasia Zhuravleva
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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19
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Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. Outer membrane protein assembly mediated by BAM-SurA complexes. Nat Commun 2024; 15:7612. [PMID: 39218969 PMCID: PMC11366764 DOI: 10.1038/s41467-024-51358-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
The outer membrane is a formidable barrier that protects Gram-negative bacteria against environmental threats. Its integrity requires the correct folding and insertion of outer membrane proteins (OMPs) by the membrane-embedded β-barrel assembly machinery (BAM). Unfolded OMPs are delivered to BAM by the periplasmic chaperone SurA, but how SurA and BAM work together to ensure successful OMP delivery and folding remains unclear. Here, guided by AlphaFold2 models, we use disulphide bond engineering in an attempt to trap SurA in the act of OMP delivery to BAM, and solve cryoEM structures of a series of complexes. The results suggest that SurA binds BAM at its soluble POTRA-1 domain, which may trigger conformational changes in both BAM and SurA that enable transfer of the unfolded OMP to the BAM lateral gate for insertion into the outer membrane. Mutations that disrupt the interaction between BAM and SurA result in outer membrane assembly defects, supporting the key role of SurA in outer membrane biogenesis.
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Affiliation(s)
- Katherine L Fenn
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Biochemistry, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Joel A Crossley
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392, Giessen, Germany
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 35392, Giessen, Germany
| | - Romany J Horne
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392, Giessen, Germany
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 35392, Giessen, Germany
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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20
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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] [MESH Headings] [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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21
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Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Essential and virulence-related protein interactions of pathogens revealed through deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589144. [PMID: 38645026 PMCID: PMC11030334 DOI: 10.1101/2024.04.12.589144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Identification of bacterial protein-protein interactions and predicting the structures of the complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here, we developed a deep learning-based pipeline that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
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22
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Pavlenok M, Nair RR, Hendrickson RC, Niederweis M. The C-terminus is essential for the stability of the mycobacterial channel protein MspA. Protein Sci 2024; 33:e4912. [PMID: 38358254 PMCID: PMC10868439 DOI: 10.1002/pro.4912] [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: 06/26/2023] [Revised: 12/15/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Outer membrane proteins perform essential functions in uptake and secretion processes in bacteria. MspA is an octameric channel protein in the outer membrane of Mycobacterium smegmatis and is structurally distinct from any other known outer membrane protein. MspA is the founding member of a family with more than 3000 homologs and is one of the most widely used proteins in nanotechnological applications due to its advantageous pore structure and extraordinary stability. While a conserved C-terminal signal sequence is essential for folding and protein assembly in the outer membrane of Gram-negative bacteria, the molecular determinants of these processes are unknown for MspA. In this study, we show that mutation and deletion of methionine 183 in the highly conserved C-terminus of MspA and mutation of the conserved tryptophan 40 lead to a complete loss of protein in heat extracts of M. smegmatis. Swapping these residues partially restores the heat stability of MspA indicating that methionine 183 and tryptophan 40 form a conserved sulfur-π electron interaction, which stabilizes the MspA monomer. Flow cytometry showed that all MspA mutants are surface-accessible demonstrating that oligomerization and membrane integration in M. smegmatis are not affected. Thus, the conserved C-terminus of MspA is essential for its thermal stability, but it is not required for protein assembly in its native membrane, indicating that this process is mediated by a mechanism distinct from that in Gram-negative bacteria. These findings will benefit the rational design of MspA-like pores to tailor their properties in current and future applications.
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Affiliation(s)
- Mikhail Pavlenok
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | | | | | - Michael Niederweis
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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23
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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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24
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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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25
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Vázquez‐Arias A, Vázquez‐Iglesias L, Pérez‐Juste I, Pérez‐Juste J, Pastoriza‐Santos I, Bodelon G. Bacterial surface display of human lectins in Escherichia coli. Microb Biotechnol 2024; 17:e14409. [PMID: 38380565 PMCID: PMC10884992 DOI: 10.1111/1751-7915.14409] [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: 05/19/2023] [Accepted: 01/02/2024] [Indexed: 02/22/2024] Open
Abstract
Lectin-glycan interactions sustain fundamental biological processes involved in development and disease. Owing to their unique sugar-binding properties, lectins have great potential in glycobiology and biomedicine. However, their relatively low affinities and broad specificities pose a significant challenge when used as analytical reagents. New approaches for expression and engineering of lectins are in demand to overcome current limitations. Herein, we report the application of bacterial display for the expression of human galectin-3 and mannose-binding lectin in Escherichia coli. The analysis of the cell surface expression and binding activity of the surface-displayed lectins, including point and deletion mutants, in combination with molecular dynamics simulation, demonstrate the robustness and suitability of this approach. Furthermore, the display of functional mannose-binding lectin in the bacterial surface proved the feasibility of this method for disulfide bond-containing lectins. This work establishes for the first time bacterial display as an efficient means for the expression and engineering of human lectins, thereby increasing the available toolbox for glycobiology research.
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Affiliation(s)
- Alba Vázquez‐Arias
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
| | - Lorena Vázquez‐Iglesias
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
| | | | - Jorge Pérez‐Juste
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
- Departamento de Química FísicaUniversidade de VigoVigoSpain
| | - Isabel Pastoriza‐Santos
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
- Departamento de Química FísicaUniversidade de VigoVigoSpain
| | - Gustavo Bodelon
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
- Departamento de Biología Funcional y Ciencias de la SaludUniversidade de VigoVigoSpain
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26
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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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27
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Saxena D, Maitra R, Bormon R, Czekanska M, Meiers J, Titz A, Verma S, Chopra S. Tackling the outer membrane: facilitating compound entry into Gram-negative bacterial pathogens. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:17. [PMID: 39843585 PMCID: PMC11721184 DOI: 10.1038/s44259-023-00016-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 10/23/2023] [Indexed: 01/17/2025]
Abstract
Emerging resistance to all available antibiotics highlights the need to develop new antibiotics with novel mechanisms of action. Most of the currently used antibiotics target Gram-positive bacteria while Gram-negative bacteria easily bypass the action of most drug molecules because of their unique outer membrane. This additional layer acts as a potent barrier restricting the entry of compounds into the cell. In this scenario, several approaches have been elucidated to increase the accumulation of compounds into Gram-negative bacteria. This review includes a brief description of the physicochemical properties that can aid compounds to enter and accumulate in Gram-negative bacteria and covers different strategies to target or bypass the outer membrane-mediated barrier in Gram-negative bacterial pathogens.
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Affiliation(s)
- Deepanshi Saxena
- Department of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, 226031, UP, India
| | - Rahul Maitra
- Department of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, 226031, UP, India
| | - Rakhi Bormon
- Department of Chemistry, IIT Kanpur, Kanpur, 208016, UP, India
| | - Marta Czekanska
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123, Saarbrücken, Germany
- Department of Chemistry, Saarland University, 66123, Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 38124, Standort Hannover-Braunschweig, Germany
| | - Joscha Meiers
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123, Saarbrücken, Germany
- Department of Chemistry, Saarland University, 66123, Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 38124, Standort Hannover-Braunschweig, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123, Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123, Saarbrücken, Germany.
- Deutsches Zentrum für Infektionsforschung (DZIF), 38124, Standort Hannover-Braunschweig, Germany.
| | - Sandeep Verma
- Department of Chemistry, IIT Kanpur, Kanpur, 208016, UP, India.
- Center for Nanoscience, IIT Kanpur, Kanpur, 208016, UP, India.
| | - Sidharth Chopra
- Department of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, 226031, UP, India.
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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28
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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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29
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Tassinari M, Rudzite M, Filloux A, Low HH. Assembly mechanism of a Tad secretion system secretin-pilotin complex. Nat Commun 2023; 14:5643. [PMID: 37704603 PMCID: PMC10499894 DOI: 10.1038/s41467-023-41200-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/25/2023] [Indexed: 09/15/2023] Open
Abstract
The bacterial Tight adherence Secretion System (TadSS) assembles surface pili that drive cell adherence, biofilm formation and bacterial predation. The structure and mechanism of the TadSS is mostly unknown. This includes characterisation of the outer membrane secretin through which the pilus is channelled and recruitment of its pilotin. Here we investigate RcpA and TadD lipoprotein from Pseudomonas aeruginosa. Light microscopy reveals RcpA colocalising with TadD in P. aeruginosa and when heterologously expressed in Escherichia coli. We use cryogenic electron microscopy to determine how RcpA and TadD assemble a secretin channel with C13 and C14 symmetries. Despite low sequence homology, we show that TadD shares a similar fold to the type 4 pilus system pilotin PilF. We establish that the C-terminal four residues of RcpA bind TadD - an interaction essential for secretin formation. The binding mechanism between RcpA and TadD appears distinct from known secretin-pilotin pairings in other secretion systems.
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Affiliation(s)
- Matteo Tassinari
- Department of Infectious Disease, Imperial College, London, SW7 2AZ, UK
- Human Technopole, Milan, Italy
| | - Marta Rudzite
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Alain Filloux
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Harry H Low
- Department of Infectious Disease, Imperial College, London, SW7 2AZ, UK.
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30
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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, TX, 77030, USA
| | - Anna Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
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31
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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: 0.5] [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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32
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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: 0.5] [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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33
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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: 18] [Impact Index Per Article: 9.0] [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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34
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Abstract
Protein translocases, such as the bacterial SecY complex, the Sec61 complex of the endoplasmic reticulum (ER) and the mitochondrial translocases, facilitate the transport of proteins across membranes. In addition, they catalyze the insertion of integral membrane proteins into the lipid bilayer. Several membrane insertases cooperate with these translocases, thereby promoting the topogenesis, folding and assembly of membrane proteins. Oxa1 and BamA family members serve as core components in the two major classes of membrane insertases. They facilitate the integration of proteins with α-helical transmembrane domains and of β-barrel proteins into lipid bilayers, respectively. Members of the Oxa1 family were initially found in the internal membranes of bacteria, mitochondria and chloroplasts. Recent studies, however, also identified several Oxa1-type insertases in the ER, where they serve as catalytically active core subunits in the ER membrane protein complex (EMC), the guided entry of tail-anchored (GET) and the GET- and EMC-like (GEL) complex. The outer membrane of bacteria, mitochondria and chloroplasts contain β-barrel proteins, which are inserted by members of the BamA family. In this Cell Science at a Glance article and the accompanying poster, we provide an overview of these different types of membrane insertases and discuss their function.
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Affiliation(s)
- Büsra Kizmaz
- Cell Biology, University of Kaiserslautern, Kaiserslautern 67663, Germany
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35
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Thewasano N, Germany EM, Maruno Y, Nakajima Y, Shiota T. Categorization of Escherichia coli Outer Membrane Proteins by Dependence on Accessory Proteins of the β-barrel Assembly Machinery Complex. J Biol Chem 2023:104821. [PMID: 37196764 PMCID: PMC10300371 DOI: 10.1016/j.jbc.2023.104821] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/20/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is populated by various outer membrane proteins (OMPs) that fold into a unique β-barrel transmembrane domain. Most OMPs are assembled into the OM by the β-barrel assembly machinery (BAM) complex. In Escherichia coli, the BAM complex is composed of two essential proteins (BamA and BamD) and three non-essential accessory proteins (BamB, BamC, and BamE). The currently proposed molecular mechanisms of the BAM complex involve only essential subunits, with the function of the accessory proteins remaining largely unknown. Here, we compared the accessory protein requirements for the assembly of seven different OMPs, 8- to 22-stranded, by our in vitro reconstitution assay using an E. coli mid-density membrane (EMM). BamE was responsible for the full efficiency of the assembly of all tested OMPs, as it enhanced the stability of essential subunit binding. BamB increased the assembly efficiency of more than 16-stranded OMPs, whereas BamC was not required for the assembly of any tested OMPs. Our categorization of the requirements of BAM complex accessory proteins in the assembly of substrate OMPs enables us to identify potential targets for the development of new antibiotics.
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Affiliation(s)
- Nakajohn Thewasano
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Edward M Germany
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yuki Maruno
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yukari Nakajima
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takuya Shiota
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
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36
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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: 29] [Impact Index Per Article: 14.5] [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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37
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Step-by-step assembly of a β-barrel protein in a bacterial membrane. Nature 2023:10.1038/d41586-023-01327-z. [PMID: 37101070 DOI: 10.1038/d41586-023-01327-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
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38
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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: 2.0] [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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39
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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: 26] [Impact Index Per Article: 13.0] [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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40
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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: 12] [Impact Index Per Article: 6.0] [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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41
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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: 7] [Impact Index Per Article: 3.5] [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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42
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Abstract
Secretory proteins are cotranslationally or posttranslationally translocated across lipid membranes via a protein-conducting channel named SecY in prokaryotes and Sec61 in eukaryotes. The vast majority of secretory proteins in bacteria are driven through the channel posttranslationally by SecA, a highly conserved ATPase. How a polypeptide chain is moved by SecA through the SecY channel is poorly understood. Here, we report electron cryomicroscopy structures of the active SecA-SecY translocon with a polypeptide substrate. The substrate is captured in different translocation states when clamped by SecA with different nucleotides. Upon binding of an ATP analog, SecA undergoes global conformational changes to push the polypeptide substrate toward the channel in a way similar to how the RecA-like helicases translocate their nucleic acid substrates. The movements of the polypeptide substrates in the SecA-SecY translocon share a similar structural basis to those in the ribosome-SecY complex during cotranslational translocation.
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43
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Structure of a TOC-TIC supercomplex spanning two chloroplast envelope membranes. Cell 2022; 185:4788-4800.e13. [PMID: 36413996 DOI: 10.1016/j.cell.2022.10.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/07/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022]
Abstract
The TOC and TIC complexes are essential translocons that facilitate the import of the nuclear genome-encoded preproteins across the two envelope membranes of chloroplast, but their exact molecular identities and assembly remain unclear. Here, we report a cryoelectron microscopy structure of TOC-TIC supercomplex from Chlamydomonas, containing a total of 14 identified components. The preprotein-conducting pore of TOC is a hybrid β-barrel co-assembled by Toc120 and Toc75, while the potential translocation path of TIC is formed by transmembrane helices from Tic20 and YlmG, rather than a classic model of Tic110. A rigid intermembrane space (IMS) scaffold bridges two chloroplast membranes, and a large hydrophilic cleft on the IMS scaffold connects TOC and TIC, forming a pathway for preprotein translocation. Our study provides structural insights into the TOC-TIC supercomplex composition, assembly, and preprotein translocation mechanism, and lays a foundation to interpret the evolutionary conservation and diversity of this fundamental translocon machinery.
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44
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Wade N, Wesseling CMJ, Innocenti P, Slingerland CJ, Koningstein GM, Luirink J, Martin NI. Synthesis and Structure-Activity Studies of β-Barrel Assembly Machine Complex Inhibitor MRL-494. ACS Infect Dis 2022; 8:2242-2252. [PMID: 36318734 PMCID: PMC9673140 DOI: 10.1021/acsinfecdis.2c00459] [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] [Indexed: 11/05/2022]
Abstract
In the hunt for new antibiotics with activity against Gram-negative pathogens, the outer membrane β-barrel assembly machine (BAM) complex has become an increasingly interesting target. The recently reported BAM complex inhibitor, MRL-494, was discovered via a screening campaign for molecules that target the outer membrane. Notably, MRL-494 was reported to be an unintended byproduct generated during the synthesis of an unrelated compound, and as such no synthesis of the compound was disclosed. We here present a convenient and reliable route for the synthesis of MRL-494 that scales well. The antibacterial activity measured for synthesized MRL-494 matches that reported in the literature. Furthermore, MRL-494 was found to exhibit potent synergistic activity with rifampicin against Gram-negative bacteria, including E. coli, K. pneumoniae, A. baumannii, and P. aeruginosa. MRL-494 was also found to cause outer membrane disruption and induction of the Rcs stress response pathway. In addition, we undertook a focused structure-activity study specifically aimed at elucidating the roles played by the two guanidine moieties contained within the structure of MRL-494.
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Affiliation(s)
- Nicola Wade
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Charlotte M. J. Wesseling
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Paolo Innocenti
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Cornelis J. Slingerland
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Gregory M. Koningstein
- Department
of Molecular Microbiology, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Joen Luirink
- Department
of Molecular Microbiology, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Nathaniel I. Martin
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands,
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45
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Di Somma A, Cané C, Moretta A, Illiano A, Pinto G, Cavasso D, Amoresano A, Paduano L, Duilio A. The antimicrobial peptide Magainin-2 interacts with BamA impairing folding of E. coli membrane proteins. Front Chem 2022; 10:1013788. [PMID: 36324521 PMCID: PMC9620421 DOI: 10.3389/fchem.2022.1013788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/05/2022] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial peptides (AMPs) are a unique and diverse group of molecules endowed with a broad spectrum of antibiotics properties that are being considered as new alternative therapeutic agents. Most of these peptides are membrane-active molecules, killing bacteria by membrane disruption. However, recently an increasing number of AMPs was shown to enter bacterial cells and target intracellular processes fundamental for bacterial life. In this paper we investigated the mechanism of action of Maganin-2 (Mag-2), a well-known antimicrobial peptide isolated from the African clawed frog Xenopus laevis, by functional proteomic approaches. Several proteins belonging to E. coli macromolecular membrane complexes were identified as Mag-2 putative interactors. Among these, we focused our attention on BamA a membrane protein belonging to the BAM complex responsible for the folding and insertion of nascent β-barrel Outer Membrane Proteins (OMPs) in the outer membrane. In silico predictions by molecular modelling, in vitro fluorescence binding and Light Scattering experiments carried out using a recombinant form of BamA confirmed the formation of a stable Mag-2/BamA complex and indicated a high affinity of the peptide for BamA. Functional implications of this interactions were investigated by two alternative and complementary approaches. The amount of outer membrane proteins OmpA and OmpF produced in E. coli following Mag-2 incubation were evaluated by both western blot analysis and quantitative tandem mass spectrometry in Multiple Reaction Monitoring scan mode. In both experiments a gradual decrease in outer membrane proteins production with time was observed as a consequence of Mag-2 treatment. These results suggested BamA as a possible good target for the rational design of new antibiotics since this protein is responsible for a crucial biological event of bacterial life and is absent in humans.
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Affiliation(s)
- Angela Di Somma
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- National Institute of Biostructures and Biosystems (INBB), Rome, Italy
| | - Carolina Cané
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Antonio Moretta
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Anna Illiano
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- National Institute of Biostructures and Biosystems (INBB), Rome, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- National Institute of Biostructures and Biosystems (INBB), Rome, Italy
| | - Domenico Cavasso
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- National Institute of Biostructures and Biosystems (INBB), Rome, Italy
| | - Luigi Paduano
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Angela Duilio
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- National Institute of Biostructures and Biosystems (INBB), Rome, Italy
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46
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Abstract
Several antibacterial compounds have recently been discovered that potentially inhibit the activity of BamA, an essential subunit of a heterooligomer (the barrel assembly machinery or BAM) that assembles outer membrane proteins (OMPs) in Gram-negative bacteria, but their mode of action is unclear. To address this issue, we examined the effect of three inhibitors on the biogenesis of a model E. coli OMP (EspP) in vivo. We found that darobactin potently inhibited the interaction of a conserved C-terminal sequence motif (the “β signal”) with BamA, but had no effect on assembly if added at a postbinding stage. In contrast, Polyphor peptide 7 and MRL-494 inhibited both binding and at least one later step of assembly. Taken together with previous studies that analyzed the binding of darobactin and Polyphor peptide 7 to BamA in vitro, our results strongly suggest that the two compounds inhibit BAM function by distinct competitive and allosteric mechanisms. In addition to providing insights into the properties of the antibacterial compounds, our results also provide direct experimental evidence that supports a model in which the binding of the β signal to BamA initiates the membrane insertion of OMPs.
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47
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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: 0.7] [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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48
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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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49
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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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50
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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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