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Niedzialkowska E, Runyan LA, Kudryashova E, Egelman EH, Kudryashov DS. Stabilization of F-actin by Salmonella effector SipA resembles the structural effects of inorganic phosphate and phalloidin. Structure 2024; 32:725-738.e8. [PMID: 38518780 PMCID: PMC11162321 DOI: 10.1016/j.str.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/08/2024] [Accepted: 02/26/2024] [Indexed: 03/24/2024]
Abstract
Entry of Salmonella into host enterocytes relies on its pathogenicity island 1 effector SipA. We found that SipA binds to F-actin in a 1:2 stoichiometry with sub-nanomolar affinity. A cryo-EM reconstruction revealed that SipA's globular core binds at the groove between actin strands, whereas the extended C-terminal arm penetrates deeply into the inter-strand space, stabilizing F-actin from within. The unusually strong binding of SipA is achieved by a combination of fast association via the core and very slow dissociation dictated by the arm. Similar to Pi, BeF3, and phalloidin, SipA potently inhibited actin depolymerization by actin depolymerizing factor (ADF)/cofilin, which correlated with increased filament stiffness, supporting the hypothesis that F-actin's mechanical properties contribute to the recognition of its nucleotide state by protein partners. The remarkably strong binding to F-actin maximizes the toxin's effects at the injection site while minimizing global influence on the cytoskeleton and preventing pathogen detection by the host cell.
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Affiliation(s)
- Ewa Niedzialkowska
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lucas A Runyan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
| | - Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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2
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Niedzialkowska E, Runyan LA, Kudryashova E, Egelman EH, Kudryashov DS. Stabilization of F-actin by Salmonella effector SipA resembles the structural effects of inorganic phosphate and phalloidin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573373. [PMID: 38234808 PMCID: PMC10793455 DOI: 10.1101/2023.12.26.573373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Entry of Salmonella into host enterocytes strictly relies on its pathogenicity island 1 effector SipA. We found that SipA binds to F-actin in a unique mode in a 1:2 stoichiometry with picomolar affinity. A cryo-EM reconstruction revealed that SipA's globular core binds at the grove between actin strands, whereas the extended C-terminal arm penetrates deeply into the inter-strand space, stabilizing F-actin from within. The unusually strong binding of SipA is achieved via a combination of fast association via the core and very slow dissociation dictated by the arm. Similarly to Pi, BeF3, and phalloidin, SipA potently inhibited actin depolymerization by ADF/cofilin, which correlated with the increased filament stiffness, supporting the hypothesis that F-actin's mechanical properties contribute to the recognition of its nucleotide state by protein partners. The remarkably strong binding to F-actin maximizes the toxin's effects at the injection site while minimizing global influence on the cytoskeleton and preventing pathogen detection by the host cell.
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Affiliation(s)
- Ewa Niedzialkowska
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lucas A. Runyan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Dmitri S. Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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3
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Zhao Z, Hu Y, Hu Y, White AP, Wang Y. Features and algorithms: facilitating investigation of secreted effectors in Gram-negative bacteria. Trends Microbiol 2023; 31:1162-1178. [PMID: 37349207 DOI: 10.1016/j.tim.2023.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Gram-negative bacteria deliver effector proteins through type III, IV, or VI secretion systems (T3SSs, T4SSs, and T6SSs) into host cells, causing infections and diseases. In general, effector proteins for each of these distinct secretion systems lack homology and are difficult to identify. Sequence analysis has disclosed many common features, helping us to understand the evolution, function, and secretion mechanisms of the effectors. In combination with various algorithms, the known common features have facilitated accurate prediction of new effectors. Ensemblers or integrated pipelines achieve a better prediction of performance, which combines multiple computational models or modules with multidimensional features. Natural language processing (NLP) models also show the merits, which could enable discovery of novel features and, in turn, facilitate more precise effector prediction, extending our knowledge about each secretion mechanism.
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Affiliation(s)
- Ziyi Zhao
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen 518060, China
| | - Yixue Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen 518060, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Aaron P White
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen 518060, China; Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen 518060, China.
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4
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Meir A, Macé K, Vegunta Y, Williams SM, Waksman G. Substrate recruitment mechanism by gram-negative type III, IV, and VI bacterial injectisomes. Trends Microbiol 2023; 31:916-932. [PMID: 37085348 DOI: 10.1016/j.tim.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/23/2023]
Abstract
Bacteria use a wide arsenal of macromolecular substrates (DNA and proteins) to interact with or infect prokaryotic and eukaryotic cells. To do so, they utilize substrate-injecting secretion systems or injectisomes. However, prior to secretion, substrates must be recruited to specialized recruitment platforms and then handed over to the secretion apparatus for secretion. In this review, we provide an update on recent advances in substrate recruitment and delivery by gram-negative bacterial recruitment platforms associated with Type III, IV, and VI secretion systems.
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Affiliation(s)
- Amit Meir
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK; Current address: MRC Centre for Virus Research, School of Infection and Immunity, University of Glasgow, Glasgow, UK.
| | - Kévin Macé
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Yogesh Vegunta
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Sunanda M Williams
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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5
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Pillay TD, Hettiarachchi SU, Gan J, Diaz-Del-Olmo I, Yu XJ, Muench JH, Thurston TL, Pearson JS. Speaking the host language: how Salmonella effector proteins manipulate the host. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001342. [PMID: 37279149 PMCID: PMC10333799 DOI: 10.1099/mic.0.001342] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023]
Abstract
Salmonella injects over 40 virulence factors, termed effectors, into host cells to subvert diverse host cellular processes. Of these 40 Salmonella effectors, at least 25 have been described as mediating eukaryotic-like, biochemical post-translational modifications (PTMs) of host proteins, altering the outcome of infection. The downstream changes mediated by an effector's enzymatic activity range from highly specific to multifunctional, and altogether their combined action impacts the function of an impressive array of host cellular processes, including signal transduction, membrane trafficking, and both innate and adaptive immune responses. Salmonella and related Gram-negative pathogens have been a rich resource for the discovery of unique enzymatic activities, expanding our understanding of host signalling networks, bacterial pathogenesis as well as basic biochemistry. In this review, we provide an up-to-date assessment of host manipulation mediated by the Salmonella type III secretion system injectosome, exploring the cellular effects of diverse effector activities with a particular focus on PTMs and the implications for infection outcomes. We also highlight activities and functions of numerous effectors that remain poorly characterized.
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Affiliation(s)
- Timesh D. Pillay
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Sahampath U. Hettiarachchi
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Jiyao Gan
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Ines Diaz-Del-Olmo
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
| | - Xiu-Jun Yu
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
| | - Janina H. Muench
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Teresa L.M. Thurston
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Jaclyn S. Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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6
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Godlee C, Holden DW. Transmembrane substrates of type three secretion system injectisomes. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001292. [PMID: 36748571 PMCID: PMC9993115 DOI: 10.1099/mic.0.001292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The type three secretion system injectisome of Gram-negative bacterial pathogens injects virulence proteins, called effectors, into host cells. Effectors of mammalian pathogens carry out a range of functions enabling bacterial invasion, replication, immune suppression and transmission. The injectisome secretes two translocon proteins that insert into host cell membranes to form a translocon pore, through which effectors are delivered. A subset of effectors also integrate into infected cell membranes, enabling a unique range of biochemical functions. Both translocon proteins and transmembrane effectors avoid cytoplasmic aggregation and integration into the bacterial inner membrane. Translocated transmembrane effectors locate and integrate into the appropriate host membrane. In this review, we focus on transmembrane translocon proteins and effectors of bacterial pathogens of mammals. We discuss what is known about the mechanisms underlying their membrane integration, as well as the functions conferred by the position of injectisome effectors within membranes.
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Affiliation(s)
- Camilla Godlee
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
- Present address: Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
- *Correspondence: Camilla Godlee, ;
| | - David W. Holden
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
- *Correspondence: David W. Holden,
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7
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Yahalom A, Shaked H, Ruthstein S, Chill JH. Inherent Minor Conformer of Bordetella Effector BteA Directs Chaperone-Mediated Unfolding. J Am Chem Soc 2022; 144:11553-11557. [PMID: 35749268 DOI: 10.1021/jacs.2c04122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The pathogen Bordetella pertussis uses a type-3 secretion system (T3SS) to inject its cytotoxic effector BteA into the host cell via a designated needle structure. Prior to injection BteA is bound to its cognate chaperone BtcA presumed to assist in effector unfolding en route to needle passage. We utilized NMR and EPR spectroscopy to uncover the molecular mechanism of BtcA-mediated unfolding of BteA. BtcA induces a global structural change in the effector, which adopts a more extended and partially unfolded conformation. EPR distance measurements further show that the structured helical-bundle form of free BteA exists in conformational equilibrium with a lowly populated minor species. The nature of this equilibrium was probed using NMR relaxation dispersion experiments. At 283 K structural effects are most pronounced for a contiguous surface spanning the A- and B-helices of BteA, extending at 303 K to a second surface including the D- and E-helices. Residues perturbed in the minor conformation coincide with those exhibiting a BtcA-induced increase in flexibility, identifying this conformation as the BtcA-bound form of the effector. Our findings hint at a conformational-selectivity mechanism for the chaperone interaction with the effector, a paradigm that may be common to effector-chaperones secretion complexes in this family of pathogens.
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Affiliation(s)
- Adi Yahalom
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Hadassa Shaked
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Sharon Ruthstein
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Jordan H Chill
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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Rahmatelahi H, El-Matbouli M, Menanteau-Ledouble S. Delivering the pain: an overview of the type III secretion system with special consideration for aquatic pathogens. Vet Res 2021; 52:146. [PMID: 34924019 PMCID: PMC8684695 DOI: 10.1186/s13567-021-01015-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
Gram-negative bacteria are known to subvert eukaryotic cell physiological mechanisms using a wide array of virulence factors, among which the type three-secretion system (T3SS) is often one of the most important. The T3SS constitutes a needle-like apparatus that the bacterium uses to inject a diverse set of effector proteins directly into the cytoplasm of the host cells where they can hamper the host cellular machinery for a variety of purposes. While the structure of the T3SS is somewhat conserved and well described, effector proteins are much more diverse and specific for each pathogen. The T3SS can remodel the cytoskeleton integrity to promote intracellular invasion, as well as silence specific eukaryotic cell signals, notably to hinder or elude the immune response and cause apoptosis. This is also the case in aquatic bacterial pathogens where the T3SS can often play a central role in the establishment of disease, although it remains understudied in several species of important fish pathogens, notably in Yersinia ruckeri. In the present review, we summarise what is known of the T3SS, with a special focus on aquatic pathogens and suggest some possible avenues for research including the potential to target the T3SS for the development of new anti-virulence drugs.
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Affiliation(s)
- Hadis Rahmatelahi
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Simon Menanteau-Ledouble
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria.
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Ø, Denmark.
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9
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Zhang Y, Liu Y, Luo J, Jie J, Deng X, Song L. The Herbal Compound Thymol Targets Multiple Salmonella Typhimurium Virulence Factors for Lon Protease Degradation. Front Pharmacol 2021; 12:674955. [PMID: 34512322 PMCID: PMC8427694 DOI: 10.3389/fphar.2021.674955] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/16/2021] [Indexed: 11/25/2022] Open
Abstract
Many important bacterial pathogens are using the type III secretion system to deliver effectors into host cells. Salmonella Typhimurium (S. Typhimurium) is a pathogenic Gram-negative bacterium with the type III secretion system as its major virulence factor. Our previous studies demonstrated that thymol, a monoterpene phenol derivative of cymene, inhibited S. Typhimurium invasion into mammalian cells and protected mice from infection. However, the antibacterial mechanism of thymol is not clear. In this study, we revealed that thymol interferes with the abundance of about 100 bacterial proteins through proteomic analysis. Among the 42 proteins whose abundance was reduced, 11 were important virulence factors associated with T3SS-1. Further analyses with SipA revealed that thymol directly interacts with this protein to induce conformational changes, which makes it susceptible to the Lon protease. In agreement with this observation, thymol effectively blocks cell invasion by S. Typhimurium. Thus, thymol represents a class of anti-virulence compounds that function by targeting pathogenic factors for degradation.
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Affiliation(s)
- Yong Zhang
- Department of Respiratory Medicine, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yan Liu
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jingjing Luo
- Department of Respiratory Medicine, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Jing Jie
- Department of Respiratory Medicine, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Xuming Deng
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Lei Song
- Department of Respiratory Medicine, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
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Abstract
Multiple gram-negative bacteria encode type III secretion systems (T3SS) that allow them to inject effector proteins directly into host cells to facilitate colonization. To be secreted, effector proteins must be at least partially unfolded to pass through the narrow needle-like channel (diameter <2 nm) of the T3SS. Fusion of effector proteins to tightly packed proteins-such as GFP, ubiquitin, or dihydrofolate reductase (DHFR)-impairs secretion and results in obstruction of the T3SS. Prior observation that unfolding can become rate-limiting for secretion has led to the model that T3SS effector proteins have low thermodynamic stability, facilitating their secretion. Here, we first show that the unfolding free energy ([Formula: see text]) of two Salmonella effector proteins, SptP and SopE2, are 6.9 and 6.0 kcal/mol, respectively, typical for globular proteins and similar to published [Formula: see text] for GFP, ubiquitin, and DHFR. Next, we mechanically unfolded individual SptP and SopE2 molecules by atomic force microscopy (AFM)-based force spectroscopy. SptP and SopE2 unfolded at low force (F unfold ≤ 17 pN at 100 nm/s), making them among the most mechanically labile proteins studied to date by AFM. Moreover, their mechanical compliance is large, as measured by the distance to the transition state (Δx ‡ = 1.6 and 1.5 nm for SptP and SopE2, respectively). In contrast, prior measurements of GFP, ubiquitin, and DHFR show them to be mechanically robust (F unfold > 80 pN) and brittle (Δx ‡ < 0.4 nm). These results suggest that effector protein unfolding by T3SS is a mechanical process and that mechanical lability facilitates efficient effector protein secretion.
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11
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Computational prediction of secreted proteins in gram-negative bacteria. Comput Struct Biotechnol J 2021; 19:1806-1828. [PMID: 33897982 PMCID: PMC8047123 DOI: 10.1016/j.csbj.2021.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022] Open
Abstract
Gram-negative bacteria harness multiple protein secretion systems and secrete a large proportion of the proteome. Proteins can be exported to periplasmic space, integrated into membrane, transported into extracellular milieu, or translocated into cytoplasm of contacting cells. It is important for accurate, genome-wide annotation of the secreted proteins and their secretion pathways. In this review, we systematically classified the secreted proteins according to the types of secretion systems in Gram-negative bacteria, summarized the known features of these proteins, and reviewed the algorithms and tools for their prediction.
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12
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Kamanova J. Bordetella Type III Secretion Injectosome and Effector Proteins. Front Cell Infect Microbiol 2020; 10:466. [PMID: 33014891 PMCID: PMC7498569 DOI: 10.3389/fcimb.2020.00466] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Pertussis, also known as whooping cough, is a resurging acute respiratory disease of humans primarily caused by the Gram-negative coccobacilli Bordetella pertussis, and less commonly by the human-adapted lineage of B. parapertussis HU. The ovine-adapted lineage of B. parapertussis OV infects only sheep, while B. bronchiseptica causes chronic and often asymptomatic respiratory infections in a broad range of mammals but rarely in humans. A largely overlapping set of virulence factors inflicts the pathogenicity of these bordetellae. Their genomes also harbor a pathogenicity island, named bsc locus, that encodes components of the type III secretion injectosome, and adjacent btr locus with the type III regulatory proteins. The Bsc injectosome of bordetellae translocates the cytotoxic BteA effector protein, also referred to as BopC, into the cells of the mammalian hosts. While the role of type III secretion activity in the persistent colonization of the lower respiratory tract by B. bronchiseptica is well recognized, the functionality of the type III secretion injectosome in B. pertussis was overlooked for many years due to the adaptation of laboratory-passaged B. pertussis strains. This review highlights the current knowledge of the type III secretion system in the so-called classical Bordetella species, comprising B. pertussis, B. parapertussis, and B. bronchiseptica, and discusses its functional divergence. Comparison with other well-studied bacterial injectosomes, regulation of the type III secretion on the transcriptional and post-transcriptional level, and activities of BteA effector protein and BopN protein, homologous to the type III secretion gatekeepers, are addressed.
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Affiliation(s)
- Jana Kamanova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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13
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Abstract
Many Gram-negative bacteria infect hosts and cause diseases by translocating a variety of type III secreted effectors (T3SEs) into the host cell cytoplasm. However, despite a dramatic increase in the number of available whole-genome sequences, it remains challenging for accurate prediction of T3SEs. Traditional prediction models have focused on atypical sequence features buried in the N-terminal peptides of T3SEs, but unfortunately, these models have had high false-positive rates. In this research, we integrated promoter information along with characteristic protein features for signal regions, chaperone-binding domains, and effector domains for T3SE prediction. Machine learning algorithms, including deep learning, were adopted to predict the atypical features mainly buried in signal sequences of T3SEs, followed by development of a voting-based ensemble model integrating the individual prediction results. We assembled this into a unified T3SE prediction pipeline, T3SEpp, which integrated the results of individual modules, resulting in high accuracy (i.e., ∼0.94) and >1-fold reduction in the false-positive rate compared to that of state-of-the-art software tools. The T3SEpp pipeline and sequence features observed here will facilitate the accurate identification of new T3SEs, with numerous benefits for future studies on host-pathogen interactions.IMPORTANCE Type III secreted effector (T3SE) prediction remains a big computational challenge. In practical applications, current software tools often suffer problems of high false-positive rates. One of the causal factors could be the relatively unitary type of biological features used for the design and training of the models. In this research, we made a comprehensive survey on the sequence-based features of T3SEs, including signal sequences, chaperone-binding domains, effector domains, and transcription factor binding promoter sites, and assembled a unified prediction pipeline integrating multi-aspect biological features within homology-based and multiple machine learning models. To our knowledge, we have compiled the most comprehensive biological sequence feature analysis for T3SEs in this research. The T3SEpp pipeline integrating the variety of features and assembling different models showed high accuracy, which should facilitate more accurate identification of T3SEs in new and existing bacterial whole-genome sequences.
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14
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Dorival J, Philys S, Giuntini E, Brailly R, de Ruyck J, Czjzek M, Biondi E, Bompard C. Structural and enzymatic characterisation of the Type III effector NopAA (=GunA) from Sinorhizobium fredii USDA257 reveals a Xyloglucan hydrolase activity. Sci Rep 2020; 10:9932. [PMID: 32555346 PMCID: PMC7303141 DOI: 10.1038/s41598-020-67069-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 04/28/2020] [Indexed: 12/03/2022] Open
Abstract
Rhizobia are nitrogen-fixing soil bacteria that can infect legume plants to establish root nodules symbiosis. To do that, a complex exchange of molecular signals occurs between plants and bacteria. Among them, rhizobial Nops (Nodulation outer proteins), secreted by a type III secretion system (T3SS) determine the host-specificity for efficient symbiosis with plant roots. Little is known about the molecular function of secreted Nops (also called effectors (T3E)) and their role in the symbiosis process. We performed the structure-function characterization of NopAA, a T3E from Sinorhizobium fredii by using a combination of X-ray crystallography, biochemical and biophysical approaches. This work displays for the first time a complete structural and biochemical characterization of a symbiotic T3E. Our results showed that NopAA has a catalytic domain with xyloglucanase activity extended by a N-terminal unfolded secretion domain that allows its secretion. We proposed that these original structural properties combined with the specificity of NopAA toward xyloglucan, a key component of root cell wall which is also secreted by roots in the soil, can give NopAA a strategic position to participate in recognition between bacteria and plant roots and to intervene in nodulation process.
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Affiliation(s)
- Jonathan Dorival
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, Bretagne, France
| | - Sonia Philys
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Elisa Giuntini
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Romain Brailly
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Jérôme de Ruyck
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Mirjam Czjzek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, Bretagne, France
| | | | - Coralie Bompard
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France.
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15
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Yahalom A, Davidov G, Kolusheva S, Shaked H, Barber-Zucker S, Zarivach R, Chill JH. Structure and membrane-targeting of a Bordetella pertussis effector N-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183054. [DOI: 10.1016/j.bbamem.2019.183054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/05/2019] [Accepted: 08/22/2019] [Indexed: 01/07/2023]
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16
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Borah SM, Jha AN. Identification and analysis of structurally critical fragments in HopS2. BMC Bioinformatics 2019; 19:552. [PMID: 30717655 PMCID: PMC7394326 DOI: 10.1186/s12859-018-2551-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/30/2018] [Indexed: 12/02/2022] Open
Abstract
Background Among the diverse roles of the Type III secretion-system (T3SS), one of the notable functions is that it serves as unique nano machineries in gram-negative bacteria that facilitate the translocation of effector proteins from bacteria into their host. These effector proteins serve as potential targets to control the pathogenicity conferred to the bacteria. Despite being ideal choices to disrupt bacterial systems, it has been quite an ordeal in the recent times to experimentally reveal and establish a concrete sequence-structure-function relationship for these effector proteins. This work focuses on the disease-causing spectrum of an effector protein, HopS2 secreted by the phytopathogen Pseudomonas syringae pv. tomato DC3000. Results The study addresses the structural attributes of HopS2 via a bioinformatics approach to by-pass some of the experimental shortcomings resulting in mining some critical regions in the effector protein. We have elucidated the functionally important regions of HopS2 with the assistance of sequence and structural analyses. The sequence based data supports the presence of important regions in HopS2 that are present in the other functional parts of Hop family proteins. Furthermore, these regions have been validated by an ab-initio structure prediction of the protein followed by 100 ns long molecular dynamics (MD) simulation. The assessment of these secondary structural regions has revealed the stability and importance of these regions in the protein structure. Conclusions The analysis has provided insights on important functional regions that may be vital to the effector functioning. In dearth of ample experimental evidence, such a bioinformatics approach has helped in the revelation of a few structural regions which will aid in future experiments to attain and evaluate the structural and functional aspects of this protein family. Electronic supplementary material The online version of this article (10.1186/s12859-018-2551-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sapna M Borah
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
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17
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Wang J, Li J, Yang B, Xie R, Marquez-Lago TT, Leier A, Hayashida M, Akutsu T, Zhang Y, Chou KC, Selkrig J, Zhou T, Song J, Lithgow T. Bastion3: a two-layer ensemble predictor of type III secreted effectors. Bioinformatics 2018; 35:2017-2028. [PMID: 30388198 PMCID: PMC7963071 DOI: 10.1093/bioinformatics/bty914] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/15/2018] [Accepted: 10/31/2018] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Type III secreted effectors (T3SEs) can be injected into host cell cytoplasm via type III secretion systems (T3SSs) to modulate interactions between Gram-negative bacterial pathogens and their hosts. Due to their relevance in pathogen-host interactions, significant computational efforts have been put toward identification of T3SEs and these in turn have stimulated new T3SE discoveries. However, as T3SEs with new characteristics are discovered, these existing computational tools reveal important limitations: (i) most of the trained machine learning models are based on the N-terminus (or incorporating also the C-terminus) instead of the proteins' complete sequences, and (ii) the underlying models (trained with classic algorithms) employed only few features, most of which were extracted based on sequence-information alone. To achieve better T3SE prediction, we must identify more powerful, informative features and investigate how to effectively integrate these into a comprehensive model. RESULTS In this work, we present Bastion3, a two-layer ensemble predictor developed to accurately identify type III secreted effectors from protein sequence data. In contrast with existing methods that employ single models with few features, Bastion3 explores a wide range of features, from various types, trains single models based on these features and finally integrates these models through ensemble learning. We trained the models using a new gradient boosting machine, LightGBM and further boosted the models' performances through a novel genetic algorithm (GA) based two-step parameter optimization strategy. Our benchmark test demonstrates that Bastion3 achieves a much better performance compared to commonly used methods, with an ACC value of 0.959, F-value of 0.958, MCC value of 0.917 and AUC value of 0.956, which comprehensively outperformed all other toolkits by more than 5.6% in ACC value, 5.7% in F-value, 12.4% in MCC value and 5.8% in AUC value. Based on our proposed two-layer ensemble model, we further developed a user-friendly online toolkit, maximizing convenience for experimental scientists toward T3SE prediction. With its design to ease future discoveries of novel T3SEs and improved performance, Bastion3 is poised to become a widely used, state-of-the-art toolkit for T3SE prediction. AVAILABILITY AND IMPLEMENTATION http://bastion3.erc.monash.edu/. CONTACT selkrig@embl.de or wyztli@163.com or or trevor.lithgow@monash.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiawei Wang
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Jiahui Li
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia,Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bingjiao Yang
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, China
| | - Ruopeng Xie
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, China
| | - Tatiana T Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, AL, USA,Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, AL, USA,Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - Morihiro Hayashida
- National Institute of Technology, Matsue College, Matsue, Shimane, Japan
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Yanju Zhang
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA, USA,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | | | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
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18
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Singh PK, Kapoor A, Lomash RM, Kumar K, Kamerkar SC, Pucadyil TJ, Mukhopadhyay A. Salmonella SipA mimics a cognate SNARE for host Syntaxin8 to promote fusion with early endosomes. J Cell Biol 2018; 217:4199-4214. [PMID: 30309979 PMCID: PMC6279372 DOI: 10.1083/jcb.201802155] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/17/2018] [Accepted: 09/18/2018] [Indexed: 01/06/2023] Open
Abstract
Intracellular pathogens can modulate host Rabs and SNAREs to support their replication and immune evasion. Singh et al. show that the Salmonella effector SipA functionally mimics an R-SNARE and recruits host Q-SNAREs to promote membrane fusion. Thus, SNARE mimicry by this intracellular pathogen effector modulates the host trafficking machinery for Salmonella survival. SipA is a major effector of Salmonella, which causes gastroenteritis and enteric fever. Caspase-3 cleaves SipA into two domains: the C-terminal domain regulates actin polymerization, whereas the function of the N terminus is unknown. We show that the cleaved SipA N terminus binds and recruits host Syntaxin8 (Syn8) to Salmonella-containing vacuoles (SCVs). The SipA N terminus contains a SNARE motif with a conserved arginine residue like mammalian R-SNAREs. SipAR204Q and SipA1–435R204Q do not bind Syn8, demonstrating that SipA mimics a cognate R-SNARE for Syn8. Consequently, Salmonella lacking SipA or that express the SipA1–435R204Q SNARE mutant are unable to recruit Syn8 to SCVs. Finally, we show that SipA mimicking an R-SNARE recruits Syn8, Syn13, and Syn7 to the SCV and promotes its fusion with early endosomes to potentially arrest its maturation. Our results reveal that SipA functionally substitutes endogenous SNAREs in order to hijack the host trafficking pathway and promote Salmonella survival.
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Affiliation(s)
| | - Anjali Kapoor
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | | | - Kamal Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
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19
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Formation of a Secretion-Competent Protein Complex by a Dynamic Wrap-around Binding Mechanism. J Mol Biol 2018; 430:3157-3169. [DOI: 10.1016/j.jmb.2018.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/20/2018] [Accepted: 07/10/2018] [Indexed: 11/18/2022]
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20
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Molecular basis for CesT recognition of type III secretion effectors in enteropathogenic Escherichia coli. PLoS Pathog 2018; 14:e1007224. [PMID: 30118511 PMCID: PMC6114900 DOI: 10.1371/journal.ppat.1007224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/29/2018] [Accepted: 07/17/2018] [Indexed: 11/19/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) use a needle-like injection apparatus known as the type III secretion system (T3SS) to deliver protein effectors into host cells. Effector translocation is highly stratified in EPEC with the translocated intimin receptor (Tir) being the first effector delivered into the host. CesT is a multi-cargo chaperone that is required for the secretion of Tir and at least 9 other effectors. However, the structural and mechanistic basis for differential effector recognition by CesT remains unclear. Here, we delineated the minimal CesT-binding region on Tir to residues 35–77 and determined the 2.74 Å structure of CesT bound to an N-terminal fragment of Tir. Our structure revealed that the CesT-binding region in the N-terminus of Tir contains an additional conserved sequence, distinct from the known chaperone-binding β-motif, that we termed the CesT-extension motif because it extends the β-sheet core of CesT. This motif is also present in the C-terminus of Tir that we confirmed to be a unique second CesT-binding region. Point mutations that disrupt CesT-binding to the N- or C-terminus of Tir revealed that the newly identified carboxy-terminal CesT-binding region was required for efficient Tir translocation into HeLa cells and pedestal formation. Furthermore, the CesT-extension motif was identified in the N-terminal region of NleH1, NleH2, and EspZ, and mutations that disrupt this motif reduced translocation of these effectors, and in some cases, overall effector stability, thus validating the universality of this CesT-extension motif. The presence of two CesT-binding regions in Tir, along with the presence of the CesT-extension motif in other highly translocated effectors, may contribute to differential cargo recognition by CesT. Enteropathogenic Escherichia coli injects effector proteins into host cells using a type III secretion system (T3SS). The translocated intimin receptor (Tir) is the first effector delivered into host cells and imparts efficient secretion of other effectors. However, the mechanism for Tir-dependent modulation of the T3SS is poorly understood. We provide evidence that the multi-cargo chaperone CesT binds to two regions in Tir at the N- and C-terminus through a specific recognition motif, and show that CesT binding to the Tir C-terminus is important for host translocation. Furthermore we show that the CesT-specific motif is conserved in a subset of highly translocated effectors. This study highlights the multi-faceted role that T3SS chaperones play in effector secretion dynamics.
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21
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Migration of Type III Secretion System Transcriptional Regulators Links Gene Expression to Secretion. mBio 2018; 9:mBio.01096-18. [PMID: 30065089 PMCID: PMC6069116 DOI: 10.1128/mbio.01096-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Many plant-pathogenic bacteria of considerable economic importance rely on type III secretion systems (T3SSs) of the Hrc-Hrp 1 family to subvert their plant hosts. T3SS gene expression is regulated through the HrpG and HrpV proteins, while secretion is controlled by the gatekeeper HrpJ. A link between the two mechanisms was so far unknown. Here, we show that a mechanistic coupling exists between the expression and secretion cascades through the direct binding of the HrpG/HrpV heterodimer, acting as a T3SS chaperone, to HrpJ. The ternary complex is docked to the cytoplasmic side of the inner bacterial membrane and orchestrates intermediate substrate secretion, without affecting early substrate secretion. The anchoring of the ternary complex to the membranes potentially keeps HrpG/HrpV away from DNA. In their multiple roles as transcriptional regulators and gatekeeper chaperones, HrpV/HrpG provide along with HrpJ potentially attractive targets for antibacterial strategies. On the basis of scientific/economic importance, Pseudomonas syringae and Erwinia amylovora are considered among the top 10 plant-pathogenic bacteria in molecular plant pathology. Both employ type III secretion systems (T3SSs) of the Hrc-Hrp 1 family to subvert their plant hosts. For Hrc-Hrp 1, no functional link was known between the key processes of T3SS gene expression and secretion. Here, we show that a mechanistic coupling exists between expression and secretion cascades, through formation of a ternary complex involving the T3SS proteins HrpG, HrpV, and HrpJ. Our results highlight the functional and structural properties of a hitherto-unknown complex which orchestrates intermediate T3SS substrate secretion and may lead to better pathogen control through novel targets for antibacterial strategies.
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22
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High-Throughput Screening of Type III Secretion Determinants Reveals a Major Chaperone-Independent Pathway. mBio 2018; 9:mBio.01050-18. [PMID: 29921672 PMCID: PMC6016238 DOI: 10.1128/mbio.01050-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Numerous Gram-negative bacterial pathogens utilize type III secretion systems (T3SSs) to inject tens of effector proteins directly into the cytosol of host cells. Through interactions with cognate chaperones, type III effectors are defined and recruited to the sorting platform, a cytoplasmic component of these membrane-embedded nanomachines. However, notably, a comprehensive review of the literature reveals that the secretion of most type III effectors has not yet been linked to a chaperone, raising questions regarding the existence of unknown chaperones as well as the universality of chaperones in effector secretion. Here, we describe the development of the first high-throughput type III secretion (T3S) assay, a semiautomated solid-plate-based assay, which enables the side-by-side comparison of secretion of over 20 Shigella effectors under a multitude of conditions. Strikingly, we found that the majority of Shigella effectors are secreted at equivalent levels by wild-type and variants of Shigella that no longer encode one or all known Shigella T3S effector chaperones. In addition, we found that Shigella effectors are efficiently secreted from a laboratory strain of Escherichia coli expressing the core Shigella type III secretion apparatus (T3SA) but no other Shigella-specific proteins. Furthermore, we observed that the sequences necessary and sufficient to define chaperone-dependent and -independent effectors are fundamentally different. Together, these findings support the existence of a major, previously unrecognized, noncanonical chaperone-independent secretion pathway that is likely common to many T3SSs. Many bacterial pathogens use specialized nanomachines, including type III secretion systems, to directly inject virulence proteins (effectors) into host cells. Here, we present the first extensive analysis of chaperone dependence in the process of type III effector secretion, providing strong evidence for the existence of a previously unrecognized chaperone-independent pathway. This noncanonical pathway is likely common to many bacteria, as an extensive review of the literature reveals that the secretion of multiple type III effectors has not yet been knowingly linked to a chaperone. While additional studies will be required to discern the molecular details of this pathway, its prevalence suggests that it can likely serve as a new target for the development of antimicrobial agents.
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23
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Molecular basis of binding between the global post-transcriptional regulator CsrA and the T3SS chaperone CesT. Nat Commun 2018; 9:1196. [PMID: 29567971 PMCID: PMC5864733 DOI: 10.1038/s41467-018-03625-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/01/2018] [Indexed: 02/05/2023] Open
Abstract
The T3SS chaperone CesT is recently shown to interact with the post-transcriptional regulator CsrA to modulate post-attachment signaling in enteropathogenic and enterohemorrhagic Escherichia coli. The molecular basis of the CesT/CsrA binding, however, remains elusive. Here, we show that CesT and CsrA both created two ligand binding sites in their homodimers, forming irregular multimeric complexes in solution. Through construction of a recombinant CsrA-dimer (Re-CsrA) that contains a single CesT binding site, the atomic binding features between CesT and CsrA are delineated via the structure of the CesT/Re-CsrA complex. In contrast to a previously reported N-terminally swapped dimer-form, CesT adopts a dimeric architecture with a swapped C-terminal helix for CsrA engagement. In CsrA, CesT binds to a surface patch that extensively overlaps with its mRNA binding site. The binding mode therefore justifies a mechanism of CsrA-modulation by CesT via competitive inhibition of the CsrA/mRNA interactions. CesT is a type III secretion system chaperone that interacts with the post-transcriptional regulator CsrA, which is important for the modulation of post-attachment signaling in enteropathogenic and enterohemorrhagic Escherichia coli. Here the authors present the structure of the CsrA/CesT complex and propose a mechanism for CsrA-modulation by CesT.
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24
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Cao H, Yang C, Quan S, Hu T, Zhang L, Zhang Y, Yang D, Liu Q. Novel T3SS effector EseK in Edwardsiella piscicida is chaperoned by EscH and EscS to express virulence. Cell Microbiol 2017; 20. [PMID: 29024267 DOI: 10.1111/cmi.12790] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 01/08/2023]
Abstract
Bacterium usually utilises type III secretion systems (T3SS) to deliver effectors directly into host cells with the aids of chaperones. Hence, it is very important to identify bacterial T3SS effectors and chaperones for better understanding of host-pathogen interactions. Edwardsiella piscicida is an invasive enteric bacterium, which infects a wide range of hosts from fish to human. Given E. piscicida encodes a functional T3SS to promote infection, very few T3SS effectors and chaperones have been identified in this bacterium so far. Here, we reported that EseK is a new T3SS effector protein translocated by E. piscicida. Bioinformatic analysis indicated that escH and escS encode two putative class I T3SS chaperones. Further investigation indicated that EscH and EscS can enhance the secretion and translocation of EseK. EscH directly binds EseK through undetermined binding domains, whereas EscS binds EseK via its N-terminal α-helix. We also found that EseK has an N-terminal chaperone-binding domain, which binds EscH and EscS to form a ternary complex. Zebrafish infection experiments showed that EseK and its chaperones EscH and EscS are necessary for bacterial colonisation in zebrafish. This work identified a new T3SS effector, EseK, and its two T3SS chaperones, EscH and EscS, in E. piscicida, which enriches our knowledge of bacterial T3SS effector-chaperone interaction and contributes to our understanding of bacterial pathogenesis.
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Affiliation(s)
- Huifang Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Cuiting Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Tianjian Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Lingzhi Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China.,Shanghai Collaborative Innovation Center for Bio-manufacturing Technology, Shanghai, China
| | - Dahai Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China.,Shanghai Collaborative Innovation Center for Bio-manufacturing Technology, Shanghai, China
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25
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Jovanovic M, Waite C, James E, Synn N, Simpson T, Kotta-Loizou I, Buck M. Functional Characterization of Key Residues in Regulatory Proteins HrpG and HrpV of Pseudomonas syringae pv. tomato DC3000. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:656-665. [PMID: 28488468 DOI: 10.1094/mpmi-03-17-0073-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The plant pathogen Pseudomonas syringae pv. tomato DC3000 uses a type III secretion system (T3SS) to transfer effector proteins into the host. The expression of T3SS proteins is controlled by the HrpL σ factor. Transcription of hrpL is σ54-dependent and bacterial enhancer-binding proteins HrpR and HrpS coactivate the hrpL promoter. The HrpV protein imposes negative control upon HrpR and HrpS through direct interaction with HrpS. HrpG interacts with HrpV and relieves such negative control. The sequence alignments across Hrp group I-type plant pathogens revealed conserved HrpV and HrpG amino acids. To establish structure-function relationships in HrpV and HrpG, either truncated or alanine substitution mutants were constructed. Key functional residues in HrpV and HrpG are found within their C-terminal regions. In HrpG, L101 and L105 are indispensable for the ability of HrpG to directly interact with HrpV and suppress HrpV-dependent negative regulation of HrpR and HrpS. In HrpV, L108 and G110 are major determinants for interactions with HrpS and HrpG. We propose that mutually exclusive binding of HrpS and HrpG to the same binding site of HrpV governs a transition from negative control to activation of the HrpRS complex leading to HrpL expression and pathogenicity of P. syringae.
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Affiliation(s)
- Milija Jovanovic
- 1 Imperial College London, Imperial College Road, London, SW7 2AZ, U.K
| | - Christopher Waite
- 1 Imperial College London, Imperial College Road, London, SW7 2AZ, U.K
| | - Ellen James
- 2 Trio Medicines Ltd., Hammersmith Medicines Research, Cumberland Avenue, London, NW10 7EW, U.K.; and
| | - Nicholas Synn
- 1 Imperial College London, Imperial College Road, London, SW7 2AZ, U.K
| | - Timothy Simpson
- 3 Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, U.K
| | - Ioly Kotta-Loizou
- 1 Imperial College London, Imperial College Road, London, SW7 2AZ, U.K
| | - Martin Buck
- 1 Imperial College London, Imperial College Road, London, SW7 2AZ, U.K
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Bartho JD, Bellini D, Wuerges J, Demitri N, Toccafondi M, Schmitt AO, Zhao Y, Walsh MA, Benini S. The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions. PLoS One 2017; 12:e0176049. [PMID: 28426806 PMCID: PMC5398634 DOI: 10.1371/journal.pone.0176049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/04/2017] [Indexed: 11/18/2022] Open
Abstract
AmyR is a stress and virulence associated protein from the plant pathogenic Enterobacteriaceae species Erwinia amylovora, and is a functionally conserved ortholog of YbjN from Escherichia coli. The crystal structure of E. amylovora AmyR reveals a class I type III secretion chaperone-like fold, despite the lack of sequence similarity between these two classes of protein and lacking any evidence of a secretion-associated role. The results indicate that AmyR, and YbjN proteins in general, function through protein-protein interactions without any enzymatic action. The YbjN proteins of Enterobacteriaceae show remarkably low sequence similarity with other members of the YbjN protein family in Eubacteria, yet a high level of structural conservation is observed. Across the YbjN protein family sequence conservation is limited to residues stabilising the protein core and dimerization interface, while interacting regions are only conserved between closely related species. This study presents the first structure of a YbjN protein from Enterobacteriaceae, the most highly divergent and well-studied subgroup of YbjN proteins, and an in-depth sequence and structural analysis of this important but poorly understood protein family.
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Affiliation(s)
- Joseph D. Bartho
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, Bolzano, Italy
| | - Dom Bellini
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Jochen Wuerges
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, Bolzano, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone Trieste, S.S 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy
| | - Mirco Toccafondi
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, Bolzano, Italy
| | - Armin O. Schmitt
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, Bolzano, Italy
- Georg-August-Universität Göttingen, Dept. Nutztierwissenschaften, Breeding informatics, Margarethe von Wrangell-Weg 7, Göttingen, Germany
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois, 1201 W. Gregory Dr., Urbana, IL, United States of America
| | - Martin A. Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, Bolzano, Italy
- * E-mail:
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27
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Abstract
Type III secretion systems (T3SSs) afford Gram-negative bacteria an intimate means of altering the biology of their eukaryotic hosts--the direct delivery of effector proteins from the bacterial cytoplasm to that of the eukaryote. This incredible biophysical feat is accomplished by nanosyringe "injectisomes," which form a conduit across the three plasma membranes, peptidoglycan layer, and extracellular space that form a barrier to the direct delivery of proteins from bacterium to host. The focus of this chapter is T3SS function at the structural level; we will summarize the core findings that have shaped our understanding of the structure and function of these systems and highlight recent developments in the field. In turn, we describe the T3SS secretory apparatus, consider its engagement with secretion substrates, and discuss the posttranslational regulation of secretory function. Lastly, we close with a discussion of the future prospects for the interrogation of structure-function relationships in the T3SS.
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Gaytán MO, Martínez-Santos VI, Soto E, González-Pedrajo B. Type Three Secretion System in Attaching and Effacing Pathogens. Front Cell Infect Microbiol 2016; 6:129. [PMID: 27818950 PMCID: PMC5073101 DOI: 10.3389/fcimb.2016.00129] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/27/2016] [Indexed: 02/06/2023] Open
Abstract
Enteropathogenic Escherichia coli and enterohemorrhagic E. coli are diarrheagenic bacterial human pathogens that cause severe gastroenteritis. These enteric pathotypes, together with the mouse pathogen Citrobacter rodentium, belong to the family of attaching and effacing pathogens that form a distinctive histological lesion in the intestinal epithelium. The virulence of these bacteria depends on a type III secretion system (T3SS), which mediates the translocation of effector proteins from the bacterial cytosol into the infected cells. The core architecture of the T3SS consists of a multi-ring basal body embedded in the bacterial membranes, a periplasmic inner rod, a transmembrane export apparatus in the inner membrane, and cytosolic components including an ATPase complex and the C-ring. In addition, two distinct hollow appendages are assembled on the extracellular face of the basal body creating a channel for protein secretion: an approximately 23 nm needle, and a filament that extends up to 600 nm. This filamentous structure allows these pathogens to get through the host cells mucus barrier. Upon contact with the target cell, a translocation pore is assembled in the host membrane through which the effector proteins are injected. Assembly of the T3SS is strictly regulated to ensure proper timing of substrate secretion. The different type III substrates coexist in the bacterial cytoplasm, and their hierarchical secretion is determined by specialized chaperones in coordination with two molecular switches and the so-called sorting platform. In this review, we present recent advances in the understanding of the T3SS in attaching and effacing pathogens.
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Affiliation(s)
- Meztlli O Gaytán
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México Ciudad de México, Mexico
| | - Verónica I Martínez-Santos
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México Ciudad de México, Mexico
| | - Eduardo Soto
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México Ciudad de México, Mexico
| | - Bertha González-Pedrajo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México Ciudad de México, Mexico
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Diepold A, Armitage JP. Type III secretion systems: the bacterial flagellum and the injectisome. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0020. [PMID: 26370933 DOI: 10.1098/rstb.2015.0020] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The flagellum and the injectisome are two of the most complex and fascinating bacterial nanomachines. At their core, they share a type III secretion system (T3SS), a transmembrane export complex that forms the extracellular appendages, the flagellar filament and the injectisome needle. Recent advances, combining structural biology, cryo-electron tomography, molecular genetics, in vivo imaging, bioinformatics and biophysics, have greatly increased our understanding of the T3SS, especially the structure of its transmembrane and cytosolic components, the transcriptional, post-transcriptional and functional regulation and the remarkable adaptivity of the system. This review aims to integrate these new findings into our current knowledge of the evolution, function, regulation and dynamics of the T3SS, and to highlight commonalities and differences between the two systems, as well as their potential applications.
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Affiliation(s)
- Andreas Diepold
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Judith P Armitage
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Campbell-Valois FX, Pontier SM. Implications of Spatiotemporal Regulation of Shigella flexneri Type Three Secretion Activity on Effector Functions: Think Globally, Act Locally. Front Cell Infect Microbiol 2016; 6:28. [PMID: 27014638 PMCID: PMC4783576 DOI: 10.3389/fcimb.2016.00028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/23/2016] [Indexed: 11/13/2022] Open
Abstract
Shigella spp. are Gram-negative bacterial pathogens that infect human colonic epithelia and cause bacterial dysentery. These bacteria express multiple copies of a syringe-like protein complex, the Type Three Secretion apparatus (T3SA), which is instrumental in the etiology of the disease. The T3SA triggers the plasma membrane (PM) engulfment of the bacteria by host cells during the initial entry process. It then enables bacteria to escape the resulting phagocytic-like vacuole. Freed bacteria form actin comets to move in the cytoplasm, which provokes bacterial collision with the inner leaflet of the PM. This phenomenon culminates in T3SA-dependent secondary uptake and vacuolar rupture in neighboring cells in a process akin to what is observed during entry and named cell-to-cell spread. The activity of the T3SA of Shigella flexneri was recently demonstrated to display an on/off regulation during the infection. While the T3SA is active when bacteria are in contact with PM-derived compartments, it switches to an inactive state when bacteria are released within the cytosol. These observations indicate that effector proteins transiting through the T3SA are therefore translocated in a highly time and space constrained fashion, likely impacting on their cellular distribution. Herein, we present what is currently known about the composition, the assembly and the regulation of the T3SA activity and discuss the consequences of the on/off regulation of T3SA on Shigella effector properties and functions during the infection. Specific examples that will be developed include the role of effectors IcsB and VirA in the escape from LC3/ATG8-positive vacuoles formed during cell-to-cell spread and of IpaJ protease activity against N-miristoylated proteins. The conservation of a similar regulation of T3SA activity in other pathogens such as Salmonella or Enteropathogenic Escherichia coli will also be briefly discussed.
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Affiliation(s)
- F-X Campbell-Valois
- Department of Chemistry and Biomolecular Sciences, University of Ottawa Ottawa, ON, Canada
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31
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Tsou LK, Lara-Tejero M, RoseFigura J, Zhang ZJ, Wang YC, Yount JS, Lefebre M, Dossa PD, Kato J, Guan F, Lam W, Cheng YC, Galán JE, Hang HC. Antibacterial Flavonoids from Medicinal Plants Covalently Inactivate Type III Protein Secretion Substrates. J Am Chem Soc 2016; 138:2209-18. [PMID: 26847396 DOI: 10.1021/jacs.5b11575] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Traditional Chinese Medicines (TCMs) have been historically used to treat bacterial infections. However, the molecules responsible for these anti-infective properties and their potential mechanisms of action have remained elusive. Using a high-throughput assay for type III protein secretion in Salmonella enterica serovar Typhimurium, we discovered that several TCMs can attenuate this key virulence pathway without affecting bacterial growth. Among the active TCMs, we discovered that baicalein, a specific flavonoid from Scutellaria baicalensis, targets S. Typhimurium pathogenicity island-1 (SPI-1) type III secretion system (T3SS) effectors and translocases to inhibit bacterial invasion of epithelial cells. Structurally related flavonoids present in other TCMs, such as quercetin, also inactivated the SPI-1 T3SS and attenuated S. Typhimurium invasion. Our results demonstrate that specific plant metabolites from TCMs can directly interfere with key bacterial virulence pathways and reveal a previously unappreciated mechanism of action for anti-infective medicinal plants.
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Affiliation(s)
- Lun K Tsou
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States.,Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes , Zhunan Town, Miaoli County 35053, Taiwan, R.O.C
| | - María Lara-Tejero
- Department of Microbial Pathogenesis, Yale University School of Medicine , New Haven, Connecticut 06536, United States
| | - Jordan RoseFigura
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
| | - Zhenrun J Zhang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
| | - Yen-Chih Wang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
| | - Jacob S Yount
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
| | - Matthew Lefebre
- Department of Microbial Pathogenesis, Yale University School of Medicine , New Haven, Connecticut 06536, United States
| | - Paul D Dossa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
| | - Junya Kato
- Department of Microbial Pathogenesis, Yale University School of Medicine , New Haven, Connecticut 06536, United States
| | - Fulan Guan
- Department of Pharmacology, Yale University School of Medicine , New Haven, Connecticut 06520, United States
| | - Wing Lam
- Department of Pharmacology, Yale University School of Medicine , New Haven, Connecticut 06520, United States
| | - Yung-Chi Cheng
- Department of Pharmacology, Yale University School of Medicine , New Haven, Connecticut 06520, United States
| | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine , New Haven, Connecticut 06536, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
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Portaliou AG, Tsolis KC, Loos MS, Zorzini V, Economou A. Type III Secretion: Building and Operating a Remarkable Nanomachine. Trends Biochem Sci 2016; 41:175-189. [DOI: 10.1016/j.tibs.2015.09.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 12/21/2022]
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Structural Features Reminiscent of ATP-Driven Protein Translocases Are Essential for the Function of a Type III Secretion-Associated ATPase. J Bacteriol 2015; 197:3007-14. [PMID: 26170413 DOI: 10.1128/jb.00434-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/03/2015] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED Many bacterial pathogens and symbionts utilize type III secretion systems to interact with their hosts. These machines have evolved to deliver bacterial effector proteins into eukaryotic target cells to modulate a variety of cellular functions. One of the most conserved components of these systems is an ATPase, which plays an essential role in the recognition and unfolding of proteins destined for secretion by the type III pathway. Here we show that structural features reminiscent of other ATP-driven protein translocases are essential for the function of InvC, the ATPase associated with a Salmonella enterica serovar Typhimurium type III secretion system. Mutational and functional analyses showed that a two-helix-finger motif and a conserved loop located at the entrance of and within the predicted pore formed by the hexameric ATPase are essential for InvC function. These findings provide mechanistic insight into the function of this highly conserved component of type III secretion machines. IMPORTANCE Type III secretion machines are essential for the virulence or symbiotic relationships of many bacteria. These machines have evolved to deliver bacterial effector proteins into host cells to modulate cellular functions, thus facilitating bacterial colonization and replication. An essential component of these machines is a highly conserved ATPase, which is necessary for the recognition and secretion of proteins destined to be delivered by the type III secretion pathway. Using modeling and structure and function analyses, we have identified structural features of one of these ATPases from Salmonella enterica serovar Typhimurium that help to explain important aspects of its function.
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Zhang W, Sun J, Ding W, Lin J, Tian R, Lu L, Liu X, Shen X, Qian PY. Extracellular matrix-associated proteins form an integral and dynamic system during Pseudomonas aeruginosa biofilm development. Front Cell Infect Microbiol 2015; 5:40. [PMID: 26029669 PMCID: PMC4429628 DOI: 10.3389/fcimb.2015.00040] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/27/2015] [Indexed: 12/13/2022] Open
Abstract
Though the essential role of extracellular matrix in biofilm development has been extensively documented, the function of matrix-associated proteins is elusive. Determining the dynamics of matrix-associated proteins would be a useful way to reveal their functions in biofilm development. Therefore, we applied iTRAQ-based quantitative proteomics to evaluate matrix-associated proteins isolated from different phases of Pseudomonas aeruginosa ATCC27853 biofilms. Among the identified 389 proteins, 54 changed their abundance significantly. The increased abundance of stress resistance and nutrient metabolism-related proteins over the period of biofilm development was consistent with the hypothesis that biofilm matrix forms micro-environments in which cells are optimally organized to resist stress and use available nutrients. Secreted proteins, including novel putative effectors of the type III secretion system were identified, suggesting that the dynamics of pathogenesis-related proteins in the matrix are associated with biofilm development. Interestingly, there was a good correlation between the abundance changes of matrix-associated proteins and their expression. Further analysis revealed complex interactions among these modulated proteins, and the mutation of selected proteins attenuated biofilm development. Collectively, this work presents the first dynamic picture of matrix-associated proteins during biofilm development, and provides evidences that the matrix-associated proteins may form an integral and well regulated system that contributes to stress resistance, nutrient acquisition, pathogenesis and the stability of the biofilm.
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Affiliation(s)
- Weipeng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Jin Sun
- Department of Biology, Hong Kong Baptist University Hong Kong, China
| | - Wei Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A & F University Yangling, China
| | - Jinshui Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A & F University Yangling, China
| | - Renmao Tian
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Liang Lu
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Xiaofen Liu
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A & F University Yangling, China
| | - Pei-Yuan Qian
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
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Wille T, Barlag B, Jakovljevic V, Hensel M, Sourjik V, Gerlach RG. A gateway-based system for fast evaluation of protein-protein interactions in bacteria. PLoS One 2015; 10:e0123646. [PMID: 25856398 PMCID: PMC4391838 DOI: 10.1371/journal.pone.0123646] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/26/2015] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions are important layers of regulation in all kingdoms of life. Identification and characterization of these interactions is one challenging task of the post-genomic era and crucial for understanding of molecular processes within a cell. Several methods have been successfully employed during the past decades to identify protein-protein interactions in bacteria, but most of them include tedious and time-consuming manipulations of DNA. In contrast, the MultiSite Gateway system is a fast tool for transfer of multiple DNA fragments between plasmids enabling simultaneous and site directed cloning of up to four fragments into one construct. Here we developed a new set of Gateway vectors including custom made entry vectors and modular Destination vectors for studying protein-protein interactions via Fluorescence Resonance Energy Transfer (FRET), Bacterial two Hybrid (B2H) and split Gaussia luciferase (Gluc), as well as for fusions with SNAP-tag and HaloTag for dual-color super-resolution microscopy. As proof of principle, we characterized the interaction between the Salmonella effector SipA and its chaperone InvB via split Gluc and B2H approach. The suitability for FRET analysis as well as functionality of fusions with SNAP- and HaloTag could be demonstrated by studying the transient interaction between chemotaxis response regulator CheY and its phosphatase CheZ.
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Affiliation(s)
- Thorsten Wille
- Junior Research Group 3, Robert Koch-Institute, Wernigerode Branch, Wernigerode, Germany
| | - Britta Barlag
- Division of Microbiology, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Vladimir Jakovljevic
- Center for Molecular Biology at the University of Heidelberg (ZMBH), DKFZ (German Cancer Research Center) -ZMBH Alliance, Heidelberg, Germany
| | - Michael Hensel
- Division of Microbiology, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Victor Sourjik
- Center for Molecular Biology at the University of Heidelberg (ZMBH), DKFZ (German Cancer Research Center) -ZMBH Alliance, Heidelberg, Germany
- Max Planck Institute for Terrestrial Microbiology & LOEWE (state offensive for the development of scientific and economic excellence) Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Roman G. Gerlach
- Junior Research Group 3, Robert Koch-Institute, Wernigerode Branch, Wernigerode, Germany
- * E-mail:
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Vujanac M, Iyer VS, Sengupta M, Ajdic D. Regulation of Streptococcus mutans PTS Bio by the transcriptional repressor NigR. Mol Oral Microbiol 2015; 30:280-94. [PMID: 25580872 DOI: 10.1111/omi.12093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2014] [Indexed: 11/29/2022]
Abstract
Streptococcus mutans is implicated in human dental caries, and the carbohydrate metabolism of this organism plays an important role in the formation of this disease. Carbohydrate transport and metabolism are essential for the survival of S. mutans in the oral cavity. It is known that a unique phosphoenolpyruvate-sugar phosphotransferase system PTS(B) (io) of S. mutans UA159 is expressed in sucrose-grown biofilms (Mol Oral Microbiol 28: 2013; 114). In this study we analyzed the transcriptional regulation of the operon (O(B) (io) ) encoding the PTS(B) (io) and showed that it was repressed by NigR, a LacI-like transcriptional regulator. Using electro-mobility shift assay, we described two operators to which NigR bound with different affinities. We also identified the transcriptional start site and showed that one of the operators overlaps with the promoter and presumably represses initiation of transcription. Mutational analyses revealed the key nucleotides in the operators required for high-affinity binding of NigR. PTS(B) (io) is expressed in S. mutans biofilms so understanding its regulation may provide improved strategies for caries treatment and prevention.
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Affiliation(s)
- M Vujanac
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - V S Iyer
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - M Sengupta
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - D Ajdic
- Miller School of Medicine, University of Miami, Miami, FL, USA
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Roblin P, Dewitte F, Villeret V, Biondi EG, Bompard C. A Salmonella type three secretion effector/chaperone complex adopts a hexameric ring-like structure. J Bacteriol 2015; 197:688-98. [PMID: 25404693 PMCID: PMC4334183 DOI: 10.1128/jb.02294-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/10/2014] [Indexed: 11/20/2022] Open
Abstract
Many bacterial pathogens use type three secretion systems (T3SS) to inject virulence factors, named effectors, directly into the cytoplasm of target eukaryotic cells. Most of the T3SS components are conserved among plant and animal pathogens, suggesting a common mechanism of recognition and secretion of effectors. However, no common motif has yet been identified for effectors allowing T3SS recognition. In this work, we performed a biochemical and structural characterization of the Salmonella SopB/SigE chaperone/effector complex by small-angle X-ray scattering (SAXS). Our results showed that the SopB/SigE complex is assembled in dynamic homohexameric-ring-shaped structures with an internal tunnel. In this ring, the chaperone maintains a disordered N-terminal end of SopB molecules, in a good position to be reached and processed by the T3SS. This ring dimensionally fits the ring-organized molecules of the injectisome, including ATPase hexameric rings; this organization suggests that this structural feature is important for ATPase recognition by T3SS. Our work constitutes the first evidence of the oligomerization of an effector, analogous to the organization of the secretion machinery, obtained in solution. As effectors share neither sequence nor structural identity, the quaternary oligomeric structure could constitute a strategy evolved to promote the specificity and efficiency of T3SS recognition.
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Affiliation(s)
- Pierre Roblin
- INRA Biopolymères, Interactions et Assemblages, Nantes, France Synchrotron SOLEIL, Gif sur Yvette, France
| | - Frédérique Dewitte
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Vincent Villeret
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Emanuele G Biondi
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Coralie Bompard
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, Université Lille Nord de France, Villeneuve d'Ascq, France
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SepD/SepL-dependent secretion signals of the type III secretion system translocator proteins in enteropathogenic Escherichia coli. J Bacteriol 2015; 197:1263-75. [PMID: 25645555 DOI: 10.1128/jb.02401-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The type III protein secretion system (T3SS) encoded by the locus of enterocyte effacement (LEE) is essential for the pathogenesis of attaching/effacing bacterial pathogens, including enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and Citrobacter rodentium. These pathogens use the T3SS to sequentially secrete three categories of proteins: the T3SS needle and inner rod protein components; the EspA, EspB, and EspD translocators; and many LEE- and non-LEE-encoded effectors. SepD and SepL are essential for translocator secretion, and mutations in either lead to hypersecretion of effectors. However, how SepD and SepL control translocator secretion and secretion hierarchy between translocators and effectors is poorly understood. In this report, we show that the secreted T3SS components, the translocators, and both LEE- and non-LEE-encoded effectors all carry N-terminal type III secretion and translocation signals. These signals all behave like those of the effectors and are sufficient for mediating type III secretion and translocation by wild-type EPEC and hypersecretion by the sepD and sepL mutants. Our results extended previous observations and suggest that the secretion hierarchy of the different substrates is determined by a signal other than the N-terminal secretion signal. We identified a domain located immediately downstream of the N-terminal secretion signal in the translocator EspB that is required for SepD/SepL-dependent secretion. We further demonstrated that this EspB domain confers SepD/SepL- and CesAB-dependent secretion on the secretion signal of effector EspZ. Our results thus suggest that SepD and SepL control and regulate secretion hierarchy between translocators and effectors by recognizing translocator-specific export signals. IMPORTANCE Many bacterial pathogens use a syringe-like protein secretion apparatus, termed the type III protein secretion system (T3SS), to secrete and inject numerous proteins directly into the host cells to cause disease. The secreted proteins perform different functions at various stages during infection and are classified into three substrate categories (T3SS components, translocators, and effectors). They all contain secretion signals at their N termini, but how their secretion hierarchy is determined is poorly understood. Here, we show that the N-terminal secretion signals from different substrate categories all behave the same and do not confer substrate specificity. We further characterize the secretion signals of the translocators and identify a translocator-specific signal, demonstrating that substrate-specific secretion signals are required in regulating T3SS substrate hierarchy.
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39
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The Salmonella type III secretion system virulence effector forms a new hexameric chaperone assembly for export of effector/chaperone complexes. J Bacteriol 2014; 197:672-5. [PMID: 25488302 DOI: 10.1128/jb.02524-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacteria hijack eukaryotic cells by injecting virulence effectors into host cytosol with a type III secretion system (T3SS). Effectors are targeted with their cognate chaperones to hexameric T3SS ATPase at the bacterial membrane's cytosolic face. In this issue of the Journal of Bacteriology, Roblin et al. (P. Roblin, F. Dewitte, V. Villeret, E. G. Biondi, and C. Bompard, J Bacteriol 197:688-698, 2015, http://dx.doi.org/10.1128/JB.02294-14) show that the T3SS chaperone SigE of Salmonella can form hexameric rings rather than dimers when bound to its cognate effector, SopB, implying a novel multimeric association for chaperone/effector complexes with their ATPase.
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40
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Gazi AD, Charova S, Aivaliotis M, Panopoulos NJ, Kokkinidis M. HrpG and HrpV proteins from the Type III secretion system of Erwinia amylovora form a stable heterodimer. FEMS Microbiol Lett 2014; 362:1-8. [PMID: 25790492 DOI: 10.1093/femsle/fnu011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Bacterial type III secretion systems (T3SSs) are specialized multicomponent nanomachines that mediate the transport of proteins either to extracellular locations or directly into eukaryotic host cell cytoplasm. Erwinia amylovora, the main agent of rosaceous plants fireblight disease, employs an Hrp/Hrc1 T3SS to accomplish its pathogenesis. The regulatory network that controls the activation of this T3SS is largely unknown in E. amylovora. However, in Pseudomonas syringae pathovars, the HrpG/HrpV complex has been shown to directly regulate the activity of transcription factor HrpS and consequently the upregulation of the Hrp/Hrc1 T3SS related genes. In this work, we report the successful recombinant production and purification of a stable E. amylovora HrpG/HrpV complex, using pPROpET, a bicistronic expression vector. Furthermore, we present the first solution structure of this complex based on small-angle X-ray scattering data.
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Affiliation(s)
- Anastasia D Gazi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece Biology Department, University of Crete, Vasilika Vouton, 71409 Heraklio, Crete, Greece
| | - Spyridoula Charova
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece
| | - Nicholas J Panopoulos
- Professor Emeritus, Biology Department, University of Crete, Vasilika Vouton, 71409 Heraklio, Crete, Greece Professor Emeritus, Department of Environmental Sciences, Policy, and Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720-3114, USA
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece Biology Department, University of Crete, Vasilika Vouton, 71409 Heraklio, Crete, Greece
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41
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Banerjee A, Dey S, Chakraborty A, Datta A, Basu A, Chakrabarti S, Datta S. Binding mode analysis of a major T3SS translocator protein PopB with its chaperone PcrH from Pseudomonas aeruginosa. Proteins 2014; 82:3273-85. [PMID: 25116453 DOI: 10.1002/prot.24666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 07/25/2014] [Accepted: 08/05/2014] [Indexed: 11/10/2022]
Abstract
Pseudomonas aeruginosa, a Gram-negative pathogen uses a specialized set of Type III secretion system (T3SS) translocator proteins to establish virulence in the host cell. An understanding of the factors that govern translocation by the translocator protein-chaperone complex is thus of immense importance. In this work, experimental and computational techniques were used to probe into the structure of the major translocator protein PopB from P. aeruginosa and to identify the important regions involved in functioning of the translocator protein. This study reveals that the binding sites of the common chaperone PcrH, needed for maintenance of the translocator PopB within the bacterial cytoplasm, which are primarily localized within the N-terminal domain. However, disordered and flexible residues located both at the N- and C-terminal domains are also observed to be involved in association with the chaperone. This intrinsic disorderliness of the terminal domains is conserved for all the major T3SS translocator proteins and is functionally important to maintain the intrinsically disordered state of the translocators. Our experimental and computational analyses suggest that a "disorder-to-order" transition of PopB protein might take place upon PcrH binding. The long helical coiled-coil part of PopB protein perhaps helps in pore formation while the flexible apical region is involved in chaperone interaction. Thus, our computational model of translocator protein PopB and its binding analyses provide crucial functional insights into the T3SS translocation mechanism.
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Affiliation(s)
- Anindyajit Banerjee
- Division of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, 700 032, West Bengal, India
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42
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Barrero-Tobon AM, Hendrixson DR. Flagellar biosynthesis exerts temporal regulation of secretion of specific Campylobacter jejuni colonization and virulence determinants. Mol Microbiol 2014; 93:957-74. [PMID: 25041103 DOI: 10.1111/mmi.12711] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 01/26/2023]
Abstract
The Campylobacter jejuni flagellum exports both proteins that form the flagellar organelle for swimming motility and colonization and virulence factors that promote commensal colonization of the avian intestinal tract or invasion of human intestinal cells respectively. We explored how the C. jejuni flagellum is a versatile secretory organelle by examining molecular determinants that allow colonization and virulence factors to exploit the flagellum for their own secretion. Flagellar biogenesis was observed to exert temporal control of secretion of these proteins, indicating that a bolus of secretion of colonization and virulence factors occurs during hook biogenesis with filament polymerization itself reducing secretion of these factors. Furthermore, we found that intramolecular and intermolecular requirements for flagellar-dependent secretion of these proteins were most reminiscent to those for flagellin secretion. Importantly, we discovered that secretion of one colonization and virulence factor, CiaI, was not required for invasion of human colonic cells, which counters previous hypotheses for how this protein functions during invasion. Instead, secretion of CiaI was essential for C. jejuni to facilitate commensal colonization of the natural avian host. Our work provides insight into the versatility of the bacterial flagellum as a secretory machine that can export proteins promoting diverse biological processes.
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Affiliation(s)
- Angelica M Barrero-Tobon
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Room NL 4.138A, Dallas, TX, 75390-9048, USA
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43
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Allison SE, Tuinema BR, Everson ES, Sugiman-Marangos S, Zhang K, Junop MS, Coombes BK. Identification of the docking site between a type III secretion system ATPase and a chaperone for effector cargo. J Biol Chem 2014; 289:23734-44. [PMID: 25035427 DOI: 10.1074/jbc.m114.578476] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A number of Gram-negative pathogens utilize type III secretion systems (T3SSs) to inject bacterial effector proteins into the host. An important component of T3SSs is a conserved ATPase that captures chaperone-effector complexes and energizes their dissociation to facilitate effector translocation. To date, there has been limited work characterizing the chaperone-T3SS ATPase interaction despite it being a fundamental aspect of T3SS function. In this study, we present the 2.1 Å resolution crystal structure of the Salmonella enterica SPI-2-encoded ATPase, SsaN. Our structure revealed a local and functionally important novel feature in helix 10 that we used to define the interaction domain relevant to chaperone binding. We modeled the interaction between the multicargo chaperone, SrcA, and SsaN and validated this model using mutagenesis to identify the residues on both the chaperone and ATPase that mediate the interaction. Finally, we quantified the benefit of this molecular interaction on bacterial fitness in vivo using chromosomal exchange of wild-type ssaN with mutants that retain ATPase activity but no longer capture the chaperone. Our findings provide insight into chaperone recognition by T3SS ATPases and demonstrate the importance of the chaperone-T3SS ATPase interaction for the pathogenesis of Salmonella.
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Affiliation(s)
- Sarah E Allison
- From the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada and the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario L8S 4K1, Canada
| | - Brian R Tuinema
- From the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada and the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario L8S 4K1, Canada
| | - Ellen S Everson
- From the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada and the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario L8S 4K1, Canada
| | - Seiji Sugiman-Marangos
- From the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada and the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario L8S 4K1, Canada
| | - Kun Zhang
- From the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada and the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario L8S 4K1, Canada
| | - Murray S Junop
- From the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada and the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario L8S 4K1, Canada
| | - Brian K Coombes
- From the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada and the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario L8S 4K1, Canada
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44
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Galán JE, Lara-Tejero M, Marlovits TC, Wagner S. Bacterial type III secretion systems: specialized nanomachines for protein delivery into target cells. Annu Rev Microbiol 2014; 68:415-38. [PMID: 25002086 DOI: 10.1146/annurev-micro-092412-155725] [Citation(s) in RCA: 367] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One of the most exciting developments in the field of bacterial pathogenesis in recent years is the discovery that many pathogens utilize complex nanomachines to deliver bacterially encoded effector proteins into target eukaryotic cells. These effector proteins modulate a variety of cellular functions for the pathogen's benefit. One of these protein-delivery machines is the type III secretion system (T3SS). T3SSs are widespread in nature and are encoded not only by bacteria pathogenic to vertebrates or plants but also by bacteria that are symbiotic to plants or insects. A central component of T3SSs is the needle complex, a supramolecular structure that mediates the passage of the secreted proteins across the bacterial envelope. Working in conjunction with several cytoplasmic components, the needle complex engages specific substrates in sequential order, moves them across the bacterial envelope, and ultimately delivers them into eukaryotic cells. The central role of T3SSs in pathogenesis makes them great targets for novel antimicrobial strategies.
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Affiliation(s)
- Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536;
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45
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Costa SCP, Lesser CF. A multifunctional region of the Shigella type 3 effector IpgB1 is important for secretion from bacteria and membrane targeting in eukaryotic cells. PLoS One 2014; 9:e93461. [PMID: 24718571 PMCID: PMC3981709 DOI: 10.1371/journal.pone.0093461] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/05/2014] [Indexed: 11/29/2022] Open
Abstract
Type 3 secretion systems are complex nanomachines used by many Gram–negative bacteria to deliver tens of proteins (effectors) directly into host cells. Once delivered into host cells, effectors often target to specific cellular loci where they usurp host cell processes to their advantage. Here, using the yeast model system, we identify the membrane localization domain (MLD) of IpgB1, a stretch of 20 amino acids enriched for hydrophobic residues essential for the targeting of this effector to the plasma membrane. Embedded within these residues are ten that define the IpgB1 chaperone-binding domain for Spa15. As observed with dedicated class IA chaperones that mask hydrophobic MLDs, Spa15, a class IB chaperone, promotes IpgB1 stability by binding this hydrophobic region. However, despite being stable, an IpgB1 allele that lacks the MLD is not recognized as a secreted substrate. Similarly, deletion of the chaperone binding domains of IpgB1 and three additional Spa15-dependent effectors result in alleles that are no longer recognized as secreted substrates despite the presence of intact N-terminal secretion signal sequences. This is in contrast with MLD-containing effectors that bind class IA dedicated chaperones, as deletion of the MLD of these effectors alleviates the chaperone requirement for secretion. These observations indicate that at least for substrates of class IB chaperones, the chaperone-effector complex plays a major role in defining type 3 secreted proteins and highlight how a single region of an effector can play important roles both within prokaryotic and eukaryotic cells.
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Affiliation(s)
- Sonia C. P. Costa
- Department of Medicine (Microbiology and Immunobiology), Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Cammie F. Lesser
- Department of Medicine (Microbiology and Immunobiology), Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, United States of America
- * E-mail:
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46
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Reddy BG, Moates DB, Kim HB, Green TJ, Kim CY, Terwilliger TC, DeLucas LJ. 1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis. Acta Crystallogr F Struct Biol Commun 2014; 70:414-7. [PMID: 24699730 PMCID: PMC3976054 DOI: 10.1107/s2053230x14003793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 02/18/2014] [Indexed: 01/22/2023] Open
Abstract
The crystallographic structure of the Mycobacterium tuberculosis (TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overall structure similar to that of the Salmonella virulence-factor chaperone InvB, with an r.m.s.d. for main-chain atoms of 2.3 Å along an aligned domain.
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Affiliation(s)
- Bharat G. Reddy
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233, USA
| | - Derek B. Moates
- Department of Biology, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233, USA
| | - Heung-Bok Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Todd J. Green
- Department of Microbiology, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233, USA
| | - Chang-Yub Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Lawrence J. DeLucas
- Department of Optometry, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233, USA
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47
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Waddell B, Southward CM, McKenna N, DeVinney R. Identification of VPA0451 as the specific chaperone for theVibrio parahaemolyticuschromosome 1 type III-secreted effector VPA0450. FEMS Microbiol Lett 2014; 353:141-50. [DOI: 10.1111/1574-6968.12416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Barbara Waddell
- Department of Microbiology, Immunology and Infectious Diseases; Snyder Institute for Chronic Diseases; University of Calgary; Calgary AB Canada
| | - Carolyn M. Southward
- Department of Microbiology, Immunology and Infectious Diseases; Snyder Institute for Chronic Diseases; University of Calgary; Calgary AB Canada
| | - Neil McKenna
- Department of Microbiology, Immunology and Infectious Diseases; Snyder Institute for Chronic Diseases; University of Calgary; Calgary AB Canada
| | - Rebekah DeVinney
- Department of Microbiology, Immunology and Infectious Diseases; Snyder Institute for Chronic Diseases; University of Calgary; Calgary AB Canada
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48
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Burkinshaw BJ, Strynadka NCJ. Assembly and structure of the T3SS. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1649-63. [PMID: 24512838 DOI: 10.1016/j.bbamcr.2014.01.035] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 02/06/2023]
Abstract
The Type III Secretion System (T3SS) is a multi-mega Dalton apparatus assembled from more than twenty components and is found in many species of animal and plant bacterial pathogens. The T3SS creates a contiguous channel through the bacterial and host membranes, allowing injection of specialized bacterial effector proteins directly to the host cell. In this review, we discuss our current understanding of T3SS assembly and structure, as well as highlight structurally characterized Salmonella effectors. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Brianne J Burkinshaw
- Department of Biochemistry and Molecular Biology, Center for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, Center for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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49
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Dey S, Datta S. Interfacial residues of SpcS chaperone affects binding of effector toxin ExoT in Pseudomonas aeruginosa: novel insights from structural and computational studies. FEBS J 2014; 281:1267-80. [PMID: 24387107 DOI: 10.1111/febs.12704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/06/2013] [Accepted: 12/23/2013] [Indexed: 12/12/2022]
Abstract
ExoT belongs to the family of type 3 secretion system (T3SS) effector toxins in Pseudomonas aeruginosa, known to be one of the major virulence determinant toxins that cause chronic and acute infections in immuno-compromised individuals, burn victims and cystic fibrosis patients. Here, we report the X-ray crystal structure of the amino terminal fragment of effector toxin ExoT, in complex with full-length homodimeric chaperone SpcS at 2.1 Å resolution. The full-length dimeric chaperone SpcS has the conserved α-β-β-β-α-β-β-α fold of class I chaperones, the characteristic hydrophobic patches for binding effector proteins and a conserved polar cavity at the dimeric interface. The stable crystallized amino terminal fragment of ExoT consists of a chaperone binding domain and a membrane localization domain that wraps around the dimeric chaperone. Site-directed mutagenesis experiments and a molecular dynamics study complement each other in revealing Asn65, Phe67 and Trp88 as critical dimeric interfacial residues that can strongly influence the effector-chaperone interactions.
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Affiliation(s)
- Supratim Dey
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Kolkata, India
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50
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Structure of a pathogenic type 3 secretion system in action. Nat Struct Mol Biol 2013; 21:82-7. [PMID: 24317488 DOI: 10.1038/nsmb.2722] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/22/2013] [Indexed: 12/20/2022]
Abstract
Type 3 secretion systems use 3.5-megadalton syringe-like, membrane-embedded 'injectisomes', each containing an ~800-Å-long needle complex to connect intracellular compartments of infectious bacteria and hosts. Here we identify requirements for substrate association with, transport through and exit from the injectisome of Salmonella enterica serovar Typhimurium. This guided the design of substrates that become trapped within the secretion path and enabled visualization of injectisomes in action in situ. We used cryo-EM to define the secretion path, providing a structural explanation as to why effector proteins must be unfolded during transport. Furthermore, trapping of a heterologous substrate in the needle prevents secretion of natural bacterial effectors. Together, the data reveal the path of protein secretion across multiple membranes and show that mechanisms rejecting unacceptable substrates can be undermined, and transport of bacterial effectors across an already assembled type 3 secretion system can be inhibited.
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