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Chen L, Khan H, Tan L, Li X, Zhang G, Im YJ. Structural basis of the activation of MARTX cysteine protease domain from Vibrio vulnificus. PLoS One 2024; 19:e0307512. [PMID: 39093838 PMCID: PMC11296635 DOI: 10.1371/journal.pone.0307512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 07/07/2024] [Indexed: 08/04/2024] Open
Abstract
The multifunctional autoprocessing repeat-in-toxin (MARTX) toxin is the primary virulence factor of Vibrio vulnificus displaying cytotoxic and hemolytic properties. The cysteine protease domain (CPD) is responsible for activating the MARTX toxin by cleaving the toxin precursor and releasing the mature toxin fragments. To investigate the structural determinants for inositol hexakisphosphate (InsP6)-mediated activation of the CPD, we determined the crystal structures of unprocessed and β-flap truncated MARTX CPDs of Vibrio vulnificus strain MO6-24/O in complex with InsP6 at 1.3 and 2.2Å resolution, respectively. The CPD displays a conserved domain with a central seven-stranded β-sheet flanked by three α-helices. The scissile bond Leu3587-Ala3588 is bound in the catalytic site of the InsP6-loaded form of the Cys3727Ala mutant. InsP6 interacts with the conserved basic cleft and the β-flap inducing the active conformation of catalytic residues. The β-flap of the post-CPD is flexible in the InsP6-unbound state. The structure of the CPD Δβ-flap showed an inactive conformation of the catalytic residues due to the absence of interaction between the active site and the β-flap. This study confirms the InsP6-mediated activation of the MARTX CPDs in which InsP6-binding induces conformational changes of the catalytic residues and the β-flap that holds the N terminus of the CPD in the active site, facilitating hydrolysis of the scissile bond.
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Affiliation(s)
- Lin Chen
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Haider Khan
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Lingchen Tan
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Xiaojie Li
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Gongchun Zhang
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Young Jun Im
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
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2
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Choi S, Lee Y, Park S, Jang SY, Park J, Oh DW, Kim SM, Kim TH, Lee GS, Cho C, Kim BS, Lee D, Kim EH, Cheong HK, Moon JH, Song JJ, Hwang J, Kim MH. Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet. Nat Commun 2024; 15:6218. [PMID: 39043696 PMCID: PMC11266601 DOI: 10.1038/s41467-024-50650-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024] Open
Abstract
Multiple bacterial genera take advantage of the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin to invade host cells. Secretion of the MARTX toxin by Vibrio vulnificus, a deadly opportunistic pathogen that causes primary septicemia, the precursor of sepsis, is a major driver of infection; however, the molecular mechanism via which the toxin contributes to septicemia remains unclear. Here, we report the crystal and cryo-electron microscopy (EM) structures of a toxin effector duet comprising the domain of unknown function in the first position (DUF1)/Rho inactivation domain (RID) complexed with human targets. These structures reveal how the duet is used by bacteria as a potent weapon. The data show that DUF1 acts as a RID-dependent transforming NADase domain (RDTND) that disrupts NAD+ homeostasis by hijacking calmodulin. The cryo-EM structure of the RDTND-RID duet complexed with calmodulin and Rac1, together with immunological analyses in vitro and in mice, provide mechanistic insight into how V. vulnificus uses the duet to suppress ROS generation by depleting NAD(P)+ and modifying Rac1 in a mutually-reinforcing manner that ultimately paralyzes first line immune responses, promotes dissemination of invaders, and induces sepsis. These data may allow development of tools or strategies to combat MARTX toxin-related human diseases.
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Affiliation(s)
- Sanghyeon Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Youngjin Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Shinhye Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Song Yee Jang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141, Korea
| | - Jongbin Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Do Won Oh
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea
| | - Su-Man Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biology Education, Chonnam National University, Gwangju, 61186, Korea
| | - Tae-Hwan Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Korea
| | - Ga Seul Lee
- Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk, 28644, Korea
| | - Changyi Cho
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Korea
| | - Byoung Sik Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Korea
| | - Donghan Lee
- Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Korea
| | - Eun-Hee Kim
- Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Korea
| | - Hae-Kap Cheong
- Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Korea
| | - Jeong Hee Moon
- Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Jungwon Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
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3
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Zeng Y, Shi W, Liu Z, Xu H, Liu L, Hang J, Wang Y, Lu M, Zhou W, Huang W, Tang F. C-terminal modification and functionalization of proteins via a self-cleavage tag triggered by a small molecule. Nat Commun 2023; 14:7169. [PMID: 37935692 PMCID: PMC10630284 DOI: 10.1038/s41467-023-42977-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
The precise modification or functionalization of the protein C-terminus is essential but full of challenges. Herein, a chemical approach to modify the C-terminus is developed by fusing a cysteine protease domain on the C-terminus of the protein of interest, which could achieve the non-enzymatic C-terminal functionalization by InsP6-triggered cysteine protease domain self-cleavage. This method demonstrates a highly efficient way to achieve protein C-terminal functionalization and is compatible with a wide range of amine-containing molecules and proteins. Additionally, a reversible C-terminal de-functionalization is found by incubating the C-terminal modified proteins with cysteine protease domain and InsP6, providing a tool for protein functionalization and de-functionalization. Last, various applications of protein C-terminal functionalization are provided in this work, as demonstrated by the site-specific assembly of nanobody drug conjugates, the construction of a bifunctional antibody, the C-terminal fluorescent labeling, and the C-terminal transpeptidation and glycosylation.
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Affiliation(s)
- Yue Zeng
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Wei Shi
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Zhi Liu
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
| | - Hao Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
| | - Liya Liu
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Jiaying Hang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Yongqin Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Mengru Lu
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Wei Zhou
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Wei Huang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Feng Tang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China.
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Wood TE, Westervelt KA, Yoon JM, Eshleman HD, Levy R, Burnes H, Slade DJ, Lesser CF, Goldberg MB. The Shigella Spp. Type III Effector Protein OspB Is a Cysteine Protease. mBio 2022; 13:e0127022. [PMID: 35638611 PMCID: PMC9239218 DOI: 10.1128/mbio.01270-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
The type III secretion system is required for virulence of many pathogenic bacteria. Bacterial effector proteins delivered into target host cells by this system modulate host signaling pathways and processes in a manner that promotes infection. Here, we define the activity of the effector protein OspB of the human pathogen Shigella spp., the etiological agent of shigellosis and bacillary dysentery. Using the yeast Saccharomyces cerevisiae as a model organism, we show that OspB sensitizes cells to inhibition of TORC1, the central regulator of growth and metabolism. In silico analyses reveal that OspB bears structural homology to bacterial cysteine proteases that target mammalian cell processes, and we define a conserved cysteine-histidine catalytic dyad required for OspB function. Using yeast genetic screens, we identify a crucial role for the arginine N-degron pathway in the yeast growth inhibition phenotype and show that inositol hexakisphosphate is an OspB cofactor. We find that a yeast substrate for OspB is the TORC1 component Tco89p, proteolytic cleavage of which generates a C-terminal fragment that is targeted for degradation via the arginine N-degron pathway; processing and degradation of Tco89p is required for the OspB phenotype. In all, we demonstrate that the Shigella T3SS effector OspB is a cysteine protease and decipher its interplay with eukaryotic cell processes. IMPORTANCEShigella spp. are important human pathogens and among the leading causes of diarrheal mortality worldwide, especially in children. Virulence depends on the Shigella type III secretion system (T3SS). Definition of the roles of the bacterial effector proteins secreted by the T3SS is key to understanding Shigella pathogenesis. The effector protein OspB contributes to a range of phenotypes during infection, yet the mechanism of action is unknown. Here, we show that S. flexneri OspB possesses cysteine protease activity in both yeast and mammalian cells, and that enzymatic activity of OspB depends on a conserved cysteine-histidine catalytic dyad. We determine how its protease activity sensitizes cells to TORC1 inhibition in yeast, finding that OspB cleaves a component of yeast TORC1, and that the degradation of the C-terminal cleavage product is responsible for OspB-mediated hypersensitivity to TORC1 inhibitors. Thus, OspB is a cysteine protease that depends on a conserved cysteine-histidine catalytic dyad.
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Affiliation(s)
- Thomas E. Wood
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathleen A. Westervelt
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jessica M. Yoon
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Heather D. Eshleman
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Roie Levy
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Henry Burnes
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel J. Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Cammie F. Lesser
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Marcia B. Goldberg
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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5
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Abstract
![]()
The paradigm of antivirulence
therapy dictates that bacterial pathogens
are specifically disarmed but not killed by neutralizing their virulence
factors. Clearance of the invading pathogen by the immune system is
promoted. As compared to antibiotics, the pathogen-selective antivirulence
drugs hold promise to minimize collateral damage to the beneficial
microbiome. Also, selective pressure for resistance is expected to
be lower because bacterial viability is not directly affected. Antivirulence
drugs are being developed for stand-alone prophylactic and therapeutic
treatments but also for combinatorial use with antibiotics. This Review
focuses on drug modalities that target bacterial exotoxins after the
secretion or release-upon-lysis. Exotoxins have a significant and
sometimes the primary role as the disease-causing virulence factor,
and thereby they are attractive targets for drug development. We describe
the key pre-clinical and clinical trial data that have led to the
approval of currently used exotoxin-targeted drugs, namely the monoclonal
antibodies bezlotoxumab (toxin B/TcdB, Clostridioides difficile), raxibacumab (anthrax toxin, Bacillus anthracis), and obiltoxaximab (anthrax toxin, Bacillus anthracis), but also to challenges with some of the promising leads. We also
highlight the recent developments in pre-clinical research sector
to develop exotoxin-targeted drug modalities, i.e., monoclonal antibodies,
antibody fragments, antibody mimetics, receptor analogs, neutralizing
scaffolds, dominant-negative mutants, and small molecules. We describe
how these exotoxin-targeted drug modalities work with high-resolution
structural knowledge and highlight their advantages and disadvantages
as antibiotic alternatives.
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Affiliation(s)
- Moona Sakari
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Arttu Laisi
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Arto T. Pulliainen
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
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6
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Ozma MA, Khodadadi E, Rezaee MA, Asgharzadeh M, Aghazadeh M, Zeinalzadeh E, Ganbarov K, Kafil H. Bacterial proteomics and its application for pathogenesis studies. Curr Pharm Biotechnol 2021; 23:1245-1256. [PMID: 34503411 DOI: 10.2174/1389201022666210908153234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 01/09/2023]
Abstract
Bacteria build their structures by implementing several macromolecules such as proteins, polysaccharides, phospholipids, and nucleic acids, which leads to preserve their lives and play an essential role in their pathogenesis. There are two genomic and proteomic methods to study various macromolecules of bacteria, which are complementary methods and provide comprehensive information. Proteomic approaches are used to identify proteins and their cell applications. Furthermore, to study bacterial proteins, macromolecules are involved in the bacteria's structures and functions. These protein-based methods provide comprehensive information about the cells, such as the external structures, internal compositions, post-translational modifications, and mechanisms of particular actions such as biofilm formation, antibiotic resistance, and adaptation to the environment, which are helpful in promoting bacterial pathogenesis. These methods use various devices such as MALDI-TOF MS, LC-MS, and two-dimensional electrophoresis, which are valuable tools for studying different structural and functional proteins of the bacteria and their mechanisms of pathogenesis that causes rapid, easy, and accurate diagnosis of the infections.
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Affiliation(s)
- Mahdi Asghari Ozma
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Ehsaneh Khodadadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Mohammad Aghazadeh
- Microbiome and Health Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Hossein Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614711. Iran
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7
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Choi S, Kim BS, Hwang J, Kim MH. Reduced virulence of the MARTX toxin increases the persistence of outbreak-associated Vibrio vulnificus in host reservoirs. J Biol Chem 2021; 296:100777. [PMID: 33992647 PMCID: PMC8191300 DOI: 10.1016/j.jbc.2021.100777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
Opportunistic bacteria strategically dampen their virulence to allow them to survive and propagate in hosts. However, the molecular mechanisms underlying virulence control are not clearly understood. Here, we found that the opportunistic pathogen Vibrio vulnificus biotype 3, which caused an outbreak of severe wound and intestinal infections associated with farmed tilapia, secretes significantly less virulent multifunctional autoprocessing repeats-in-toxin (MARTX) toxin, which is the most critical virulence factor in other clinical Vibrio strains. The biotype 3 MARTX toxin contains a cysteine protease domain (CPD) evolutionarily retaining a unique autocleavage site and a distinct β-flap region. CPD autoproteolytic activity is attenuated following its autocleavage because of the β-flap region. This β-flap blocks the active site, disabling further autoproteolytic processing and release of the modularly structured effector domains within the toxin. Expression of this altered CPD consequently results in attenuated release of effectors by the toxin and significantly reduces the virulence of V. vulnificus biotype 3 in cells and in mice. Bioinformatic analysis revealed that this virulence mechanism is shared in all biotype 3 strains. Thus, these data provide new insights into the mechanisms by which opportunistic bacteria persist in an environmental reservoir, prolonging the potential to cause outbreaks.
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Affiliation(s)
- Sanghyeon Choi
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Byoung Sik Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul, Korea
| | - Jungwon Hwang
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
| | - Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
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8
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Quijano-Rubio A, Yeh HW, Park J, Lee H, Langan RA, Boyken SE, Lajoie MJ, Cao L, Chow CM, Miranda MC, Wi J, Hong HJ, Stewart L, Oh BH, Baker D. De novo design of modular and tunable protein biosensors. Nature 2021; 591:482-487. [PMID: 33503651 PMCID: PMC8074680 DOI: 10.1038/s41586-021-03258-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023]
Abstract
Naturally occurring protein switches have been repurposed for the development of biosensors and reporters for cellular and clinical applications1. However, the number of such switches is limited, and reengineering them is challenging. Here we show that a general class of protein-based biosensors can be created by inverting the flow of information through de novo designed protein switches in which the binding of a peptide key triggers biological outputs of interest2. The designed sensors are modular molecular devices with a closed dark state and an open luminescent state; analyte binding drives the switch from the closed to the open state. Because the sensor is based on the thermodynamic coupling of analyte binding to sensor activation, only one target binding domain is required, which simplifies sensor design and allows direct readout in solution. We create biosensors that can sensitively detect the anti-apoptosis protein BCL-2, the IgG1 Fc domain, the HER2 receptor, and Botulinum neurotoxin B, as well as biosensors for cardiac troponin I and an anti-hepatitis B virus antibody with the high sensitivity required to detect these molecules clinically. Given the need for diagnostic tools to track the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)3, we used the approach to design sensors for the SARS-CoV-2 spike protein and antibodies against the membrane and nucleocapsid proteins. The former, which incorporates a de novo designed spike receptor binding domain (RBD) binder4, has a limit of detection of 15 pM and a luminescence signal 50-fold higher than the background level. The modularity and sensitivity of the platform should enable the rapid construction of sensors for a wide range of analytes, and highlights the power of de novo protein design to create multi-state protein systems with new and useful functions.
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Affiliation(s)
- Alfredo Quijano-Rubio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Hsien-Wei Yeh
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Jooyoung Park
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Hansol Lee
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Robert A. Langan
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Scott E. Boyken
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Marc J. Lajoie
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Longxing Cao
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Cameron M. Chow
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Marcos C. Miranda
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Jimin Wi
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Hyo Jeong Hong
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Lance Stewart
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Byung-Ha Oh
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,Correspondence and requests for materials should be addressed to D.B. or B.-H.O
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA,Correspondence and requests for materials should be addressed to D.B. or B.-H.O
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9
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Quijano-Rubio A, Yeh HW, Park J, Lee H, Langan RA, Boyken SE, Lajoie MJ, Cao L, Chow CM, Miranda MC, Wi J, Hong HJ, Stewart L, Oh BH, Baker D. De novo design of modular and tunable allosteric biosensors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32743576 DOI: 10.1101/2020.07.18.206946] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Naturally occurring allosteric protein switches have been repurposed for developing novel biosensors and reporters for cellular and clinical applications 1 , but the number of such switches is limited, and engineering them is often challenging as each is different. Here, we show that a very general class of allosteric protein-based biosensors can be created by inverting the flow of information through de novo designed protein switches in which binding of a peptide key triggers biological outputs of interest 2 . Using broadly applicable design principles, we allosterically couple binding of protein analytes of interest to the reconstitution of luciferase activity and a bioluminescent readout through the association of designed lock and key proteins. Because the sensor is based purely on thermodynamic coupling of analyte binding to switch activation, only one target binding domain is required, which simplifies sensor design and allows direct readout in solution. We demonstrate the modularity of this platform by creating biosensors that, with little optimization, sensitively detect the anti-apoptosis protein Bcl-2, the hIgG1 Fc domain, the Her2 receptor, and Botulinum neurotoxin B, as well as biosensors for cardiac Troponin I and an anti-Hepatitis B virus (HBV) antibody that achieve the sub-nanomolar sensitivity necessary to detect clinically relevant concentrations of these molecules. Given the current need for diagnostic tools for tracking COVID-19 3 , we use the approach to design sensors of antibodies against SARS-CoV-2 protein epitopes and of the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. The latter, which incorporates a de novo designed RBD binder, has a limit of detection of 15pM with an up to seventeen fold increase in luminescence upon addition of RBD. The modularity and sensitivity of the platform should enable the rapid construction of sensors for a wide range of analytes and highlights the power of de novo protein design to create multi-state protein systems with new and useful functions.
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10
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Differential effects of 'resurrecting' Csp pseudoproteases during Clostridioides difficile spore germination. Biochem J 2020; 477:1459-1478. [PMID: 32242623 PMCID: PMC7200643 DOI: 10.1042/bcj20190875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 01/02/2023]
Abstract
Clostridioides difficile is a spore-forming bacterial pathogen that is the leading cause of hospital-acquired gastroenteritis. C. difficile infections begin when its spore form germinates in the gut upon sensing bile acids. These germinants induce a proteolytic signaling cascade controlled by three members of the subtilisin-like serine protease family, CspA, CspB, and CspC. Notably, even though CspC and CspA are both pseudoproteases, they are nevertheless required to sense germinants and activate the protease, CspB. Thus, CspC and CspA are part of a growing list of pseudoenzymes that play important roles in regulating cellular processes. However, despite their importance, the structural properties of pseudoenzymes that allow them to function as regulators remain poorly understood. Our recently solved crystal structure of CspC revealed that its pseudoactive site residues align closely with the catalytic triad of CspB, suggesting that it might be possible to ‘resurrect' the ancestral protease activity of the CspC and CspA pseudoproteases. Here, we demonstrate that restoring the catalytic triad to these pseudoproteases fails to resurrect their protease activity. We further show that the pseudoactive site substitutions differentially affect the stability and function of the CspC and CspA pseudoproteases: the substitutions destabilized CspC and impaired spore germination without affecting CspA stability or function. Thus, our results surprisingly reveal that the presence of a catalytic triad does not necessarily predict protease activity. Since homologs of C. difficile CspA occasionally carry an intact catalytic triad, our results indicate that bioinformatic predictions of enzyme activity may underestimate pseudoenzymes in rare cases.
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11
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Wang X, Shen J, Jiang F, Jin Q. The Photorhabdus Virulence Cassettes RRSP-Like Effector Interacts With Cyclin-Dependent Kinase 1 and Causes Mitotic Defects in Mammalian Cells. Front Microbiol 2020; 11:366. [PMID: 32231646 PMCID: PMC7082817 DOI: 10.3389/fmicb.2020.00366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/19/2020] [Indexed: 12/20/2022] Open
Abstract
The "Photorhabdus virulence cassettes" (PVCs) secreted by Photorhabdus are defined as "extracellular contractile injection systems" (eCISs) and can deliver effectors to eukaryotic hosts for cytotoxicity. Previously, we demonstrated the cryogenic electron microscopy (cryo-EM) structure and assembly process of an intact PVC particle from Photorhabdus asymbiotica. In this work, we characterized the biological functions of a PVC effector, which is defined as a homologous protein of Ras/Rap1-specific endopeptidase domain (RRSP) in the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin from Vibrio vulnificus. In this work, we found that the RRSP homologous protein (RRSPPa) was associated with inhibition of cell proliferation and increased cell apoptosis and death of HeLa cells. Furthermore, we discovered that RRSPPa disturbed mitotic progression, including the induction of cell cycle alteration, retardation of cell abscission time, and regression of the cleavage furrow. In addition, we revealed that RRSPPa could target the cyclin-dependent kinase 1 (CDK1) protein and block activation of CDK1 through inhibition of Thr161 phosphorylation, which partially explained the crucial role of this effector in cell mitosis.
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Affiliation(s)
| | | | - Feng Jiang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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12
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Woida PJ, Satchell KJF. The Vibrio cholerae MARTX toxin silences the inflammatory response to cytoskeletal damage before inducing actin cytoskeleton collapse. Sci Signal 2020; 13:13/614/eaaw9447. [PMID: 31937566 DOI: 10.1126/scisignal.aaw9447] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Multifunctional autoprocessing repeats-in-toxin (MARTX) toxins are pore-forming bacterial toxins that translocate multiple functionally independent effector domains into a target eukaryotic cell. Vibrio cholerae colonizes intestinal epithelial cells (IECs) and uses a MARTX toxin with three effector domains-an actin cross-linking domain (ACD), a Rho inactivation domain (RID), and an α/β hydrolase domain (ABH)-to suppress innate immunity and enhance colonization. We investigated whether these multiple catalytic enzymes delivered from a single toxin functioned in a coordinated manner to suppress intestinal innate immunity. Using cultured human IECs, we demonstrated that ACD-induced cytoskeletal collapse activated extracellular signal-regulated kinase, p38, and c-Jun amino-terminal kinase mitogen-activated protein kinase (MAPK) signaling to elicit a robust proinflammatory response characterized by the secretion of interleukin-8 (IL-8; also called CXCL8) and the expression of CXCL8, tumor necrosis factor (TNF), and other proinflammatory genes. However, RID and ABH, which are naturally delivered together with ACD, blocked MAPK activation through Rac1 and thus prevented ACD-induced inflammation. RID also abolished IL-8 secretion induced by heat-killed bacteria, TNF, or latrunculin A. Thus, MARTX toxins use enzymatic multifunctionality to silence the host response to bacterial factors and to the damage caused by the toxins. Furthermore, these data show how V. cholerae MARTX toxin suppresses intestinal inflammation and contributes to cholera being classically defined as a noninflammatory diarrheal disease.
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Affiliation(s)
- Patrick J Woida
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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13
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Makes caterpillars floppy-like effector-containing MARTX toxins require host ADP-ribosylation factor (ARF) proteins for systemic pathogenicity. Proc Natl Acad Sci U S A 2019; 116:18031-18040. [PMID: 31427506 PMCID: PMC6731672 DOI: 10.1073/pnas.1905095116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
MARTX toxins present across multiple bacterial genera are primary virulence factors that facilitate initial colonization, dissemination, and lethality in a wide range of hosts, including humans. Upon entry into host cells, the toxins undergo a processing event to release their disease-related modularly structured effector domains. However, the mechanisms underlying processing and activation of diverse effector domains within the toxins remain unclear. Here, we use biochemical and structural biological approaches, in combination with cellular microbiological experiments, to demonstrate how Makes caterpillars floppy-like effector (MCF) or its homolog-containing MARTX toxins process effector modules and fully activate effectors. MCF-containing toxins target ADP-ribosylation factor proteins ubiquitously expressed in cells to activate and disseminate effectors across subcellular compartments simultaneously, eventually leading to systemic pathogenicity. Upon invading target cells, multifunctional autoprocessing repeats-in-toxin (MARTX) toxins secreted by bacterial pathogens release their disease-related modularly structured effector domains. However, it is unclear how a diverse repertoire of effector domains within these toxins are processed and activated. Here, we report that Makes caterpillars floppy-like effector (MCF)-containing MARTX toxins require ubiquitous ADP-ribosylation factor (ARF) proteins for processing and activation of intermediate effector modules, which localize in different subcellular compartments following limited processing of holo effector modules by the internal cysteine protease. Effector domains structured tandemly with MCF in intermediate modules become disengaged and fully activated by MCF, which aggressively interacts with ARF proteins present at the same location as intermediate modules and is converted allosterically into a catalytically competent protease. MCF-mediated effector processing leads ultimately to severe virulence in mice via an MCF-mediated ARF switching mechanism across subcellular compartments. This work provides insight into how bacteria take advantage of host systems to induce systemic pathogenicity.
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14
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Xu Y, Wang S, Hu Q, Gao S, Ma X, Zhang W, Shen Y, Chen F, Lai L, Pei J. CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction. Nucleic Acids Res 2019; 46:W374-W379. [PMID: 29750256 PMCID: PMC6031032 DOI: 10.1093/nar/gky380] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/30/2018] [Indexed: 12/02/2022] Open
Abstract
CavityPlus is a web server that offers protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys. CavPharmer uses a receptor-based pharmacophore modelling program, Pocket, to automatically extract pharmacophore features within cavities. CorrSite identifies potential allosteric ligand-binding sites based on motion correlation analyses between cavities. CovCys automatically detects druggable cysteine residues, which is especially useful to identify novel binding sites for designing covalent allosteric ligands. Overall, CavityPlus provides an integrated platform for analysing comprehensive properties of protein binding cavities. Such analyses are useful for many aspects of drug design and discovery, including target selection and identification, virtual screening, de novo drug design, and allosteric and covalent-binding drug design. The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.
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Affiliation(s)
- Youjun Xu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shiwei Wang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Qiwan Hu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shuaishi Gao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaomin Ma
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Weilin Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yihang Shen
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fangjin Chen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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15
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Kudryashova E, Seveau SM, Kudryashov DS. Targeting and inactivation of bacterial toxins by human defensins. Biol Chem 2017; 398:1069-1085. [PMID: 28593905 DOI: 10.1515/hsz-2017-0106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/18/2017] [Indexed: 11/15/2022]
Abstract
Defensins, as a prominent family of antimicrobial peptides (AMP), are major effectors of the innate immunity with a broad range of immune modulatory and antimicrobial activities. In particular, defensins are the only recognized fast-response molecules that can neutralize a broad range of bacterial toxins, many of which are among the deadliest compounds on the planet. For a decade, the mystery of how a small and structurally conserved group of peptides can neutralize a heterogeneous group of toxins with little to no sequential and structural similarity remained unresolved. Recently, it was found that defensins recognize and target structural plasticity/thermodynamic instability, fundamental physicochemical properties that unite many bacterial toxins and distinguish them from the majority of host proteins. Binding of human defensins promotes local unfolding of the affected toxins, destabilizes their secondary and tertiary structures, increases susceptibility to proteolysis, and leads to their precipitation. While the details of toxin destabilization by defensins remain obscure, here we briefly review properties and activities of bacterial toxins known to be affected by or resilient to defensins, and discuss how recognized features of defensins correlate with the observed inactivation.
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16
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Kwak MJ, Kim JD, Kim H, Kim C, Bowman JW, Kim S, Joo K, Lee J, Jin KS, Kim YG, Lee NK, Jung JU, Oh BH. Architecture of the type IV coupling protein complex of Legionella pneumophila. Nat Microbiol 2017; 2:17114. [PMID: 28714967 PMCID: PMC6497169 DOI: 10.1038/nmicrobiol.2017.114] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 06/14/2017] [Indexed: 12/14/2022]
Abstract
Many bacteria, including Legionella pneumophila, rely on the type IV secretion system to translocate a repertoire of effector proteins into the hosts for their survival and growth. Type IV coupling protein (T4CP) is a hexameric ATPase that links translocating substrates to the transenvelope secretion conduit. Yet, how a large number of effector proteins are selectively recruited and processed by T4CPs remains enigmatic. DotL, the T4CP of L. pneumophila, contains an ATPase domain and a C-terminal extension whose function is unknown. Unlike T4CPs involved in plasmid DNA translocation, DotL appeared to function by forming a multiprotein complex with four other proteins. Here, we show that the C-terminal extension of DotL interacts with DotN, IcmS, IcmW and an additionally identified subunit LvgA, and that this pentameric assembly binds Legionella effector proteins. We determined the crystal structure of this assembly and built an architecture of the T4CP holocomplex by combining a homology model of the ATPase domain of DotL. The holocomplex is a hexamer of a bipartite structure composed of a membrane-proximal ATPase domain and a membrane-distal substrate-recognition assembly. The presented information demonstrates the architecture and functional dissection of the multiprotein T4CP complexes and provides important insights into their substrate recruitment and processing.
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Affiliation(s)
- Mi-Jeong Kwak
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - J. Dongun Kim
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyunmin Kim
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Cheolhee Kim
- Department of Physics, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Korea
| | - James W. Bowman
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 1975 Zonal Avenue, Los Angeles, California 90033, USA
| | - Seonghoon Kim
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Keehyoung Joo
- Center for Advanced Computation, School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Korea
| | - Jooyoung Lee
- Center for Advanced Computation, School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Korea
| | - Nam Ki Lee
- Department of Physics, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Korea
| | - Jae U. Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 1975 Zonal Avenue, Los Angeles, California 90033, USA
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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17
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Affiliation(s)
- Megan Garland
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Sebastian Loscher
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Matthew Bogyo
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
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18
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Biancucci M, Dolores JS, Wong J, Grimshaw S, Anderson WF, Satchell KJF, Kwon K. New ligation independent cloning vectors for expression of recombinant proteins with a self-cleaving CPD/6xHis-tag. BMC Biotechnol 2017; 17:1. [PMID: 28056928 PMCID: PMC5216533 DOI: 10.1186/s12896-016-0323-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/09/2016] [Indexed: 12/30/2022] Open
Abstract
Background Recombinant protein purification is a crucial step for biochemistry and structural biology fields. Rapid robust purification methods utilize various peptide or protein tags fused to the target protein for affinity purification using corresponding matrices and to enhance solubility. However, affinity/solubility-tags often need to be removed in order to conduct functional and structural studies, adding complexities to purification protocols. Results In this work, the Vibrio cholerae MARTX toxin Cysteine Protease Domain (CPD) was inserted in a ligation-independent cloning (LIC) vector to create a C-terminal 6xHis-tagged inducible autoprocessing enzyme tag, called “the CPD-tag”. The pCPD and alternative pCPD/ccdB cloning vectors allow for easy insertion of DNA and expression of the target protein fused to the CPD-tag, which is removed at the end of the purification step by addition of the inexpensive small molecule inositol hexakisphosphate to induce CPD autoprocessing. This process is demonstrated using a small bacterial membrane localization domain and for high yield purification of the eukaryotic small GTPase KRas. Subsequently, pCPD was tested with 40 proteins or sub-domains selected from a high throughput crystallization pipeline. Conclusion pCPD vectors are easily used LIC compatible vectors for expression of recombinant proteins with a C-terminal CPD/6xHis-tag. Although intended only as a strategy for rapid tag removal, this pilot study revealed the CPD-tag may also increase expression and solubility of some recombinant proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0323-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Biancucci
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Ward 6-205, Chicago, IL, 60611, USA
| | - Jazel S Dolores
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Ward 6-205, Chicago, IL, 60611, USA.,Present address: Northwestern Memorial Hospital, Chicago, IL, USA
| | - Jennifer Wong
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Ward 6-205, Chicago, IL, 60611, USA.,Present address: Indiana University, Bloomington, IN, USA
| | - Sarah Grimshaw
- Infectious Diseases Group, J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA.,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Ward 6-205, Chicago, IL, 60611, USA. .,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Keehwan Kwon
- Infectious Diseases Group, J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA. .,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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19
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Kleingardner EC, Asher WB, Bren KL. Efficient and Flexible Preparation of Biosynthetic Microperoxidases. Biochemistry 2016; 56:143-148. [DOI: 10.1021/acs.biochem.6b00915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Erin C. Kleingardner
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Wesley B. Asher
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
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20
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Belyy A, Raoux-Barbot D, Saveanu C, Namane A, Ogryzko V, Worpenberg L, David V, Henriot V, Fellous S, Merrifield C, Assayag E, Ladant D, Renault L, Mechold U. Actin activates Pseudomonas aeruginosa ExoY nucleotidyl cyclase toxin and ExoY-like effector domains from MARTX toxins. Nat Commun 2016; 7:13582. [PMID: 27917880 PMCID: PMC5150216 DOI: 10.1038/ncomms13582] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/13/2016] [Indexed: 12/15/2022] Open
Abstract
The nucleotidyl cyclase toxin ExoY is one of the virulence factors injected by the Pseudomonas aeruginosa type III secretion system into host cells. Inside cells, it is activated by an unknown eukaryotic cofactor to synthesize various cyclic nucleotide monophosphates. ExoY-like adenylate cyclases are also found in Multifunctional-Autoprocessing Repeats-in-ToXin (MARTX) toxins produced by various Gram-negative pathogens. Here we demonstrate that filamentous actin (F-actin) is the hitherto unknown cofactor of ExoY. Association with F-actin stimulates ExoY activity more than 10,000 fold in vitro and results in stabilization of actin filaments. ExoY is recruited to actin filaments in transfected cells and alters F-actin turnover. Actin also activates an ExoY-like adenylate cyclase MARTX effector domain from Vibrio nigripulchritudo. Finally, using a yeast genetic screen, we identify actin mutants that no longer activate ExoY. Our results thus reveal a new sub-group within the class II adenylyl cyclase family, namely actin-activated nucleotidyl cyclase (AA-NC) toxins.
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Affiliation(s)
- Alexander Belyy
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
- Department of Bacterial Infections, Gamaleya Research Center, Moscow 123098, Russia
| | - Dorothée Raoux-Barbot
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Cosmin Saveanu
- Institut Pasteur, CNRS UMR3525, Génétique des Interactions Macromoléculaires, Département de Génomes et Génétique, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Abdelkader Namane
- Institut Pasteur, CNRS UMR3525, Génétique des Interactions Macromoléculaires, Département de Génomes et Génétique, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Vasily Ogryzko
- Institut Gustave Roussy, CNRS UMR 8126, Unité de Signaling, Nuclei and Innovations in Oncology, 94805 Villejuif, France
| | - Lina Worpenberg
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Violaine David
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Veronique Henriot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Souad Fellous
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Christien Merrifield
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Elodie Assayag
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Daniel Ladant
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Louis Renault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Undine Mechold
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
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Abstract
Multifunctional-autoprocessing repeats-in-toxin (MARTX) toxins are a heterogeneous group of toxins found in a number of Vibrio species and other Gram-negative bacteria. The toxins are composed of conserved repeat regions and an autoprocessing protease domain that together function as a delivery platform for transfer of cytotoxic and cytopathic domains into target eukaryotic cell cytosol. Within the cells, the effectors can alter biological processes such as signaling or cytoskeletal structure, presumably to the benefit of the bacterium. Ten effector domains are found in the various Vibrio MARTX toxins, although any one toxin carries only two to five effector domains. The specific toxin variant expressed by a species can be modified by homologous recombination to acquire or lose effector domains, such that different strains within the same species can express distinct variants of the toxins. This review examines the conserved structural elements of the MARTX toxins and details the different toxin arrangements carried by Vibrio species and strains. The catalytic function of domains and how the toxins are linked to pathogenesis of human and animals is described.
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Reexamining the Germination Phenotypes of Several Clostridium difficile Strains Suggests Another Role for the CspC Germinant Receptor. J Bacteriol 2015; 198:777-86. [PMID: 26668265 DOI: 10.1128/jb.00908-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/09/2015] [Indexed: 12/17/2022] Open
Abstract
UNLABELLED Clostridium difficile spore germination is essential for colonization and disease. The signals that initiate C. difficile spore germination are a combination of taurocholic acid (a bile acid) and glycine. Interestingly, the chenodeoxycholic acid class (CDCA) bile acids competitively inhibit taurocholic acid-mediated germination, suggesting that compounds that inhibit spore germination could be developed into drugs that prophylactically prevent C. difficile infection or reduce recurring disease. However, a recent report called into question the utility of such a strategy to prevent infection by describing C. difficile strains that germinated in the apparent absence of bile acids or germinated in the presence of the CDCA inhibitor. Because the mechanisms of C. difficile spore germination are beginning to be elucidated, the mechanism of germination in these particular strains could yield important information on how C. difficile spores initiate germination. Therefore, we quantified the interaction of these strains with taurocholic acid and CDCA, the rates of spore germination, the release of DPA from the spore core, and the abundance of the germinant receptor complex (CspC, CspB, and SleC). We found that strains previously observed to germinate in the absence of taurocholic acid correspond to more potent 50% effective concentrations (EC50 values; the concentrations that achieve a half-maximum germination rate) of the germinant and are still inhibited by CDCA, possibly explaining the previous observations. By comparing the germination kinetics and the abundance of proteins in the germinant receptor complex, we revised our original model for CspC-mediated activation of spore germination and propose that CspC may activate spore germination and then inhibit downstream processes. IMPORTANCE Clostridium difficile forms metabolically dormant spores that persist in the health care environment. In susceptible hosts, C. difficile spores germinate in response to certain bile acids and glycine. Blocking germination by C. difficile spores is an attractive strategy to prevent the initiation of disease or to block recurring infection. However, certain C. difficile strains have been identified whose spores germinate in the absence of bile acids or are not blocked by known inhibitors of C. difficile spore germination (calling into question the utility of such strategies). Here, we further investigate these strains and reestablish that bile acid activators and inhibitors of germination affect these strains and use these data to suggest another role for the C. difficile bile acid germinant receptor.
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Agarwal S, Kim H, Chan RB, Agarwal S, Williamson R, Cho W, Paolo GD, Paolo GD, Satchell KJF. Autophagy and endosomal trafficking inhibition by Vibrio cholerae MARTX toxin phosphatidylinositol-3-phosphate-specific phospholipase A1 activity. Nat Commun 2015; 6:8745. [PMID: 26498860 PMCID: PMC4640098 DOI: 10.1038/ncomms9745] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/25/2015] [Indexed: 12/16/2022] Open
Abstract
Vibrio cholerae, responsible for acute gastroenteritis secretes a large multifunctional-autoprocessing repeat-in-toxin (MARTX) toxin linked to evasion of host immune system, facilitating colonization of small intestine. Unlike other effector domains of the multifunctional toxin that target cytoskeleton, the function of alpha-beta hydrolase (ABH) remained elusive. This study demonstrates that ABH is an esterase/lipase with catalytic Ser–His–Asp triad. ABH binds with high affinity to phosphatidylinositol-3-phosphate (PtdIns3P) and cleaves the fatty acid in PtdIns3P at the sn1 position in vitro making it the first PtdIns3P-specific phospholipase A1 (PLA1). Expression of ABH in vivo reduces intracellular PtdIns3P levels and its PtdIns3P-specific PLA1 activity blocks endosomal and autophagic pathways. In accordance with recent studies acknowledging the potential of extracellular pathogens to evade or exploit autophagy to prevent their clearance and facilitate survival, this is the first report highlighting the role of ABH in inhibiting autophagy and endosomal trafficking induced by extracellular V. cholerae. The MARTX toxin of V. cholerae processes itself to deliver three distinct effector domains to the cytosol. Here the authors show that the third effector domain is a phosphatidylinositol-3-phosphate (PtdIns3P)-specific phospholipase that inhibits autophagy in target cells.
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Affiliation(s)
- Shivani Agarwal
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, Illinois 60611, USA
| | - Hyunjin Kim
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA
| | - Robin B Chan
- Department of Pathology and Cell Biology, 630 West 168th Street, Columbia University, New York, New York 10032, USA
| | - Shivangi Agarwal
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, Illinois 60611, USA
| | - Rebecca Williamson
- Department of Pathology and Cell Biology, 630 West 168th Street, Columbia University, New York, New York 10032, USA
| | - Wonhwa Cho
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA
| | - Gilbert Di Paolo
- Department of Pathology and Cell Biology, 630 West 168th Street, Columbia University, New York, New York 10032, USA
| | - Gilbert D Paolo
- Department of Pathology and Cell Biology, 630 West 168th Street, Columbia University, New York, New York 10032, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, Illinois 60611, USA
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Gavin HE, Satchell KJF. MARTX toxins as effector delivery platforms. Pathog Dis 2015; 73:ftv092. [PMID: 26472741 DOI: 10.1093/femspd/ftv092] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2015] [Indexed: 12/14/2022] Open
Abstract
Bacteria frequently manipulate their host environment via delivery of microbial 'effector' proteins to the cytosol of eukaryotic cells. In the case of the multifunctional autoprocessing repeats-in-toxins (MARTX) toxin, this phenomenon is accomplished by a single, >3500 amino acid polypeptide that carries information for secretion, translocation, autoprocessing and effector activity. MARTX toxins are secreted from bacteria by dedicated Type I secretion systems. The released MARTX toxins form pores in target eukaryotic cell membranes for the delivery of up to five cytopathic effectors, each of which disrupts a key cellular process. Targeted cellular processes include modulation or modification of small GTPases, manipulation of host cell signaling and disruption of cytoskeletal integrity. More recently, MARTX toxins have been shown to be capable of heterologous protein translocation. Found across multiple bacterial species and genera--frequently in pathogens lacking Type 3 or Type 4 secretion systems--MARTX toxins in multiple cases function as virulence factors. Innovative research at the intersection of toxin biology and bacterial genetics continues to elucidate the intricacies of the toxin as well as the cytotoxic mechanisms of its diverse effector collection.
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Affiliation(s)
- Hannah E Gavin
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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25
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Agarwal S, Agarwal S, Biancucci M, Satchell KJF. Induced autoprocessing of the cytopathic Makes caterpillars floppy-like effector domain of the Vibrio vulnificus MARTX toxin. Cell Microbiol 2015; 17:1494-509. [PMID: 25912102 DOI: 10.1111/cmi.12451] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 12/22/2022]
Abstract
The multifunctional-autoprocessing repeats-in-toxin (MARTX(Vv)) toxin that harbours a varied repertoire of effector domains is the primary virulence factor of Vibrio vulnificus. Although ubiquitously present among Biotype I toxin variants, the 'Makes caterpillars floppy-like' effector domain (MCF(Vv)) is previously unstudied. Using transient expression and protein delivery, MCF(Vv) and MCF(Ah) from the Aeromonas hydrophila MARTX(Ah)) toxin are shown for the first time to induce cell rounding. Alanine mutagenesis across the C-terminal subdomain of MCF(Vv) identified an Arg-Cys-Asp (RCD) tripeptide motif shown to comprise a cysteine protease catalytic site essential for autoprocessing of MCF(Vv). The autoprocessing could be recapitulated in vitro by the addition of host cell lysate to recombinant MCF(Vv), indicating induced autoprocessing by cellular factors. The RCD motif is also essential for cytopathicity, suggesting autoprocessing is essential first to activate the toxin and then to process a cellular target protein resulting in cell rounding. Sequence homology places MCF(Vv) within the C58 cysteine protease family that includes the type III secretion effectors YopT from Yersinia spp. and AvrPphB from Pseudomonas syringae. However, the catalytic site RCD motif is unique compared with other C58 peptidases and is here proposed to represent a new subgroup of autopeptidase found within a number of putative large bacterial toxins.
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Affiliation(s)
- Shivangi Agarwal
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Shivani Agarwal
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Marco Biancucci
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
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26
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Distinct roles of the repeat-containing regions and effector domains of the Vibrio vulnificus multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin. mBio 2015; 6:mBio.00324-15. [PMID: 25827415 PMCID: PMC4453568 DOI: 10.1128/mbio.00324-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Vibrio vulnificus is a seafood-borne pathogen that destroys the intestinal epithelium, leading to rapid bacterial dissemination and death. The most important virulence factor is the multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin comprised of effector domains in the center region flanked by long repeat-containing regions which are well conserved among MARTX toxins and predicted to translocate effector domains. Here, we examined the role of the repeat-containing regions using a modified V. vulnificus MARTX (MARTXVv) toxin generated by replacing all the internal effector domains with β-lactamase (Bla). Bla activity was detected in secretions from the bacterium and also in the cytosol of intoxicated epithelial cells. The modified MARTXVv toxin without effector domains retained its necrotic activity but lost its cell-rounding activity. Further, deletion of the carboxyl-terminal repeat-containing region blocked toxin secretion from the bacterium. Deletion of the amino-terminal repeat-containing region had no effect on secretion but completely abolished translocation and necrosis. Neither secretion nor translocation was affected by enzymatically inactivating the cysteine protease domain of the toxin. These data demonstrate that the amino-terminal and carboxyl-terminal repeat-containing regions of the MARTXVv toxin are necessary and sufficient for the delivery of effector domains and epithelial cell lysis in vitro but that effector domains are required for other cytopathic functions. Furthermore, Ca2+-dependent secretion of the modified MARTXVv toxin suggests that nonclassical RTX-like repeats found in the carboxyl-terminal repeat-containing region are functionally similar to classical RTX repeats found in other RTX proteins. Up to 95% of deaths from seafood-borne infections in the United States are due solely to one pathogen, V. vulnificus. Among its various virulence factors, the MARTXVv toxin has been characterized as a critical exotoxin for successful pathogenesis of V. vulnificus in mouse infection models. Similarly to MARTX toxins of other pathogens, MARTXVv toxin is comprised of repeat-containing regions, central effector domains, and an autoprocessing cysteine protease domain. Yet how each of these regions contributes to essential activities of the toxins has not been fully identified for any of MARTX toxins. Using modified MARTXVv toxin fused with β-lactamase as a reporter enzyme, the portion(s) responsible for toxin secretion from bacteria, effector domain translocation into host cells, rapid host cell rounding, and necrotic host cell death was identified. The results are relevant for understanding how MARTXVv toxin serves as both a necrotic pore-forming toxin and an effector delivery platform.
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McLuskey K, Mottram J. Comparative structural analysis of the caspase family with other clan CD cysteine peptidases. Biochem J 2015; 466:219-32. [PMID: 25697094 PMCID: PMC4357240 DOI: 10.1042/bj20141324] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/19/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
Abstract
Clan CD forms a structural group of cysteine peptidases, containing seven individual families and two subfamilies of structurally related enzymes. Historically, it is most notable for containing the mammalian caspases, on which the structures of the clan were founded. Interestingly, the caspase family is split into two subfamilies: the caspases, and a second subfamily containing both the paracaspases and the metacaspases. Structural data are now available for both the paracaspases and the metacaspases, allowing a comprehensive structural analysis of the entire caspase family. In addition, a relative plethora of structural data has recently become available for many of the other families in the clan, allowing both the structures and the structure-function relationships of clan CD to be fully explored. The present review compares the enzymes in the caspase subfamilies with each other, together with a comprehensive comparison of all the structural families in clan CD. This reveals a diverse group of structures with highly conserved structural elements that provide the peptidases with a variety of substrate specificities and activation mechanisms. It also reveals conserved structural elements involved in substrate binding, and potential autoinhibitory functions, throughout the clan, and confirms that the metacaspases are structurally diverse from the caspases (and paracaspases), suggesting that they should form a distinct family of clan CD peptidases.
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Key Words
- caspase
- clan cd
- crystallography
- metacaspase
- peptidase
- protein structure
- ap, activation peptide
- card, caspase recruitment domain
- chf, caspase/haemoglobinase fold
- cpd, cysteine peptidase domain
- csd, c-terminal subdomain
- dd, death domain
- ded, death effector domain
- insp6, myo-inositol hexakisphosphate
- lsam, legumain stabilization and activity modulation
- lsd1, lesion-simulating disease 1
- malt1, mucosa-associated lymphoid tissue translocation protein 1
- martx, multi-functional, autoprocessing repeat in toxin
- rmsd, root-mean-square deviation
- sse, secondary structural element
- xiap, x-linked inhibitor of apoptosis
- z-vrpr-fmk, benzoxycarbonyl-val-arg-pro-arg-fluoromethylketone
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Affiliation(s)
- Karen McLuskey
- *Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Jeremy C. Mottram
- *Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
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28
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Dolores JS, Agarwal S, Egerer M, Satchell KJF. Vibrio cholerae MARTX toxin heterologous translocation of beta-lactamase and roles of individual effector domains on cytoskeleton dynamics. Mol Microbiol 2015; 95:590-604. [PMID: 25427654 DOI: 10.1111/mmi.12879] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2014] [Indexed: 12/17/2022]
Abstract
The Vibrio cholerae MARTXVc toxin delivers three effector domains to eukaryotic cells. To study toxin delivery and function of individual domains, the rtxA gene was modified to encode toxin with an in-frame beta-lactamase (Bla) fusion. The hybrid RtxA::Bla toxin was Type I secreted from bacteria; and then Bla was translocated into eukaryotic cells and delivered by autoprocessing, demonstrating that the MARTXVc toxin is capable of heterologous protein transfer. Strains that produce hybrid RtxA::Bla toxins that carry one effector domain in addition to Bla were found to more efficiently translocate Bla. In cell biological assays, the actin cross-linking domain (ACD) and Rho-inactivation domain (RID) are found to cross-link actin and inactivate RhoA, respectively, when other effector domains are absent, with toxin autoprocessing required for high efficiency. The previously unstudied alpha-beta hydrolase domain (ABH) is shown here to activate CDC42, although the effect is ameliorated when RID is also present. Despite all effector domains acting on cytoskeleton assembly, the ACD was sufficient to rapidly inhibit macrophage phagocytosis. Both the ACD and RID independently disrupted polarized epithelial tight junction integrity. The sufficiency of ACD but strong selection for retention of RID and ABH suggests these two domains may primarily function by modulating cell signaling.
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Affiliation(s)
- Jazel S Dolores
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
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29
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Human defensins facilitate local unfolding of thermodynamically unstable regions of bacterial protein toxins. Immunity 2014; 41:709-21. [PMID: 25517613 DOI: 10.1016/j.immuni.2014.10.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/17/2014] [Indexed: 02/08/2023]
Abstract
Defensins are short cationic, amphiphilic, cysteine-rich peptides that constitute the front-line immune defense against various pathogens. In addition to exerting direct antibacterial activities, defensins inactivate several classes of unrelated bacterial exotoxins. To date, no coherent mechanism has been proposed to explain defensins' enigmatic efficiency toward various toxins. In this study, we showed that binding of neutrophil ?-defensin HNP1 to affected bacterial toxins caused their local unfolding, potentiated their thermal melting and precipitation, exposed new regions for proteolysis, and increased susceptibility to collisional quenchers without causing similar effects on tested mammalian structural and enzymatic proteins. Enteric ?-defensin HD5 and ?-defensin hBD2 shared similar toxin-unfolding effects with HNP1, albeit to different degrees. We propose that protein susceptibility to inactivation by defensins is contingent to their thermolability and conformational plasticity and that defensin-induced unfolding is a key element in the general mechanism of toxin inactivation by human defensins.
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30
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Gall DL, Ralph J, Donohue TJ, Noguera D. A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:12454-63. [PMID: 25232892 PMCID: PMC4207535 DOI: 10.1021/es503886d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Lignin biosynthesis occurs via radical coupling of guaiacyl and syringyl hydroxycinnamyl alcohol monomers (i.e., "monolignols") through chemical condensation with the growing lignin polymer. With each chain-extension step, monolignols invariably couple at their β-positions, generating chiral centers. Here, we report on activities of bacterial glutathione-S-transferase (GST) enzymes that cleave β-aryl ether bonds in lignin dimers that are composed of different monomeric units. Our data reveal that these sequence-related enzymes from Novosphingobium sp. strain PP1Y, Novosphingobium aromaticivorans strain DSM12444, and Sphingobium sp. strain SYK-6 have conserved functions as β-etherases, catalyzing cleavage of each of the four dimeric α-keto-β-aryl ether-linked substrates (i.e., guaiacyl-β-guaiacyl, guaiacyl-β-syringyl, syringyl-β-guaiacyl, and syringyl-β-syringyl). Although each β-etherase cleaves β-guaiacyl and β-syringyl substrates, we have found that each is stereospecific for a given β-enantiomer in a racemic substrate; LigE and LigP β-etherase homologues exhibited stereospecificity toward β(R)-enantiomers whereas LigF and its homologues exhibited β(S)-stereospecificity. Given the diversity of lignin's monomeric units and the racemic nature of lignin polymers, we propose that bacterial catabolic pathways have overcome the existence of diverse lignin-derived substrates in nature by evolving multiple enzymes with broad substrate specificities. Thus, each bacterial β-etherase is able to cleave β-guaiacyl and β-syringyl ether-linked compounds while retaining either β(R)- or β(S)-stereospecificity.
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Affiliation(s)
- Daniel L. Gall
- Department
of Civil & Environmental Engineering, University of Wisconsin, Madison, Wisconsin 53706, United States
- U.S.
Department of Energy’s Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison Wisconsin 53726, United States
- Phone: 608-265-8465; e-mail:
| | - John Ralph
- U.S.
Department of Energy’s Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison Wisconsin 53726, United States
- Department
of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Timothy J. Donohue
- U.S.
Department of Energy’s Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison Wisconsin 53726, United States
- Department
of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Daniel
R. Noguera
- Department
of Civil & Environmental Engineering, University of Wisconsin, Madison, Wisconsin 53706, United States
- U.S.
Department of Energy’s Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison Wisconsin 53726, United States
- Environmental
Chemistry and Technology Program, University
of Wisconsin, Madison, Wisconsin 53706, United States
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31
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Screening of potent antibacterial agents targeting Clostridium difficile virulence factor toxin B: an in silico approach. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Antic I, Biancucci M, Satchell KJF. Cytotoxicity of the Vibrio vulnificus MARTX toxin effector DUF5 is linked to the C2A subdomain. Proteins 2014; 82:2643-56. [PMID: 24935440 DOI: 10.1002/prot.24628] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/02/2014] [Accepted: 06/11/2014] [Indexed: 12/19/2022]
Abstract
The multifunctional-autoprocessing repeats-in-toxin (MARTX) toxins are bacterial protein toxins that serve as delivery platforms for cytotoxic effector domains. The domain of unknown function in position 5 (DUF5) effector domain is present in at least six different species' MARTX toxins and as a hypothetical protein in Photorhabdus spp. Its presence increases the potency of the Vibrio vulnificus MARTX toxin in mouse virulence studies, indicating DUF5 directly contributes to pathogenesis. In this work, DUF5 is shown to be cytotoxic when transiently expressed in HeLa cells. DUF5 localized to the plasma membrane dependent upon its C1 domain and the cells become rounded dependent upon its C2 domain. Both full-length DUF5 and the C2 domain caused growth inhibition when expressed in Saccharomyces cerevisiae. A structural model of DUF5 was generated based on the structure of Pasteurella multocida toxin facilitating localization of the cytotoxic activity to a 186 amino acid subdomain termed C2A. Within this subdomain, an alanine scanning mutagenesis revealed aspartate-3721 and arginine-3841 as residues critical for cytotoxicity. These residues were also essential for HeLa cell intoxication when purified DUF5 fused to anthrax toxin lethal factor was delivered cytosolically. Thermal shift experiments indicated that these conserved residues are important to maintain protein structure, rather than for catalysis. The Aeromonas hydrophila MARTX toxin DUF5(Ah) domain was also cytotoxic, while the weakly conserved C1-C2 domains from P. multocida toxin were not. Overall, this study is the first demonstration that DUF5 as found in MARTX toxins has cytotoxic activity that depends on conserved residues in the C2A subdomain.
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Affiliation(s)
- Irena Antic
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611
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Kudryashova E, Heisler D, Zywiec A, Kudryashov DS. Thermodynamic properties of the effector domains of MARTX toxins suggest their unfolding for translocation across the host membrane. Mol Microbiol 2014; 92:1056-71. [PMID: 24724536 DOI: 10.1111/mmi.12615] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2014] [Indexed: 11/28/2022]
Abstract
MARTX (multifunctional autoprocessing repeats-in-toxin) family toxins are produced by Vibrio cholerae, Vibrio vulnificus, Aeromonas hydrophila and other Gram-negative bacteria. Effector domains of MARTX toxins cross the cytoplasmic membrane of a host cell through a putative pore formed by the toxin's glycine-rich repeats. The structure of the pore is unknown and the translocation mechanism of the effector domains is poorly understood. We examined the thermodynamic stability of the effector domains of V. cholerae and A. hydrophila MARTX toxins to elucidate the mechanism of their translocation. We found that all but one domain in each toxin are thermodynamically unstable and several acquire a molten globule state near human physiological temperatures. Fusion of the most stable cysteine protease domain to the adjacent effector domain reduces its thermodynamic stability ∼ 1.4-fold (from D G H 2 O 21.8 to 16.1 kJ mol(-1) ). Precipitation of several individual domains due to thermal denaturation is reduced upon their fusion into multi-domain constructs. We speculate that low thermostability of the MARTX effector domains correlates with that of many other membrane-penetrating toxins and implies their unfolding for cell entry. This study extends the list of thermolabile bacterial toxins, suggesting that this quality is essential and could be susceptible for selective targeting of pathogenic toxins.
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Affiliation(s)
- Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
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34
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Gall DL, Kim H, Lu F, Donohue TJ, Noguera DR, Ralph J. Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway. J Biol Chem 2014; 289:8656-67. [PMID: 24509858 PMCID: PMC3961688 DOI: 10.1074/jbc.m113.536250] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Glutathione-dependent enzymes play important protective, repair, or metabolic roles in cells. In particular, enzymes in the glutathione S-transferase (GST) superfamily function in stress responses, defense systems, or xenobiotic detoxification. Here, we identify novel features of bacterial GSTs that cleave β-aryl ether bonds typically found in plant lignin. Our data reveal several original features of the reaction cycle of these GSTs, including stereospecific substrate recognition and stereoselective formation of β-S-thioether linkages. Products of recombinant GSTs (LigE, LigP, and LigF) are β-S-glutathionyl-α-keto-thioethers that are degraded by a β-S-thioetherase (LigG). All three Lig GSTs produced the ketone product (β-S-glutathionyl-α-veratrylethanone) from an achiral side chain-truncated model substrate (β-guaiacyl-α-veratrylethanone). However, when β-etherase assays were conducted with a racemic model substrate, β-guaiacyl-α-veratrylglycerone, LigE- or LigP-catalyzed reactions yielded only one of two potential product (β-S-glutathionyl-α-veratrylglycerone) epimers, whereas the other diastereomer (differing in configuration at the β-position (i.e. its β-epimer)) was produced only in the LigF-catalyzed reaction. Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF). Further, LigG catalyzed glutathione-dependent β-S-thioether cleavage with β-S-glutathionyl-α-veratrylethanone and with β(R)-configured β-S-glutathionyl-α-veratrylglycerone but exhibited no or significantly reduced β-S-thioether-cleaving activity with the β(S)-epimer, demonstrating that LigG is a stereospecific β-thioetherase. We therefore propose that multiple Lig enzymes are needed in this β-aryl etherase pathway in order to cleave the racemic β-ether linkages that are present in the backbone of the lignin polymer.
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Affiliation(s)
- Daniel L Gall
- From the Departments of Civil and Environmental Engineering
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35
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Abstract
The development of affinity tags has greatly simplified protein purification procedures. A variety of affinity tags are now available to improve expression, solubility, and/or tag removal. In this chapter, we describe a method for purifying recombinant proteins expressed in Escherichia coli that uses a highly specific, inducible, C-terminal autoprocessing protease tag. This method streamlines affinity purification, cleavage, and tag separation into a one-step purification procedure, avoiding the need to remove fusion tags from target proteins with exogenous proteases. In addition to accelerating protein purification, we show that this method can enhance the expression, stability, and solubility of select proteins.
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Affiliation(s)
- Aimee Shen
- Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, VT, 05405, USA,
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36
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Miyoshi SI. Extracellular proteolytic enzymes produced by human pathogenic vibrio species. Front Microbiol 2013; 4:339. [PMID: 24302921 PMCID: PMC3831164 DOI: 10.3389/fmicb.2013.00339] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/26/2013] [Indexed: 12/19/2022] Open
Abstract
Bacteria in the genus Vibrio produce extracellular proteolytic enzymes to obtain nutrients via digestion of various protein substrates. However, the enzymes secreted by human pathogenic species have been documented to modulate the bacterial virulence. Several species including Vibrio cholerae and V. vulnificus are known to produce thermolysin-like metalloproteases termed vibriolysin. The vibriolysin from V. vulnificus, a causative agent of serious systemic infection, is a major toxic factor eliciting the secondary skin damage characterized by formation of the hemorrhagic brae. The vibriolysin from intestinal pathogens may play indirect roles in pathogenicity because it can activate protein toxins and hemagglutinin by the limited proteolysis and can affect the bacterial attachment to or detachment from the intestinal surface by degradation of the mucus layer. Two species causing wound infections, V. alginolyticus and V. parahaemolyticus, produce another metalloproteases so-called collagenases. Although the detailed pathological roles have not been studied, the collagenase is potent to accelerate the bacterial dissemination through digestion of the protein components of the extracellular matrix. Some species produce cymotrypsin-like serine proteases, which may also affect the bacterial virulence potential. The intestinal pathogens produce sufficient amounts of the metalloprotease at the small intestinal temperature; however, the metalloprotease production by extra-intestinal pathogens is much higher around the body surface temperature. On the other hand, the serine protease is expressed only in the absence of the metalloprotease.
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Affiliation(s)
- Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Okayama, Japan
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37
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Machado MF, Marcondes MF, Juliano MA, McLuskey K, Mottram JC, Moss CX, Juliano L, Oliveira V. Substrate specificity and the effect of calcium on Trypanosoma brucei metacaspase 2. FEBS J 2013; 280:2608-21. [PMID: 23506317 PMCID: PMC3779824 DOI: 10.1111/febs.12248] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/19/2013] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
Abstract
Metacaspases are cysteine peptidases found only in yeast, plants and lower eukaryotes, including the protozoa. To investigate the extended substrate specificity and effects of Ca(2+) on the activation of these enzymes, detailed kinetic, biochemical and structural analyses were carried out on metacaspase 2 from Trypanosoma brucei (TbMCA2). These results reveal that TbMCA2 has an unambiguous preference for basic amino acids at the P1 position of peptide substrates and that this is most probably a result of hydrogen bonding from the P1 residue to Asp95 and Asp211 in TbMCA2. In addition, TbMCA2 also has a preference for charged residues at the P2 and P3 positions and for small residues at the prime side of a peptide substrate. Studies into the effects of Ca(2+) on the enzyme revealed the presence of two Ca(2+) binding sites and a reversible structural modification of the enzyme upon Ca(2+) binding. In addition, the concentration of Ca(2+) used for activation of TbMCA2 was found to produce a differential effect on the activity of TbMCA2, but only when a series of peptides that differed in P2 were examined, suggesting that Ca(2+) activation of TbMCA2 has a structural effect on the enzyme in the vicinity of the S2 binding pocket. Collectively, these data give new insights into the substrate specificity and Ca(2+) activation of TbMCA2. This provides important functional details and leads to a better understanding of metacaspases, which are known to play an important role in trypanosomes and make attractive drug targets due to their absence in humans.
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Affiliation(s)
- Maurício F.M. Machado
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669 – 7° andar, São Paulo, Brazil
| | - Marcelo F. Marcondes
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669 – 7° andar, São Paulo, Brazil
| | - Maria A. Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669 – 7° andar, São Paulo, Brazil
| | - Karen McLuskey
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Jeremy C. Mottram
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Catherine X. Moss
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Luiz Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669 – 7° andar, São Paulo, Brazil
| | - Vitor Oliveira
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669 – 7° andar, São Paulo, Brazil
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Analysis of Vibrio cholerae genome sequences reveals unique rtxA variants in environmental strains and an rtxA-null mutation in recent altered El Tor isolates. mBio 2013; 4:e00624. [PMID: 23592265 PMCID: PMC3634609 DOI: 10.1128/mbio.00624-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Vibrio cholerae genome sequences were analyzed for variation in the rtxA gene that encodes the multifunctional autoprocessing RTX (MARTX) toxin. To accommodate genomic analysis, a discrepancy in the annotated rtxA start site was resolved experimentally. The correct start site is an ATG downstream from rtxC resulting in a gene of 13,638 bp and deduced protein of 4,545 amino acids. Among the El Tor O1 and closely related O139 and O37 genomes, rtxA was highly conserved, with nine alleles differing by only 1 to 6 nucleotides in 100 years. In contrast, 12 alleles from environment-associated isolates are highly variable, at 1 to 3% by nucleotide and 3 to 7% by amino acid. The difference in variation rates did not represent a bias for conservation of the El Tor rtxA compared to that of other strains but rather reflected the lack of gene variation in overall genomes. Three alleles were identified that would affect the function of the MARTX toxin. Two environmental isolates carry novel arrangements of effector domains. These include a variant from RC385 that would suggest an adenylate cyclase toxin and from HE-09 that may have actin ADP-ribosylating activity. Within the recently emerged altered El Tor strains that have a classical ctxB gene, a mutation arose in rtxA that introduces a premature stop codon that disabled toxin function. This null mutant is the genetic background for subsequent emergence of the ctxB7 allele resulting in the strain that spread into Haiti in 2010. Thus, similar to classical strains, the altered El Tor pandemic strains eliminated rtxA after acquiring a classical ctxB. IMPORTANCE Pathogen evolution involves both gain and loss of factors that influence disease. In the environment, bacteria evolve rapidly, with nucleotide diversity arising by genetic modification. Such is occurring with Vibrio cholerae, exemplified by extensive diversity and unique variants of the rtxA-encoded multifunctional autoprocessing RTX (MARTX) toxin among environment-associated strains that cause localized diarrheal outbreaks and food-borne disease. In contrast, seventh pandemic El Tor V. cholerae strains associated with severe diarrhea have changed minimally until the altered El Tor emerged as the most frequent cause of cholera, including in the 2010 Haiti epidemic. These strains have increased virulence attributed to a new variant of the major virulence factor, cholera toxin. It is revealed that these strains also have an inactivated MARTX toxin gene. A similar inactivation occurred during classical cholera pandemics, highlighting that evolution of El Tor cholera is following a similar path of increased dependence on cholera toxin, while eliminating other secreted factors.
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39
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Hor LI, Chen CL. Cytotoxins of Vibrio vulnificus: Functions and roles in pathogenesis. Biomedicine (Taipei) 2013. [DOI: 10.1016/j.biomed.2012.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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40
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Merdanovic M, Mönig T, Ehrmann M, Kaiser M. Diversity of allosteric regulation in proteases. ACS Chem Biol 2013. [PMID: 23181429 DOI: 10.1021/cb3005935] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Allostery is a fundamental regulatory mechanism that is based on a functional modulation of a site by a distant site. Allosteric regulation can be triggered by binding of diverse allosteric effectors, ranging from small molecules to macromolecules, and is therefore offering promising opportunities for functional modulation in a wide range of applications including the development of chemical probes or drug discovery. Here, we provide an overview of key classes of allosteric protease effectors, their corresponding molecular mechanisms, and their practical implications.
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Affiliation(s)
- Melisa Merdanovic
- Department of Microbiology
II and ‡Department
of Chemical Biology, Center for Medical Biotechnology,
Faculty of Biology, University of Duisburg-Essen, Universtitätsstr.
2, 45117 Essen, Germany
| | - Timon Mönig
- Department of Microbiology
II and ‡Department
of Chemical Biology, Center for Medical Biotechnology,
Faculty of Biology, University of Duisburg-Essen, Universtitätsstr.
2, 45117 Essen, Germany
| | - Michael Ehrmann
- Department of Microbiology
II and ‡Department
of Chemical Biology, Center for Medical Biotechnology,
Faculty of Biology, University of Duisburg-Essen, Universtitätsstr.
2, 45117 Essen, Germany
| | - Markus Kaiser
- Department of Microbiology
II and ‡Department
of Chemical Biology, Center for Medical Biotechnology,
Faculty of Biology, University of Duisburg-Essen, Universtitätsstr.
2, 45117 Essen, Germany
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41
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Ahrens S, Geissler B, Satchell KJF. Identification of a His-Asp-Cys catalytic triad essential for function of the Rho inactivation domain (RID) of Vibrio cholerae MARTX toxin. J Biol Chem 2012. [PMID: 23184949 DOI: 10.1074/jbc.m112.396309] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vibrio cholerae is the causative agent of the severe diarrheal disease cholera. For V. cholerae to colonize the intestinal epithelium, accessory toxins such as the multifunctional autoprocessing repeats-in-toxin (MARTX(Vc)) toxin are required. MARTX toxins are composite toxins comprised of arrayed effector domains that carry out distinct functions inside the host cell. Among the three effector domains of MARTX(Vc) is the Rho inactivation domain (RID(Vc)) known to cause cell rounding through inactivation of small RhoGTPases. Using alanine scanning mutagenesis in the activity subdomain of RID(Vc), four residues, His-2782, Leu-2851, Asp-2854, and Cys-3022, were identified as impacting RID(Vc) function in depolymerization of the actin cytoskeleton and inactivation of RhoA. Tyr-2807 and Tyr-3015 were identified as important potentially for forming the active structure for substrate contact but are not involved in catalysis or post translational modifications. Finally, V. cholerae strains modified to carry a catalytically inactive RID(Vc) show that the rate and efficiency of MARTX(Vc) actin cross-linking activity does not depend on a functional RID(Vc), demonstrating that these domains function independently in actin depolymerization. Overall, our results indicate a His-Asp-Cys catalytic triad is essential for function of the RID effector domain family shared by MARTX toxins produced by many Gram-negative bacteria.
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Affiliation(s)
- Sebastian Ahrens
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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42
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Abstract
Metacaspases are distantly related caspase-family cysteine peptidases implicated in programmed cell death in plants and lower eukaryotes. They differ significantly from caspases because they are calcium-activated, arginine-specific peptidases that do not require processing or dimerization for activity. To elucidate the basis of these differences and to determine the impact they might have on the control of cell death pathways in lower eukaryotes, the previously undescribed crystal structure of a metacaspase, an inactive mutant of metacaspase 2 (MCA2) from Trypanosoma brucei, has been determined to a resolution of 1.4 Å. The structure comprises a core caspase fold, but with an unusual eight-stranded β-sheet that stabilizes the protein as a monomer. Essential aspartic acid residues, in the predicted S1 binding pocket, delineate the arginine-specific substrate specificity. In addition, MCA2 possesses an unusual N terminus, which encircles the protein and traverses the catalytic dyad, with Y31 acting as a gatekeeper residue. The calcium-binding site is defined by samarium coordinated by four aspartic acid residues, whereas calcium binding itself induces an allosteric conformational change that could stabilize the active site in a fashion analogous to subunit processing in caspases. Collectively, these data give insights into the mechanistic basis of substrate specificity and mode of activation of MCA2 and provide a detailed framework for understanding the role of metacaspases in cell death pathways of lower eukaryotes.
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43
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Ivarsson ME, Leroux JC, Castagner B. Targeting bacterial toxins. Angew Chem Int Ed Engl 2012; 51:4024-45. [PMID: 22441768 DOI: 10.1002/anie.201104384] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/21/2011] [Indexed: 12/18/2022]
Abstract
Protein toxins constitute the main virulence factors of several species of bacteria and have proven to be attractive targets for drug development. Lead candidates that target bacterial toxins range from small molecules to polymeric binders, and act at each of the multiple steps in the process of toxin-mediated pathogenicity. Despite recent and significant advances in the field, a rationally designed drug that targets toxins has yet to reach the market. This Review presents the state of the art in bacterial toxin targeted drug development with a critical consideration of achieved breakthroughs and withstanding challenges. The discussion focuses on A-B-type protein toxins secreted by four species of bacteria, namely Clostridium difficile (toxins A and B), Vibrio cholerae (cholera toxin), enterohemorrhagic Escherichia coli (Shiga toxin), and Bacillus anthracis (anthrax toxin), which are the causative agents of diseases for which treatments need to be improved.
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Affiliation(s)
- Mattias E Ivarsson
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zurich, Wolfgang-Pauli-Strasse 10, Zurich, Switzerland
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44
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45
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Shen A. Clostridium difficile toxins: mediators of inflammation. J Innate Immun 2012; 4:149-58. [PMID: 22237401 DOI: 10.1159/000332946] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 09/06/2011] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile is a significant problem in hospital settings as the most common cause of nosocomial diarrhea worldwide. C. difficile infections (CDIs) are characterized by an acute intestinal inflammatory response with neutrophil infiltration. These symptoms are primarily caused by the glucosylating toxins, TcdA and TcdB. In the past decade, the frequency and severity of CDIs have increased markedly due to the emergence of so-called hypervirulent strains that overproduce cytotoxic glucosylating toxins relative to historical strains. In addition, these strains produce a third toxin, binary toxin or C. difficile transferase (CDT), that may contribute to hypervirulence. Both the glucosylating toxins and CDT covalently modify target cell proteins to cause disassembly of the actin cytoskeleton and induce severe inflammation. This review summarizes our current knowledge of the mechanisms by which glucosylating toxins and CDT disrupt target cell function, alter host physiology and stimulate immune responses.
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Affiliation(s)
- Aimee Shen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vt. 05401, USA.
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46
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Deu E, Verdoes M, Bogyo M. New approaches for dissecting protease functions to improve probe development and drug discovery. Nat Struct Mol Biol 2012; 19:9-16. [PMID: 22218294 DOI: 10.1038/nsmb.2203] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteases are well-established targets for pharmaceutical development because of their known enzymatic mechanism and their regulatory roles in many pathologies. However, many potent clinical lead compounds have been unsuccessful either because of a lack of specificity or because of our limited understanding of the biological roles of the targeted protease. In order to successfully develop protease inhibitors as drugs, it is necessary to understand protease functions and to expand the platform of inhibitor development beyond active site-directed design and in vitro optimization. Several newly developed technologies will enhance assessment of drug selectivity in living cells and animal models, allowing researchers to focus on compounds with high specificity and minimal side effects in vivo. In this review, we highlight advances in the development of chemical probes, proteomic methods and screening tools that we feel will help facilitate this paradigm shift in drug discovery.
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Affiliation(s)
- Edgar Deu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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47
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Satchell KJ. Structure and Function of MARTX Toxins and Other Large Repetitive RTX Proteins. Annu Rev Microbiol 2011; 65:71-90. [DOI: 10.1146/annurev-micro-090110-102943] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Karla J.F. Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611;
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48
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Tam Dang TH, Fagan RP, Fairweather NF, Tate EW. Novel inhibitors of surface layer processing in Clostridium difficile. Bioorg Med Chem 2011; 20:614-21. [PMID: 21752656 DOI: 10.1016/j.bmc.2011.06.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 04/20/2011] [Accepted: 06/14/2011] [Indexed: 01/05/2023]
Abstract
Clostridium difficile, a leading cause of hospital-acquired bacterial infection, is coated in a dense surface layer (S-layer) that is thought to provide both physicochemical protection and a scaffold for host-pathogen interactions. The key structural components of the S-layer are two proteins derived from a polypeptide precursor, SlpA, via proteolytic cleavage by the protease Cwp84. Here, we report the design, synthesis and in vivo characterization of a panel of protease inhibitors and activity-based probes (ABPs) designed to target S-layer processing in live C. difficile cells. Inhibitors based on substrate-mimetic peptides bearing a C-terminal Michael acceptor warhead were found to be promising candidates for further development.
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Affiliation(s)
- T H Tam Dang
- Department of Chemistry, Imperial College London, London SW72AZ, United Kingdom
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49
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Abstract
Bacteria of the genus Vibrio are normal habitants of the aquatic environment but the some species are believed to be human pathogens. Pathogenic vibrios produce various pathogenic factors, and the proteases are also recognized to play pathogenic roles in the infection: the direct roles by digesting many kinds of host proteins or indirect roles by processing other pathogenic protein factors. Especially VVP from Vibrio vulnificus is thought to be a major pathogenic factor of the vibrio. Although HA/P, the V. cholerae hemagglutinin/protease, is not a direct toxic factor of cholera vibrio, its significance is an undeniable fact. Production of HA/P is regulated together with major pathogenic factors such as CT (cholera toxin) or TCP (toxin co-regulated pilus) by a quorum-sensing system. HA/P is necessary for full expression of pathogenicity of the vibrio by supporting growth and translocation in the digestive tract. Processing of protein toxins such as CT or El Tor hemolysin is also an important pathogenic role.
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Affiliation(s)
- Sumio Shinoda
- Faculty of Science, Okayama University of Science, Okayama University of Science, Ridai-cho, Okayama 700-005, Japan.
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50
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Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB. ACTA ACUST UNITED AC 2011; 17:1201-11. [PMID: 21095570 DOI: 10.1016/j.chembiol.2010.09.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 09/30/2010] [Accepted: 09/30/2010] [Indexed: 01/05/2023]
Abstract
Clostridium difficile is a leading cause of nosocomial infections. The major virulence factors of this pathogen are the multi-domain toxins TcdA and TcdB. These toxins contain a cysteine protease domain (CPD) that autoproteolytically releases a cytotoxic effector domain upon binding intracellular inositol hexakisphosphate. Currently, there are no known inhibitors of this protease. Here, we describe the rational design of covalent small molecule inhibitors of TcdB CPD. We identified compounds that inactivate TcdB holotoxin function in cells and solved the structure of inhibitor-bound protease to 2.0 Å. This structure reveals the molecular basis of CPD substrate recognition and informed the synthesis of activity-based probes for this enzyme. The inhibitors presented will guide the development of therapeutics targeting C. difficile, and the probes will serve as tools for studying the unique activation mechanism of bacterial toxin CPDs.
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