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Mondal AK, Chattopadhyay K. Structures and functions of the membrane-damaging pore-forming proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:241-288. [PMID: 35034720 DOI: 10.1016/bs.apcsb.2021.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pore-forming proteins (PFPs) of the diverse life forms have emerged as the potent cell-killing entities owing to their specialized membrane-damaging properties. PFPs have the unique ability to perforate the plasma membranes of their target cells, and they exert this functionality by creating oligomeric pores in the membrane lipid bilayer. Pathogenic bacteria employ PFPs as toxins to execute their virulence mechanisms, whereas in the higher vertebrates PFPs are deployed as the part of the immune system and to generate inflammatory responses. PFPs are the unique dimorphic proteins that are generally synthesized as water-soluble molecules, and transform into membrane-inserted oligomeric pore assemblies upon interacting with the target membranes. In spite of sharing very little sequence similarity, PFPs from diverse organisms display incredible structural similarity. Yet, at the same time, structure-function mechanisms of the PFPs document remarkable versatility. Such notions establish PFPs as the fascinating model system to explore variety of unsolved issues pertaining to the structure-function paradigm of the proteins that interact and act in the membrane environment. In this article, we discuss our current understanding regarding the structural basis of the pore-forming functions of the diverse class of PFPs. We attempt to highlight the similarities and differences in their structures, membrane pore-formation mechanisms, and their implications for the various biological processes, ranging from the bacterial virulence mechanisms to the inflammatory immune response generation in the higher animals.
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Affiliation(s)
- Anish Kumar Mondal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
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202
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Verma P, Chattopadhyay K. Current Perspective on the Membrane-Damaging Action of Thermostable Direct Hemolysin, an Atypical Bacterial Pore-forming Toxin. Front Mol Biosci 2021; 8:717147. [PMID: 34368235 PMCID: PMC8343067 DOI: 10.3389/fmolb.2021.717147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Thermostable direct hemolysin (TDH) is the major virulence determinant of the gastroenteric bacterial pathogen Vibrio parahaemolyticus. TDH is a membrane-damaging pore-forming toxin (PFT). TDH shares remarkable structural similarity with the actinoporin family of eukaryotic PFTs produced by the sea anemones. Unlike most of the PFTs, it exists as tetramer in solution, and such assembly state is crucial for its functionality. Although the structure of the tetrameric assembly of TDH in solution is known, membrane pore structure is not available yet. Also, the specific membrane-interaction mechanisms of TDH, and the exact role of any receptor(s) in such process, still remain unclear. In this mini review, we discuss some of the unique structural and physicochemical properties of TDH, and their implications for the membrane-damaging action of the toxin. We also present our current understanding regarding the membrane pore-formation mechanism of this atypical bacterial PFT.
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Affiliation(s)
- Pratima Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, India
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203
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Zou JT, Jing HM, Yuan Y, Lei LH, Chen ZF, Gou Q, Xiong QS, Zhang XL, Zhao Z, Zhang XK, Zeng H, Zou QM, Zhang JY. Pore-forming alpha-hemolysin efficiently improves the immunogenicity and protective efficacy of protein antigens. PLoS Pathog 2021; 17:e1009752. [PMID: 34288976 PMCID: PMC8294524 DOI: 10.1371/journal.ppat.1009752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
Highly immunogenic exotoxins are used as carrier proteins because they efficiently improve the immunogenicity of polysaccharides. However, their efficiency with protein antigens remains unclear. In the current study, the candidate antigen PA0833 from Pseudomonas aeruginosa was fused to the α-hemolysin mutant HlaH35A from Staphylococcus aureus to form a HlaH35A-PA0833 fusion protein (HPF). Immunization with HPF resulted in increased PA0833-specific antibody titers, higher protective efficacy, and decreased bacterial burden and pro-inflammatory cytokine secretion compared with PA0833 immunization alone. Using fluorescently labeled antigens to track antigen uptake and delivery, we found that HlaH35A fusion significantly improved antigen uptake in injected muscles and antigen delivery to draining lymph nodes. Both in vivo and in vitro studies demonstrated that the increased antigen uptake after immunization with HPF was mainly due to monocyte- and macrophage-dependent macropinocytosis, which was probably the result of HPF binding to ADAM10, the Hla host receptor. Furthermore, a transcriptome analysis showed that several immune signaling pathways were activated by HPF, shedding light on the mechanism whereby HlaH35A fusion improves immunogenicity. Finally, the improvement in immunogenicity by HlaH35A fusion was also confirmed with two other antigens, GlnH from Klebsiella pneumoniae and the model antigen OVA, indicating that HlaH35A could serve as a universal carrier protein to improve the immunogenicity of protein antigens.
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Affiliation(s)
- Jin-Tao Zou
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Hai-Ming Jing
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Yue Yuan
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Lang-Huan Lei
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
- Department of Critical Care Medicine, Children’s Hospital of Chongqing Medical University, Chongqing, PR China
| | - Zhi-Fu Chen
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Qiang Gou
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Qing-Shan Xiong
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Xiao-Li Zhang
- Department of Clinical Hematology, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Zhuo Zhao
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Xiao-Kai Zhang
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Hao Zeng
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
| | - Quan-Ming Zou
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
- * E-mail: (Q-MZ); (J-YZ)
| | - Jin-Yong Zhang
- National Engineering Research Center of Immunological Products & Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, PR China
- * E-mail: (Q-MZ); (J-YZ)
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204
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Liu L, Deng CJ, Duan YL, Ye CJ, Gong DH, Guo XL, Lee WH, Zhou J, Li SA, Zhang Y. An Aerolysin-like Pore-Forming Protein Complex Targets Viral Envelope to Inactivate Herpes Simplex Virus Type 1. THE JOURNAL OF IMMUNOLOGY 2021; 207:888-901. [PMID: 34290105 DOI: 10.4049/jimmunol.2001056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 05/20/2021] [Indexed: 01/12/2023]
Abstract
Because most of animal viruses are enveloped, cytoplasmic entry of these viruses via fusion with cellular membrane initiates their invasion. However, the strategies in which host cells counteract cytoplasmic entry of such viruses are incompletely understood. Pore-forming toxin aerolysin-like proteins (ALPs) exist throughout the animal kingdom, but their functions are mostly unknown. In this study, we report that βγ-crystallin fused aerolysin-like protein and trefoil factor complex (βγ-CAT), an ALP and trefoil factor complex from the frog Bombina maxima, directly blocks enveloped virus invasion by interfering with cytoplasmic entry. βγ-CAT targeted acidic glycosphingolipids on the HSV type 1 (HSV-1) envelope to induce pore formation, as indicated by the oligomer formation of protein and potassium and calcium ion efflux. Meanwhile, βγ-CAT formed ring-like oligomers of ∼10 nm in diameter on the liposomes and induced dye release from liposomes that mimic viral envelope. Unexpectedly, transmission electron microscopy analysis showed that the βγ-CAT-treated HSV-1 was visibly as intact as the vehicle-treated HSV-1, indicating that βγ-CAT did not lyse the viral envelope. However, the cytoplasmic entry of the βγ-CAT-treated HSV-1 into HeLa cells was totally hindered. In vivo, topical application of βγ-CAT attenuated the HSV-1 corneal infection in mice. Collectively, these results uncovered that βγ-CAT possesses the capacity to counteract enveloped virus invasion with its featured antiviral-acting manner. Our findings will also largely help to illustrate the putative antiviral activity of animal ALPs.
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Affiliation(s)
- Long Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Cheng-Jie Deng
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ya-Li Duan
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chen-Jun Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dao-Hua Gong
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiao-Long Guo
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen-Hui Lee
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jumin Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China;
| | - Sheng-An Li
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China; and
| | - Yun Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Science/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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205
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Pospiech M, Owens SE, Miller DJ, Austin-Muttitt K, Mullins JGL, Cronin JG, Allemann RK, Sheldon IM. Bisphosphonate inhibitors of squalene synthase protect cells against cholesterol-dependent cytolysins. FASEB J 2021; 35:e21640. [PMID: 33991130 DOI: 10.1096/fj.202100164r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 01/29/2023]
Abstract
Certain species of pathogenic bacteria damage tissues by secreting cholesterol-dependent cytolysins, which form pores in the plasma membranes of animal cells. However, reducing cholesterol protects cells against these cytolysins. As the first committed step of cholesterol biosynthesis is catalyzed by squalene synthase, we explored whether inhibiting this enzyme protected cells against cholesterol-dependent cytolysins. We first synthesized 22 different nitrogen-containing bisphosphonate molecules that were designed to inhibit squalene synthase. Squalene synthase inhibition was quantified using a cell-free enzyme assay, and validated by computer modeling of bisphosphonate molecules binding to squalene synthase. The bisphosphonates were then screened for their ability to protect HeLa cells against the damage caused by the cholesterol-dependent cytolysin, pyolysin. The most effective bisphosphonate reduced pyolysin-induced leakage of lactate dehydrogenase into cell supernatants by >80%, and reduced pyolysin-induced cytolysis from >75% to <25%. In addition, this bisphosphonate reduced pyolysin-induced leakage of potassium from cells, limited changes in the cytoskeleton, prevented mitogen-activated protein kinases cell stress responses, and reduced cellular cholesterol. The bisphosphonate also protected cells against another cholesterol-dependent cytolysin, streptolysin O, and protected lung epithelial cells and primary dermal fibroblasts against cytolysis. Our findings imply that treatment with bisphosphonates that inhibit squalene synthase might help protect tissues against pathogenic bacteria that secrete cholesterol-dependent cytolysins.
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Affiliation(s)
- Mateusz Pospiech
- Swansea University Medical School, Swansea University, Swansea, UK
| | - Siân E Owens
- Swansea University Medical School, Swansea University, Swansea, UK
| | | | | | | | - James G Cronin
- Swansea University Medical School, Swansea University, Swansea, UK
| | | | - I Martin Sheldon
- Swansea University Medical School, Swansea University, Swansea, UK
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206
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Chalivendra S. Microbial Toxins in Insect and Nematode Pest Biocontrol. Int J Mol Sci 2021; 22:ijms22147657. [PMID: 34299280 PMCID: PMC8303606 DOI: 10.3390/ijms22147657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 12/24/2022] Open
Abstract
Invertebrate pests, such as insects and nematodes, not only cause or transmit human and livestock diseases but also impose serious crop losses by direct injury as well as vectoring pathogenic microbes. The damage is global but greater in developing countries, where human health and food security are more at risk. Although synthetic pesticides have been in use, biological control measures offer advantages via their biodegradability, environmental safety and precise targeting. This is amply demonstrated by the successful and widespread use of Bacillusthuringiensis to control mosquitos and many plant pests, the latter by the transgenic expression of insecticidal proteins from B. thuringiensis in crop plants. Here, I discuss the prospects of using bacterial and fungal toxins for pest control, including the molecular basis of their biocidal activity.
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207
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Palacios-Ortega J, García-Linares S, Rivera-de-Torre E, Heras-Márquez D, Gavilanes JG, Slotte JP, Martínez-Del-Pozo Á. Structural foundations of sticholysin functionality. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140696. [PMID: 34246789 DOI: 10.1016/j.bbapap.2021.140696] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023]
Abstract
Actinoporins constitute a family of α pore-forming toxins produced by sea anemones. The soluble fold of these proteins consists of a β-sandwich flanked by two α-helices. Actinoporins exert their activity by specifically recognizing sphingomyelin at their target membranes. Once there, they penetrate the membrane with their N-terminal α-helices, a process that leads to the formation of cation-selective pores. These pores kill the target cells by provoking an osmotic shock on them. In this review, we examine the role and relevance of the structural features of actinoporins, down to the residue level. We look at the specific amino acids that play significant roles in the function of actinoporins and their fold. Particular emphasis is given to those residues that display a high degree of conservation across the actinoporin sequences known to date. In light of the latest findings in the field, the membrane requirements for pore formation, the effect of lipid composition, and the process of pore formation are also discussed.
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Affiliation(s)
- Juan Palacios-Ortega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain; Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
| | - Sara García-Linares
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - Esperanza Rivera-de-Torre
- Department of Biochemistry and Biotechnology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Diego Heras-Márquez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - José G Gavilanes
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Álvaro Martínez-Del-Pozo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
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208
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Swanson NA, Lokareddy RK, Li F, Hou CFD, Leptihn S, Pavlenok M, Niederweis M, Pumroy RA, Moiseenkova-Bell VY, Cingolani G. Cryo-EM structure of the periplasmic tunnel of T7 DNA-ejectosome at 2.7 Å resolution. Mol Cell 2021; 81:3145-3159.e7. [PMID: 34214465 DOI: 10.1016/j.molcel.2021.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/27/2021] [Accepted: 06/01/2021] [Indexed: 11/15/2022]
Abstract
Hershey and Chase used bacteriophage T2 genome delivery inside Escherichia coli to demonstrate that DNA, not protein, is the genetic material. Seventy years later, our understanding of viral genome delivery in prokaryotes remains limited, especially for short-tailed phages of the Podoviridae family. These viruses expel mysterious ejection proteins found inside the capsid to form a DNA-ejectosome for genome delivery into bacteria. Here, we reconstitute the phage T7 DNA-ejectosome components gp14, gp15, and gp16 and solve the periplasmic tunnel structure at 2.7 Å resolution. We find that gp14 forms an outer membrane pore, gp15 assembles into a 210 Å hexameric DNA tube spanning the host periplasm, and gp16 extends into the host cytoplasm forming a ∼4,200 residue hub. Gp16 promotes gp15 oligomerization, coordinating peptidoglycan hydrolysis, DNA binding, and lipid insertion. The reconstituted gp15:gp16 complex lacks channel-forming activity, suggesting that the pore for DNA passage forms only transiently during genome ejection.
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Affiliation(s)
- Nicholas A Swanson
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Sebastian Leptihn
- Zhejiang University-University of Edinburgh Institute, School of Medicine, Hangzhou, China
| | - Mikhail Pavlenok
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
| | - Ruth A Pumroy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.
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209
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Ilangumaran Ponmalar I, Ayappa KG, Basu JK. Bacterial protein listeriolysin O induces nonmonotonic dynamics because of lipid ejection and crowding. Biophys J 2021; 120:3040-3049. [PMID: 34214525 DOI: 10.1016/j.bpj.2021.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 01/15/2023] Open
Abstract
Membrane-bound protein complexes involving pore forming toxins (PFTs) released by virulent bacteria are known to form transmembrane pores leading to host cell lysis. Developing alternative strategies against PFT mediated bacterial virulence factors requires an understanding of the cellular membrane response. However, membrane disruption and related lipid reorganization events during attack by PFTs remain largely unexplored. We report counterintuitive and nonmonotonic variations in lipid diffusion, measured using confocal fluorescence correlation spectroscopy, due to interplay of lipid ejection and crowding by membrane-bound oligomers of a prototypical cholesterol-dependent cytolysin, listeriolysin O (LLO). The observed dynamical crossover is correlated with concentration dependent transitions of LLO oligomeric state populations from rings to arc-like pore complexes, predicted using a proposed two-state free area-based diffusion model. At low PFT concentrations, a hitherto unexplored regime of increased lipid diffusivity is attributed to lipid ejection events because of a preponderance of ring-like pore states. At higher protein concentrations in which membrane-inserted arc-like pores dominate, lipid ejection is less efficient and the ensuing crowding results in a lowering of lipid diffusion. These variations in lipid dynamics are corroborated by macroscopic rheological response measurements of PFT bound vesicles. Our study correlates PFT oligomeric state transitions, membrane remodeling, and mechanical property variations, providing unique insights into the pore forming mechanisms of cholesterol-dependent cytolysins.
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Affiliation(s)
| | - K Ganapathy Ayappa
- Center for BioSystems Science and Engineering Bengaluru, India; Department of Chemical Engineering Bengaluru, India.
| | - Jaydeep K Basu
- Department of Physics, Indian Institute of Science, Bengaluru, India.
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210
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Draberova L, Tumova M, Draber P. Molecular Mechanisms of Mast Cell Activation by Cholesterol-Dependent Cytolysins. Front Immunol 2021; 12:670205. [PMID: 34248949 PMCID: PMC8260682 DOI: 10.3389/fimmu.2021.670205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022] Open
Abstract
Mast cells are potent immune sensors of the tissue microenvironment. Within seconds of activation, they release various preformed biologically active products and initiate the process of de novo synthesis of cytokines, chemokines, and other inflammatory mediators. This process is regulated at multiple levels. Besides the extensively studied IgE and IgG receptors, toll-like receptors, MRGPR, and other protein receptor signaling pathways, there is a critical activation pathway based on cholesterol-dependent, pore-forming cytolytic exotoxins produced by Gram-positive bacterial pathogens. This pathway is initiated by binding the exotoxins to the cholesterol-rich membrane, followed by their dimerization, multimerization, pre-pore formation, and pore formation. At low sublytic concentrations, the exotoxins induce mast cell activation, including degranulation, intracellular calcium concentration changes, and transcriptional activation, resulting in production of cytokines and other inflammatory mediators. Higher toxin concentrations lead to cell death. Similar activation events are observed when mast cells are exposed to sublytic concentrations of saponins or some other compounds interfering with the membrane integrity. We review the molecular mechanisms of mast cell activation by pore-forming bacterial exotoxins, and other compounds inducing cholesterol-dependent plasma membrane perturbations. We discuss the importance of these signaling pathways in innate and acquired immunity.
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Affiliation(s)
- Lubica Draberova
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Magda Tumova
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Petr Draber
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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211
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Hammond K, Cipcigan F, Al Nahas K, Losasso V, Lewis H, Cama J, Martelli F, Simcock PW, Fletcher M, Ravi J, Stansfeld PJ, Pagliara S, Hoogenboom BW, Keyser UF, Sansom MSP, Crain J, Ryadnov MG. Switching Cytolytic Nanopores into Antimicrobial Fractal Ruptures by a Single Side Chain Mutation. ACS NANO 2021; 15:9679-9689. [PMID: 33885289 PMCID: PMC8219408 DOI: 10.1021/acsnano.1c00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Disruption of cell membranes is a fundamental host defense response found in virtually all forms of life. The molecular mechanisms vary but generally lead to energetically favored circular nanopores. Here, we report an elaborate fractal rupture pattern induced by a single side-chain mutation in ultrashort (8-11-mers) helical peptides, which otherwise form transmembrane pores. In contrast to known mechanisms, this mode of membrane disruption is restricted to the upper leaflet of the bilayer where it exhibits propagating fronts of peptide-lipid interfaces that are strikingly similar to viscous instabilities in fluid flow. The two distinct disruption modes, pores and fractal patterns, are both strongly antimicrobial, but only the fractal rupture is nonhemolytic. The results offer wide implications for elucidating differential membrane targeting phenomena defined at the nanoscale.
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Affiliation(s)
- Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Department of Physics & Astronomy, University College London, London WC1E 6BT, UK
| | | | - Kareem Al Nahas
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | | | - Helen Lewis
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Jehangir Cama
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
- College of Engineering, Mathematics and Phys Sciences, University of Exeter, Exeter EX4 4QF, UK
| | | | - Patrick W Simcock
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Marcus Fletcher
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Jascindra Ravi
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | | | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Department of Physics & Astronomy, University College London, London WC1E 6BT, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jason Crain
- IBM Research Europe, Hartree Centre, Daresbury WA4 4AD, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- Department of Physics, King’s College London, London, WC2R 2LS, UK
- Corresponding author: Prof Maxim G Ryadnov; National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK, Tel: (+44) 20 89436078;
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212
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Lopez Chiloeches M, Bergonzini A, Frisan T. Bacterial Toxins Are a Never-Ending Source of Surprises: From Natural Born Killers to Negotiators. Toxins (Basel) 2021; 13:426. [PMID: 34204481 PMCID: PMC8235270 DOI: 10.3390/toxins13060426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
The idea that bacterial toxins are not only killers but also execute more sophisticated roles during bacteria-host interactions by acting as negotiators has been highlighted in the past decades. Depending on the toxin, its cellular target and mode of action, the final regulatory outcome can be different. In this review, we have focused on two families of bacterial toxins: genotoxins and pore-forming toxins, which have different modes of action but share the ability to modulate the host's immune responses, independently of their capacity to directly kill immune cells. We have addressed their immuno-suppressive effects with the perspective that these may help bacteria to avoid clearance by the host's immune response and, concomitantly, limit detrimental immunopathology. These are optimal conditions for the establishment of a persistent infection, eventually promoting asymptomatic carriers. This immunomodulatory effect can be achieved with different strategies such as suppression of pro-inflammatory cytokines, re-polarization of the immune response from a pro-inflammatory to a tolerogenic state, and bacterial fitness modulation to favour tissue colonization while preventing bacteraemia. An imbalance in each of those effects can lead to disease due to either uncontrolled bacterial proliferation/invasion, immunopathology, or both.
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Affiliation(s)
| | | | - Teresa Frisan
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; (M.L.C.); (A.B.)
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213
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Lv F, Qi F, Zhang Z, Wen M, Kale J, Piai A, Du L, Wang S, Zhou L, Yang Y, Wu B, Liu Z, Del Rosario J, Pogmore J, Chou JJ, Andrews DW, Lin J, OuYang B. An amphipathic Bax core dimer forms part of the apoptotic pore wall in the mitochondrial␣membrane. EMBO J 2021; 40:e106438. [PMID: 34101209 PMCID: PMC8280806 DOI: 10.15252/embj.2020106438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/17/2021] [Accepted: 04/27/2021] [Indexed: 02/01/2023] Open
Abstract
Bax proteins form pores in the mitochondrial outer membrane to initiate apoptosis. This might involve their embedding in the cytosolic leaflet of the lipid bilayer, thus generating tension to induce a lipid pore with radially arranged lipids forming the wall. Alternatively, Bax proteins might comprise part of the pore wall. However, there is no unambiguous structural evidence for either hypothesis. Using NMR, we determined a high-resolution structure of the Bax core region, revealing a dimer with the nonpolar surface covering the lipid bilayer edge and the polar surface exposed to water. The dimer tilts from the bilayer normal, not only maximizing nonpolar interactions with lipid tails but also creating polar interactions between charged residues and lipid heads. Structure-guided mutations demonstrate the importance of both types of protein-lipid interactions in Bax pore assembly and core dimer configuration. Therefore, the Bax core dimer forms part of the proteolipid pore wall to permeabilize mitochondria.
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Affiliation(s)
- Fujiao Lv
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fei Qi
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Zhi Zhang
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Maorong Wen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Justin Kale
- Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Alessandro Piai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lingyu Du
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Shuqing Wang
- School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Liujuan Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yaqing Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Juan Del Rosario
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Justin Pogmore
- Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - David W Andrews
- Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Jialing Lin
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Stephenson Cancer Center, Oklahoma City, OK, USA
| | - Bo OuYang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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214
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Wu X, Rapoport TA. Translocation of Proteins through a Distorted Lipid Bilayer. Trends Cell Biol 2021; 31:473-484. [PMID: 33531207 PMCID: PMC8122044 DOI: 10.1016/j.tcb.2021.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/13/2022]
Abstract
Membranes surrounding cells or organelles represent barriers to proteins and other molecules. However, specific proteins can cross membranes by different translocation systems, the best studied being the Sec61/SecY channel. This channel forms a hydrophilic, hourglass-shaped membrane channel, with a lateral gate towards the surrounding lipid. However, recent studies show that an aqueous pore is not required in other cases of protein translocation. The Hrd1 complex, mediating the retrotranslocation of misfolded proteins from the endoplasmic reticulum (ER) lumen into the cytosol, contains multispanning proteins with aqueous luminal and cytosolic cavities, and lateral gates juxtaposed in a thinned membrane region. A locally thinned, distorted lipid bilayer also allows protein translocation in other systems, suggesting a new paradigm to overcome the membrane barrier.
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Affiliation(s)
- Xudong Wu
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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215
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Batsale M, Bahammou D, Fouillen L, Mongrand S, Joubès J, Domergue F. Biosynthesis and Functions of Very-Long-Chain Fatty Acids in the Responses of Plants to Abiotic and Biotic Stresses. Cells 2021; 10:cells10061284. [PMID: 34064239 PMCID: PMC8224384 DOI: 10.3390/cells10061284] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/22/2022] Open
Abstract
Very-long-chain fatty acids (i.e., fatty acids with more than 18 carbon atoms; VLCFA) are important molecules that play crucial physiological and structural roles in plants. VLCFA are specifically present in several membrane lipids and essential for membrane homeostasis. Their specific accumulation in the sphingolipids of the plasma membrane outer leaflet is of primordial importance for its correct functioning in intercellular communication. VLCFA are found in phospholipids, notably in phosphatidylserine and phosphatidylethanolamine, where they could play a role in membrane domain organization and interleaflet coupling. In epidermal cells, VLCFA are precursors of the cuticular waxes of the plant cuticle, which are of primary importance for many interactions of the plant with its surrounding environment. VLCFA are also major components of the root suberin barrier, which has been shown to be fundamental for nutrient homeostasis and plant adaptation to adverse conditions. Finally, some plants store VLCFA in the triacylglycerols of their seeds so that they later play a pivotal role in seed germination. In this review, taking advantage of the many studies conducted using Arabidopsis thaliana as a model, we present our current knowledge on the biosynthesis and regulation of VLCFA in plants, and on the various functions that VLCFA and their derivatives play in the interactions of plants with their abiotic and biotic environment.
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216
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Liposomes Prevent In Vitro Hemolysis Induced by Streptolysin O and Lysenin. MEMBRANES 2021; 11:membranes11050364. [PMID: 34069894 PMCID: PMC8157566 DOI: 10.3390/membranes11050364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/08/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
The need for alternatives to antibiotics in the fight against infectious diseases has inspired scientists to focus on antivirulence factors instead of the microorganisms themselves. In this respect, prior work indicates that tiny, enclosed bilayer lipid membranes (liposomes) have the potential to compete with cellular targets for toxin binding, hence preventing their biological attack and aiding with their clearance. The effectiveness of liposomes as decoy targets depends on their availability in the host and how rapidly they are cleared from the circulation. Although liposome PEGylation may improve their circulation time, little is known about how such a modification influences their interactions with antivirulence factors. To fill this gap in knowledge, we investigated regular and long-circulating liposomes for their ability to prevent in vitro red blood cell hemolysis induced by two potent lytic toxins, lysenin and streptolysin O. Our explorations indicate that both regular and long-circulating liposomes are capable of similarly preventing lysis induced by streptolysin O. In contrast, PEGylation reduced the effectiveness against lysenin-induced hemolysis and altered binding dynamics. These results suggest that toxin removal by long-circulating liposomes is feasible, yet dependent on the particular virulence factor under scrutiny.
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217
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Constructing ion channels from water-soluble α-helical barrels. Nat Chem 2021; 13:643-650. [PMID: 33972753 PMCID: PMC7611114 DOI: 10.1038/s41557-021-00688-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 03/05/2021] [Indexed: 12/21/2022]
Abstract
The design of peptides that assemble in membranes to form functional ion channels is challenging. Specifically, hydrophobic interactions must be designed between the peptides and at the peptide-lipid interfaces simultaneously. Here, we take a multi-step approach towards this problem. First, we use rational de novo design to generate water-soluble α-helical barrels with polar interiors, and confirm their structures using high-resolution X-ray crystallography. These α-helical barrels have water-filled lumens like those of transmembrane channels. Then, we modify the sequences to facilitate their insertion into lipid bilayers. Single-channel electrical recordings and fluorescent imaging of the peptides in membranes show monodisperse, cation-selective channels of unitary conductance. Surprisingly, however, an X-ray structure solved from lipidic cubic phase for one peptide reveals an alternative state with tightly packed helices and a constricted channel. To reconcile these observations, we perform computational analyses to compare the properties of possible different states of the peptide.
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218
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Garcia-Sanchez JA, Ewbank JJ, Visvikis O. Ubiquitin-related processes and innate immunity in C. elegans. Cell Mol Life Sci 2021; 78:4305-4333. [PMID: 33630111 PMCID: PMC11072174 DOI: 10.1007/s00018-021-03787-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/18/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023]
Abstract
Innate immunity is an evolutionary ancient defence strategy that serves to eliminate infectious agents while maintaining host health. It involves a complex network of sensors, signaling proteins and immune effectors that detect the danger, then relay and execute the immune programme. Post-translational modifications relying on conserved ubiquitin and ubiquitin-like proteins are an integral part of the system. Studies using invertebrate models of infection, such as the nematode Caenorhabditis elegans, have greatly contributed to our understanding of how ubiquitin-related processes act in immune sensing, regulate immune signaling pathways, and participate to host defence responses. This review highlights the interest of working with a genetically tractable model organism and illustrates how C. elegans has been used to identify ubiquitin-dependent immune mechanisms, discover novel ubiquitin-based resistance strategies that mediate pathogen clearance, and unravel the role of ubiquitin-related processes in tolerance, preserving host fitness during pathogen attack. Special emphasis is placed on processes that are conserved in mammals.
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Affiliation(s)
- Juan A Garcia-Sanchez
- INSERM, C3M, Côte D'Azur University, Nice, France
- INSERM, CNRS, CIML, Turing Centre for Living Systems, Aix-Marseille University, Marseille, France
| | - Jonathan J Ewbank
- INSERM, CNRS, CIML, Turing Centre for Living Systems, Aix-Marseille University, Marseille, France.
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219
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Qiu P, Zhou J, Zhang J, Dong Y, Liu Y. Exosome: The Regulator of the Immune System in Sepsis. Front Pharmacol 2021; 12:671164. [PMID: 33995102 PMCID: PMC8113812 DOI: 10.3389/fphar.2021.671164] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Sepsis is a syndrome comprised of a series of life-threatening organ dysfunctions caused by a maladjusted body response to infection with no effective treatment. There is growing evidence that the immune system plays a core role in sepsis. Pathogens cause abnormal host immune response and eventually lead to immunosuppression, which is an important cause of death in patients with sepsis. Exosomes are vesicles derived from double invagination of plasma membrane, associating with immune responses closely. The cargos delivered by exosomes into recipient cells, especially immune cells, effectively alter their response and functions in sepsis. In this review, we focus on the effects and mechanisms of exosomes on multiple immune cells, as well as the role of immune cell-derived exosomes in sepsis. This is helpful for us to have an in-depth understanding of the mechanism of immune disorders in sepsis. Exosomes is also expected to become a novel target and therapeutic approach for sepsis.
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Affiliation(s)
- Peng Qiu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jing Zhou
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jin Zhang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Youjing Dong
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yang Liu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China
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220
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Klompen AML, Kayal E, Collins AG, Cartwright P. Phylogenetic and Selection Analysis of an Expanded Family of Putatively Pore-Forming Jellyfish Toxins (Cnidaria: Medusozoa). Genome Biol Evol 2021; 13:6248095. [PMID: 33892512 PMCID: PMC8214413 DOI: 10.1093/gbe/evab081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 12/20/2022] Open
Abstract
Many jellyfish species are known to cause a painful sting, but box jellyfish (class Cubozoa) are a well-known danger to humans due to exceptionally potent venoms. Cubozoan toxicity has been attributed to the presence and abundance of cnidarian-specific pore-forming toxins called jellyfish toxins (JFTs), which are highly hemolytic and cardiotoxic. However, JFTs have also been found in other cnidarians outside of Cubozoa, and no comprehensive analysis of their phylogenetic distribution has been conducted to date. Here, we present a thorough annotation of JFTs from 147 cnidarian transcriptomes and document 111 novel putative JFTs from over 20 species within Medusozoa. Phylogenetic analyses show that JFTs form two distinct clades, which we call JFT-1 and JFT-2. JFT-1 includes all known potent cubozoan toxins, as well as hydrozoan and scyphozoan representatives, some of which were derived from medically relevant species. JFT-2 contains primarily uncharacterized JFTs. Although our analyses detected broad purifying selection across JFTs, we found that a subset of cubozoan JFT-1 sequences are influenced by gene-wide episodic positive selection compared with homologous toxins from other taxonomic groups. This suggests that duplication followed by neofunctionalization or subfunctionalization as a potential mechanism for the highly potent venom in cubozoans. Additionally, published RNA-seq data from several medusozoan species indicate that JFTs are differentially expressed, spatially and temporally, between functionally distinct tissues. Overall, our findings suggest a complex evolutionary history of JFTs involving duplication and selection that may have led to functional diversification, including variability in toxin potency and specificity.
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Affiliation(s)
- Anna M L Klompen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA
| | - Ehsan Kayal
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Allen G Collins
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,National Systematics Laboratory of NOAA's Fisheries Service, Silver Spring, Maryland, USA
| | - Paulyn Cartwright
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA
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221
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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222
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Ammendolia DA, Bement WM, Brumell JH. Plasma membrane integrity: implications for health and disease. BMC Biol 2021; 19:71. [PMID: 33849525 PMCID: PMC8042475 DOI: 10.1186/s12915-021-00972-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Plasma membrane integrity is essential for cellular homeostasis. In vivo, cells experience plasma membrane damage from a multitude of stressors in the extra- and intra-cellular environment. To avoid lethal consequences, cells are equipped with repair pathways to restore membrane integrity. Here, we assess plasma membrane damage and repair from a whole-body perspective. We highlight the role of tissue-specific stressors in health and disease and examine membrane repair pathways across diverse cell types. Furthermore, we outline the impact of genetic and environmental factors on plasma membrane integrity and how these contribute to disease pathogenesis in different tissues.
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Affiliation(s)
- Dustin A Ammendolia
- Cell Biology Program, Hospital for Sick Children, 686 Bay Street PGCRL, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - William M Bement
- Center for Quantitative Cell Imaging and Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John H Brumell
- Cell Biology Program, Hospital for Sick Children, 686 Bay Street PGCRL, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A1, Canada. .,SickKids IBD Centre, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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223
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Challenges of automation and scale: Bioinformatics and the evaluation of proteins to support genetically modified product safety assessments. J Invertebr Pathol 2021; 186:107587. [PMID: 33838205 DOI: 10.1016/j.jip.2021.107587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Bioinformatic analyses of protein sequences play an important role in the discovery and subsequent safety assessment of insect control proteins in Genetically Modified (GM) crops. Due to the rapid adoption of high-throughput sequencing methods over the last decade, the number of protein sequences in GenBank and other public databases has increased dramatically. Many of these protein sequences are the product of whole genome sequencing efforts, coupled with automated protein sequence prediction and annotation pipelines. Published genome sequencing studies provide a rich and expanding foundation of new source organisms and proteins for insect control or other desirable traits in GM products. However, data generated by automated pipelines can also confound regulatory safety assessments that employ bioinformatics. Largely this issue does not arise due to underlying sequence, but rather its annotation or associated metadata, and the downstream integration of that data into existing repositories. Observations made during bioinformatic safety assessments are described.
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224
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Abstract
Secretory pore-forming proteins (PFPs) have been identified in organisms from all kingdoms of life. Our studies with the toad species Bombina maxima found an interaction network among aerolysin family PFPs (af-PFPs) and trefoil factors (TFFs). As a toad af-PFP, BmALP1 can be reversibly regulated between active and inactive forms, with its paralog BmALP3 acting as a negative regulator. BmALP1 interacts with BmTFF3 to form a cellular active complex called βγ-CAT. This PFP complex is characterized by acting on endocytic pathways and forming pores on endolysosomes, including stimulating cell macropinocytosis. In addition, cell exocytosis can be induced and/or modulated in the presence of βγ-CAT. Depending on cell contexts and surroundings, these effects can facilitate the toad in material uptake and vesicular transport, while maintaining mucosal barrier function as well as immune defense. Based on experimental evidence, we hereby propose a secretory endolysosome channel (SELC) pathway conducted by a secreted PFP in cell endocytic and exocytic systems, with βγ-CAT being the first example of a SELC protein. With essential roles in cell interactions and environmental adaptations, the proposed SELC protein pathway should be conserved in other living organisms.
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Affiliation(s)
- Yun Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Qi-Quan Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zhong Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Cheng-Jie Deng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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225
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Abstract
Obligate intracellular malaria parasites reside within a vacuolar compartment generated during invasion which is the principal interface between pathogen and host. To subvert their host cell and support their metabolism, these parasites coordinate a range of transport activities at this membrane interface that are critically important to parasite survival and virulence, including nutrient import, waste efflux, effector protein export, and uptake of host cell cytosol. Here, we review our current understanding of the transport mechanisms acting at the malaria parasite vacuole during the blood and liver-stages of development with a particular focus on recent advances in our understanding of effector protein translocation into the host cell by the Plasmodium Translocon of EXported proteins (PTEX) and small molecule transport by the PTEX membrane-spanning pore EXP2. Comparison to Toxoplasma gondii and other related apicomplexans is provided to highlight how similar and divergent mechanisms are employed to fulfill analogous transport activities.
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Affiliation(s)
- Josh R. Beck
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, United States of America
| | - Chi-Min Ho
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
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226
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Pinaud S, Tetreau G, Poteaux P, Galinier R, Chaparro C, Lassalle D, Portet A, Simphor E, Gourbal B, Duval D. New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata. Front Immunol 2021; 12:635131. [PMID: 33868258 PMCID: PMC8047071 DOI: 10.3389/fimmu.2021.635131] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - in Biomphalaria glabrata snail, the intermediate host of the trematode Schistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family. Twenty-three biomphalysin genes were identified. All are expressed and exhibited a tissue-specific expression pattern. An in silico structural analysis was performed to highlight the central role played by two distinct domains i) a large lobe involved in the lytic function of these snail toxins which constrained their evolution and ii) a small lobe which is structurally variable between biomphalysin toxins and that matched to various functional domains involved in moiety recognition of targets cells. A functional approach suggests that the repertoire of biomphalysins that bind to pathogens, depends on the type of pathogen encountered. These results underline a neo-and sub-functionalization of the biomphalysin toxins, which have the potential to increase the range of effectors in the snail’s immune arsenal.
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Affiliation(s)
- Silvain Pinaud
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Guillaume Tetreau
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Pierre Poteaux
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Richard Galinier
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Cristian Chaparro
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Damien Lassalle
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Anaïs Portet
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Elodie Simphor
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Benjamin Gourbal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - David Duval
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
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227
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Banerji R, Karkee A, Kanojiya P, Saroj SD. Pore-forming toxins of foodborne pathogens. Compr Rev Food Sci Food Saf 2021; 20:2265-2285. [PMID: 33773026 DOI: 10.1111/1541-4337.12737] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 01/04/2023]
Abstract
Pore-forming toxins (PFTs) are water-soluble molecules that have been identified as the most crucial virulence factors during bacterial pathogenesis. PFTs disrupt the host cell membrane to internalize or to deliver other bacterial or virulence factors for establishing infections. Disruption of the host cell membrane by PFTs can lead to uncontrollable exchanges between the extracellular and the intracellular matrix, thereby disturbing the cellular homeostasis. Recent studies have provided insights into the molecular mechanism of PFTs during pathogenesis. Evidence also suggests the activation of several signal transduction pathways in the host cell on recognition of PFTs. Additionally, numerous distinctive host defense mechanisms as well as membrane repair mechanisms have been reported; however, studies reveal that PFTs aid in host immune evasion of the bacteria through numerous pathways. PFTs have been primarily associated with foodborne pathogens. Infection and death from diseases by consuming contaminated food are a constant threat to public health worldwide, affecting socioeconomic development. Moreover, the emergence of new foodborne pathogens has led to the rise of bacterial antimicrobial resistance affecting the population. Hence, this review focuses on the role of PFTs secreted by foodborne pathogens. The review highlights the molecular mechanism of foodborne bacterial PFTs, assisting bacterial survival from the host immune responses and understanding the downstream mechanism in the activation of various signaling pathways in the host upon PFT recognition. PFT research is a remarkable and an important field for exploring novel and broad applications of antimicrobial compounds as therapeutics.
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Affiliation(s)
- Rajashri Banerji
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Astha Karkee
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Poonam Kanojiya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
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228
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The molecular mechanisms of listeriolysin O-induced lipid membrane damage. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183604. [PMID: 33722646 DOI: 10.1016/j.bbamem.2021.183604] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/22/2022]
Abstract
Listeria monocytogenes is an intracellular food-borne pathogen that causes listeriosis, a severe and potentially life-threatening disease. Listeria uses a number of virulence factors to proliferate and spread to various cells and tissues. In this process, three bacterial virulence factors, the pore-forming protein listeriolysin O and phospholipases PlcA and PlcB, play a crucial role. Listeriolysin O belongs to a family of cholesterol-dependent cytolysins that are mostly expressed by gram-positive bacteria. Its unique structural features in an otherwise conserved three-dimensional fold, such as the acidic triad and proline-glutamate-serine-threonine-like sequence, enable the regulation of its intracellular activity as well as distinct extracellular functions. The stability of listeriolysin O is pH- and temperature-dependent, and this provides another layer of control of its activity in cells. Moreover, many recent studies have demonstrated a unique mechanism of pore formation by listeriolysin O, i.e., the formation of arc-shaped oligomers that can subsequently fuse to form membrane defects of various shapes and sizes. During listerial invasion of host cells, these membrane defects can disrupt phagosome membranes, allowing bacteria to escape into the cytosol and rapidly multiply. The activity of listeriolysin O is profoundly dependent on the amount and accessibility of cholesterol in the lipid membrane, which can be modulated by the phospholipase PlcB. All these prominent features of listeriolysin O play a role during different stages of the L. monocytogenes life cycle by promoting the proliferation of the pathogen while mitigating excessive damage to its replicative niche in the cytosol of the host cell.
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229
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Žerovnik E. Viroporins vs. Other Pore-Forming Proteins: What Lessons Can We Take? Front Chem 2021; 9:626059. [PMID: 33681145 PMCID: PMC7930612 DOI: 10.3389/fchem.2021.626059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Pore-forming proteins (PFPs) exist in virtually all domains of life, and by disrupting cellular membranes, depending on the pore size, they cause ion dis-balance, small substances, or even protein efflux/influx, influencing cell’s signaling routes and fate. Such pore-forming proteins exist from bacteria to viruses and also shape host defense systems, including innate immunity. There is strong evidence that amyloid toxicity is also caused by prefibrillar oligomers making “amyloid pores” into cellular membranes. For most of the PFPs, a 2-step mechanism of protein-membrane interaction takes place on the “lipid rafts,” membrane microdomains rich in gangliosides and cholesterol. In this mini-review paper, common traits of different PFPs are looked at. Possible ways for therapy of channelopathies and/or modulating immunity relevant to the new threat of SARS-CoV-2 infections could be learnt from such comparisons.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Ljubljana, Slovenia
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230
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Abstract
In its natural habitat, C. elegans encounters a wide variety of microbes, including food, commensals and pathogens. To be able to survive long enough to reproduce, C. elegans has developed a complex array of responses to pathogens. These activities are coordinated on scales that range from individual organelles to the entire organism. Often, the response is triggered within cells, by detection of infection-induced damage, mainly in the intestine or epidermis. C. elegans has, however, a capacity for cell non-autonomous regulation of these responses. This frequently involves the nervous system, integrating pathogen recognition, altering host biology and governing avoidance behavior. Although there are significant differences with the immune system of mammals, some mechanisms used to limit pathogenesis show remarkable phylogenetic conservation. The past 20 years have witnessed an explosion of host-pathogen interaction studies using C. elegans as a model. This review will discuss the broad themes that have emerged and highlight areas that remain to be fully explored.
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Affiliation(s)
- Céline N Martineau
- Aix Marseille Université, Inserm, CNRS, CIML, Turing Centre for Living Systems, Marseille, France
| | | | - Nathalie Pujol
- Aix Marseille Université, Inserm, CNRS, CIML, Turing Centre for Living Systems, Marseille, France.
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231
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Desikan R, Behera A, Maiti PK, Ayappa KG. Using multiscale molecular dynamics simulations to obtain insights into pore forming toxin mechanisms. Methods Enzymol 2021; 649:461-502. [PMID: 33712196 DOI: 10.1016/bs.mie.2021.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse-grained MARTINI models and structure-based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein-protein and protein-lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.
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Affiliation(s)
- Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Amit Behera
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, India
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India; Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
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232
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Tang Y, Guo H, Vermeulen AJ, Heuck AP. Topological analysis of type 3 secretion translocons in native membranes. Methods Enzymol 2021; 649:397-429. [PMID: 33712194 DOI: 10.1016/bs.mie.2021.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PFPs (Pore-forming proteins) perforate cellular membranes to create an aqueous pore and allow the passage of ions and polar molecules. The molecular mechanisms for many of these PFPs have been elucidated by combining high resolution structural information of these proteins with biochemical and biophysical approaches. However, some PFPs do not adopt stable conformations and are difficult to study in vitro. An example of these proteins are the bacterial Type 3 Secretion (T3S) translocators. The translocators are secreted by the bacterium and insert into the target cell membrane to form a translocon pore providing a portal for the passage of T3S toxins into eukaryotic cells. Given the important role that the T3S systems play in pathogenesis, methods to study these translocon pores in cellular membranes are needed. Using a combination of protein modifications and methods to selectively permeate and solubilized eukaryotic membranes, we have established an experimental procedure to analyze the topology of the Pseudomonas aeruginosa T3S translocon using P. aeruginosa strain variants and HeLa cell lines.
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Affiliation(s)
- Yuzhou Tang
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, United States
| | - Hanling Guo
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, United States
| | - Arjan J Vermeulen
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, United States
| | - Alejandro P Heuck
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, United States.
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233
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Abstract
Pore-forming proteins (PFPs) include virulence factors that are produced by many pathogenic bacteria. However, PFPs also comprise non-virulence factors, such as apoptotic Bcl2-like proteins, and also occur in non-pathogenic bacteria and indeed in all kingdoms of life. Pore-forming proteins are an ancient class of proteins, which are tremendously powerful in damaging cell membranes. In general, upon binding to lipid membranes, they convert from the soluble monomeric form into an oligomeric state, and then undergo a dramatic conformational change to form transmembrane pores. Thus, PFPs render the plasma membrane of their target cells permeable to solutes, potentially leading to cell death, or to more subtle manipulations of cellular functions. Recent cryo-EM and X-ray crystallography studies revealed high-resolution structures of several PFPs in their pre-pore and pore states, however many aspects regarding the cues that induce pore formation, the pre-pore to pore conformational transition, the mechanism of membrane permeation and associated dynamics are still less well understood, and direct visualization of the dynamics of these transitions are missing. Using high-speed atomic force microscopy (HS-AFM), the kinetics of oligomerization and the pre-pore to pore transition dynamics of various PFPs, such as Listeriolysin O (LLO), lysenin, and Perforin-2 (PFN2), could be studied. These studies revealed that LLO does not form pores of regular shape or size, but rather forms membrane inserted arcs that propagate and damage lipid membranes as lineactants. In contrast, lysenin forms stable pre-pore and pore nonameric rings and HS-AFM allowed to study their diffusion on and the pH-dependent insertion into the membrane. Similarly, PFN2 underwent pre-pore to pore transition upon acidification. The openness of the HS-AFM system allowed the transition to be imaged in real time and revealed that all observed molecules transitioned into the pore state within 3s. In this chapter, we detail protocols to prepare lipids, form supported lipid bilayers, and provide guidelines for real-time, real-space HS-AFM observations of PFPs in action.
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234
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Evans JC, Tweten RK. How protein engineering has revealed the molecular mechanisms of pore-forming toxins. Methods Enzymol 2021; 649:47-70. [PMID: 33712197 DOI: 10.1016/bs.mie.2021.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Pore-forming proteins are found in prokaryotes, vertebrates, and invertebrates, and when involved in pathogenic processes they are classified as pore-forming toxins (PFTs). The use of gene engineering methods in combination with the information provided by the high-resolution crystal structures of the PFTs have allowed investigators to gain a deep understanding of their pore-forming mechanisms. In this chapter, we discuss how protein engineering has helped us and others to reveal the molecular mechanisms of pore formation by prokaryotic PFTs with an emphasis on our experiences with the cholesterol-dependent cytolysins (CDCs).
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Affiliation(s)
- Jordan C Evans
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Rodney K Tweten
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.
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235
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Caaveiro JMM, Tsumoto K. Molecular basis for the activation of actinoporins by lipids. Methods Enzymol 2021; 649:277-306. [PMID: 33712190 DOI: 10.1016/bs.mie.2021.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Actinoporins are a family of homologous pore forming proteins from sea anemones. They are one of the few families of eukaryotic toxins that have been characterized in depth. Actinoporins are activated by lipids in the context of bilayers, especially in cell and in model membranes containing the lipid sphingomyelin. These proteins must undergo conformational changes induced upon interaction with lipids in the membrane, where they form cytotoxic pores causing cell death and lethality. Herein we review a list of procedures and techniques to study this family of toxins, with the goal of elucidating the physicochemical, thermodynamic and structural basis for their activation by lipids. The emerging picture indicates that actinoporins undergo a stepwise process that includes binding to the membrane, oligomerization, and pore formation, in this order. The key transformation from the inactive oligomer to the active pore is catalyzed by sphingomyelin, explaining the key role of this lipid in the function of actinoporins.
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Affiliation(s)
- Jose M M Caaveiro
- Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japan.
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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236
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Hub JS. Joint Reaction Coordinate for Computing the Free-Energy Landscape of Pore Nucleation and Pore Expansion in Lipid Membranes. J Chem Theory Comput 2021; 17:1229-1239. [PMID: 33427469 DOI: 10.1021/acs.jctc.0c01134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Topological transitions of membranes, such as pore formation or membrane fusion, play key roles in biology, biotechnology, and in medical applications. Calculating the related free-energy landscapes has been complicated by the fact that such processes involve a sequence of transitions along highly distinct directions in conformational space, making it difficult to define good reaction coordinates (RCs) for the overall process. In this study, a new RC capable of driving both pore nucleation and pore expansion in lipid membranes is presented. The potential of mean force (PMF) along the RC computed with molecular dynamics simulations provides a comprehensive view on the free-energy landscape of pore formation, including a barrier for pore nucleation; the size, free energy, and metastability of the open pore; and the energetic cost for further pore expansion against the line tension of the pore rim. The RC is illustrated by quantifying the effects of (i) simulation system size and (ii) the addition of dimethyl sulfoxide on the free-energy landscape of pore formation. PMF calculations along the RC provide mechanistic and energetic understanding of pore formation, hence they will be useful to rationalize the effects of membrane-active peptides, electric fields, and membrane composition on transmembrane pores.
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Affiliation(s)
- Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken D-66123, Germany
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237
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Li Y, Li Y, Mengist HM, Shi C, Zhang C, Wang B, Li T, Huang Y, Xu Y, Jin T. Structural Basis of the Pore-Forming Toxin/Membrane Interaction. Toxins (Basel) 2021; 13:toxins13020128. [PMID: 33572271 PMCID: PMC7914777 DOI: 10.3390/toxins13020128] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/13/2021] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
With the rapid growth of antibiotic-resistant bacteria, it is urgent to develop alternative therapeutic strategies. Pore-forming toxins (PFTs) belong to the largest family of virulence factors of many pathogenic bacteria and constitute the most characterized classes of pore-forming proteins (PFPs). Recent studies revealed the structural basis of several PFTs, both as soluble monomers, and transmembrane oligomers. Upon interacting with host cells, the soluble monomer of bacterial PFTs assembles into transmembrane oligomeric complexes that insert into membranes and affect target cell-membrane permeability, leading to diverse cellular responses and outcomes. Herein we have reviewed the structural basis of pore formation and interaction of PFTs with the host cell membrane, which could add valuable contributions in comprehensive understanding of PFTs and searching for novel therapeutic strategies targeting PFTs and interaction with host receptors in the fight of bacterial antibiotic-resistance.
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Affiliation(s)
- Yajuan Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; (Y.L.); (C.S.); (B.W.); (T.L.); (Y.H.)
| | - Yuelong Li
- Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China; (Y.L.); (H.M.M.); (C.Z.)
| | - Hylemariam Mihiretie Mengist
- Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China; (Y.L.); (H.M.M.); (C.Z.)
| | - Cuixiao Shi
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; (Y.L.); (C.S.); (B.W.); (T.L.); (Y.H.)
| | - Caiying Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China; (Y.L.); (H.M.M.); (C.Z.)
| | - Bo Wang
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; (Y.L.); (C.S.); (B.W.); (T.L.); (Y.H.)
| | - Tingting Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; (Y.L.); (C.S.); (B.W.); (T.L.); (Y.H.)
| | - Ying Huang
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; (Y.L.); (C.S.); (B.W.); (T.L.); (Y.H.)
| | - Yuanhong Xu
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; (Y.L.); (C.S.); (B.W.); (T.L.); (Y.H.)
- Correspondence: (Y.X.); (T.J.); Tel.: +86-13505694447 (Y.X.); +86-17605607323 (T.J.)
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China; (Y.L.); (H.M.M.); (C.Z.)
- Correspondence: (Y.X.); (T.J.); Tel.: +86-13505694447 (Y.X.); +86-17605607323 (T.J.)
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238
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Larpin Y, Besançon H, Babiychuk VS, Babiychuk EB, Köffel R. Small Pore-Forming Toxins Different Membrane Area Binding and Ca 2+ Permeability of Pores Determine Cellular Resistance of Monocytic Cells. Toxins (Basel) 2021; 13:toxins13020126. [PMID: 33572185 PMCID: PMC7914786 DOI: 10.3390/toxins13020126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 01/06/2023] Open
Abstract
Pore-forming toxins (PFTs) form multimeric trans-membrane pores in cell membranes that differ in pore channel diameter (PCD). Cellular resistance to large PFTs (>20 nm PCD) was shown to rely on Ca2+ influx activated membrane repair mechanisms. Small PFTs (<2 nm PCD) were shown to exhibit a high cytotoxic activity, but host cell response and membrane repair mechanisms are less well studied. We used monocytic immune cell lines to investigate the cellular resistance and host membrane repair mechanisms to small PFTs lysenin (Eisenia fetida) and aerolysin (Aeromonas hydrophila). Lysenin, but not aerolysin, is shown to induce Ca2+ influx from the extracellular space and to activate Ca2+ dependent membrane repair mechanisms. Moreover, lysenin binds to U937 cells with higher efficiency as compared to THP-1 cells, which is in line with a high sensitivity of U937 cells to lysenin. In contrast, aerolysin equally binds to U937 or THP-1 cells, but in different plasma membrane areas. Increased aerolysin induced cell death of U937 cells, as compared to THP-1 cells, is suggested to be a consequence of cap-like aerolysin binding. We conclude that host cell resistance to small PFTs attack comprises binding efficiency, pore localization, and capability to induce Ca2+ dependent membrane repair mechanisms.
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239
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Dixit M, Lazaridis T. Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint. J Chem Phys 2021; 153:054101. [PMID: 32770888 DOI: 10.1063/5.0016682] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The free energy of pore formation in lipid bilayers has been previously calculated using a variety of reaction coordinates. Here, we use free energy perturbation of a cylindrical lipid exclusion restraint to compute the free energy profile as a function of pore radius in dimyristoylphosphatidylcholine (DMPC) and dioleoylphosphatidylcholine (DOPC) bilayers. Additionally restraining the headgroups to lie on the membrane surface allows us to also calculate the free energy profile of hydrophobic pores, i.e., cylindrical pores lined by acyl chains. For certain pore radii, the free energy of wetting of hydrophobic pores is calculated using the density bias method. It is found that wetting of hydrophobic pores becomes thermodynamically favorable at 5.0 Å for DMPC and 6.5 Å for DOPC, although significant barriers prevent spontaneous wetting of the latter on a nanosecond time scale. The free energy of transformation of hydrophilic pores to hydrophobic ones is also calculated using free energy perturbation of headgroup restraints along the bilayer normal. This quantity, along with wetting and pore growth free energies, provides complete free energy profiles as a function of radius. Pore line tension values for the hydrophilic pores obtained from the slope of the free energy profiles are 37.6 pN for DMPC and 53.7 pN for DOPC. The free energy profiles for the hydrophobic pores are analyzed in terms of elementary interfacial tensions. It is found that a positive three-phase line tension is required to explain the results. The estimated value for this three-phase line tension (51.2 pN) lies within the expected range.
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Affiliation(s)
- Mayank Dixit
- Department of Chemistry, City College of New York, 160 Convent Ave., New York, New York 10031, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Ave., New York, New York 10031, USA
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Lima C, Falcao MAP, Andrade-Barros AI, Seni-Silva AC, Grund LZ, Balogh E, Conceiçao K, Queniaux VF, Ryffel B, Lopes-Ferreira M. Natterin an aerolysin-like fish toxin drives IL-1β-dependent neutrophilic inflammation mediated by caspase-1 and caspase-11 activated by the inflammasome sensor NLRP6. Int Immunopharmacol 2021; 91:107287. [PMID: 33378723 DOI: 10.1016/j.intimp.2020.107287] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
Natterin is an aerolysin-like pore-forming toxin responsible for the toxic effects of the venom of the medically significant fish Thalassophryne nattereri. Using a combination of pharmacologic and genetic loss-of-function approaches we conduct a systematic investigation of the regulatory mechanisms that control Natterin-induced neutrophilic inflammation in the peritonitis model. Our data confirmed the capacity of Natterin to induce a strong and sustained neutrophilic inflammation leading to systemic inflammatory lung infiltration and revealed overlapping regulatory paths in its control. We found that Natterin induced the extracellular release of mature IL-1β and the sustained production of IL-33 by bronchial epithelial cells. We confirmed the dependence of both ST2/IL-33 and IL-17A/IL-17RA signaling on the local and systemic neutrophils migration, as well as the crucial role of IL-1α, caspase-1 and caspase-11 for neutrophilic inflammation. The inflammation triggered by Natterin was a gasdermin-D-dependent inflammasome process, despite the cells did not die by pyroptosis. Finally, neutrophilic inflammation was mediated by non-canonical NLRP6 and NLRC4 adaptors through ASC interaction, independent of NLRP3. Our data highlight that the inflammatory process dependent on non-canonical inflammasome activation can be a target for pharmacological intervention in accidents by T. nattereri, which does not have adequate specific therapy.
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Affiliation(s)
- Carla Lima
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CETICs/FAPESP), Butantan Institute, Vital Brazil Avenue, 1500. Butantan, 05503-009 São Paulo. Brazil.
| | - Maria Alice Pimentel Falcao
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CETICs/FAPESP), Butantan Institute, Vital Brazil Avenue, 1500. Butantan, 05503-009 São Paulo. Brazil
| | - Aline Ingrid Andrade-Barros
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CETICs/FAPESP), Butantan Institute, Vital Brazil Avenue, 1500. Butantan, 05503-009 São Paulo. Brazil
| | - Ana Carolina Seni-Silva
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CETICs/FAPESP), Butantan Institute, Vital Brazil Avenue, 1500. Butantan, 05503-009 São Paulo. Brazil
| | - Lidiane Zito Grund
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CETICs/FAPESP), Butantan Institute, Vital Brazil Avenue, 1500. Butantan, 05503-009 São Paulo. Brazil
| | - Eniko Balogh
- Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei Krt 98, 4012 Debrecen, Hungary
| | - Katia Conceiçao
- Peptide Biochemistry Laboratory, UNIFESP, São José dos Campos. Brazil
| | - Valerie F Queniaux
- Allergy and Lung Inflammation Unit of the Molecular and Experimental Immunology and Neurogenetics (INEM, UMR7355, CNRS and University Orléans), Orléans, 45071 Orléans Cedex 2, France
| | - Bernhard Ryffel
- Allergy and Lung Inflammation Unit of the Molecular and Experimental Immunology and Neurogenetics (INEM, UMR7355, CNRS and University Orléans), Orléans, 45071 Orléans Cedex 2, France
| | - Monica Lopes-Ferreira
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CETICs/FAPESP), Butantan Institute, Vital Brazil Avenue, 1500. Butantan, 05503-009 São Paulo. Brazil
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The Food Poisoning Toxins of Bacillus cereus. Toxins (Basel) 2021; 13:toxins13020098. [PMID: 33525722 PMCID: PMC7911051 DOI: 10.3390/toxins13020098] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Bacillus cereus is a ubiquitous soil bacterium responsible for two types of food-associated gastrointestinal diseases. While the emetic type, a food intoxication, manifests in nausea and vomiting, food infections with enteropathogenic strains cause diarrhea and abdominal pain. Causative toxins are the cyclic dodecadepsipeptide cereulide, and the proteinaceous enterotoxins hemolysin BL (Hbl), nonhemolytic enterotoxin (Nhe) and cytotoxin K (CytK), respectively. This review covers the current knowledge on distribution and genetic organization of the toxin genes, as well as mechanisms of enterotoxin gene regulation and toxin secretion. In this context, the exceptionally high variability of toxin production between single strains is highlighted. In addition, the mode of action of the pore-forming enterotoxins and their effect on target cells is described in detail. The main focus of this review are the two tripartite enterotoxin complexes Hbl and Nhe, but the latest findings on cereulide and CytK are also presented, as well as methods for toxin detection, and the contribution of further putative virulence factors to the diarrheal disease.
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242
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Pore-forming toxins in infection and immunity. Biochem Soc Trans 2021; 49:455-465. [PMID: 33492383 DOI: 10.1042/bst20200836] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/02/2021] [Accepted: 01/06/2021] [Indexed: 12/14/2022]
Abstract
The integrity of the plasma membranes is extremely crucial for the survival and proper functioning of the cells. Organisms from all kingdoms of life employ specialized pore-forming proteins and toxins (PFPs and PFTs) that perforate cell membranes, and cause detrimental effects. PFPs/PFTs exert their damaging actions by forming oligomeric pores in the membrane lipid bilayer. PFPs/PFTs play important roles in diverse biological processes. Many pathogenic bacteria secrete PFTs for executing their virulence mechanisms. The immune system of the higher vertebrates employs PFPs to kill pathogen-infected cells and transformed cancer cells. The most obvious consequence of membrane pore-formation by the PFPs/PFTs is the killing of the target cells due to the disruption of the permeability barrier function of the plasma membranes. PFPs/PFTs can also activate diverse cellular processes that include activation of the stress-response pathways, induction of programmed cell death, and inflammation. Upon attack by the PFTs, host cells may also activate pathways to repair the injured membranes, restore cellular homeostasis, and trigger inflammatory immune responses. In this article, we present an overview of the diverse cellular responses that are triggered by the PFPs/PFTs, and their implications in the process of pathogen infection and immunity.
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243
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Li S, Akrap N, Cerboni S, Porritt MJ, Wimberger S, Lundin A, Möller C, Firth M, Gordon E, Lazovic B, Sieńska A, Pane LS, Coelho MA, Ciotta G, Pellegrini G, Sini M, Xu X, Mitra S, Bohlooly-Y M, Taylor BJM, Sienski G, Maresca M. Universal toxin-based selection for precise genome engineering in human cells. Nat Commun 2021; 12:497. [PMID: 33479216 PMCID: PMC7820243 DOI: 10.1038/s41467-020-20810-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023] Open
Abstract
Prokaryotic restriction enzymes, recombinases and Cas proteins are powerful DNA engineering and genome editing tools. However, in many primary cell types, the efficiency of genome editing remains low, impeding the development of gene- and cell-based therapeutic applications. A safe strategy for robust and efficient enrichment of precisely genetically engineered cells is urgently required. Here, we screen for mutations in the receptor for Diphtheria Toxin (DT) which protect human cells from DT. Selection for cells with an edited DT receptor variant enriches for simultaneously introduced, precisely targeted gene modifications at a second independent locus, such as nucleotide substitutions and DNA insertions. Our method enables the rapid generation of a homogenous cell population with bi-allelic integration of a DNA cassette at the selection locus, without clonal isolation. Toxin-based selection works in both cancer-transformed and non-transformed cells, including human induced pluripotent stem cells and human primary T-lymphocytes, as well as it is applicable also in vivo, in mice with humanized liver. This work represents a flexible, precise, and efficient selection strategy to engineer cells using CRISPR-Cas and base editing systems.
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Affiliation(s)
- Songyuan Li
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Nina Akrap
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science and Experimental Medicine, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Michelle J Porritt
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Lundin
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Carl Möller
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- R&D Data Infrastructure & Tools, AstraZeneca, Cambridge, UK
| | - Euan Gordon
- Discovery Biology SWE, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bojana Lazovic
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Aleksandra Sieńska
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Luna Simona Pane
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Giovanni Ciotta
- Discovery Biology UK, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Giovanni Pellegrini
- CVRM pathology, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Marcella Sini
- CVRM pathology, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Xiufeng Xu
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Suman Mitra
- Inserm UMR1277 CNRS UMR9020 - CANTHER, Institut pour la Recherche sur le Cancer de Lille, Lille, France
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Benjamin J M Taylor
- Discovery Biology UK, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Grzegorz Sienski
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Marcello Maresca
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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244
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Jing W, Lo Pilato J, Kay C, Man SM. Activation mechanisms of inflammasomes by bacterial toxins. Cell Microbiol 2021; 23:e13309. [PMID: 33426791 DOI: 10.1111/cmi.13309] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/16/2020] [Accepted: 12/12/2020] [Indexed: 12/13/2022]
Abstract
Inflammasomes are cytosolic innate immune complexes, which assemble in mammalian cells in response to microbial components and endogenous danger signals. A major family of inflammasome activators is bacterial toxins. Inflammasome sensor proteins, such as the nucleotide-binding oligomerisation domain-like receptor (NLR) family members NLRP1b and NLRP3, and the tripartite motif family member Pyrin+ efflux triggered by pore-forming toxins or by other toxin-induced homeostasis-altering events such as lysosomal rupture. Pyrin senses perturbation of host cell functions induced by certain enzymatic toxins resulting in impairment of RhoA GTPase activity. Assembly of the inflammasome complex activates the cysteine protease caspase-1, leading to the proteolytic cleavage of the proinflammatory cytokines IL-1β and IL-18, and the pore-forming protein gasdermin D causing pyroptosis. In this review, we discuss the latest progress in our understanding on the activation mechanisms of inflammasome complexes by bacterial toxins and effector proteins and explore avenues for future research into the relationships between inflammasomes and bacterial toxins.
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Affiliation(s)
- Weidong Jing
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jordan Lo Pilato
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Callum Kay
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Si Ming Man
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
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López-Molina S, do Nascimento NA, Silva-Filha MHNL, Guerrero A, Sánchez J, Pacheco S, Gill SS, Soberón M, Bravo A. In vivo nanoscale analysis of the dynamic synergistic interaction of Bacillus thuringiensis Cry11Aa and Cyt1Aa toxins in Aedes aegypti. PLoS Pathog 2021; 17:e1009199. [PMID: 33465145 PMCID: PMC7846010 DOI: 10.1371/journal.ppat.1009199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/29/2021] [Accepted: 11/30/2020] [Indexed: 12/22/2022] Open
Abstract
The insecticidal Cry11Aa and Cyt1Aa proteins are produced by Bacillus thuringiensis as crystal inclusions. They work synergistically inducing high toxicity against mosquito larvae. It was proposed that these crystal inclusions are rapidly solubilized and activated in the gut lumen, followed by pore formation in midgut cells killing the larvae. In addition, Cyt1Aa functions as a Cry11Aa binding receptor, inducing Cry11Aa oligomerization and membrane insertion. Here, we used fluorescent labeled crystals, protoxins or activated toxins for in vivo localization at nano-scale resolution. We show that after larvae were fed solubilized proteins, these proteins were not accumulated inside the gut and larvae were not killed. In contrast, if larvae were fed soluble non-toxic mutant proteins, these proteins were found inside the gut bound to gut-microvilli. Only feeding with crystal inclusions resulted in high larval mortality, suggesting that they have a role for an optimal intoxication process. At the macroscopic level, Cry11Aa completely degraded the gastric caeca structure and, in the presence of Cyt1Aa, this effect was observed at lower toxin-concentrations and at shorter periods. The labeled Cry11Aa crystal protein, after midgut processing, binds to the gastric caeca and posterior midgut regions, and also to anterior and medium regions where it is internalized in ordered "net like" structures, leading finally to cell break down. During synergism both Cry11Aa and Cyt1Aa toxins showed a dynamic layered array at the surface of apical microvilli, where Cry11Aa is localized in the lower layer closer to the cell cytoplasm, and Cyt1Aa is layered over Cry11Aa. This array depends on the pore formation activity of Cry11Aa, since the non-toxic mutant Cry11Aa-E97A, which is unable to oligomerize, inverted this array. Internalization of Cry11Aa was also observed during synergism. These data indicate that the mechanism of action of Cry11Aa is more complex than previously anticipated, and may involve additional steps besides pore-formation activity.
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Affiliation(s)
- Samira López-Molina
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | | | | | - Adán Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico
| | - Jorge Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Sabino Pacheco
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Sarjeet S. Gill
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, California, United States of America
| | - Mario Soberón
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Alejandra Bravo
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
- * E-mail:
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246
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Passive Immunization with Recombinant Antibody VLRB-PirA vp/PirB vp-Enriched Feeds against Vibrio parahaemolyticus Infection in Litopenaeus vannamei Shrimp. Vaccines (Basel) 2021; 9:vaccines9010055. [PMID: 33467013 PMCID: PMC7829966 DOI: 10.3390/vaccines9010055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 11/17/2022] Open
Abstract
The causative agent of acute hepatopancreatic necrosis disease (AHPND) is the bacterium, Vibrio parahaemolyticus, which secretes toxins into the gastrointestinal tract of its host. Vibrio parahaemolyticus toxins A and B (PirAvp/PirBvp) have been implicated in the pathogenesis of this disease, and are, therefore, the focus of studies developing treatments for AHPND. We previously produced recombinant antibodies based on the hagfish variable lymphocyte receptor B (VLRB) capable of neutralizing some viruses, suggesting that this type of antibody may have a potential application for treatment of AHPND. Here, recombinant PirAvp/PirBvp, produced using a bacterial expression system, were used as antigens to screen a hagfish VLRB cDNA library to obtain PirAvp/PirBvp-specific antibodies. A cell line secreting these antibodies was established by screening and cloning the DNA extracted from hagfish B cells. Supernatants collected from cells secreting the PirAvp/PirBvp antibodies were collected and concentrated, and used to passively immunize shrimp to neutralize the toxins PirAvp or PirBvp associated with AHPND. Briefly, 10 μg of PirAvp and PirBvp antibodies, 7C12 and 9G10, respectively, were mixed with the shrimp feed, and fed to shrimp for three days consecutive days prior to experimentally infecting the shrimp with V. parahaemolyticus (containing toxins A and B), and resulting mortalities recorded for six days. Results showed significantly higher level of survival in shrimp fed with the PirBvp-9G10 antibody (60%) compared to the group fed the PirAvp-7C12 antibody (3%) and the control group (0%). This suggests that VLRB antibodies may be a suitable alternative to immunoglobulin-based antibodies, as passive immunization treatments for effective management of AHPND outbreaks within shrimp farms.
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247
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Palacios-Ortega J, Rivera-de-Torre E, Gavilanes JG, Slotte JP, Martínez-Del-Pozo Á, García-Linares S. Biophysical approaches to study actinoporin-lipid interactions. Methods Enzymol 2021; 649:307-339. [PMID: 33712191 DOI: 10.1016/bs.mie.2020.12.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-lipid interactions are crucial events from a biochemical point of view, like the interaction of proteins with the cell plasma membrane, and their study is of great importance. Actinoporins are a very powerful tool to study this kind of interactions, since they are soluble proteins in an aqueous environment, capable of inserting into membranes when they have the adequate composition. In fact, actinoporins have been used to study protein-lipid interactions for many years now. Sometimes it is not possible to use real biological membranes in the experiments, so model membranes need to be used. This article aims to give a thorough description of many of the techniques used to study actinoporin-lipid interactions, using both biological and model membranes: Hemolysis, release of vesicles content, surface plasmon resonance, isothermal titration calorimetry, fluorescence-based measurements, etc. Some of these techniques measure the actinoporins activity and some measure their binding properties. The combination of all the techniques described can offer valuable information about the thermodynamics and the kinetics of the actinoporin-lipid interaction.
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Affiliation(s)
- Juan Palacios-Ortega
- Department of Biochemistry and Molecular Biology, Complutense University, Madrid, Spain; Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Esperanza Rivera-de-Torre
- Department of Biochemistry and Molecular Biology, Complutense University, Madrid, Spain; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - José G Gavilanes
- Department of Biochemistry and Molecular Biology, Complutense University, Madrid, Spain
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | | | - Sara García-Linares
- Department of Biochemistry and Molecular Biology, Complutense University, Madrid, Spain.
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248
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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249
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Sathyanarayana P, Visweswariah SS, Ayappa KG. Mechanistic Insights into Pore Formation by an α-Pore Forming Toxin: Protein and Lipid Bilayer Interactions of Cytolysin A. Acc Chem Res 2021; 54:120-131. [PMID: 33291882 DOI: 10.1021/acs.accounts.0c00551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pore forming toxins (PFTs) are the largest class of bacterial toxins playing a central role in bacterial pathogenesis. They are proteins specifically designed to form nanochannels in the membranes of target cells, ultimately resulting in cell death and establishing infection. PFTs are broadly classified as α- and β-PFTs, depending on secondary structures that form the transmembrane channel. A unique feature about this class of proteins is the drastic conformational changes and complex oligomerization pathways that occur upon exposure to the plasma membrane. A molecular understanding of pore formation has implications in designing novel intervention strategies to combat rising antimicrobial resistance, targeted-cancer therapy, as well as designing nanopores for specialized technologies. Central to unraveling the pore formation pathway is the availability of high resolution crystal structures. In this regard, β-toxins are better understood, when compared with α-toxins whose pore forming mechanisms are complicated by an incomplete knowledge of the driving forces for amphiphatic membrane-inserted helices to organize into functional pores. With the publication of the first crystal structure for an α-toxin, cytolysin A (ClyA), in 2009 we embarked on an extensive multiscale study to unravel its pore forming mechanism. This Account represents the collective mechanistic knowledge gained in our laboratories using a variety of experimental and theoretical techniques which include large scale molecular dynamics (MD) simulations, kinetic modeling studies, single-molecule fluorescence imaging, and super-resolution spectroscopy. We reported MD simulations of the ClyA protomer, oligomeric intermediates, and full pore complex in a lipid bilayer and mapped the conformational transitions that accompany membrane binding. Using single-molecule fluorescence imaging, the conformational transition was experimentally verified by analysis of various diffusion states of membrane bound ClyA. Importantly, we have uncovered a hitherto unknown putative cholesterol binding motif in the membrane-inserted helix of ClyA. Distinct binding pockets for cholesterol formed by adjacent membrane-inserted helices are revealed in MD simulations. Cholesterol appears to play a dual role by stabilizing both the membrane-inserted protomer as well as oligomeric intermediates. Molecular dynamics simulations and kinetic modeling studies suggest that the membrane-inserted arcs oligomerize reversibly to form the predominant transmembrane oligomeric intermediates during pore formation. We posit that this mechanistic understanding of the complex action of α-PFTs has implications in unraveling pore assembly across the wider family of bacterial toxins. With emerging antimicrobial resistance, alternate therapies may rely on disrupting pore functionality or oligomerization of these pathogenic determinants utilized by bacteria, and our study includes assessing the potential for dendrimers as pore blockers.
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Affiliation(s)
- Pradeep Sathyanarayana
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India 560012
| | - Sandhya S. Visweswariah
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India 560012
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India 560012
| | - K. Ganapathy Ayappa
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India 560012
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India 560012
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250
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Schureck MA, Darling JE, Merk A, Shao J, Daggupati G, Srinivasan P, Olinares PDB, Rout MP, Chait BT, Wollenberg K, Subramaniam S, Desai SA. Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake. eLife 2021; 10:e65282. [PMID: 33393463 PMCID: PMC7840181 DOI: 10.7554/elife.65282] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
Malaria parasites use the RhopH complex for erythrocyte invasion and channel-mediated nutrient uptake. As the member proteins are unique to Plasmodium spp., how they interact and traffic through subcellular sites to serve these essential functions is unknown. We show that RhopH is synthesized as a soluble complex of CLAG3, RhopH2, and RhopH3 with 1:1:1 stoichiometry. After transfer to a new host cell, the complex crosses a vacuolar membrane surrounding the intracellular parasite and becomes integral to the erythrocyte membrane through a PTEX translocon-dependent process. We present a 2.9 Å single-particle cryo-electron microscopy structure of the trafficking complex, revealing that CLAG3 interacts with the other subunits over large surface areas. This soluble complex is tightly assembled with extensive disulfide bonding and predicted transmembrane helices shielded. We propose a large protein complex stabilized for trafficking but poised for host membrane insertion through large-scale rearrangements, paralleling smaller two-state pore-forming proteins in other organisms.
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Affiliation(s)
- Marc A Schureck
- Laboratory of Malaria and Vector Research, NIAID, National Institutes of HealthRockvilleUnited States
| | - Joseph E Darling
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Jinfeng Shao
- Laboratory of Malaria and Vector Research, NIAID, National Institutes of HealthRockvilleUnited States
| | - Geervani Daggupati
- Department of Molecular Microbiology and Immunology, and Johns Hopkins Malaria Institute, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Prakash Srinivasan
- Department of Molecular Microbiology and Immunology, and Johns Hopkins Malaria Institute, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | - Kurt Wollenberg
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British ColumbiaVancouverCanada
| | - Sanjay A Desai
- Laboratory of Malaria and Vector Research, NIAID, National Institutes of HealthRockvilleUnited States
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