1
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Soto JE, Lara-Tejero M. The sorting platform in the type III secretion pathway: From assembly to function. Bioessays 2023; 45:e2300078. [PMID: 37329195 DOI: 10.1002/bies.202300078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
The type III secretion system (T3SS) is a specialized nanomachine that enables bacteria to secrete proteins in a specific order and directly deliver a specific set of them, collectively known as effectors, into eukaryotic organisms. The core structure of the T3SS is a syringe-like apparatus composed of multiple building blocks, including both membrane-associated and soluble proteins. The cytosolic components organize together in a chamber-like structure known as the sorting platform (SP), responsible for recruiting, sorting, and initiating the substrates destined to engage this secretion pathway. In this article, we provide an overview of recent findings on the SP's structure and function, with a particular focus on its assembly pathway. Furthermore, we discuss the molecular mechanisms behind the recruitment and hierarchical sorting of substrates by this cytosolic complex. Overall, the T3SS is a highly specialized and complex system that requires precise coordination to function properly. A deeper understanding of how the SP orchestrates T3S could enhance our comprehension of this complex nanomachine, which is central to the host-pathogen interface, and could aid in the development of novel strategies to fight bacterial infections.
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Affiliation(s)
- Jose Eduardo Soto
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - María Lara-Tejero
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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2
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Choudhury A, Saha S, Maiti NC, Datta S. Exploring structural features and potential lipid interactions of Pseudomonas aeruginosa type three secretion effector PemB by spectroscopic and calorimetric experiments. Protein Sci 2023; 32:e4627. [PMID: 36916835 PMCID: PMC10044109 DOI: 10.1002/pro.4627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023]
Abstract
Type Three Secretion System (T3SS) is a sophisticated nano-scale weapon utilized by several gram negative bacteria under stringent spatio-temporal regulation to manipulate and evade host immune systems in order to cause infection. To the best of our knowledge, this present study is the first report where we embark upon characterizing inherent features of native type three secretion effector protein PemB through biophysical techniques. Herein, first, we demonstrate binding affinity of PemB for phosphoinositides through isothermal calorimetric titrations. Second, we shed light on its strong homo-oligomerization propensity in aqueous solution through multiple biophysical methods. Third, we also employ several spectroscopic techniques to delineate its disordered and helical conformation. Lastly, we perform a phylogenetic analysis of this new effector to elucidate evolutionary relationship with other organisms. Taken together, our results shall surely contribute to our existing knowledge of Pseudomonas aeruginosa secretome.
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Affiliation(s)
- Arkaprabha Choudhury
- Department of Structural Biology and BioinformaticsCSIR‐Indian Institute of Chemical Biology (CSIR‐IICB)Kolkata700032India
- Biological SciencesAcademy of Scientific and Innovative Research (AcSIR)201002GhaziabadIndia
| | - Saumen Saha
- Department of Structural Biology and BioinformaticsCSIR‐Indian Institute of Chemical Biology (CSIR‐IICB)Kolkata700032India
| | - Nakul Chandra Maiti
- Department of Structural Biology and BioinformaticsCSIR‐Indian Institute of Chemical Biology (CSIR‐IICB)Kolkata700032India
- Biological SciencesAcademy of Scientific and Innovative Research (AcSIR)201002GhaziabadIndia
| | - Saumen Datta
- Department of Structural Biology and BioinformaticsCSIR‐Indian Institute of Chemical Biology (CSIR‐IICB)Kolkata700032India
- Biological SciencesAcademy of Scientific and Innovative Research (AcSIR)201002GhaziabadIndia
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3
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Tseytin I, Lezerovich S, David N, Sal-Man N. Interactions and substrate selectivity within the SctRST complex of the type III secretion system of enteropathogenic Escherichia coli. Gut Microbes 2022; 14:2013763. [PMID: 34965187 PMCID: PMC8726614 DOI: 10.1080/19490976.2021.2013763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 02/04/2023] Open
Abstract
Many bacterial pathogens employ a protein complex, termed the type III secretion system (T3SS), to inject bacterial effectors into host cells. These effectors manipulate various cellular processes to promote bacterial growth and survival. The T3SS complex adopts a nano-syringe shape that is assembled across the bacterial membranes, with an extracellular needle extending toward the host cell membrane. The assembly of the T3SS is initiated by the association of three proteins, known as SctR, SctS, and SctT, which create an entry portal to the translocation channel within the bacterial inner membrane. Using the T3SS of enteropathogenic Escherichia coli, we investigated, by mutational and functional analyses, the role of two structural construction sites formed within the SctRST complex and revealed that they are mutation-resistant components that are likely to act as seals preventing leakage of ions and metabolites rather than as substrate gates. In addition, we identified two residues in the SctS protein, Pro23, and Lys54, that are critical for the proper activity of the T3SS. We propose that Pro23 is critical for the physical orientation of the SctS transmembrane domains that create the tip of the SctRST complex and for their positioning with regard to other T3SS substructures. Surprisingly, we found that SctS Lys54, which was previously suggested to mediate the SctS self-oligomerization, is critical for T3SS activity due to its essential role in SctS-SctT hetero-interactions.
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Affiliation(s)
- Irit Tseytin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shir Lezerovich
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Nofar David
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Muthuramalingam M, Whittier SK, Lovell S, Battaile KP, Tachiyama S, Johnson DK, Picking WL, Picking WD. The Structures of SctK and SctD from Pseudomonas aeruginosa Reveal the Interface of the Type III Secretion System Basal Body and Sorting Platform. J Mol Biol 2020; 432:166693. [PMID: 33122003 PMCID: PMC10550303 DOI: 10.1016/j.jmb.2020.10.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
Many Gram-negative bacterial pathogens use type III secretion systems (T3SS) to inject proteins into eukaryotic cells to subvert normal cellular functions. The T3SS apparatus (injectisome) shares a common architecture in all systems studied thus far, comprising three major components - the cytoplasmic sorting platform, envelope-spanning basal body and external needle with tip complex. The sorting platform consists of an ATPase (SctN) connected to "pods" (SctQ) having six-fold symmetry via radial spokes (SctL). These pods interface with the 24-fold symmetric SctD inner membrane ring (IR) via an adaptor protein (SctK). Here we report the first high-resolution structure of a SctK protein family member, PscK from Pseudomonas aeruginosa, as well as the structure of its interacting partner, the cytoplasmic domain of PscD (SctD). The cytoplasmic domain of PscD forms a forkhead-associated (FHA) fold, like that of its homologues from other T3SS. PscK, on the other hand, forms a helix-rich structure that does not resemble any known protein fold. Based on these structural findings, we present the first model for an interaction between proteins from the sorting platform and the IR. We also test the importance of the PscD residues predicted to mediate this electrostatic interaction using a two-hybrid analysis. The functional need for these residues in vivo was then confirmed by monitoring secretion of the effector ExoU. These structures will contribute to the development of atomic-resolution models of the entire sorting platform and to our understanding of the mechanistic interface between the sorting platform and the basal body of the injectisome.
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Affiliation(s)
| | - Sean K Whittier
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, United States
| | - Kevin P Battaile
- IMCA-CAT, Hauptman Woodward Medical Research Institute, Argonne, IL 60439, United States
| | - Shoichi Tachiyama
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - David K Johnson
- Computational Chemical Biology Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, United States
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - William D Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States.
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5
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Jensen JL, Yamini S, Rietsch A, Spiller BW. "The structure of the Type III secretion system export gate with CdsO, an ATPase lever arm". PLoS Pathog 2020; 16:e1008923. [PMID: 33048983 PMCID: PMC7584215 DOI: 10.1371/journal.ppat.1008923] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 10/23/2020] [Accepted: 08/24/2020] [Indexed: 01/10/2023] Open
Abstract
Type III protein secretion systems (T3SS) deliver effector proteins from the Gram-negative bacterial cytoplasm into a eukaryotic host cell through a syringe-like, multi-protein nanomachine. Cytosolic components of T3SS include a portion of the export apparatus, which traverses the inner membrane and features the opening of the secretion channel, and the sorting complex for substrate recognition and for providing the energetics required for protein secretion. Two components critical for efficient effector export are the export gate protein and the ATPase, which are proposed to be linked by the central stalk protein of the ATPase. We present the structure of the soluble export gate homo-nonamer, CdsV, in complex with the central stalk protein, CdsO, of its cognate ATPase, both derived from Chlamydia pneumoniae. This structure defines the interface between these essential T3S proteins and reveals that CdsO engages the periphery of the export gate that may allow the ATPase to catalyze an opening between export gate subunits to allow cargo to enter the export apparatus. We also demonstrate through structure-based mutagenesis of the homologous export gate in Pseudomonas aeruginosa that mutation of this interface disrupts effector secretion. These results provide novel insights into the molecular mechanisms governing active substrate recognition and translocation through a T3SS. Many pathogenic Gram-negative bacteria utilize T3SS to export virulence factors in a well-regulated manner. Most component proteins of the T3SS are highly structurally conserved, capable of recognizing and secreting diverse effectors, which are recruited to the cytoplasmic sorting complex by chaperones. This work describes the molecular architecture of two essential components of a T3SS, identifies the interface between the components, and establishes the necessity of this interaction for effector secretion.
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Affiliation(s)
- Jaime L. Jensen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Shavait Yamini
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - Arne Rietsch
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, United States of America
| | - Benjamin W. Spiller
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
- * E-mail:
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Russo BC, Duncan JK, Wiscovitch AL, Hachey AC, Goldberg MB. Activation of Shigella flexneri type 3 secretion requires a host-induced conformational change to the translocon pore. PLoS Pathog 2019; 15:e1007928. [PMID: 31725799 PMCID: PMC6879154 DOI: 10.1371/journal.ppat.1007928] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 11/26/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022] Open
Abstract
Type 3 secretion systems (T3SSs) are conserved bacterial nanomachines that inject virulence proteins (effectors) into eukaryotic cells during infection. Due to their ability to inject heterologous proteins into human cells, these systems are being developed as therapeutic delivery devices. The T3SS assembles a translocon pore in the plasma membrane and then docks onto the pore. Docking activates effector secretion through the pore and into the host cytosol. Here, using Shigella flexneri, a model pathogen for the study of type 3 secretion, we determined the molecular mechanisms by which host intermediate filaments trigger docking and enable effector secretion. We show that the interaction of intermediate filaments with the translocon pore protein IpaC changed the pore's conformation in a manner that was required for docking. Intermediate filaments repositioned residues of the Shigella pore protein IpaC that are located on the surface of the pore and in the pore channel. Restricting these conformational changes blocked docking in an intermediate filament-dependent manner. These data demonstrate that a host-induced conformational change to the pore enables T3SS docking and effector secretion, providing new mechanistic insight into the regulation of type 3 secretion.
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Affiliation(s)
- Brian C. Russo
- Center for Bacterial Pathogenesis, Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jeffrey K. Duncan
- Center for Bacterial Pathogenesis, Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Alexandra L. Wiscovitch
- Center for Bacterial Pathogenesis, Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Research Scholar Initiative, The Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Austin C. Hachey
- Center for Bacterial Pathogenesis, Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Marcia B. Goldberg
- Center for Bacterial Pathogenesis, Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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8
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Lau N, Haeberle AL, O’Keeffe BJ, Latomanski EA, Celli J, Newton HJ, Knodler LA. SopF, a phosphoinositide binding effector, promotes the stability of the nascent Salmonella-containing vacuole. PLoS Pathog 2019; 15:e1007959. [PMID: 31339948 PMCID: PMC6682159 DOI: 10.1371/journal.ppat.1007959] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 08/05/2019] [Accepted: 07/02/2019] [Indexed: 12/19/2022] Open
Abstract
The enteric bacterial pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), utilizes two type III secretion systems (T3SSs) to invade host cells, survive and replicate intracellularly. T3SS1 and its dedicated effector proteins are required for bacterial entry into non-phagocytic cells and establishment and trafficking of the nascent Salmonella-containing vacuole (SCV). Here we identify the first T3SS1 effector required to maintain the integrity of the nascent SCV as SopF. SopF associates with host cell membranes, either when translocated by bacteria or ectopically expressed. Recombinant SopF binds to multiple phosphoinositides in protein-lipid overlays, suggesting that it targets eukaryotic cell membranes via phospholipid interactions. In yeast, the subcellular localization of SopF is dependent on the activity of Mss4, a phosphatidylinositol 4-phosphate 5-kinase that generates PI(4,5)P2 from PI(4)P, indicating that membrane recruitment of SopF requires specific phospholipids. Ectopically expressed SopF partially colocalizes with specific phosphoinositide pools present on the plasma membrane in mammalian cells and with cytoskeletal-associated markers at the leading edge of cells. Translocated SopF concentrates on plasma membrane ruffles and around intracellular bacteria, presumably on the SCV. SopF is not required for bacterial invasion of non-phagocytic cells but is required for maintenance of the internalization vacuole membrane as infection with a S. Typhimurium ΔsopF mutant led to increased lysis of the SCV compared to wild type bacteria. Our structure-function analysis shows that the carboxy-terminal seven amino acids of SopF are essential for its membrane association in host cells and to promote SCV membrane stability. We also describe that SopF and another T3SS1 effector, SopB, act antagonistically to modulate nascent SCV membrane dynamics. In summary, our study highlights that a delicate balance of type III effector activities regulates the stability of the Salmonella internalization vacuole.
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Affiliation(s)
- Nicole Lau
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
| | - Amanda L. Haeberle
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
| | - Brittany J. O’Keeffe
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
| | - Eleanor A. Latomanski
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Celli
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
| | - Hayley J. Newton
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (LAK); (HJN)
| | - Leigh A. Knodler
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
- * E-mail: (LAK); (HJN)
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9
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Jennings E, Esposito D, Rittinger K, Thurston TLM. Structure-function analyses of the bacterial zinc metalloprotease effector protein GtgA uncover key residues required for deactivating NF-κB. J Biol Chem 2018; 293:15316-15329. [PMID: 30049795 PMCID: PMC6166728 DOI: 10.1074/jbc.ra118.004255] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/23/2018] [Indexed: 12/03/2022] Open
Abstract
The closely related type III secretion system zinc metalloprotease effector proteins GtgA, GogA, and PipA are translocated into host cells during Salmonella infection. They then cleave nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) transcription factor subunits, dampening activation of the NF-κB signaling pathway and thereby suppressing host immune responses. We demonstrate here that GtgA, GogA, and PipA cleave a subset of NF-κB subunits, including p65, RelB, and cRel but not NF-κB1 and NF-κB2, whereas the functionally similar type III secretion system effector NleC of enteropathogenic and enterohemorrhagic Escherichia coli cleaved all five NF-κB subunits. Mutational analysis of NF-κB subunits revealed that a single nonconserved residue in NF-κB1 and NF-κB2 that corresponds to the P1' residue Arg-41 in p65 prevents cleavage of these subunits by GtgA, GogA, and PipA, explaining the observed substrate specificity of these enzymes. Crystal structures of GtgA in its apo-form and in complex with the p65 N-terminal domain explained the importance of the P1' residue. Furthermore, the pattern of interactions suggested that GtgA recognizes NF-κB subunits by mimicking the shape and negative charge of the DNA phosphate backbone. Moreover, structure-based mutational analysis of GtgA uncovered amino acids that are required for the interaction of GtgA with p65, as well as those that are required for full activity of GtgA in suppressing NF-κB activation. This study therefore provides detailed and critical insight into the mechanism of substrate recognition by this family of proteins important for bacterial virulence.
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Affiliation(s)
- Elliott Jennings
- From the Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ and
| | - Diego Esposito
- the Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom
| | - Katrin Rittinger
- the Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom
| | - Teresa L M Thurston
- From the Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ and
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10
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Bergeron JRC, Brockerman JA, Vuckovic M, Deng W, Okon M, Finlay BB, McIntosh LP, Strynadka NCJ. Characterization of the two conformations adopted by the T3SS inner-membrane protein PrgK. Protein Sci 2018; 27:1680-1691. [PMID: 30095200 DOI: 10.1002/pro.3447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 11/07/2022]
Abstract
The pathogenic bacterium Salmonella enterica serovar Typhimurium utilizes two type III secretion systems (T3SS) to inject effector proteins into target cells upon infection. The T3SS secretion apparatus (the injectisome) is a large macromolecular assembly composed of over twenty proteins, many in highly oligomeric states. A sub-structure of the injectisome, termed the basal body, spans both membranes and the periplasmic space of the bacterium. It is primarily composed of three integral membranes proteins, InvG, PrgH, and PrgK, that form ring structures through which components are secreted. In particular, PrgK possesses a periplasmic region consisting of two globular domains joined by a linker polypeptide. We showed previously that in isolation, this region adopts two distinct conformations, of with only one is observed in the assembled basal body complex. Here, using NMR spectroscopy, we further characterize these two conformations. In particular, we demonstrate that the interaction of the linker region with the first globular domain, as found in the intact basal body, is dependent upon the cis conformation of the Leu77-Pro78 peptide. Furthermore, this interaction is pH-dependent due to coupling with hydrogen bond formation between Tyr75 and His42 in its neutral Nδ1 H tautomeric form. This pH-dependent interaction may play a role in the regulation of the secretion apparatus disassembly in the context of bacterial infection.
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Affiliation(s)
- Julien R C Bergeron
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jacob A Brockerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wanyin Deng
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - B Brett Finlay
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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11
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Kato J, Dey S, Soto JE, Butan C, Wilkinson MC, De Guzman RN, Galan JE. A protein secreted by the Salmonella type III secretion system controls needle filament assembly. eLife 2018; 7:e35886. [PMID: 30015613 PMCID: PMC6066329 DOI: 10.7554/elife.35886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022] Open
Abstract
Type III protein secretion systems (T3SS) are encoded by several pathogenic or symbiotic bacteria. The central component of this nanomachine is the needle complex. Here we show in a Salmonella Typhimurium T3SS that assembly of the needle filament of this structure requires OrgC, a protein encoded within the T3SS gene cluster. Absence of OrgC results in significantly reduced number of needle substructures but does not affect needle length. We show that OrgC is secreted by the T3SS and that exogenous addition of OrgC can complement a ∆orgC mutation. We also show that OrgC interacts with the needle filament subunit PrgI and accelerates its polymerization into filaments in vitro. The structure of OrgC shows a novel fold with a shared topology with a domain from flagellar capping proteins. These findings identify a novel component of T3SS and provide new insight into the assembly of the type III secretion machine.
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Affiliation(s)
- Junya Kato
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Supratim Dey
- Department of Molecular BiosciencesUniversity of KansasLawrenceUnited States
| | - Jose E Soto
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Carmen Butan
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Mason C Wilkinson
- Department of Molecular BiosciencesUniversity of KansasLawrenceUnited States
| | - Roberto N De Guzman
- Department of Molecular BiosciencesUniversity of KansasLawrenceUnited States
| | - Jorge E Galan
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
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12
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Nadler H, Shaulov L, Blitsman Y, Mordechai M, Jopp J, Sal-Man N, Berkovich R. Deciphering the Mechanical Properties of Type III Secretion System EspA Protein by Single Molecule Force Spectroscopy. Langmuir 2018; 34:6261-6270. [PMID: 29726683 DOI: 10.1021/acs.langmuir.8b01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial pathogens inject virulence factors into host cells during bacterial infections using type III secretion systems. In enteropathogenic Escherichia coli, this system contains an external filament, formed by a self-oligomerizing protein called E. coli secreted protein A (EspA). The EspA filament penetrates the thick viscous mucus layer to facilitate the attachment of the bacteria to the gut-epithelium. To do that, the EspA filament requires noteworthy mechanical endurance considering the mechanical shear stresses found within the intestinal tract. To date, the mechanical properties of the EspA filament and the structural and biophysical knowledge of monomeric EspA are very limited, mostly due to the strong tendency of the protein to self-oligomerize. To overcome this limitation, we employed a single molecule force spectroscopy (SMFS) technique and studied the mechanical properties of EspA. Force extension dynamic of (I91)4-EspA-(I91)4 chimera revealed two structural unfolding events occurring at low forces during EspA unfolding, thus indicating no unique mechanical stability of the monomeric protein. SMFS examination of purified monomeric EspA protein, treated by a gradually refolding protocol, exhibited similar mechanical properties as the EspA protein within the (I91)4-EspA-(I91)4 chimera. Overall, our results suggest that the mechanical integrity of the EspA filament likely originates from the interactions between EspA monomers and not from the strength of an individual monomer.
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Affiliation(s)
- Hila Nadler
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Lihi Shaulov
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Yossi Blitsman
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Moran Mordechai
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Jürgen Jopp
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Neta Sal-Man
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Ronen Berkovich
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
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13
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Bzdzion L, Krezel H, Wrzeszcz K, Grzegorek I, Nowinska K, Chodaczek G, Swietnicki W. Design of small molecule inhibitors of type III secretion system ATPase EscN from enteropathogenic Escherichia coli. Acta Biochim Pol 2016; 64:49-63. [PMID: 27864920 DOI: 10.18388/abp.2016_1265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 09/06/2016] [Accepted: 09/22/2016] [Indexed: 11/10/2022]
Abstract
Enteropathogenic E. coli (EPEC) is a human pathogen using type III secretion system for delivery of proteins directly into the human host. The system contains a single ATPase, EscN, which is essential for uncoupling of proteins from their complexes with chaperones before the delivery. The structure of EscN ATPase (PDB code: 2obm) was used to screen computationally for small molecule inhibitors blocking its active site. Two lead candidates were examined but only one, Compound 54, was selected for further optimization. After extended QSAR optimization, two derivatives were found to be competitive inhibitors of EscN capable of blocking ATPase activity with a Ki below 50 µM. One candidate, WEN05-03, with a Ki=16±2 µM, was also minimally toxic to mammalian cells as determined by other assays. In the cell infection model of HeLa cells with EPEC, Compound WEN05-03 completely blocked actin cluster formation at 100 µM concentration, when analyzed by confocal microscopy. The second best inhibitor of EscN ATPase activity was WEN04-34 with a Ki=46±2 µM. However, the compound was highly toxic to the BALB/3T3 cell line. In summary, the work identifies a compound blocking bacterial ATPase in its active site without causing cellular toxicity to the host cells. It is the first report showing feasibility of using bacterial virulence system ATPase as a target for safe, non-toxic compounds and offering a proof-of-concept for non-antibiotic alternatives.
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Affiliation(s)
- Lukasz Bzdzion
- Department of Biotechnology, Wroclaw Research Centre EIT+ Ltd., Wrocław, Poland
| | - Hanna Krezel
- Department of Biotechnology, Wroclaw Research Centre EIT+ Ltd., Wrocław, Poland
| | - Karol Wrzeszcz
- Department of Biotechnology, Wroclaw Research Centre EIT+ Ltd., Wrocław, Poland
| | - Irmina Grzegorek
- Department of Biotechnology, Wroclaw Research Centre EIT+ Ltd., Wrocław, Poland
| | - Katarzyna Nowinska
- Department of Biotechnology, Wroclaw Research Centre EIT+ Ltd., Wrocław, Poland
| | - Grzegorz Chodaczek
- Department of Biotechnology, Wroclaw Research Centre EIT+ Ltd., Wrocław, Poland
| | - Wieslaw Swietnicki
- Department of Biotechnology, Wroclaw Research Centre EIT+ Ltd., Wrocław, Poland
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
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14
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Fricke P, Mance D, Chevelkov V, Giller K, Becker S, Baldus M, Lange A. High resolution observed in 800 MHz DNP spectra of extremely rigid type III secretion needles. J Biomol NMR 2016; 65:121-126. [PMID: 27351550 DOI: 10.1007/s10858-016-0044-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/22/2016] [Indexed: 05/05/2023]
Abstract
The cryogenic temperatures at which dynamic nuclear polarization (DNP) solid-state NMR experiments need to be carried out cause line-broadening, an effect that is especially detrimental for crowded protein spectra. By increasing the magnetic field strength from 600 to 800 MHz, the resolution of DNP spectra of type III secretion needles (T3SS) could be improved by 22 %, indicating that inhomogeneous broadening is not the dominant effect that limits the resolution of T3SS needles under DNP conditions. The outstanding spectral resolution of this system under DNP conditions can be attributed to its low overall flexibility.
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Affiliation(s)
- Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie, 13125, Berlin, Germany
| | - Deni Mance
- NMR Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie, 13125, Berlin, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Marc Baldus
- NMR Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie, 13125, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
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15
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Meriläinen G, Koski MK, Wierenga RK. The extended structure of the periplasmic region of CdsD, a structural protein of the type III secretion system of Chlamydia trachomatis. Protein Sci 2016; 25:987-98. [PMID: 26914207 PMCID: PMC4838655 DOI: 10.1002/pro.2906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/19/2016] [Indexed: 11/10/2022]
Abstract
The type III secretion system (T3SS) is required for the virulence of many gram-negative bacterial human pathogens. It is composed of several structural proteins, forming the secretion needle and its basis, the basal body. In Chlamydia spp., the T3SS inner membrane ring (IM-ring) of the basal body is formed by the periplasmic part of CdsD (outer ring) and CdsJ (inner ring). Here we describe the crystal structure of the C-terminal, periplasmic part of CdsD, not including the last 60 residues. Two crystal forms were obtained, grown in three different crystallization conditions. In both crystal forms there is one molecule per asymmetric unit adopting a similar extended structure. The structures consist of three periplasmic domains (PDs) of similar αββαβ topology as seen also in the structures of the homologous PrgH (Salmonella typhimurium) and YscD (Yersinia enterocolitica). Only in the C2 crystal form, there is a C-terminal additional helix after the PD3 domain. The relative orientation of the three subsequent CdsD PD domains with respect to each other is more extended than in PrgH but less extended than in YscD. Small-angle X-ray scattering data show that also in solution this CdsD construct adopts the same elongated shape. In both crystal forms the CdsD molecules are packed in a parallel fashion, using translational crystallographic symmetry. The most extensive crystal contacts are preserved in both crystal forms, suggesting a possible mode of assembly of the CdsD periplasmic part into a 24-mer complex forming the outer ring of the IM-ring of the T3SS.
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Affiliation(s)
- Gitte Meriläinen
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, 90014 University of OuluOuluFinland
| | - M. Kristian Koski
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, 90014 University of OuluOuluFinland
| | - Rik K. Wierenga
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, 90014 University of OuluOuluFinland
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16
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Kaur K, Chatterjee S, De Guzman RN. Characterization of the Shigella and Salmonella Type III Secretion System Tip-Translocon Protein-Protein Interaction by Paramagnetic Relaxation Enhancement. Chembiochem 2016; 17:745-752. [PMID: 26749041 PMCID: PMC4918631 DOI: 10.1002/cbic.201500556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Indexed: 12/21/2022]
Abstract
Many Gram-negative pathogens, such as Shigella and Salmonella, assemble the type III secretion system (T3SS) to inject virulence proteins directly into eukaryotic cells to initiate infectious diseases. The needle apparatus of the T3SS consists of a base, an extracellular needle, a tip protein complex, and a translocon. The atomic structure of the assembled tip complex and the translocon is unknown. Here, we show by NMR paramagnetic relaxation enhancement (PRE) that the mixed α-β domain at the distal region of the Shigella and Salmonella tip proteins interacts with the N-terminal ectodomain of their major translocon proteins. Our results reveal the binding surfaces involved in the tip-translocon protein-protein interaction and provide insights about the assembly of the needle apparatus of the T3SS.
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Affiliation(s)
- Kawaljit Kaur
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Srirupa Chatterjee
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Roberto N De Guzman
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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17
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Nariya MK, Israeli J, Shi JJ, Deeds EJ. Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System. PLoS Comput Biol 2016; 12:e1004851. [PMID: 27078235 PMCID: PMC4831731 DOI: 10.1371/journal.pcbi.1004851] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/06/2016] [Indexed: 12/28/2022] Open
Abstract
Type III Secretion Systems (T3SS) are complex bacterial structures that provide gram-negative pathogens with a unique virulence mechanism whereby they grow a needle-like structure in order to inject bacterial effector proteins into the cytoplasm of a host cell. Numerous experiments have been performed to understand the structural details of this nanomachine during the past decade. Despite the concerted efforts of molecular and structural biologists, several crucial aspects of the assembly of this structure, such as the regulation of the length of the needle itself, remain unclear. In this work, we used a combination of mathematical and computational techniques to better understand length control based on the timing of substrate switching, which is a possible mechanism for how bacteria ensure that the T3SS needles are neither too short nor too long. In particular, we predicted the form of the needle length distribution based on this mechanism, and found excellent agreement with available experimental data from Salmonella typhimurium with only a single free parameter. Although our findings provide preliminary evidence in support of the substrate switching model, they also make a set of quantitative predictions that, if tested experimentally, would assist in efforts to unambiguously characterize the regulatory mechanisms that control the growth of this crucial virulence factor.
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Affiliation(s)
- Maulik K. Nariya
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas, United States of America
| | - Johnny Israeli
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas, United States of America
| | - Jack J. Shi
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas, United States of America
| | - Eric J. Deeds
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Sante Fe Institute, Santa Fe, New Mexico, United States of America
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18
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Tsurumaru H, Hashimoto S, Okizaki K, Kanesaki Y, Yoshikawa H, Yamakawa T. A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj4 Genotype Soybeans. Appl Environ Microbiol 2015; 81:5812-9. [PMID: 26092458 PMCID: PMC4551253 DOI: 10.1128/aem.00823-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/12/2015] [Indexed: 11/20/2022] Open
Abstract
The nodulation of Bradyrhizobium japonicum Is-34 is restricted by Rj4 genotype soybeans (Glycine max). To identify the genes responsible for this incompatibility, Tn5 mutants of B. japonicum Is-34 that were able to overcome this nodulation restriction were obtained. Analysis of the Tn5 mutants revealed that Tn5 was inserted into a region containing the MA20_12780 gene. In addition, direct disruption of this gene using marker exchange overcame the nodulation restriction by Rj4 genotype soybeans. The MA20_12780 gene has a tts box motif in its upstream region, indicating a possibility that this gene encodes a type III secretion system (T3SS) effector protein. Bioinformatic characterization revealed that the MA20_12780 protein contains the small ubiquitin-like modifier (SUMO) protease domain of the C48 peptidase (ubiquitin-like protease 1 [Ulp1]) family. The results of the present study indicate that a putative T3SS effector encoded by the MA20_12780 gene causes the incompatibility with Rj4 genotype soybeans, and they suggest the possibility that the nodulation restriction of B. japonicum Is-34 may be due to Rj4 genotype soybeans recognizing the putative T3SS effector (MA20_12780 protein) as a virulence factor.
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Affiliation(s)
- Hirohito Tsurumaru
- Graduate School of Life Science, Tohoku University, Miyagi, Japan Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Syougo Hashimoto
- Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kouhei Okizaki
- Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yu Kanesaki
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Takeo Yamakawa
- Department of Biosciences and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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