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Chiu YC, Yeh MC, Wang CH, Chen YA, Chang H, Lin HY, Ho MC, Lin SM. Structural basis for calcium-stimulating pore formation of Vibrio α-hemolysin. Nat Commun 2023; 14:5946. [PMID: 37741869 PMCID: PMC10517994 DOI: 10.1038/s41467-023-41579-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: 05/30/2023] [Accepted: 09/10/2023] [Indexed: 09/25/2023] Open
Abstract
Vibrio α-hemolysins (αHLs) are β-pore-forming toxins secreted by Vibrio pathogens, crucial for the facilitation of bacterial infections through host cell lysis. These toxins are produced as inactive precursors, requiring proteolytic maturation and membrane association for activation within host tissues. Here, we investigate Vibrio campbellii αHL (VcαHL), and establish that its hemolytic activity is significantly stimulated by calcium ions, with an EC50 that aligns with physiological calcium concentrations. Furthermore, we illustrate the vital contribution of calcium ions to the oligomerization of VcαHL on membranes. Using X-ray crystallography and cryo-electron microscopy, we decipher both the immature and assembled structures of VcαHL and elucidate the conformational changes corresponding to toxin assembly. We also identify a calcium-binding module that is integral for VcαHL's calcium-dependent activation. These findings provide insights into the regulatory mechanisms of VcαHL and have the potential to inform the development of targeted therapeutic strategies against Vibrio infections.
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Affiliation(s)
- Yu-Chuan Chiu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Min-Chi Yeh
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-An Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Hsiang Chang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Han-You Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan
| | - Shih-Ming Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan.
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Panda A, Brown C, Gupta K. Studying Membrane Protein-Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1917-1927. [PMID: 37432128 PMCID: PMC10932607 DOI: 10.1021/jasms.3c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Native mass spectrometry (nMS) has emerged as a key analytical tool to study the organizational states of proteins and their complexes with both endogenous and exogenous ligands. Specifically, for membrane proteins, it provides a key analytical dimension to determine the identity of bound lipids and to decipher their effects on the observed structural assembly. We recently developed an approach to study membrane proteins directly from intact and tunable lipid membranes where both the biophysical properties of the membrane and its lipid compositions can be customized. Extending this, we use our liposome-nMS platform to decipher the lipid specificity of membrane proteins through their multiorganelle trafficking pathways. To demonstrate this, we used VAMP2 and reconstituted it in the endoplasmic reticulum (ER), Golgi, synaptic vesicle (SV), and plasma membrane (PM) mimicking liposomes. By directly studying VAMP2 from these customized liposomes, we show how the same transmembrane protein can bind to different sets of lipids in different organellar-mimicking membranes. Considering that the cellular trafficking pathway of most eukaryotic integral membrane proteins involves residence in multiple organellar membranes, this study highlights how the lipid-specificity of the same integral membrane protein may change depending on the membrane context. Further, leveraging the capability of the platform to study membrane proteins from liposomes with curated biophysical properties, we show how we can disentangle chemical versus biophysical properties, of individual lipids in regulating membrane protein assembly.
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Affiliation(s)
- Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Caroline Brown
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
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Mishra S, Roy A, Dutta S. Cryo-EM-based structural insights into supramolecular assemblies of γ-hemolysin from S. aureus reveal the pore formation mechanism. Structure 2023:S0969-2126(23)00085-0. [PMID: 37019111 DOI: 10.1016/j.str.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/31/2023] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
γ-Hemolysin (γ-HL) is a hemolytic and leukotoxic bicomponent β-pore-forming toxin (β-PFT), a potent virulence factor from the Staphylococcus aureus Newman strain. In this study, we performed single-particle cryoelectron microscopy (cryo-EM) of γ-HL in a lipid environment. We observed clustering and square lattice packing of octameric HlgAB pores on the membrane bilayer and an octahedral superassembly of octameric pore complexes that we resolved at resolution of 3.5 Å. Our atomic model further demonstrated the key residues involved in hydrophobic zipping between the rim domains of adjacent octameric complexes, providing additional structural stability in PFTs post oligomerization. We also observed extra densities at the octahedral and octameric interfaces, providing insights into the plausible lipid-binding residues involved for HlgA and HlgB components. Furthermore, the hitherto elusive N-terminal region of HlgA was also resolved in our cryo-EM map, and an overall mechanism of pore formation for bicomponent β-PFTs is proposed.
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Affiliation(s)
- Suman Mishra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Anupam Roy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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Sengupta N, P S, Dutta S. Cryo-EM reveals the membrane-binding phenomenon of EspB, a virulence factor of the Mycobacterial Type VII secretion system. J Biol Chem 2023; 299:104589. [PMID: 36889587 PMCID: PMC10140165 DOI: 10.1016/j.jbc.2023.104589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/08/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) utilizes sophisticated machinery called the type VII secretion system to translocate virulence factors across its complex lipid membrane. EspB, a ∼36 kDa secreted substrate of the ESX-1 apparatus, was shown to cause ESAT-6-independent host cell death. Despite the current wealth of high-resolution structural information of the ordered N-terminal domain, the mechanism of EspB-mediated virulence remains poorly characterized. Here we document EspB interaction with phosphatidic acid (PA) and phosphatidylserine (PS) in the context of membranes, through a biophysical approach including TEM and cryo-EM. We were also able to show PA, PS-dependent conversion of monomers to oligomers at physiological pH. Our data suggest that EspB adheres to biological membranes with limited PA and PS. Electron microscopy of yeast mitochondria with EspB indicates a mitochondrial-membrane binding property of this ESX-1 substrate. Further, we determined the 3D structures of EspB with and without PA and observed plausible stabilization of the low complexity C-terminal domain in the presence of PA. Collectively, our cryo-EM-based structural and functional studies of EspB provide further insight into the host-Mtb interaction.
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Affiliation(s)
- Nayanika Sengupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Surekha P
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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Mishra S, Kundu N, Pramanick I, Kumar A, Chattopadhyay K, Dutta S. Structural insights into thermostable direct hemolysin of Vibrio parahaemolyticus using single-particle cryo-EM. Proteins 2023; 91:137-146. [PMID: 36000388 DOI: 10.1002/prot.26416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 01/07/2023]
Abstract
Thermostable direct hemolysin (TDH) is a ~19 kDa, hemolytic pore-forming toxin from the gram-negative marine bacterium Vibrio parahaemolyticus, one of the causative agents of seafood-borne acute gastroenteritis and septicemia. Previous studies have established that TDH exists as a tetrameric assembly in physiological state; however, there is limited knowledge regarding the molecular arrangement of its disordered N-terminal region (NTR)-the absence of which has been shown to compromise TDH's hemolytic and cytotoxic abilities. In our current study, we have employed single-particle cryo-electron microscopy to resolve the solution-state structures of wild-type TDH and a TDH construct with deletion of the NTR (NTD), in order to investigate structural aspects of NTR on the overall tetrameric architecture. We observed that both TDH and NTD electron density maps, resolved at global resolutions of 4.5 and 4.2 Å, respectively, showed good correlation in their respective oligomeric architecture. Additionally, we were able to locate extra densities near the pore opening of TDH which might correspond to the disordered NTR. Surprisingly, under cryogenic conditions, we were also able to observe novel supramolecular assemblies of TDH tetramers, which we were able to resolve to 4.3 Å. We further investigated the tetrameric and inter-tetrameric interaction interfaces to elaborate upon the key residues involved in both TDH tetramers and TDH super assemblies. Our current structural study will aid in understanding the mechanistic aspects of this pore-forming toxin and the role of its disordered NTR in membrane interaction.
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Affiliation(s)
- Suman Mishra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Nidhi Kundu
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Ishika Pramanick
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Anil Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Mondal AK, Lata K, Singh M, Chatterjee S, Chauhan A, Puravankara S, Chattopadhyay K. Cryo-EM elucidates mechanism of action of bacterial pore-forming toxins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184013. [PMID: 35908609 DOI: 10.1016/j.bbamem.2022.184013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Pore-forming toxins (PFTs) rupture plasma membranes and kill target cells. PFTs are secreted as soluble monomers that undergo drastic structural rearrangements upon interacting with the target membrane and generate transmembrane oligomeric pores. A detailed understanding of the molecular mechanisms of the pore-formation process remains unclear due to limited structural insights regarding the transmembrane oligomeric pore states of the PFTs. However, recent advances in the field of cryo-electron microscopy (cryo-EM) have led to the high-resolution structure determination of the oligomeric pore forms of diverse PFTs. Here, we discuss the pore-forming mechanisms of various PFTs, specifically the mechanistic details contributed by the cryo-EM-based structural studies.
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Affiliation(s)
- Anish Kumar Mondal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
| | - Kusum Lata
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
| | - Mahendra Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
| | - Shamaita Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
| | - Aakanksha Chauhan
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
| | - Sindhoora Puravankara
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India.
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Mondal AK, Sengupta N, Singh M, Biswas R, Lata K, Lahiri I, Dutta S, Chattopadhyay K. Glu289 residue in the pore-forming motif of Vibrio cholerae cytolysin is important for efficient β-barrel pore formation. J Biol Chem 2022; 298:102441. [PMID: 36055404 PMCID: PMC9520032 DOI: 10.1016/j.jbc.2022.102441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 11/19/2022] Open
Abstract
Vibrio cholerae cytolysin (VCC) is a potent membrane-damaging β-barrel pore-forming toxin (β-PFT). Upon binding to the target membranes, VCC monomers first assemble into oligomeric pre-pore intermediates, and subsequently transform into transmembrane β-barrel pores. VCC harbors a designated pore-forming motif, which, during oligomeric pore formation, inserts into the membrane and generates a transmembrane β-barrel scaffold. It remains an enigma how the molecular architecture of the pore-forming motif regulates the VCC pore-formation mechanism. Here, we show that a specific pore-forming motif residue, E289, plays crucial regulatory roles in the pore-formation mechanism of VCC. We find that the mutation of E289A drastically compromises pore-forming activity, without affecting the structural integrity and membrane-binding potential of the toxin monomers. Although our single-particle cryo-EM analysis reveals wild type-like oligomeric β-barrel pore formation by E289A-VCC in the membrane, we demonstrate that the mutant shows severely delayed kinetics in terms of pore-forming ability that can be rescued with elevated temperature conditions. We find that the pore-formation efficacy of E289A-VCC appears to be more profoundly dependent on temperature as compared to that of the wild type toxin. Our results suggest that the E289A mutation traps membrane-bound toxin molecules in the pre-pore-like intermediate state that is hindered from converting into the functional β-barrel pores by a large energy barrier, thus highlighting the importance of this residue for the pore-formation mechanism of VCC.
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Affiliation(s)
- Anish Kumar Mondal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Manauli, Punjab, India
| | - Nayanika Sengupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Mahendra Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Manauli, Punjab, India
| | - Rupam Biswas
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kusum Lata
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Manauli, Punjab, India
| | - Indrajit Lahiri
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Manauli, Punjab, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Manauli, Punjab, India.
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