1
|
Xian W, Fu J, Zhang Q, Li C, Zhao YB, Tang Z, Yuan Y, Wang Y, Zhou Y, Brzoic PS, Zheng N, Ouyang S, Luo ZQ, Liu X. The Shigella kinase effector OspG modulates host ubiquitin signaling to escape septin-cage entrapment. Nat Commun 2024; 15:3890. [PMID: 38719850 PMCID: PMC11078946 DOI: 10.1038/s41467-024-48205-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Shigella flexneri is a Gram-negative bacterium causing severe bloody dysentery. Its pathogenesis is largely dictated by a plasmid-encoded type III secretion system (T3SS) and its associated effectors. Among these, the effector OspG has been shown to bind to the ubiquitin conjugation machinery (E2~Ub) to activate its kinase activity. However, the cellular targets of OspG remain elusive despite years of extensive efforts. Here we show by unbiased phosphoproteomics that a major target of OspG is CAND1, a regulatory protein controlling the assembly of cullin-RING ubiquitin ligases (CRLs). CAND1 phosphorylation weakens its interaction with cullins, which is expected to impact a large panel of CRL E3s. Indeed, global ubiquitome profiling reveals marked changes in the ubiquitination landscape when OspG is introduced. Notably, OspG promotes ubiquitination of a class of cytoskeletal proteins called septins, thereby inhibiting formation of cage-like structures encircling cytosolic bacteria. Overall, we demonstrate that pathogens have evolved an elaborate strategy to modulate host ubiquitin signaling to evade septin-cage entrapment.
Collapse
Affiliation(s)
- Wei Xian
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Jiaqi Fu
- Department of Respiratory Medicine, Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, 130021, Changchun, China
| | - Qinxin Zhang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Chuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Yan-Bo Zhao
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhiheng Tang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Yi Yuan
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Ying Wang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Yan Zhou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Peter S Brzoic
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Songying Ouyang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China.
| |
Collapse
|
2
|
Vieira MFM, Hernandez G, Zhong Q, Arbesú M, Veloso T, Gomes T, Martins ML, Monteiro H, Frazão C, Frankel G, Zanzoni A, Cordeiro TN. The pathogen-encoded signalling receptor Tir exploits host-like intrinsic disorder for infection. Commun Biol 2024; 7:179. [PMID: 38351154 PMCID: PMC10864410 DOI: 10.1038/s42003-024-05856-9] [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: 11/23/2022] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
The translocated intimin receptor (Tir) is an essential type III secretion system (T3SS) effector of attaching and effacing pathogens contributing to the global foodborne disease burden. Tir acts as a cell-surface receptor in host cells, rewiring intracellular processes by targeting multiple host proteins. We investigated the molecular basis for Tir's binding diversity in signalling, finding that Tir is a disordered protein with host-like binding motifs. Unexpectedly, also are several other T3SS effectors. By an integrative approach, we reveal that Tir dimerises via an antiparallel OB-fold within a highly disordered N-terminal cytosolic domain. Also, it has a long disordered C-terminal cytosolic domain partially structured at host-like motifs that bind lipids. Membrane affinity depends on lipid composition and phosphorylation, highlighting a previously unrecognised host interaction impacting Tir-induced actin polymerisation and cell death. Furthermore, multi-site tyrosine phosphorylation enables Tir to engage host SH2 domains in a multivalent fuzzy complex, consistent with Tir's scaffolding role and binding promiscuity. Our findings provide insights into the intracellular Tir domains, highlighting the ability of T3SS effectors to exploit host-like protein disorder as a strategy for host evasion.
Collapse
Affiliation(s)
- Marta F M Vieira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Guillem Hernandez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Qiyun Zhong
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Miguel Arbesú
- Department of NMR-supported Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- InstaDeep Ltd, 5 Merchant Square, London, UK
| | - Tiago Veloso
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Tiago Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Maria L Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Hugo Monteiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Gad Frankel
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Andreas Zanzoni
- Aix-Marseille Université, Inserm, TAGC, UMR_S1090, Marseille, France
| | - Tiago N Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.
| |
Collapse
|
3
|
Nandi I, Aroeti B. Mitogen-Activated Protein Kinases (MAPKs) and Enteric Bacterial Pathogens: A Complex Interplay. Int J Mol Sci 2023; 24:11905. [PMID: 37569283 PMCID: PMC10419152 DOI: 10.3390/ijms241511905] [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: 06/18/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Diverse extracellular and intracellular cues activate mammalian mitogen-activated protein kinases (MAPKs). Canonically, the activation starts at cell surface receptors and continues via intracellular MAPK components, acting in the host cell nucleus as activators of transcriptional programs to regulate various cellular activities, including proinflammatory responses against bacterial pathogens. For instance, binding host pattern recognition receptors (PRRs) on the surface of intestinal epithelial cells to bacterial pathogen external components trigger the MAPK/NF-κB signaling cascade, eliciting cytokine production. This results in an innate immune response that can eliminate the bacterial pathogen. However, enteric bacterial pathogens evolved sophisticated mechanisms that interfere with such a response by delivering virulent proteins, termed effectors, and toxins into the host cells. These proteins act in numerous ways to inactivate or activate critical components of the MAPK signaling cascades and innate immunity. The consequence of such activities could lead to successful bacterial colonization, dissemination, and pathogenicity. This article will review enteric bacterial pathogens' strategies to modulate MAPKs and host responses. It will also discuss findings attempting to develop anti-microbial treatments by targeting MAPKs.
Collapse
Affiliation(s)
| | - Benjamin Aroeti
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190410, Israel;
| |
Collapse
|
4
|
Targeting of microvillus protein Eps8 by the NleH effector kinases from enteropathogenic E. coli. Proc Natl Acad Sci U S A 2022; 119:e2204332119. [PMID: 35976880 PMCID: PMC9407544 DOI: 10.1073/pnas.2204332119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Attaching and effacing (AE) lesion formation on enterocytes by enteropathogenic Escherichia coli (EPEC) requires the EPEC type III secretion system (T3SS). Two T3SS effectors injected into the host cell during infection are the atypical kinases, NleH1 and NleH2. However, the host targets of NleH1 and NleH2 kinase activity during infection have not been reported. Here phosphoproteomics identified Ser775 in the microvillus protein Eps8 as a bona fide target of NleH1 and NleH2 phosphorylation. Both kinases interacted with Eps8 through previously unrecognized, noncanonical "proline-rich" motifs, PxxDY, that bound the Src Homology 3 (SH3) domain of Eps8. Structural analysis of the Eps8 SH3 domain bound to a peptide containing one of the proline-rich motifs from NleH showed that the N-terminal part of the peptide adopts a type II polyproline helix, and its C-terminal "DY" segment makes multiple contacts with the SH3 domain. Ser775 phosphorylation by NleH1 or NleH2 hindered Eps8 bundling activity and drove dispersal of Eps8 from the AE lesion during EPEC infection. This finding suggested that NleH1 and NleH2 altered the cellular localization of Eps8 and the cytoskeletal composition of AE lesions during EPEC infection.
Collapse
|
5
|
Kotsaridis K, Tsakiri D, Sarris PF. Understanding enemy's weapons to an effective prevention: common virulence effects across microbial phytopathogens kingdoms. Crit Rev Microbiol 2022:1-15. [PMID: 35709325 DOI: 10.1080/1040841x.2022.2083939] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Plant-pathogens interaction is an ongoing confrontation leading to the emergence of new diseases. The majority of the invading microorganisms inject effector proteins into the host cell, to bypass the sophisticated defense system of the host. However, the effectors could also have other specialized functions, which can disrupt various biological pathways of the host cell. Pathogens can enrich their effectors arsenal to increase infection success or expand their host range. This usually is accomplished by the horizontal gene transfer. Nowadays, the development of specialized software that can predict proteins structure, has changed the experimental designing in effectors' function research. Different effectors of distinct plant pathogens tend to fold alike and have the same function and focussed structural studies on microbial effectors can help to uncover their catalytic/functional activities, while the structural similarity can enable cataloguing the great number of pathogens' effectors. In this review, we collectively present phytopathogens' effectors with known enzymatic functions and proteins structure, originated from all the kingdoms of microbial plant pathogens. Presentation of their common domains and motifs is also included. We believe that the in-depth understanding of the enemy's weapons will help the development of new strategies to prevent newly emerging or re-emerging plant pathogens.
Collapse
Affiliation(s)
| | | | - Panagiotis F Sarris
- Department of Biology, University of Crete, Crete, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Crete, Greece.,Biosciences, University of Exeter, Exeter, UK
| |
Collapse
|
6
|
Yadav M, Srinivasan M, Tulsian NK, Liu YX, Lin Q, Rosenshine I, Sivaraman J. Binding specificity of type three secretion system effector NleH2 to multi-cargo chaperone CesT and their phosphorylation. Protein Sci 2021; 30:2433-2444. [PMID: 34662450 DOI: 10.1002/pro.4210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Gram-negative pathogens like Enteropathogenic Escherichia coli (EPEC) utilize the type three secretion system (T3SS) to translocate various effector proteins that are needed to "hijack" the host system for pathogenic survival. Specialized T3SS chaperones inside bacterial cells stabilize these effector proteins and facilitate their translocation. CesT is a unique multi-cargo chaperone that interacts with and translocates ~10 different effector proteins. Here, we report the specific interaction between CesT and its key effector, NleH2, and explore the potential role of NleH2 as a kinase for CesT phosphorylation. First, we identified the chaperone-binding domain (CBD; 19-97aa) of NleH2, and mapped the specific interaction sites for both CesT and NleH2. The N- and C-terminal residues of the CBD interact with the dimeric interface of CesT. Further, we compared the CesT binding to NleH2, to that of another key effector Tir and with the global carbon regulator CsrA. Notably, the effectors have the binding regions at the β-sheet core and dimer interface of CesT, whereas the CsrA regulator interacts predominantly through the C-terminal region, which is found ~17 Å away from the effectors-binding sites. Next, we showed that NleH2 remains an active kinase even as a complex with CesT and is responsible for its autophosphorylation as well as phosphorylation of CesT at Tyr153. Collectively, our findings enhance the understanding of the role of multi-cargo chaperone CesT in orchestrating effector translocation through T3SS.
Collapse
Affiliation(s)
- Manisha Yadav
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Nikhil K Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Yu Xuan Liu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore
| |
Collapse
|
7
|
Wang S, Li S, Wang J, Li Q, Xin XF, Zhou S, Wang Y, Li D, Xu J, Luo ZQ, He SY, Sun W. A bacterial kinase phosphorylates OSK1 to suppress stomatal immunity in rice. Nat Commun 2021; 12:5479. [PMID: 34531388 PMCID: PMC8445998 DOI: 10.1038/s41467-021-25748-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
The Xanthomonas outer protein C2 (XopC2) family of bacterial effectors is widely found in plant pathogens and Legionella species. However, the biochemical activity and host targets of these effectors remain enigmatic. Here we show that ectopic expression of XopC2 promotes jasmonate signaling and stomatal opening in transgenic rice plants, which are more susceptible to Xanthomonas oryzae pv. oryzicola infection. Guided by these phenotypes, we discover that XopC2 represents a family of atypical kinases that specifically phosphorylate OSK1, a universal adaptor protein of the Skp1-Cullin-F-box ubiquitin ligase complexes. Intriguingly, OSK1 phosphorylation at Ser53 by XopC2 exclusively increases the binding affinity of OSK1 to the jasmonate receptor OsCOI1b, and specifically enhances the ubiquitination and degradation of JAZ transcription repressors and plant disease susceptibility through inhibiting stomatal immunity. These results define XopC2 as a prototypic member of a family of pathogenic effector kinases and highlight a smart molecular mechanism to activate jasmonate signaling.
Collapse
Affiliation(s)
- Shanzhi Wang
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Shuai Li
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Jiyang Wang
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Qian Li
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Xiu-Fang Xin
- grid.17088.360000 0001 2150 1785DOE Plant Research Laboratory, Michigan State University, East Lansing, MI USA ,grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), CAS John Innes Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Shanghai, China
| | - Shuang Zhou
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Yanping Wang
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Dayong Li
- grid.464353.30000 0000 9888 756XCollege of Plant Protection, Jilin Agricultural University, Changchun, Jilin China
| | - Jiaqing Xu
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhao-Qing Luo
- grid.169077.e0000 0004 1937 2197Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN USA
| | - Sheng Yang He
- grid.17088.360000 0001 2150 1785DOE Plant Research Laboratory, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Howard Hughes Medical Institute, Michigan State University, East Lansing, MI USA
| | - Wenxian Sun
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China ,grid.464353.30000 0000 9888 756XCollege of Plant Protection, Jilin Agricultural University, Changchun, Jilin China
| |
Collapse
|
8
|
Identification of a Family of Vibrio Type III Secretion System Effectors That Contain a Conserved Serine/Threonine Kinase Domain. mSphere 2021; 6:e0059921. [PMID: 34346702 PMCID: PMC8386410 DOI: 10.1128/msphere.00599-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Vibrio parahaemolyticus is a marine Gram-negative bacterium that is a leading cause of seafood-borne gastroenteritis. Pandemic strains of V. parahaemolyticus rely on a specialized protein secretion machinery known as the type III secretion system 2 (T3SS2) to cause disease. The T3SS2 mediates the delivery of effector proteins into the cytosol of infected cells, where they subvert multiple cellular pathways. Here, we identify a new T3SS2 effector protein encoded by VPA1328 (VP_RS21530) in V. parahaemolyticus RIMD2210633. Bioinformatic analysis revealed that VPA1328 is part of a larger family of uncharacterized T3SS effector proteins with homology to the VopG effector protein in Vibrio cholerae AM-19226. These VopG-like proteins are found in many but not all T3SS2 gene clusters and are distributed among diverse Vibrio species, including V. parahaemolyticus, V. cholerae, V. mimicus, and V. diabolicus and also in Shewanella baltica. Structure-based prediction analyses uncovered the presence of a conserved C-terminal kinase domain in VopG orthologs, similar to the serine/threonine kinase domain found in the NleH family of T3SS effector proteins. However, in contrast to NleH effector proteins, in tissue culture-based infections, VopG did not impede host cell death or suppress interleukin 8 (IL-8) secretion, suggesting a yet undefined role for VopG during V. parahaemolyticus infection. Collectively, our work reveals that VopG effector proteins, a new family of likely serine/threonine kinases, is widely distributed in the T3SS2 effector armamentarium among marine bacteria. IMPORTANCE Vibrio parahaemolyticus is the leading bacterial cause of seafood-borne gastroenteritis worldwide. The pathogen relies on a type III secretion system to deliver a variety of effector proteins into the cytosol of infected cells to subvert cellular function. In this study, we identified a novel Vibrio parahaemolyticus effector protein that is similar to the VopG effector of Vibrio cholerae. VopG-like effectors were found in diverse Vibrio species and contain a conserved serine/threonine kinase domain that bears similarity to the kinase domain in the enterohemorrhagic Escherichia coli (EHEC) and Shigella NleH effectors that manipulate host cell survival pathways and host immune responses. Together our findings identify a new family of Vibrio effector proteins and highlight the role of horizontal gene transfer events among marine bacteria in shaping T3SS gene clusters.
Collapse
|
9
|
The expanding world of protein kinase-like families in bacteria: forty families and counting. Biochem Soc Trans 2021; 48:1337-1352. [PMID: 32677675 DOI: 10.1042/bst20190712] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022]
Abstract
The protein kinase-like clan/superfamily is a large group of regulatory, signaling and biosynthetic enzymes that were historically regarded as typically eukaryotic proteins, although bacterial members have also been known for a long time. In this review, we explore the diversity of bacterial protein kinase like families, and discuss functional versatility of these enzymes, both the ones acting within the bacterial cell, and those acting within eukaryotic cells as effectors during infection. We focus on novel bacterial kinase-like families discovered in the last five years. A bioinformatics perspective is held here, hence sequence and structure comparison overview is presented, and also a comparison of genomic neighbourhoods of the families. We perform a phylum-level census of the families. Also, we discuss apparent pseudokinases that turned out to perform alternative catalytic functions by repurposing their atypical kinase-like active sites. We also highlight some 'unpopular' kinase-like families that await characterisation.
Collapse
|
10
|
Gazi AD, Kokkinidis M, Fadouloglou VE. α-Helices in the Type III Secretion Effectors: A Prevalent Feature with Versatile Roles. Int J Mol Sci 2021; 22:ijms22115412. [PMID: 34063760 PMCID: PMC8196651 DOI: 10.3390/ijms22115412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Type III Secretion Systems (T3SSs) are multicomponent nanomachines located at the cell envelope of Gram-negative bacteria. Their main function is to transport bacterial proteins either extracellularly or directly into the eukaryotic host cell cytoplasm. Type III Secretion effectors (T3SEs), latest to be secreted T3S substrates, are destined to act at the eukaryotic host cell cytoplasm and occasionally at the nucleus, hijacking cellular processes through mimicking eukaryotic proteins. A broad range of functions is attributed to T3SEs, ranging from the manipulation of the host cell's metabolism for the benefit of the bacterium to bypassing the host's defense mechanisms. To perform this broad range of manipulations, T3SEs have evolved numerous novel folds that are compatible with some basic requirements: they should be able to easily unfold, pass through the narrow T3SS channel, and refold to an active form when on the other side. In this review, the various folds of T3SEs are presented with the emphasis placed on the functional and structural importance of α-helices and helical domains.
Collapse
Affiliation(s)
- Anastasia D. Gazi
- Unit of Technology & Service Ultrastructural Bio-Imaging (UTechS UBI), Institut Pasteur, 75015 Paris, France
- Correspondence: (A.D.G.); (V.E.F.)
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion, 70013 Crete, Greece;
- Department of Biology, Voutes University Campus, University of Crete, Heraklion, 70013 Crete, Greece
| | - Vasiliki E. Fadouloglou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Correspondence: (A.D.G.); (V.E.F.)
| |
Collapse
|
11
|
Selvaraj C, Vierra M, Dinesh DC, Abhirami R, Singh SK. Structural insights of macromolecules involved in bacteria-induced apoptosis in the pathogenesis of human diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 126:1-38. [PMID: 34090612 DOI: 10.1016/bs.apcsb.2021.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Numbers of pathogenic bacteria can induce apoptosis in human host cells and modulate the cellular pathways responsible for inducing or inhibiting apoptosis. These pathogens are significantly recognized by host proteins and provoke the multitude of several signaling pathways and alter the cellular apoptotic stimuli. This process leads the bacterial entry into the mammalian cells and evokes a variety of responses like phagocytosis, release of mitochondrial cytochrome c, secretion of bacterial effectors, release of both apoptotic and inflammatory cytokines, and the triggering of apoptosis. Several mechanisms are involved in bacteria-induced apoptosis including, initiation of the endogenous death machinery, pore-forming proteins, and secretion of superantigens. Either small molecules or proteins may act as a binding partner responsible for forming the protein complexes and regulate enzymatic activity via protein-protein interactions. The bacteria induce apoptosis, attack the human cell and gain control over various types of cells and tissue. Since these processes are intricate in the defense mechanisms of host organisms against pathogenic bacteria and play an important function in host-pathogen interactions. In this chapter, we focus on the various bacterial-induced apoptosis mechanisms in host cells and discuss the important proteins and bacterial effectors that trigger the host cell apoptosis. The structural characterization of bacterial effector proteins and their interaction with human host cells are also considered.
Collapse
Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Marisol Vierra
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, United States
| | | | - Rajaram Abhirami
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| |
Collapse
|
12
|
Grishin A, Voth K, Gagarinova A, Cygler M. Structural biology of the invasion arsenal of Gram-negative bacterial pathogens. FEBS J 2021; 289:1385-1427. [PMID: 33650300 DOI: 10.1111/febs.15794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022]
Abstract
In the last several years, there has been a tremendous progress in the understanding of host-pathogen interactions and the mechanisms by which bacterial pathogens modulate behavior of the host cell. Pathogens use secretion systems to inject a set of proteins, called effectors, into the cytosol of the host cell. These effectors are secreted in a highly regulated, temporal manner and interact with host proteins to modify a multitude of cellular processes. The number of effectors varies between pathogens from ~ 30 to as many as ~ 350. The functional redundancy of effectors encoded by each pathogen makes it difficult to determine the cellular effects or function of individual effectors, since their individual knockouts frequently produce no easily detectable phenotypes. Structural biology of effector proteins and their interactions with host proteins, in conjunction with cell biology approaches, has provided invaluable information about the cellular function of effectors and underlying molecular mechanisms of their modes of action. Many bacterial effectors are functionally equivalent to host proteins while being structurally divergent from them. Other effector proteins display new, previously unobserved functionalities. Here, we summarize the contribution of the structural characterization of effectors and effector-host protein complexes to our understanding of host subversion mechanisms used by the most commonly investigated Gram-negative bacterial pathogens. We describe in some detail the enzymatic activities discovered among effector proteins and how they affect various cellular processes.
Collapse
Affiliation(s)
- Andrey Grishin
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Kevin Voth
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| |
Collapse
|
13
|
Riebisch AK, Mühlen S. Attaching and effacing pathogens: the effector ABC of immune subversion. Future Microbiol 2020; 15:945-958. [PMID: 32716209 DOI: 10.2217/fmb-2019-0274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The innate immune response resembles an essential barrier to bacterial infection. Many bacterial pathogens have, therefore, evolved mechanisms to evade from or subvert the host immune response in order to colonize, survive and multiply. The attaching and effacing pathogens enteropathogenic Escherichia coli, enterohaemorrhagic E. coli, Escherichia albertii and Citrobacter rodentium are Gram-negative extracellular gastrointestinal pathogens. They use a type III secretion system to inject effector proteins into the host cell to manipulate a variety of cellular processes. Over the last decade, considerable progress was made in identifying and characterizing the effector proteins of attaching and effacing pathogens that are involved in the inhibition of innate immune signaling pathways, in determining their host cell targets and elucidating the mechanisms they employ. Their functions will be reviewed here.
Collapse
Affiliation(s)
- Anna Katharina Riebisch
- Systems-Oriented Immunology & Inflammation Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.,Institute for Molecular & Clinical Immunology, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany.,Department of Molecular Immunology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Sabrina Mühlen
- Institute for Infectiology, University of Münster, 48149 Münster, Germany.,German Center for Infection Research (DZIF), Associated Site University of Münster, 48149 Münster, Germany
| |
Collapse
|
14
|
A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity. Cell 2019; 179:205-218.e21. [PMID: 31522888 DOI: 10.1016/j.cell.2019.08.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 06/21/2019] [Accepted: 08/09/2019] [Indexed: 01/01/2023]
Abstract
The molecular chaperone HSP90 facilitates the folding of several client proteins, including innate immune receptors and protein kinases. HSP90 is an essential component of plant and animal immunity, yet pathogenic strategies that directly target the chaperone have not been described. Here, we identify the HopBF1 family of bacterial effectors as eukaryotic-specific HSP90 protein kinases. HopBF1 adopts a minimal protein kinase fold that is recognized by HSP90 as a host client. As a result, HopBF1 phosphorylates HSP90 to completely inhibit the chaperone's ATPase activity. We demonstrate that phosphorylation of HSP90 prevents activation of immune receptors that trigger the hypersensitive response in plants. Consequently, HopBF1-dependent phosphorylation of HSP90 is sufficient to induce severe disease symptoms in plants infected with the bacterial pathogen, Pseudomonas syringae. Collectively, our results uncover a family of bacterial effector kinases with toxin-like properties and reveal a previously unrecognized betrayal mechanism by which bacterial pathogens modulate host immunity.
Collapse
|
15
|
Park JB, Kim YH, Yoo Y, Kim J, Jun SH, Cho JW, El Qaidi S, Walpole S, Monaco S, García-García AA, Wu M, Hays MP, Hurtado-Guerrero R, Angulo J, Hardwidge PR, Shin JS, Cho HS. Structural basis for arginine glycosylation of host substrates by bacterial effector proteins. Nat Commun 2018; 9:4283. [PMID: 30327479 PMCID: PMC6191443 DOI: 10.1038/s41467-018-06680-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/19/2018] [Indexed: 01/11/2023] Open
Abstract
The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-κB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although they differ in protein substrate specificity. Here we report that these enzymes are retaining glycosyltransferases composed of a helix-loop-helix (HLH) domain, a lid domain, and a catalytic domain. A conserved HEN motif (His-Glu-Asn) in the active site is important for enzyme catalysis and bacterial virulence. We observe differences between SseK1 and SseK2 in interactions with substrates and identify substrate residues that are critical for enzyme recognition. Long Molecular Dynamics simulations suggest that the HLH domain determines substrate specificity and the lid-domain regulates the opening of the active site. Overall, our data suggest a front-face SNi mechanism, explain differences in activities among these effectors, and have implications for future drug development against enteric pathogens.
Collapse
Affiliation(s)
- Jun Bae Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Young Hun Kim
- Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Youngki Yoo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Juyeon Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Sung-Hoon Jun
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Center for Electron Microscopy Research, Korea Basic Science Institute, Ochang, Chungbuk, 28119, Republic of Korea
| | - Jin Won Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Ana A García-García
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain
| | - Miaomiao Wu
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Michael P Hays
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Ramon Hurtado-Guerrero
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain. .,Fundación ARAID, 50018, Zaragoza, Spain.
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Jeon-Soo Shin
- Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea. .,Severance Biomedical Science Institute and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| |
Collapse
|
16
|
Grishin AM, Barber KR, Gu RX, Tieleman DP, Shaw GS, Cygler M. Regulation of Shigella Effector Kinase OspG through Modulation of Its Dynamic Properties. J Mol Biol 2018; 430:2096-2112. [DOI: 10.1016/j.jmb.2018.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/03/2018] [Accepted: 05/09/2018] [Indexed: 01/01/2023]
|
17
|
Kralicek SE, Nguyen M, Rhee KJ, Tapia R, Hecht G. EPEC NleH1 is significantly more effective in reversing colitis and reducing mortality than NleH2 via differential effects on host signaling pathways. J Transl Med 2018; 98:477-488. [PMID: 29396422 PMCID: PMC5920738 DOI: 10.1038/s41374-017-0016-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 12/31/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a foodborne pathogen that uses a type III secretion system to translocate effector molecules into host intestinal epithelial cells (IECs) subverting several host cell processes and signaling cascades. Interestingly, EPEC infection induces only modest intestinal inflammation in the host. The homologous EPEC effector proteins, NleH1 and NleH2, suppress the nuclear factor-κB (NF-κB) pathway and apoptosis in vitro. Increased apoptosis and activation of NF-κB and MAP kinases (MAPK) contribute to the pathogenesis of inflammatory bowel diseases (IBD). The aim of this study was to determine if NleH1 and NleH2 also block MAPK pathways in vitro and in vivo, and to compare the effects of these bacterial proteins on a murine model of colitis. Cultured IECs were infected with various strains of EPEC expressing NleH1 and NleH2, or not, and the activation of ERK1/2 and p38 was determined. In addition, the impact of infection with various strains of EPEC on murine DSS colitis was assessed by change in body weight, colon length, histology, and survival. Activation of apoptosis and MAPK signaling were also evaluated. Our data show that NleH1, but not NleH2, suppresses ERK1/2 and p38 activation in vitro. Interestingly, NleH1 affords significantly greater protection against and hastens recovery from dextran sodium sulfate (DSS)-induced colitis compared to NleH2. Strikingly, colitis-associated mortality was abolished by infection with EPEC strains expressing NleH1. Interestingly, in vivo NleH1 suppresses activation of ERK1/2 and p38 and blocks apoptosis independent of the kinase domain that inhibits NF-κB. In contrast, NleH2 suppresses only caspase-3 and p38, but not ERK1/2. We conclude that NleH1 affords greater protection against and improves recovery from DSS colitis compared to NleH2 due to its ability to suppress ERK1/2 in addition to NF-κB, p38, and apoptosis. These findings warrant further investigation of anti-inflammatory bacterial proteins as novel treatments for IBD.
Collapse
Affiliation(s)
- Sarah E. Kralicek
- Department of Medicine, Division of Gastroenterology and Nutrition, Loyola University Chicago, Maywood, IL, USA
| | - Mai Nguyen
- Cortexyme Inc, South San Francisco, CA, USA
| | - Ki-Jong Rhee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University at Wonju, Wonju, Gangwon-do, Republic of Korea
| | - Rocio Tapia
- Department of Medicine, Division of Gastroenterology and Nutrition, Loyola University Chicago, Maywood, IL, USA
| | - Gail Hecht
- Department of Medicine, Division of Gastroenterology and Nutrition, Loyola University Chicago, Maywood, IL, USA. .,Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA. .,Edward Hines Jr. VA Hospital, Hines, IL, USA.
| |
Collapse
|
18
|
Cooperative Immune Suppression by Escherichia coli and Shigella Effector Proteins. Infect Immun 2018; 86:IAI.00560-17. [PMID: 29339461 DOI: 10.1128/iai.00560-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The enteric attaching and effacing (A/E) pathogens enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) and the invasive pathogens enteroinvasive E. coli (EIEC) and Shigella encode type III secretion systems (T3SS) used to inject effector proteins into human host cells during infection. Among these are a group of effectors required for NF-κB-mediated host immune evasion. Recent studies have identified several effector proteins from A/E pathogens and EIEC/Shigella that are involved in suppression of NF-κB and have uncovered their cellular and molecular functions. A novel mechanism among these effectors from both groups of pathogens is to coordinate effector function during infection. This cooperativity among effector proteins explains how bacterial pathogens are able to effectively suppress innate immune defense mechanisms in response to diverse classes of immune receptor signaling complexes (RSCs) stimulated during infection.
Collapse
|
19
|
El Qaidi S, Wu M, Zhu C, Hardwidge PR. Salmonella, E. coli, and Citrobacter Type III Secretion System Effector Proteins that Alter Host Innate Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1111:205-218. [PMID: 30411307 DOI: 10.1007/5584_2018_289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bacteria deliver virulence proteins termed 'effectors' to counteract host innate immunity. Protein-protein interactions within the host cell ultimately subvert the generation of an inflammatory response to the infecting pathogen. Here we briefly describe a subset of T3SS effectors produced by enterohemorrhagic Escherichia coli (EHEC), enteropathogenic E. coli (EPEC), Citrobacter rodentium, and Salmonella enterica that inhibit innate immune pathways. These effectors are interesting for structural and mechanistic reasons, as well as for their potential utility in being engineered to treat human autoimmune disorders associated with perturbations in NF-κB signaling.
Collapse
Affiliation(s)
- Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Miaomiao Wu
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Congrui Zhu
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
20
|
Tawk C, Sharan M, Eulalio A, Vogel J. A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins. Sci Rep 2017; 7:9328. [PMID: 28839189 PMCID: PMC5570926 DOI: 10.1038/s41598-017-09527-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/27/2017] [Indexed: 12/15/2022] Open
Abstract
Many pathogenic bacteria utilize specialized secretion systems to deliver proteins called effectors into eukaryotic cells for manipulation of host pathways. The vast majority of known effector targets are host proteins, whereas a potential targeting of host nucleic acids remains little explored. There is only one family of effectors known to target DNA directly, and effectors binding host RNA are unknown. Here, we take a two-pronged approach to search for RNA-binding effectors, combining biocomputational prediction of RNA-binding domains (RBDs) in a newly assembled comprehensive dataset of bacterial secreted proteins, and experimental screening for RNA binding in mammalian cells. Only a small subset of effectors were predicted to carry an RBD, indicating that if RNA targeting was common, it would likely involve new types of RBDs. Our experimental evaluation of effectors with predicted RBDs further argues for a general paucity of RNA binding activities amongst bacterial effectors. We obtained evidence that PipB2 and Lpg2844, effector proteins of Salmonella and Legionella species, respectively, may harbor novel biochemical activities. Our study presenting the first systematic evaluation of the RNA-targeting potential of bacterial effectors offers a basis for discussion of whether or not host RNA is a prominent target of secreted bacterial proteins.
Collapse
Affiliation(s)
- Caroline Tawk
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Malvika Sharan
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ana Eulalio
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany.
| |
Collapse
|
21
|
Pearson JS, Giogha C, Wong Fok Lung T, Hartland EL. The Genetics of EnteropathogenicEscherichia coliVirulence. Annu Rev Genet 2016; 50:493-513. [DOI: 10.1146/annurev-genet-120215-035138] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jaclyn S. Pearson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia; , , ,
| | - Cristina Giogha
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia; , , ,
| | - Tania Wong Fok Lung
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia; , , ,
| | - Elizabeth L. Hartland
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia; , , ,
| |
Collapse
|
22
|
DeForte S, Reddy KD, Uversky VN. Quarterly intrinsic disorder digest (January-February-March, 2014). INTRINSICALLY DISORDERED PROTEINS 2016; 4:e1153395. [PMID: 28232896 DOI: 10.1080/21690707.2016.1153395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This is the 5th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during the period of January, February, and March of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
Collapse
Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Krishna D Reddy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Biology Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| |
Collapse
|
23
|
Flayhan A, Bergé C, Baïlo N, Doublet P, Bayliss R, Terradot L. The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase. Sci Rep 2015; 5:14602. [PMID: 26419332 PMCID: PMC4588518 DOI: 10.1038/srep14602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/28/2015] [Indexed: 01/24/2023] Open
Abstract
Bacterial pathogens subvert signalling pathways to promote invasion and/or replication into the host. LegK1-4 proteins are eukaryotic-like serine/threonine kinases that are translocated by the Dot/Icm type IV secretion system (T4SS) of several Legionella pneumophila strains. We present the crystal structures of an active fragment of the LegK4 protein in apo and substrate-bound states. The structure of LegK41–445 reveals a eukaryotic-like kinase domain flanked by a novel cap domain and a four-helix bundle. The protein self-assembles through interactions mediated by helices αF and αG that generate a dimeric interface not previously observed in a protein kinase. The helix αG is displaced compared to previous kinase structures, and its role in stabilization of the activation loop is taken on by the dimerisation interface. The apo-form of the protein has an open conformation with a disordered P-loop but a structured activation segment in absence of targeted phosphorylation. The nucleotide-binding site of LegK4 contains an unusual set of residues that mediate non-canonical interactions with AMP-PNP. Nucleotide binding results in limited changes in the active site, suggesting that LegK4 constitutive kinase activity does not depend on phosphorylation of the activation loop but on the stabilizing effects of the dimer.
Collapse
Affiliation(s)
- Ali Flayhan
- UMR 5086 BMSSI CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Célia Bergé
- UMR 5086 BMSSI CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Nathalie Baïlo
- Legionella Pathogenesis Group, International Center for Infectiology Research, Université de Lyon Lyon, France.,INSERM U1111 Lyon, France.,Ecole Normale Suptérieure de Lyon Lyon, France.,Centre International de Recherche en Infectiologie, Université Lyon 1 Lyon, France.,CNRS, UMR5308 Lyon, France
| | - Patricia Doublet
- Legionella Pathogenesis Group, International Center for Infectiology Research, Université de Lyon Lyon, France.,INSERM U1111 Lyon, France.,Ecole Normale Suptérieure de Lyon Lyon, France.,Centre International de Recherche en Infectiologie, Université Lyon 1 Lyon, France.,CNRS, UMR5308 Lyon, France
| | - Richard Bayliss
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Laurent Terradot
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| |
Collapse
|
24
|
Luo J, Hu J, Zhang Y, Hu Q, Li S. Hijacking of death receptor signaling by bacterial pathogen effectors. Apoptosis 2015; 20:216-23. [PMID: 25528554 DOI: 10.1007/s10495-014-1068-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Death receptors such as Tumor necrosis factor receptor 1, FAS and TNF-associated apoptosis-inducing ligand-R1/2 play a major role in counteracting with bacterial pathogen infection through regulation of inflammation and programmed cell death. The highly regulated death receptor signaling is frequently targeted by gram-negative bacterial pathogens such as Salmonella, Shigella, enteropathogenic Escherichia coli and enterohamorrhagic Escherichia coli, which harbor a conserved type III secretion system that delivers a repertoire of effector proteins to manipulate host signal transductions for their own benefit. This review focuses on how bacterial gut pathogens hijack death receptor signaling to inhibit host NF-κB and programmed cell death pathways.
Collapse
Affiliation(s)
- Jie Luo
- Taihe Hospital, Hubei University of Medicine, #32 Renmin South Rd, Shiyan, 442000, Hubei, China
| | | | | | | | | |
Collapse
|
25
|
Grishin AM, Beyrakhova KA, Cygler M. Structural insight into effector proteins of Gram-negative bacterial pathogens that modulate the phosphoproteome of their host. Protein Sci 2015; 24:604-20. [PMID: 25565677 DOI: 10.1002/pro.2636] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 12/29/2014] [Indexed: 12/16/2022]
Abstract
Invading pathogens manipulate cellular process of the host cell to establish a safe replicative niche. To this end they secrete a spectrum of proteins called effectors that modify cellular environment through a variety of mechanisms. One of the most important mechanisms is the manipulation of cellular signaling through modifications of the cellular phosphoproteome. Phosphorylation/dephosphorylation plays a pivotal role in eukaryotic cell signaling, with ∼ 500 different kinases and ∼ 130 phosphatases in the human genome. Pathogens affect the phosphoproteome either directly through the action of bacterial effectors, and/or indirectly through downstream effects of host proteins modified by the effectors. Here we review the current knowledge of the structure, catalytic mechanism and function of bacterial effectors that modify directly the phosphorylation state of host proteins. These effectors belong to four enzyme classes: kinases, phosphatases, phospholyases and serine/threonine acetylases.
Collapse
Affiliation(s)
- Andrey M Grishin
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada, S7N 5E5
| | | | | |
Collapse
|
26
|
Grishin AM, Condos TEC, Barber KR, Campbell-Valois FX, Parsot C, Shaw GS, Cygler M. Structural basis for the inhibition of host protein ubiquitination by Shigella effector kinase OspG. Structure 2014; 22:878-88. [PMID: 24856362 DOI: 10.1016/j.str.2014.04.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 03/19/2014] [Accepted: 04/09/2014] [Indexed: 11/30/2022]
Abstract
Shigella invasion of its human host is assisted by T3SS-delivered effector proteins. The OspG effector kinase binds ubiquitin and ubiquitin-loaded E2-conjugating enzymes, including UbcH5b and UbcH7, and attenuates the host innate immune NF-kB signaling. We present the structure of OspG bound to the UbcH7∼Ub conjugate. OspG has a minimal kinase fold lacking the activation loop of regulatory kinases. UbcH7∼Ub binds OspG at sites remote from the kinase active site, yet increases its kinase activity. The ubiquitin is positioned in the "open" conformation with respect to UbcH7 using its I44 patch to interact with the C terminus of OspG. UbcH7 binds to OspG using two conserved loops essential for E3 ligase recruitment. The interaction of the UbcH7∼Ub with OspG is remarkably similar to the interaction of an E2∼Ub with a HECT E3 ligase. OspG interferes with the interaction of UbcH7 with the E3 parkin and inhibits the activity of the E3.
Collapse
Affiliation(s)
- Andrey M Grishin
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Tara E C Condos
- Department of Biochemistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Kathryn R Barber
- Department of Biochemistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | | | - Claude Parsot
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 75724 Paris, France; INSERM, U786, 75015, Paris, France
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada.
| |
Collapse
|