1
|
Chowdhury G, Ghosh D, Zhou Y, Deb AK, Mukhopadhyay AK, Dutta S, Chakraborty S. Field evaluation of a simple and rapid diagnostic test, RLDT to detect Shigella and enterotoxigenic E. coli in Indian children. Sci Rep 2024; 14:8816. [PMID: 38627472 PMCID: PMC11021469 DOI: 10.1038/s41598-024-59181-6] [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: 08/24/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The diagnostic assays currently used to detect Shigella spp. (Shigella) and enterotoxigenic Escherichia coli (ETEC) are complex or elaborate which make them difficult to apply in resource poor settings where these diseases are endemic. The simple and rapid nucleic acid amplification-based assay "Rapid LAMP-based Diagnostic Test (RLDT)" was evaluated to detect Shigella spp (Shigella) and enterotoxigenic Escherichia coli (ETEC) and determine the epidemiology of these pathogens in Kolkata, India. Stool samples (n = 405) from children under five years old with diarrhea seeking care at the hospitals were tested, and 85(21%) and 68(17%) by RLDT, 91(23%) and 58(14%) by quantitative PCR (qPCR) and 35(9%) and 15(4%) by culture, were positive for Shigella and ETEC, respectively. The RLDT showed almost perfect agreement with qPCR, Kappa 0.96 and 0.89; sensitivity 93% and 98%; specificity 100% and 97% for Shigella and ETEC, respectively. While RLDT detected additional 12% Shigella and 13% ETEC than culture, all culture positives for Shigella and ETEC except one each were also positive by the RLDT, sensitivity 97% and 93% respectively. RLDT is a simple, sensitive, and rapid assay that could be implemented with minimum training in the endemic regions to strengthen the disease surveillance system and rapid outbreak detection.
Collapse
Affiliation(s)
- Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Debjani Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Yiyi Zhou
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alok K Deb
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India.
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| |
Collapse
|
2
|
Kyono Y, Magboo JD, Daley EA, Flowers SA. Antipsychotic quetiapine alters the mouse fecal resistome by impacting antibiotic efflux, cell membrane, and cell wall synthesis genes. Microbiol Spectr 2024; 12:e0380423. [PMID: 38099619 PMCID: PMC10782992 DOI: 10.1128/spectrum.03804-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study significantly contributes to our understanding of how certain medications can unintentionally contribute to a major global health issue, i.e., antibiotic resistance. Quetiapine, a widely used antipsychotic medication, was found to increase key resistance mechanisms of gut bacteria to antibiotics in mice. Specifically, these data suggest that quetiapine may target elements of the bacterial cell membrane. If similar effects are found in humans, this medicine could unexpectedly make it harder to treat certain infections. This research emphasizes the importance of being mindful about not just antibiotics themselves, but also about other medications that could inadvertently contribute to this problem. Ultimately, these findings underline the necessity for more in-depth research on the broader impact of pharmaceuticals.
Collapse
Affiliation(s)
- Yasuhiro Kyono
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jonathan D. Magboo
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Elizabeth A. Daley
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stephanie A. Flowers
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| |
Collapse
|
3
|
Chowdhury G, Ghosh D, Zhou Y, Deb AK, Mukhopadhyay AK, Dutta S, Chakraborty S. Field evaluation of a simple and rapid diagnostic test, RLDT to detect Shigella and enterotoxigenic E. coli in Indian children. RESEARCH SQUARE 2023:rs.3.rs-3293791. [PMID: 37886599 PMCID: PMC10602125 DOI: 10.21203/rs.3.rs-3293791/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The diagnostic assays currently used to detect Shigella spp. (Shigella) and enterotoxigenic Escherichia coli (ETEC) are complex or elaborate which make them difficult to apply in resource poor settings where these diseases are endemic. The simple and rapid nucleic acid amplification-based assay "Rapid LAMP-based Diagnostic Test (RLDT)" was evaluated to detect Shigella spp (Shigella) and enterotoxigenic Escherichia coli (ETEC) and determine the epidemiology of these pathogens in Kolkata, India. Stool samples (n = 405) from children under five years old with diarrhea seeking care at the hospitals were tested, and 85(21%) and 68(17%) by RLDT, 91(23%) and 58(14%) by quantitative PCR (qPCR) and 35(9%) and 15(4%) by culture, were positive for Shigella and ETEC, respectively. The RLDT showed almost perfect agreement with qPCR, Kappa 0.96 and 0.89; sensitivity 93% and 98%; specificity 100% and 97% for Shigella and ETEC, respectively. While RLDT detected 12% more Shigella and 13% more ETEC than culture, all culture positives for Shigella and ETEC except one each were also positive by the RLDT, sensitivity 97% and 93% respectively. RLDT is a simple, sensitive, and rapid assay that could be implemented with minimum training in the endemic regions to strengthen the disease surveillance system and rapid outbreak detection.
Collapse
Affiliation(s)
| | - Debjani Ghosh
- ICMR-National Institute of Cholera and Enteric Diseases
| | - YiYi Zhou
- Johns Hopkins Bloomberg School of Public Health
| | - Alok K Deb
- ICMR-National Institute of Cholera and Enteric Diseases
| | | | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases
| | | |
Collapse
|
4
|
Ouyang X, Chen J, Sun Z, Wang R, Wu X, Li B, Song C, Liu P, Zhang M. Ubiquitin E3 ligase activity of Ralstonia solanacearum effector RipAW is not essential for induction of plant defense in Nicotiana benthamiana. Front Microbiol 2023; 14:1201444. [PMID: 37293211 PMCID: PMC10244751 DOI: 10.3389/fmicb.2023.1201444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/04/2023] [Indexed: 06/10/2023] Open
Abstract
As one of the most destructive bacterial phytopathogens, Ralstonia solanacearum causes substantial annual yield losses of many important crops. Deciphering the functional mechanisms of type III effectors, the crucial factors mediating R. solanacearum-plant interactions, will provide a valuable basis for protecting crop plants from R. solanacearum. Recently, the NEL (novel E3 ligase) effector RipAW was found to induce cell death on Nicotiana benthamiana in a E3 ligase activity-dependent manner. Here, we further deciphered the role of the E3 ligase activity in RipAW-triggered plant immunity. We found that RipAWC177A, the E3 ligase mutant of RipAW, could not induce cell death but retained the ability of triggering plant immunity in N. benthamiana, indicating that the E3 ligase activity is not essential for RipAW-triggered immunity. By generating truncated mutants of RipAW, we further showed that the N-terminus, NEL domain and C-terminus are all required but not sufficient for RipAW-induced cell death. Furthermore, all truncated mutants of RipAW triggered ETI immune responses in N. benthamiana, confirming that the E3 ligase activity is not essential for RipAW-triggered plant immunity. Finally, we demonstrated that RipAW- and RipAWC177A-triggered immunity in N. benthamiana requires SGT1 (suppressor of G2 allele of skp1), but not EDS1 (enhanced disease susceptibility), NRG1 (N requirement gene 1), NRC (NLR required for cell death) proteins or SA (salicylic acid) pathway. Our findings provide a typical case in which the effector-induced cell death can be uncoupled with immune responses, shedding new light on effector-triggered plant immunity. Our data also provide clues for further in-depth study of mechanism underlying RipAW-induced plant immunity.
Collapse
Affiliation(s)
- Xue Ouyang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Jialan Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhimao Sun
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Rongbo Wang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xuan Wu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Benjin Li
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Congfeng Song
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Peiqing Liu
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Meixiang Zhang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| |
Collapse
|
5
|
Pakbin B, Brück WM, Brück TB. Molecular Mechanisms of Shigella Pathogenesis; Recent Advances. Int J Mol Sci 2023; 24:ijms24032448. [PMID: 36768771 PMCID: PMC9917014 DOI: 10.3390/ijms24032448] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Shigella species are the main cause of bacillary diarrhoea or shigellosis in humans. These organisms are the inhabitants of the human intestinal tract; however, they are one of the main concerns in public health in both developed and developing countries. In this study, we reviewed and summarised the previous studies and recent advances in molecular mechanisms of pathogenesis of Shigella Dysenteriae and non-Dysenteriae species. Regarding the molecular mechanisms of pathogenesis and the presence of virulence factor encoding genes in Shigella strains, species of this bacteria are categorised into Dysenteriae and non-Dysenteriae clinical groups. Shigella species uses attachment, invasion, intracellular motility, toxin secretion and host cell interruption mechanisms, causing mild diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome diseases in humans through the expression of effector delivery systems, protein effectors, toxins, host cell immune system evasion and iron uptake genes. The investigation of these genes and molecular mechanisms can help us to develop and design new methods to detect and differentiate these organisms in food and clinical samples and determine appropriate strategies to prevent and treat the intestinal and extraintestinal infections caused by these enteric pathogens.
Collapse
Affiliation(s)
- Babak Pakbin
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748 Garching bei München, Germany
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
| | - Wolfram Manuel Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
- Correspondence: (W.M.B.); (T.B.B.)
| | - Thomas B. Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748 Garching bei München, Germany
- Correspondence: (W.M.B.); (T.B.B.)
| |
Collapse
|
6
|
Abstract
The major function of the mammalian immune system is to prevent and control infections caused by enteropathogens that collectively have altered human destiny. In fact, as the gastrointestinal tissues are the major interface of mammals with the environment, up to 70% of the human immune system is dedicated to patrolling them The defenses are multi-tiered and include the endogenous microflora that mediate colonization resistance as well as physical barriers intended to compartmentalize infections. The gastrointestinal tract and associated lymphoid tissue are also protected by sophisticated interleaved arrays of active innate and adaptive immune defenses. Remarkably, some bacterial enteropathogens have acquired an arsenal of virulence factors with which they neutralize all these formidable barriers to infection, causing disease ranging from mild self-limiting gastroenteritis to in some cases devastating human disease.
Collapse
Affiliation(s)
- Micah J. Worley
- Department of Biology, University of Louisville, Louisville, Kentucky, USA,CONTACT Micah J. Worley Department of Biology, University of Louisville, 139 Life Sciences Bldg, Louisville, Kentucky, USA
| |
Collapse
|
7
|
Das A, Doss K, Mandal J. CRISPR-cas heterogeneity and plasmid incompatibility types in relation to virulence determinants of Shigella. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Virulence factors (VFs) are the most potent weapon in the molecular armoury of
Shigella
. In bacteria, the mobile genetic elements (MGEs) are contributors to the evolution of different types of clustered regularly interspaced short palindromic repeats-CRISPR associated genes (CRISPR-cas) variants and plasmid incompatibility types. The present study explored the virulence potential of
Shigella
in relation to the CRISPR-cas pattern and incompatibility types among the isolates.
Hypothesis/Gap Statement. The profile of the CRISPR-cas systems among clinical isolates of
Shigella
in India has not been reported earlier. Limited knowledge is available on the pattern of plasmid incompatibility groups among clinical isolates
Shigella
. The bias is always towards studying the genetic elements associated with AMR, but the present study highlights CRISPR-cas and incompatibility types among
Shigella
in association with virulence.
Aim. We aimed to investigate the distribution of virulence factors, CRISPR-cas pattern followed by plasmid incompatibility types among
Shigella
isolates.
Methodology. Between 2012–2017, a total of 187 isolates of
Shigella
were included in the study. The virulence genes' distribution was carried out. CRISPR-cas profiling followed by analysis of the repeats and spacers was carried out. PCR-based replicon typing was used to determine the incompatibility types. The interplay was statistically determined using STATA.
Results. The distribution of virulence genes showed varied pattern with ipaH present in all the isolates followed by ompA (93.6 %), virF (66.8 %), ial and sen (60.4 %), set1A (39.6 %) and set1B (39 %). CRISPR 1, CRISPR 3 and Cas6-Cas5 region were dominantly conserved. Twenty-two types of spacers were identified. The CRISPR3 repeat appeared to have a highly conserved sequence. CRISPR2 being the least common CRISPR type showed a strong association with an array of virulence genes (ial-set1A-set1B-virF) while CRISPR1 being the most dominant showed the least association with virulence genes (sen-virF). The dominant plasmids were found to be belonging to the inc FII group. The incompatibility groups FII, IncIγ, U, FIIS, FIIK, K, A/C, I1alpha was found to be associated with a greater number of virulence genes.
Conclusion. The isolates showed increasing diversity in their gene content that contributes to increasing heterogeneity among the isolates, which is a known virulence strategy among pathogens.
Collapse
Affiliation(s)
- Ankita Das
- Department of Microbiology, Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
| | - Kamali Doss
- Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
| | - Jharna Mandal
- Department of Microbiology, Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
| |
Collapse
|
8
|
Ohmura-Hoshino M, Miyaki Y, Yashima S. A one-step multiplex PCR-based assay for simultaneous detection and classification of virulence factors to identify five diarrheagenic E. coli pathotypes. Heliyon 2022; 8:e10231. [PMID: 36046532 PMCID: PMC9421181 DOI: 10.1016/j.heliyon.2022.e10231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/22/2022] [Accepted: 08/04/2022] [Indexed: 12/02/2022] Open
Abstract
Human diarrhea-causing strains of Escherichia coli are referred to as diarrheagenic E. coli (DEC). DEC can be divided into five main categories based on distinct epidemiological and clinical features, specific virulence determinants, and association with certain serotypes. In the present study, a simple and rapid one-step single reaction multiplex PCR (mPCR) assay was developed for the simultaneous identification and differentiation of five currently established DEC pathotypes causing gastrointestinal diseases. The mPCR incorporated 10 primer pairs to amplify 10 virulence genes specific to the different pathotypes (i.e., stx1 and stx2 for EHEC, elt and sth for ETEC, eaeA and bfpA for EPEC, aggR and astA for EAEC, and ipaH and invE for EIEC) and to generate DNA fragments of sufficiently different sizes to be unequivocally resolved. All strains were detected at concentrations ranging from 104 to 107 CFU/mL. To demonstrate the utility of the mPCR assay, 236 clinically isolated strains of DEC from two hospitals were successfully categorized. One-step mPCR technique reduced the cost and effort involved in the identification of various virulence factors in DEC. Thus, we demonstrated that the newly developed mPCR assay has the potential to be introduced as a diagnostic tool that can be utilized for the detection of DEC as an additional check in clinical laboratories and for confirmation in health and environment institutes, health centers, and reference laboratories. We developed a one-step single reaction mPCR to detect DEC strains. 10 prominently expressed genes characteristic to the five pathotypes were assayed. All the strains were detected at concentrations ranging from 104 to 107 CFU/mL. We show cost- and time-effective detection of DEC in clinical cultured samples.
Collapse
Affiliation(s)
- Mari Ohmura-Hoshino
- Department of Medical Technology, School of Nursing and Medical Care, Yokkaichi Nursing and Medical Care University, Yokkaichi, Japan
| | | | | |
Collapse
|
9
|
Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Sci Rep 2022; 12:6868. [PMID: 35477739 PMCID: PMC9046306 DOI: 10.1038/s41598-022-10827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/31/2022] [Indexed: 11/08/2022] Open
Abstract
Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.
Collapse
|
10
|
Efficient production of immunologically active Shigella invasion plasmid antigens IpaB and IpaH using a cell-free expression system. Appl Microbiol Biotechnol 2021; 106:401-414. [PMID: 34932164 PMCID: PMC8688910 DOI: 10.1007/s00253-021-11701-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022]
Abstract
Abstract Shigella spp. invade the colonic epithelium and cause bacillary dysentery in humans. Individuals living in areas that lack access to clean water and sanitation are the most affected. Even though infection can be treated with antibiotics, Shigella antimicrobial drug resistance complicates clinical management. Despite decades of effort, there are no licensed vaccines to prevent shigellosis. The highly conserved invasion plasmid antigens (Ipa), which are components of the Shigella type III secretion system, participate in bacterial epithelial cell invasion and have been pursued as vaccine targets. However, expression and purification of these proteins in conventional cell-based systems have been challenging due to solubility issues and extremely low recovery yields. These difficulties have impeded manufacturing and clinical advancement. In this study, we describe a new method to express Ipa proteins using the Xpress+TM cell-free protein synthesis (CFPS) platform. Both IpaB and the C-terminal domain of IpaH1.4 (IpaH-CTD) were efficiently produced with this technology at yields > 200 mg/L. Furthermore, the expression was linearly scaled in a bioreactor under controlled conditions, and proteins were successfully purified using multimode column chromatography to > 95% purity as determined by SDS-PAGE. Biophysical characterization of the cell-free synthetized IpaB and IpaH-CTD using SEC-MALS analysis showed well-defined oligomeric states of the proteins in solution. Functional analysis revealed similar immunoreactivity as compared to antigens purified from E. coli. These results demonstrate the efficiency of CFPS for Shigella protein production; the practicality and scalability of this method will facilitate production of antigens for Shigella vaccine development and immunological analysis. Key points • First report of Shigella IpaB and IpaH produced at high purity and yield using CFPS • CFPS-IpaB and IpaH perform similarly to E. coli–produced proteins in immunoassays • CFPS-IpaB and IpaH react with Shigella-specific human antibodies and are immunogenic in mice. Graphical abstract ![]()
Collapse
|
11
|
Tripathi-Giesgen I, Behrends C, Alpi AF. The ubiquitin ligation machinery in the defense against bacterial pathogens. EMBO Rep 2021; 22:e52864. [PMID: 34515402 PMCID: PMC8567218 DOI: 10.15252/embr.202152864] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/21/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin system is an important part of the host cellular defense program during bacterial infection. This is in particular evident for a number of bacteria including Salmonella Typhimurium and Mycobacterium tuberculosis which—inventively as part of their invasion strategy or accidentally upon rupture of seized host endomembranes—become exposed to the host cytosol. Ubiquitylation is involved in the detection and clearance of these bacteria as well as in the activation of innate immune and inflammatory signaling. Remarkably, all these defense responses seem to emanate from a dense layer of ubiquitin which coats the invading pathogens. In this review, we focus on the diverse group of host cell E3 ubiquitin ligases that help to tailor this ubiquitin coat. In particular, we address how the divergent ubiquitin conjugation mechanisms of these ligases contribute to the complexity of the anti‐bacterial coating and the recruitment of different ubiquitin‐binding effectors. We also discuss the activation and coordination of the different E3 ligases and which strategies bacteria evolved to evade the activities of the host ubiquitin system.
Collapse
Affiliation(s)
- Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy), Medical Faculty, Ludwig-Maximilians-University München, München, Germany
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| |
Collapse
|
12
|
Luchetti G, Roncaioli JL, Chavez RA, Schubert AF, Kofoed EM, Reja R, Cheung TK, Liang Y, Webster JD, Lehoux I, Skippington E, Reeder J, Haley B, Tan MW, Rose CM, Newton K, Kayagaki N, Vance RE, Dixit VM. Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection. Cell Host Microbe 2021; 29:1521-1530.e10. [PMID: 34492225 DOI: 10.1016/j.chom.2021.08.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/08/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
The pore-forming protein gasdermin D (GSDMD) executes lytic cell death called pyroptosis to eliminate the replicative niche of intracellular pathogens. Evolution favors pathogens that circumvent this host defense mechanism. Here, we show that the Shigella ubiquitin ligase IpaH7.8 functions as an inhibitor of GSDMD. Shigella is an enteroinvasive bacterium that causes hemorrhagic gastroenteritis in primates, but not rodents. IpaH7.8 contributes to species specificity by ubiquitinating human, but not mouse, GSDMD and targeting it for proteasomal degradation. Accordingly, infection of human epithelial cells with IpaH7.8-deficient Shigella flexneri results in increased GSDMD-dependent cell death compared with wild type. Consistent with pyroptosis contributing to murine disease resistance, eliminating GSDMD from NLRC4-deficient mice, which are already sensitized to oral infection with Shigella flexneri, leads to further enhanced bacterial replication and increased disease severity. This work highlights a species-specific pathogen arms race focused on maintenance of host cell viability.
Collapse
Affiliation(s)
- Giovanni Luchetti
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Justin L Roncaioli
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA
| | - Roberto A Chavez
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA
| | - Alexander F Schubert
- Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eric M Kofoed
- Department of Immunology and Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Oncology Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tommy K Cheung
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yuxin Liang
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Isabelle Lehoux
- Department of Biomolecular Resources, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Elizabeth Skippington
- Department of OMNI Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janina Reeder
- Department of OMNI Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Man Wah Tan
- Department of Immunology and Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nobuhiko Kayagaki
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Russell E Vance
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley CA 94720, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| |
Collapse
|
13
|
Halimeh FB, Rafei R, Osman M, Kassem II, Diene SM, Dabboussi F, Rolain JM, Hamze M. Historical, current, and emerging tools for identification and serotyping of Shigella. Braz J Microbiol 2021; 52:2043-2055. [PMID: 34524650 PMCID: PMC8441030 DOI: 10.1007/s42770-021-00573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
The Shigella genus includes serious foodborne disease etiologic agents, with 4 species and 54 serotypes. Identification at species and serotype levels is a crucial task in microbiological laboratories. Nevertheless, the genetic similarity between Shigella spp. and Escherichia coli challenges the correct identification and serotyping of Shigella spp., with subsequent negative repercussions on surveillance, epidemiological investigations, and selection of appropriate treatments. For this purpose, multiple techniques have been developed historically ranging from phenotype-based methods and single or multilocus molecular techniques to whole-genome sequencing (WGS). To facilitate the selection of the most relevant method, we herein provide a global overview of historical and emerging identification and serotyping techniques with a particular focus on the WGS-based approaches. This review highlights the excellent discriminatory power of WGS to more accurately elucidate the epidemiology of Shigella spp., disclose novel promising genomic targets for surveillance methods, and validate previous well-established methods.
Collapse
Affiliation(s)
- Fatima Bachir Halimeh
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14850, USA
| | - Issmat I Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA
| | - Seydina M Diene
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Marc Rolain
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
| |
Collapse
|
14
|
Sun J, Wang X, Lin H, Wan L, Chen J, Yang X, Li D, Zhang Y, He X, Wang B, Dong M, Zhong H, Wei C. Shigella escapes lysosomal degradation through inactivation of Rab31 by IpaH4.5. J Med Microbiol 2021; 70. [PMID: 34296983 DOI: 10.1099/jmm.0.001382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Shigella flexneri is an intracellular bacterial pathogen that utilizes a type III secretion apparatus to inject effector proteins into host cells.Hypothesis/Gap Statement. The T3SS effector IpaH4.5 is important for the virulence of Shigella.Aim. This study aimed to elucidate the molecular mechanism and host target of the IpaH4.5 as well as its roles in S. flexneri infection.Methodology. The GAP assay was used to identify substrate Rab GTPases of IpaH4.5. A coimmunoprecipitation assay was applied to identify the interaction of Rab GTPases with IpaH4.5. A confocal microscopy analysis was used to assess the effects of IpaH4.5 on mannose 6-phosphate receptor (MPR) trafficking. To identify the effects of IpaH4.5 GAP activity on the activity of lysosomal cathepsin B, the Magic Red-RR assay was used. Finally, the intracellular persistence assay was used to identify IpaH4.5 GAP activity in S. flexneri intracellular growth.Results. We found that the effector IpaH4.5 disrupts MPR trafficking and lysosomal function, thereby counteracting host lysosomal degradation. IpaH4.5 harbours TBC-like dual-finger motifs and exhibits potent RabGAP activities towards Rab31. IpaH4.5 disrupts the transport of the cation-dependent mannose 6-phosphate receptor (CD-MPR) from the Golgi to the endosome by targeting Rab31, thereby attenuating lysosomal function. As a result, the intracellular persistence of S. flexneri requires IpaH4.5 TBC-like GAP activity to mediate bacterial escape from host lysosome-mediated elimination.Conclusion. We identified an unknown function of IpaH4.5 and its potential role in S. flexneri infection.
Collapse
Affiliation(s)
- Jin Sun
- Basic Medical College, Qingdao University, Qingdao, PR China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Xiaolin Wang
- Basic Medical College, Qingdao University, Qingdao, PR China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Haotian Lin
- Basic Medical College, Qingdao University, Qingdao, PR China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Luming Wan
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Ji Chen
- Basic Medical College, Qingdao University, Qingdao, PR China
| | - Xiaopan Yang
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Dongyu Li
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Yanhong Zhang
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Xiang He
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Bin Wang
- Basic Medical College, Qingdao University, Qingdao, PR China
| | - Mingxin Dong
- Basic Medical College, Qingdao University, Qingdao, PR China
| | - Hui Zhong
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Congwen Wei
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| |
Collapse
|
15
|
Zhu Z, Wang W, Cao M, Zhu Q, Ma T, Zhang Y, Liu G, Zhou X, Li B, Shi Y, Zhang J. Virulence factors and molecular characteristics of Shigella flexneri isolated from calves with diarrhea. BMC Microbiol 2021; 21:214. [PMID: 34271864 PMCID: PMC8285881 DOI: 10.1186/s12866-021-02277-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background The natural hosts of Shigella are typically humans and other primates, but it has been shown that the host range of Shigella has expanded to many animals. Although Shigella is becoming a major threat to animals, there is limited information on the genetic background of local strains. The purpose of this study was to assess the presence of virulence factors and the molecular characteristics of S. flexneri isolated from calves with diarrhea. Results Fifty-four S. flexneri isolates from Gansun, Shanxi, Qinghai, Xinjiang and Tibet obtained during 2014 to 2016 possessed four typical biochemical characteristics of Shigella. The prevalences of ipaH, virA, ipaBCD, ial, sen, set1A, set1B and stx were 100 %, 100 %, 77.78 %, 79.63 %, 48.15 %, 48.15 and 0 %, respectively. Multilocus variable number tandem repeat analysis (MLVA) based on 8 variable number of tandem repeat (VNTR) loci discriminated the isolates into 39 different MLVA types (MTs), pulsed field gel electrophoresis (PFGE) based on NotI digestion divided the 54 isolates into 31 PFGE types (PTs), and multilocus sequence typing (MLST) based on 15 housekeeping genes differentiated the isolates into 7 MLST sequence types (STs). Conclusions The findings from this study enrich our knowledge of the molecular characteristics of S. flexneri collected from calves with diarrhea, which will be important for addressing clinical and epidemiological issues regarding shigellosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02277-0.
Collapse
Affiliation(s)
- Zhen Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China.,College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Weiwei Wang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Mingze Cao
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Qiqi Zhu
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Tenghe Ma
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Yongying Zhang
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Guanhui Liu
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Xuzheng Zhou
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Bing Li
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Yuxiang Shi
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Jiyu Zhang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China.
| |
Collapse
|
16
|
Li W, Jiang L, Liu X, Guo R, Ma S, Wang J, Ma S, Li S, Li H. YhjC is a novel transcriptional regulator required for Shigella flexneri virulence. Virulence 2021; 12:1661-1671. [PMID: 34152261 PMCID: PMC8218686 DOI: 10.1080/21505594.2021.1936767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Shigella is an intracellular pathogen that primarily infects the human colon and causes shigellosis. Shigella virulence relies largely on the type III secretion system (T3SS) and secreted effectors. VirF, the master Shigella virulence regulator, is essential for the expression of T3SS-related genes. In this study, we found that YhjC, a LysR-type transcriptional regulator, is required for Shigella virulence through activating the transcription of virF. Pathogenicity of the yhjC mutant, including colonization in the colons of guinea pigs as well as its ability for host cell adhesion and invasion, was significantly lowered. Expression levels of virF and nearly all VirF-dependent genes were downregulated by yhjC deletion, indicating that YhjC can activate virF transcription. Electrophoretic mobility shift assay analysis demonstrated that YhjC could bind directly to the virF promoter region. Therefore, YhjC is a novel virulence regulator that positively regulates the virF expression and promotes Shigella virulence. Additionally, genome-wide expression analysis identified the presence of other genes in the large virulence plasmid and a genome exhibiting differential expression in response to yhjC deletion, with 169 downregulated and 99 upregulated genes, indicating that YhjC also functioned as a global regulatory factor.
Collapse
Affiliation(s)
- Wanwu Li
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China.,Shandong Center for Food and Drug Evaluation & Certification, Jinan, China
| | - Lingyan Jiang
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Xiaoqian Liu
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Rui Guo
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China
| | - Shuai Ma
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Jingting Wang
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Shuangshuang Ma
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Shujie Li
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Huiying Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China.,School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| |
Collapse
|
17
|
García A, Fox JG. A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts. Comp Med 2021; 71:3-45. [PMID: 33419487 PMCID: PMC7898170 DOI: 10.30802/aalas-cm-20-000054] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/17/2020] [Accepted: 09/19/2020] [Indexed: 11/05/2022]
Abstract
E. coli is one of the most common species of bacteria colonizing humans and animals. The singularity of E. coli 's genus and species underestimates its multifaceted nature, which is represented by different strains, each with different combinations of distinct virulence factors. In fact, several E. coli pathotypes, or hybrid strains, may be associated with both subclinical infection and a range of clinical conditions, including enteric, urinary, and systemic infections. E. coli may also express DNA-damaging toxins that could impact cancer development. This review summarizes the different E. coli pathotypes in the context of their history, hosts, clinical signs, epidemiology, and control. The pathotypic characterization of E. coli in the context of disease in different animals, including humans, provides comparative and One Health perspectives that will guide future clinical and research investigations of E. coli infections.
Collapse
Key Words
- aa, aggregative adherence
- a/e, attaching and effacing
- aepec, atypical epec
- afa, afimbrial adhesin
- aida-i, adhesin involved in diffuse adherence
- aiec, adherent invasive e. coli
- apec, avian pathogenic e. coli
- atcc, american type culture collection
- bfp, bundle-forming pilus
- cd, crohn disease
- cdt, cytolethal distending toxin gene
- clb, colibactin
- cnf, cytotoxic necrotizing factor
- cs, coli surface (antigens)
- daec, diffusely adhering e. coli
- db, dutch belted
- eae, e. coli attaching and effacing gene
- eaec, enteroaggregative e. coli
- eaf, epec adherence factor (plasmid)
- eahec, entero-aggregative-hemorrhagic e. coli
- east-1, enteroaggregative e. coli heat-stable enterotoxin
- e. coli, escherichia coli
- ed, edema disease
- ehec, enterohemorrhagic e. coli
- eiec, enteroinvasive e. coli
- epec, enteropathogenic e. coli
- esbl, extended-spectrum β-lactamase
- esp, e. coli secreted protein
- etec, enterotoxigenic e. coli
- expec, extraintestinal pathogenic e. coli
- fyua, yersiniabactin receptor gene
- gi, gastrointestinal
- hly, hemolysin
- hus, hemolytic uremic syndrome
- ibd, inflammatory bowel disease
- la, localized adherence
- lee, locus of enterocyte effacement
- lpf, long polar fimbriae
- lt, heat-labile (enterotoxin)
- mlst, multilocus sequence typing
- ndm, new delhi metallo-β-lactamase
- nzw, new zealand white
- pap, pyelonephritis-associated pilus
- pks, polyketide synthase
- sfa, s fimbrial adhesin
- slt, shiga-like toxin
- st, heat-stable (enterotoxin)
- stec, stx-producing e. coli
- stx, shiga toxin
- tepec, typical epec
- upec, uropathogenic e. coli
- uti, urinary tract infection
Collapse
Affiliation(s)
- Alexis García
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts;,
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| |
Collapse
|
18
|
Ye Y, Xiong Y, Huang H. Substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of bacterial ubiquitin ligase IpaH9.8. Commun Biol 2020; 3:752. [PMID: 33303953 PMCID: PMC7728815 DOI: 10.1038/s42003-020-01492-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
IpaH enzymes are bacterial E3 ligases targeting host proteins for ubiquitylation. Two autoinhibition modes of IpaH enzymes have been proposed based on the relative positioning of the Leucine-rich repeat domain (LRR) with respect to the NEL domain. In mode 1, substrate-binding competitively displaces the interactions between theLRR and NEL to relieve autoinhibition. However, the molecular basis for mode 2 is unclear. Here, we present the crystal structures of Shigella IpaH9.8 and the LRR of IpaH9.8 in complex with the substrate of human guanylate-binding protein 1 (hGBP1). A hydrophobic cluster in the C-terminus of IpaH9.8LRR forms a hydrophobic pocket involved in binding the NEL domain, and the binding is important for IpaH9.8 autoinhibition. Substrate-binding destabilizes the hydrophobic cluster by inducing conformational changes of IpaH9.8LRR. Arg166 and Phe187 in IpaH9.8LRR function as sensors for substrate-binding. Collectively, our findings provide insights into the molecular mechanisms for the actication of IpaH9.8 in autoinhibition mode 2. Ye, Xiong et al. present crystal structures of bacterial E3 ubiquitin ligase IpaH9.8 and IpaH9.8LRR–hGBP1. They find that substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of IpaH9.8. This study provides insights into the mechanisms underlying substrate-induced activation of IpaH9.8.
Collapse
Affiliation(s)
- Yuxin Ye
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055, Shenzhen, China. .,Shenzhen Bay Laboratory Pingshan Translational Medicine Center, Shenzhen, China. .,Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, 518055, Shenzhen, China.
| | - Yuxian Xiong
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055, Shenzhen, China.,Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, 518055, Shenzhen, China
| | - Hao Huang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055, Shenzhen, China. .,Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, 518055, Shenzhen, China.
| |
Collapse
|
19
|
Wang X, Sun J, Wan L, Yang X, Lin H, Zhang Y, He X, Zhong H, Guan K, Min M, Sun Z, Yang X, Wang B, Dong M, Wei C. The Shigella Type III Secretion Effector IpaH4.5 Targets NLRP3 to Activate Inflammasome Signaling. Front Cell Infect Microbiol 2020; 10:511798. [PMID: 33117724 PMCID: PMC7561375 DOI: 10.3389/fcimb.2020.511798] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
Activation of the NLRP3 inflammasome requires the expression of NLRP3, which is strictly regulated by its capacity to directly recognize microbial-derived substances. Even though the involvement of caspase-1 activation in macrophages via NLRP3 and NLRC4 has been discovered, the accurate mechanisms by which Shigella infection triggers NLRP3 activation remain inadequately understood. Here, we demonstrate that IpaH4.5, a Shigella T3SS effector, triggers inflammasome activation by regulating NLRP3 expression through the E3 ubiquitin ligase activity of IpaH4.5. First, we found that IpaH4.5 interacted with NLRP3. As a result, IpaH4.5 modulated NLRP3 protein stability and inflammasome activation. Bacteria lacking IpaH4.5 had dramatically reduced ability to induce pyroptosis. Our results identify a previously unrecognized target of IpaH4.5 in the regulation of inflammasome signaling and clarify the molecular basis for the cytosolic response to the T3SS effector.
Collapse
Affiliation(s)
- Xiaolin Wang
- Basic Medical College, Qingdao University, Qingdao, China.,Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Jin Sun
- Basic Medical College, Qingdao University, Qingdao, China.,Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Luming Wan
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiaopan Yang
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Haotian Lin
- Basic Medical College, Qingdao University, Qingdao, China.,Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yanhong Zhang
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiang He
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Hui Zhong
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Kai Guan
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Min Min
- Department of Gastroenterology and Hepatology, The Fifth Medical Center of Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Zhenxue Sun
- Third Medical Center of Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Xiaoli Yang
- Third Medical Center of Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Bin Wang
- Basic Medical College, Qingdao University, Qingdao, China
| | - Mingxin Dong
- Basic Medical College, Qingdao University, Qingdao, China
| | - Congwen Wei
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| |
Collapse
|
20
|
Whelan R, McVicker G, Leo JC. Staying out or Going in? The Interplay between Type 3 and Type 5 Secretion Systems in Adhesion and Invasion of Enterobacterial Pathogens. Int J Mol Sci 2020; 21:E4102. [PMID: 32521829 PMCID: PMC7312957 DOI: 10.3390/ijms21114102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Enteric pathogens rely on a variety of toxins, adhesins and other virulence factors to cause infections. Some of the best studied pathogens belong to the Enterobacterales order; these include enteropathogenic and enterohemorrhagic Escherichia coli, Shigella spp., and the enteropathogenic Yersiniae. The pathogenesis of these organisms involves two different secretion systems, a type 3 secretion system (T3SS) and type 5 secretion systems (T5SSs). The T3SS forms a syringe-like structure spanning both bacterial membranes and the host cell plasma membrane that translocates toxic effector proteins into the cytoplasm of the host cell. T5SSs are also known as autotransporters, and they export part of their own polypeptide to the bacterial cell surface where it exerts its function, such as adhesion to host cell receptors. During infection with these enteropathogens, the T3SS and T5SS act in concert to bring about rearrangements of the host cell cytoskeleton, either to invade the cell, confer intracellular motility, evade phagocytosis or produce novel structures to shelter the bacteria. Thus, in these bacteria, not only the T3SS effectors but also T5SS proteins could be considered "cytoskeletoxins" that bring about profound alterations in host cell cytoskeletal dynamics and lead to pathogenic outcomes.
Collapse
Affiliation(s)
| | | | - Jack C. Leo
- Antimicrobial Resistance, Omics and Microbiota Group, Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK; (R.W.); (G.M.)
| |
Collapse
|
21
|
Bacterial Factors Targeting the Nucleus: The Growing Family of Nucleomodulins. Toxins (Basel) 2020; 12:toxins12040220. [PMID: 32244550 PMCID: PMC7232420 DOI: 10.3390/toxins12040220] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/23/2020] [Accepted: 03/29/2020] [Indexed: 12/18/2022] Open
Abstract
Pathogenic bacteria secrete a variety of proteins that manipulate host cell function by targeting components of the plasma membrane, cytosol, or organelles. In the last decade, several studies identified bacterial factors acting within the nucleus on gene expression or other nuclear processes, which has led to the emergence of a new family of effectors called “nucleomodulins”. In human and animal pathogens, Listeria monocytogenes for Gram-positive bacteria and Anaplasma phagocytophilum, Ehrlichia chaffeensis, Chlamydia trachomatis, Legionella pneumophila, Shigella flexneri, and Escherichia coli for Gram-negative bacteria, have led to pioneering discoveries. In this review, we present these paradigms and detail various mechanisms and core elements (e.g., DNA, histones, epigenetic regulators, transcription or splicing factors, signaling proteins) targeted by nucleomodulins. We particularly focus on nucleomodulins interacting with epifactors, such as LntA of Listeria and ankyrin repeat- or tandem repeat-containing effectors of Rickettsiales, and nucleomodulins from various bacterial species acting as post-translational modification enzymes. The study of bacterial nucleomodulins not only generates important knowledge about the control of host responses by microbes but also creates new tools to decipher the dynamic regulations that occur in the nucleus. This research also has potential applications in the field of biotechnology. Finally, this raises questions about the epigenetic effects of infectious diseases.
Collapse
|
22
|
Liu S, Feng J, Pu J, Xu X, Lu S, Yang J, Wang Y, Jin D, Du X, Meng X, Luo X, Sun H, Xiong Y, Ye C, Lan R, Xu J. Genomic and molecular characterisation of Escherichia marmotae from wild rodents in Qinghai-Tibet plateau as a potential pathogen. Sci Rep 2019; 9:10619. [PMID: 31337784 PMCID: PMC6650469 DOI: 10.1038/s41598-019-46831-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/03/2019] [Indexed: 12/25/2022] Open
Abstract
Wildlife is a reservoir of emerging infectious diseases of humans and domestic animals. Marmota himalayana mainly resides 2800-4000 m above sea level in the Qinghai-Tibetan Plateau, and is the primary animal reservoir of plague pathogen Yersinia pestis. Recently we isolated a new species, Escherichia marmotae from the faeces of M. himalayana. In this study we characterised E. marmotae by genomic analysis and in vitro virulence testing to determine its potential as a human pathogen. We sequenced the genomes of the seven E. marmotae strains and found that they contained a plasmid that carried a Shigella-like type III secretion system (T3SS) and their effectors, and shared the same O antigen gene cluster as Shigella dysenterae 8 and E. coli O38. We also showed that E. marmotae was invasive to HEp-2 cells although it was much less invasive than Shigella. Thus E. marmotae is likely to be an invasive pathogen. However, E. marmotae has a truncated IpaA invasin, and lacks the environmental response regulator VirF and the IcsA-actin based intracellular motility, rendering it far less invasive in comparison to Shigella. E. marmotae also carried a diverse set of virulence factors in addition to the T3SS, including an IS1414 encoded enterotoxin gene astA with 37 copies, E. coli virulence genes lifA/efa, cif, and epeA, and the sfp gene cluster, Yersinia T3SS effector yopJ, one Type II secretion system and two Type VI secretion systems. Therefore, E. marmotae is a potential invasive pathogen.
Collapse
Affiliation(s)
- Sha Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China.,Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Jie Feng
- Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing, 100101, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Xuefang Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Yiting Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Xiaochen Du
- Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing, 100101, China
| | - Xiangli Meng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Xia Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Hui Sun
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Changyun Ye
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China. .,Shanghai Institute of Emerging and Re-emerging infectious diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, China.
| |
Collapse
|
23
|
|
24
|
McDowell MA, Byrne AM, Mylona E, Johnson R, Sagfors A, Crepin VF, Lea S, Frankel G. The S. Typhi effector StoD is an E3/E4 ubiquitin ligase which binds K48- and K63-linked diubiquitin. Life Sci Alliance 2019; 2:2/3/e201800272. [PMID: 31142637 PMCID: PMC6545606 DOI: 10.26508/lsa.201800272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 11/24/2022] Open
Abstract
Salmonella Typhi is estimated to cause 100,000–200,000 deaths annually, yet its infection strategy remains elusive. This article reports of the first Typhi-specific effector, which has an E3/E4 ubiquitin ligase activity and can uniquely bind K48- and K63-linked diubiquitin. Salmonella enterica (e.g., serovars Typhi and Typhimurium) relies on translocation of effectors via type III secretion systems (T3SS). Specialization of typhoidal serovars is thought to be mediated via pseudogenesis. Here, we show that the Salmonella Typhi STY1076/t1865 protein, named StoD, a homologue of the enteropathogenic Escherichia coli/enterohemorrhagic E. coli/Citrobacter rodentium NleG, is a T3SS effector. The StoD C terminus (StoD-C) is a U-box E3 ubiquitin ligase, capable of autoubiquitination in the presence of multiple E2s. The crystal structure of the StoD N terminus (StoD-N) at 2.5 Å resolution revealed a ubiquitin-like fold. In HeLa cells expressing StoD, ubiquitin is redistributed into puncta that colocalize with StoD. Binding assays showed that StoD-N and StoD-C bind the same exposed surface of the β-sheet of ubiquitin, suggesting that StoD could simultaneously interact with two ubiquitin molecules. Consistently, StoD interacted with both K63- (KD = 5.6 ± 1 μM) and K48-linked diubiquitin (KD = 15 ± 4 μM). Accordingly, we report the first S. Typhi–specific T3SS effector. We suggest that StoD recognizes and ubiquitinates pre-ubiquitinated targets, thus subverting intracellular signaling by functioning as an E4 enzyme.
Collapse
Affiliation(s)
| | - Alexander Mp Byrne
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Elli Mylona
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Rebecca Johnson
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Agnes Sagfors
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Valerie F Crepin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Susan Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| |
Collapse
|
25
|
Ludwicki MB, Li J, Stephens EA, Roberts RW, Koide S, Hammond PT, DeLisa MP. Broad-Spectrum Proteome Editing with an Engineered Bacterial Ubiquitin Ligase Mimic. ACS CENTRAL SCIENCE 2019; 5:852-866. [PMID: 31139721 PMCID: PMC6535771 DOI: 10.1021/acscentsci.9b00127] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Indexed: 05/03/2023]
Abstract
Manipulation of the ubiquitin-proteasome pathway to achieve targeted silencing of cellular proteins has emerged as a reliable and customizable strategy for remodeling the mammalian proteome. One such approach involves engineering bifunctional proteins called ubiquibodies that are comprised of a synthetic binding protein fused to an E3 ubiquitin ligase, thus enabling post-translational ubiquitination and degradation of a target protein independent of its function. Here, we have designed a panel of new ubiquibodies based on E3 ubiquitin ligase mimics from bacterial pathogens that are capable of effectively interfacing with the mammalian proteasomal degradation machinery for selective removal of proteins of interest. One of these, the Shigella flexneri effector protein IpaH9.8 fused to a fibronectin type III (FN3) monobody that specifically recognizes green fluorescent protein (GFP), was observed to potently eliminate GFP and its spectral derivatives as well as 15 different FP-tagged mammalian proteins that varied in size (27-179 kDa) and subcellular localization (cytoplasm, nucleus, membrane-associated, and transmembrane). To demonstrate therapeutically relevant delivery of ubiquibodies, we leveraged a bioinspired molecular assembly method whereby synthetic mRNA encoding the GFP-specific ubiquibody was coassembled with poly A binding proteins and packaged into nanosized complexes using biocompatible, structurally defined polypolypeptides bearing cationic amine side groups. The resulting nanoplexes delivered ubiquibody mRNA in a manner that caused efficient target depletion in cultured mammalian cells stably expressing GFP as well as in transgenic mice expressing GFP ubiquitously. Overall, our results suggest that IpaH9.8-based ubiquibodies are a highly modular proteome editing technology with the potential for pharmacologically modulating disease-causing proteins.
Collapse
Affiliation(s)
- Morgan B. Ludwicki
- Robert F. Smith
School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New
York 14853, United
States
| | - Jiahe Li
- Department of Chemical Engineering and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erin A. Stephens
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Richard W. Roberts
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University
Langone Medical Center, New York, New York 10016, United States
- Department of Biochemistry and Molecular
Pharmacology, New York University School
of Medicine, New York, New York 10016, United States
| | - Paula T. Hammond
- Department of Chemical Engineering and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Matthew P. DeLisa
- Robert F. Smith
School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New
York 14853, United
States
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
26
|
Abstract
ABSTRACT
Shigella
is a genus of Gram-negative enteropathogens that have long been, and continue to be, an important public health concern worldwide. Over the past several decades,
Shigella
spp. have also served as model pathogens in the study of bacterial pathogenesis, and
Shigella flexneri
has become one of the best-studied pathogens on a molecular, cellular, and tissue level. In the arms race between
Shigella
and the host immune system,
Shigella
has developed highly sophisticated mechanisms to subvert host cell processes in order to promote infection, escape immune detection, and prevent bacterial clearance. Here, we give an overview of
Shigella
pathogenesis while highlighting innovative techniques and methods whose application has significantly advanced our understanding of
Shigella
pathogenesis in recent years.
Collapse
|
27
|
McVicker G, Hollingshead S, Pilla G, Tang CM. Maintenance of the virulence plasmid in Shigella flexneri is influenced by Lon and two functional partitioning systems. Mol Microbiol 2019; 111:1355-1366. [PMID: 30767313 PMCID: PMC6519299 DOI: 10.1111/mmi.14225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2019] [Indexed: 11/30/2022]
Abstract
Members of the genus Shigella carry a large plasmid, pINV, which is essential for virulence. In Shigella flexneri, pINV harbours three toxin‐antitoxin (TA) systems, CcdAB, GmvAT and VapBC that promote vertical transmission of the plasmid. Type II TA systems, such as those on pINV, consist of a toxic protein and protein antitoxin. Selective degradation of the antitoxin by proteases leads to the unopposed action of the toxin once genes encoding a TA system have been lost, such as following failure to inherit a plasmid harbouring a TA system. Here, we investigate the role of proteases in the function of the pINV TA systems and demonstrate that Lon, but not ClpP, is required for their activity during plasmid stability. This provides the first evidence that acetyltransferase family TA systems, such as GmvAT, can be regulated by Lon. Interestingly, S. flexneri pINV also harbours two putative partitioning systems, ParAB and StbAB. We show that both systems are functional for plasmid maintenance although their activity is masked by other systems on pINV. Using a model vector based on the pINV replicon, we observe temperature‐dependent differences between the two partitioning systems that contribute to our understanding of the maintenance of virulence in Shigella species.
Collapse
Affiliation(s)
- Gareth McVicker
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sarah Hollingshead
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Giulia Pilla
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| |
Collapse
|
28
|
Bastedo DP, Lo T, Laflamme B, Desveaux D, Guttman DS. Diversity and Evolution of Type III Secreted Effectors: A Case Study of Three Families. Curr Top Microbiol Immunol 2019; 427:201-230. [DOI: 10.1007/82_2019_165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
29
|
Rüter C, Lubos ML, Norkowski S, Schmidt MA. All in—Multiple parallel strategies for intracellular delivery by bacterial pathogens. Int J Med Microbiol 2018; 308:872-881. [DOI: 10.1016/j.ijmm.2018.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/01/2018] [Accepted: 06/16/2018] [Indexed: 02/06/2023] Open
|
30
|
Functional diversification of the NleG effector family in enterohemorrhagic Escherichia coli. Proc Natl Acad Sci U S A 2018; 115:10004-10009. [PMID: 30217892 DOI: 10.1073/pnas.1718350115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The pathogenic strategy of Escherichia coli and many other gram-negative pathogens relies on the translocation of a specific set of proteins, called effectors, into the eukaryotic host cell during infection. These effectors act in concert to modulate host cell processes in favor of the invading pathogen. Injected by the type III secretion system (T3SS), the effector arsenal of enterohemorrhagic E. coli (EHEC) O157:H7 features at least eight individual NleG effectors, which are also found across diverse attaching and effacing pathogens. NleG effectors share a conserved C-terminal U-box E3 ubiquitin ligase domain that engages with host ubiquitination machinery. However, their specific functions and ubiquitination targets have remained uncharacterized. Here, we identify host proteins targeted for ubiquitination-mediated degradation by two EHEC NleG family members, NleG5-1 and NleG2-3. NleG5-1 localizes to the host cell nucleus and targets the MED15 subunit of the Mediator complex, while NleG2-3 resides in the host cytosol and triggers degradation of Hexokinase-2 and SNAP29. Our structural studies of NleG5-1 reveal a distinct N-terminal α/β domain that is responsible for interacting with host protein targets. The core of this domain is conserved across the NleG family, suggesting this domain is present in functionally distinct NleG effectors, which evolved diversified surface residues to interact with specific host proteins. This is a demonstration of the functional diversification and the range of host proteins targeted by the most expanded effector family in the pathogenic arsenal of E. coli.
Collapse
|
31
|
Xu CC, Zhang D, Hann DR, Xie ZP, Staehelin C. Biochemical properties and in planta effects of NopM, a rhizobial E3 ubiquitin ligase. J Biol Chem 2018; 293:15304-15315. [PMID: 30120198 DOI: 10.1074/jbc.ra118.004444] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/25/2018] [Indexed: 01/18/2023] Open
Abstract
Nodulation outer protein M (NopM) is an IpaH family type three (T3) effector secreted by the nitrogen-fixing nodule bacterium Sinorhizobium sp. strain NGR234. Previous work indicated that NopM is an E3 ubiquitin ligase required for an optimal symbiosis between NGR234 and the host legume Lablab purpureus Here, we continued to analyze the function of NopM. Recombinant NopM was biochemically characterized using an in vitro ubiquitination system with Arabidopsis thaliana proteins. In this assay, NopM forms unanchored polyubiquitin chains and possesses auto-ubiquitination activity. In a NopM variant lacking any lysine residues, auto-ubiquitination was not completely abolished, indicating noncanonical auto-ubiquitination of the protein. In addition, we could show intermolecular ubiquitin transfer from NopM to C338A (enzymatically inactive NopM form) in vitro Bimolecular fluorescence complementation analysis provided clues about NopM-NopM interactions at plasma membranes in planta NopM, but not C338A, expressed in tobacco cells induced cell death, suggesting that E3 ubiquitin ligase activity of NopM induced effector-triggered immunity responses. Likewise, expression of NopM in Lotus japonicus caused reduced nodule formation, whereas expression of C338A showed no obvious effects on symbiosis. Further experiments indicated that serine residue 26 of NopM is phosphorylated in planta and that NopM can be phosphorylated in vitro by salicylic acid-induced protein kinase (NtSIPK), a mitogen-activated protein kinase (MAPK) of tobacco. Hence, NopM is a phosphorylated T3 effector that can interact with itself, with ubiquitin, and with MAPKs.
Collapse
Affiliation(s)
- Chang-Chao Xu
- From the State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Di Zhang
- From the State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Dagmar R Hann
- the Institute of Genetics, Ludwig-Maximilians-Universität München, D-82152 Martinsried, Germany, and
| | - Zhi-Ping Xie
- From the State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China, .,the Shenzhen Research and Development Center of State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Baoan, Shenzhen 518057, China
| | - Christian Staehelin
- From the State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China, .,the Shenzhen Research and Development Center of State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Baoan, Shenzhen 518057, China
| |
Collapse
|
32
|
Abstract
Guanylate-binding proteins (GBPs) confer protection against intracellular pathogens. In this issue of Cell Host & Microbe, Wandel et al. (2017) report that cytosolic Shigella becomes trapped within a GBP coat that prevents bacterial cell-to-cell spread. However, this defense mechanism is counteracted by the bacterial E3 ubiquitin ligase IpaH9.8.
Collapse
Affiliation(s)
| | - Jost Enninga
- Institut Pasteur, Dynamics of Host-Pathogen Interactions Unit, Paris, France.
| |
Collapse
|
33
|
Pasqua M, Michelacci V, Di Martino ML, Tozzoli R, Grossi M, Colonna B, Morabito S, Prosseda G. The Intriguing Evolutionary Journey of Enteroinvasive E. coli (EIEC) toward Pathogenicity. Front Microbiol 2017; 8:2390. [PMID: 29259590 PMCID: PMC5723341 DOI: 10.3389/fmicb.2017.02390] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/20/2017] [Indexed: 01/01/2023] Open
Abstract
Among the intestinal pathogenic Escherichia coli, enteroinvasive E. coli (EIEC) are a group of intracellular pathogens able to enter epithelial cells of colon, multiplicate within them, and move between adjacent cells with a mechanism similar to Shigella, the ethiological agent of bacillary dysentery. Despite EIEC belong to the same pathotype of Shigella, they neither have the full set of traits that define Shigella nor have undergone the extensive gene decay observed in Shigella. Molecular analysis confirms that EIEC are widely distributed among E. coli phylogenetic groups and correspond to bioserotypes found in many E. coli serogroups. Like Shigella, also in EIEC the critical event toward a pathogenic life-style consisted in the acquisition by horizontal gene transfer of a large F-type plasmid (pINV) containing the genes required for invasion, intracellular survival, and spreading through the intestinal mucosa. In Shigella, the ample gain in virulence determinants has been counteracted by a substantial loss of functions that, although important for the survival in the environment, are redundant or deleterious for the life inside the host. The pathoadaptation process that has led Shigella to modify its metabolic profile and increase its pathogenic potential is still in infancy in EIEC, although maintenance of some features typical of E. coli might favor their emerging relevance as intestinal pathogens worldwide, as documented by recent outbreaks in industrialized countries. In this review, we will discuss the evolution of EIEC toward Shigella-like invasive forms going through the epidemiology, including the emergence of new virulent strains, their genome organization, and the complex interactions they establish with the host.
Collapse
Affiliation(s)
- Martina Pasqua
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Valeria Michelacci
- European Union Reference Laboratory for Escherichia coli, Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Letizia Di Martino
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Rosangela Tozzoli
- European Union Reference Laboratory for Escherichia coli, Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Milena Grossi
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Bianca Colonna
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Stefano Morabito
- European Union Reference Laboratory for Escherichia coli, Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Gianni Prosseda
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| |
Collapse
|
34
|
Ubiquitination and degradation of GBPs by a Shigella effector to suppress host defence. Nature 2017; 551:378-383. [PMID: 29144452 DOI: 10.1038/nature24467] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 10/03/2017] [Indexed: 12/27/2022]
Abstract
Interferon-inducible guanylate-binding proteins (GBPs) mediate cell-autonomous antimicrobial defences. Shigella flexneri, a Gram-negative cytoplasmic free-living bacterium that causes bacillary dysentery, encodes a repertoire of highly similar type III secretion system effectors called invasion plasmid antigen Hs (IpaHs). IpaHs represent a large family of bacterial ubiquitin-ligases, but their function is poorly understood. Here we show that S. flexneri infection induces rapid proteasomal degradation of human guanylate binding protein-1 (hGBP1). We performed a transposon screen to identify a mutation in the S. flexneri gene ipaH9.8 that prevented hGBP1 degradation. IpaH9.8 targets hGBP1 for degradation via Lys48-linked ubiquitination. IpaH9.8 targets multiple GBPs in the cytoplasm independently of their nucleotide-bound states and their differential function in antibacterial defence, promoting S. flexneri replication and resulting in the death of infected mice. In the absence of IpaH9.8, or when binding of GBPs to IpaH9.8 was disrupted, GBPs such as hGBP1 and mouse GBP2 (mGBP2) translocated to intracellular S. flexneri and inhibited bacterial replication. Like wild-type mice, mutant mice deficient in GBP1-3, 5 and 7 succumbed to S. flexneri infection, but unlike wild-type mice, mice deficient in these GBPs were also susceptible to S. flexneri lacking ipaH9.8. The mode of IpaH9.8 action highlights the functional importance of GBPs in antibacterial defences. IpaH9.8 and S. flexneri provide a unique system for dissecting GBP-mediated immunity.
Collapse
|
35
|
Nakano M, Oda K, Mukaihara T. Ralstonia solanacearum novel E3 ubiquitin ligase (NEL) effectors RipAW and RipAR suppress pattern-triggered immunity in plants. MICROBIOLOGY (READING, ENGLAND) 2017; 163:992-1002. [PMID: 28708051 DOI: 10.1099/mic.0.000495] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Ralstonia solanacearum is the causal agent of bacterial wilt in solanaceous crops. This pathogen injects more than 70 effector proteins into host plant cells via the Hrp type III secretion system to cause a successful infection. However, the function of these effectors in plant cells, especially in the suppression of plant immunity, remains largely unknown. In this study, we characterized two Ralstonia solanacearum effectors, RipAW and RipAR, which share homology with the IpaH family of effectors from animal and plant pathogenic bacteria, that have a novel E3 ubiquitin ligase (NEL) domain. Recombinant RipAW and RipAR show E3 ubiquitin ligase activity in vitro. RipAW and RipAR localized to the cytoplasm of plant cells and significantly suppressed pattern-triggered immunity (PTI) responses such as the production of reactive oxygen species and the expression of defence-related genes when expressed in leaves of Nicotiana benthamiana. Mutation in the conserved cysteine residue in the NEL domain of RipAW completely abolished the E3 ubiquitin ligase activity in vitro and the ability to suppress PTI responses in plant leaves. These results indicate that RipAW suppresses plant PTI responses through the E3 ubiquitin ligase activity. Unlike other members of the IpaH family of effectors, RipAW and RipAR had no leucine-rich repeat motifs in their amino acid sequences. A conserved C-terminal region of RipAW is indispensable for PTI suppression. Transgenic Arabidopsis plants expressing RipAW and RipAR showed increased disease susceptibility, suggesting that RipAW and RipAR contribute to bacterial virulence in plants.
Collapse
Affiliation(s)
- Masahito Nakano
- Research Institute for Biological Sciences, Okayama (RIBS), 7549-1 Yoshikawa, Kibichuo-cho, Okayama 716-1241, Japan
| | - Kenji Oda
- Research Institute for Biological Sciences, Okayama (RIBS), 7549-1 Yoshikawa, Kibichuo-cho, Okayama 716-1241, Japan
| | - Takafumi Mukaihara
- Research Institute for Biological Sciences, Okayama (RIBS), 7549-1 Yoshikawa, Kibichuo-cho, Okayama 716-1241, Japan
| |
Collapse
|
36
|
Lin YH, Machner MP. Exploitation of the host cell ubiquitin machinery by microbial effector proteins. J Cell Sci 2017; 130:1985-1996. [PMID: 28476939 PMCID: PMC5482977 DOI: 10.1242/jcs.188482] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pathogenic bacteria are in a constant battle for survival with their host. In order to gain a competitive edge, they employ a variety of sophisticated strategies that allow them to modify conserved host cell processes in ways that favor bacterial survival and growth. Ubiquitylation, the covalent attachment of the small modifier ubiquitin to target proteins, is such a pathway. Ubiquitylation profoundly alters the fate of a myriad of cellular proteins by inducing changes in their stability or function, subcellular localization or interaction with other proteins. Given the importance of ubiquitylation in cell development, protein homeostasis and innate immunity, it is not surprising that this post-translational modification is exploited by a variety of effector proteins from microbial pathogens. Here, we highlight recent advances in our understanding of the many ways microbes take advantage of host ubiquitylation, along with some surprising deviations from the canonical theme. The lessons learned from the in-depth analyses of these host-pathogen interactions provide a fresh perspective on an ancient post-translational modification that we thought was well understood.This article is part of a Minifocus on Ubiquitin Regulation and Function. For further reading, please see related articles: 'Mechanisms of regulation and diversification of deubiquitylating enzyme function' by Pawel Leznicki and Yogesh Kulathu (J. Cell Sci.130, 1997-2006). 'Cell scientist to watch - Mads Gyrd-Hansen' (J. Cell Sci.130, 1981-1983).
Collapse
Affiliation(s)
- Yi-Han Lin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthias P Machner
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
37
|
Vanhove AS, Hang S, Vijayakumar V, Wong ACN, Asara JM, Watnick PI. Vibrio cholerae ensures function of host proteins required for virulence through consumption of luminal methionine sulfoxide. PLoS Pathog 2017; 13:e1006428. [PMID: 28586382 PMCID: PMC5473594 DOI: 10.1371/journal.ppat.1006428] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/16/2017] [Accepted: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Vibrio cholerae is a diarrheal pathogen that induces accumulation of lipid droplets in enterocytes, leading to lethal infection of the model host Drosophila melanogaster. Through untargeted lipidomics, we provide evidence that this process is the product of a host phospholipid degradation cascade that induces lipid droplet coalescence in enterocytes. This infection-induced cascade is inhibited by mutation of the V. cholerae glycine cleavage system due to intestinal accumulation of methionine sulfoxide (MetO), and both dietary supplementation with MetO and enterocyte knock-down of host methionine sulfoxide reductase A (MsrA) yield increased resistance to infection. MsrA converts both free and protein-associated MetO to methionine. These findings support a model in which dietary MetO competitively inhibits repair of host proteins by MsrA. Bacterial virulence strategies depend on functional host proteins. We propose a novel virulence paradigm in which an intestinal pathogen ensures the repair of host proteins essential for pathogenesis through consumption of dietary MetO.
Collapse
Affiliation(s)
- Audrey S. Vanhove
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston MA, United States of America
| | - Saiyu Hang
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston MA, United States of America
| | - Vidhya Vijayakumar
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston MA, United States of America
| | - Adam CN Wong
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston MA, United States of America
| | - John M. Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, 3 Blackfan Circle, Boston MA, United States of America
- Department of Medicine, Harvard Medical School, Boston MA, United States of America
| | - Paula I. Watnick
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston MA, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA United States of America
- * E-mail:
| |
Collapse
|
38
|
Mechanism of catalysis, E2 recognition, and autoinhibition for the IpaH family of bacterial E3 ubiquitin ligases. Proc Natl Acad Sci U S A 2017; 114:1311-1316. [PMID: 28115697 DOI: 10.1073/pnas.1611595114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
IpaH enzymes are secreted bacterial effectors that function within host cells as E3 ubiquitin (Ub) ligases. Catalytic activity is imparted by a conserved novel E3 ligase (NEL) domain that is unique to Gram-negative pathogens and whose activity is repressed by a flanking substrate-binding leucine-rich repeat (LRR) domain when substrate is absent. How the NEL domain catalyzes the conjugation of Ub onto substrates, recognizes host E2s, and maintains its autoinhibited state remain poorly understood. Here we used mutagenesis and enzyme kinetic analyses to address these gaps in knowledge. Mutagenesis of conserved residues on two remote surfaces of the NEL domain identified functional clusters proximal to and distal to the active site cysteine. By analyzing the kinetics of Ub charging and discharging, we identified proximal active site residues that function as either the catalytic acid or catalytic base for aminolysis. Further analysis revealed that distal site residues mediate the direct binding of E2. In studying the full-length protein, we also have uncovered that IpaH family autoinhibition is achieved by a short-circuiting mechanism wherein the LRR domain selectively blocks productive aminolysis, but not the nonproductive discharge of Ub from the E3 to solvent. This mode of autoinhibition, which is not shared by the HECT domain ligase Smurf2, leads to the unanticipated depletion of E2∼Ub and thus a concomitant dominant-negative effect on other E3s in vitro, raising the possibility that short circuiting also may serve to restrict the function of host E3s in cells.
Collapse
|
39
|
Ashida H, Sasakawa C. Bacterial E3 ligase effectors exploit host ubiquitin systems. Curr Opin Microbiol 2016; 35:16-22. [PMID: 27907841 DOI: 10.1016/j.mib.2016.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/08/2016] [Accepted: 11/08/2016] [Indexed: 12/31/2022]
Abstract
Ubiquitination is a crucial post-translational protein modification involved in regulation of various cellular processes in eukaryotes. In particular, ubiquitination is involved in multiple aspects of bacterial infection and host defense mechanisms. In parallel with the identification of ubiquitination as a component of host defense systems, recently accumulated evidence shows that many bacterial pathogens exploit host ubiquitin systems to achieve successful infection. Here, we highlight the strategies by which bacteria subvert host ubiquitin systems by mimicking E3 ubiquitin ligase activity.
Collapse
Affiliation(s)
- Hiroshi Ashida
- Division of Bacterial Infection Immunology, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan.
| | - Chihiro Sasakawa
- Nippon Institute for Biological Science, 9-2221-1 Shinmachi, Ome, 198-0024, Tokyo, Japan; Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, 260-8673, Chiba, Japan
| |
Collapse
|
40
|
Di Martino ML, Falconi M, Micheli G, Colonna B, Prosseda G. The Multifaceted Activity of the VirF Regulatory Protein in the Shigella Lifestyle. Front Mol Biosci 2016; 3:61. [PMID: 27747215 PMCID: PMC5041530 DOI: 10.3389/fmolb.2016.00061] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/15/2016] [Indexed: 12/20/2022] Open
Abstract
Shigella is a highly adapted human pathogen, mainly found in the developing world and causing a severe enteric syndrome. The highly sophisticated infectious strategy of Shigella banks on the capacity to invade the intestinal epithelial barrier and cause its inflammatory destruction. The cellular pathogenesis and clinical presentation of shigellosis are the sum of the complex action of a large number of bacterial virulence factors mainly located on a large virulence plasmid (pINV). The expression of pINV genes is controlled by multiple environmental stimuli through a regulatory cascade involving proteins and sRNAs encoded by both the pINV and the chromosome. The primary regulator of the virulence phenotype is VirF, a DNA-binding protein belonging to the AraC family of transcriptional regulators. The virF gene, located on the pINV, is expressed only within the host, mainly in response to the temperature transition occurring when the bacterium transits from the outer environment to the intestinal milieu. VirF then acts as anti-H-NS protein and directly activates the icsA and virB genes, triggering the full expression of the invasion program of Shigella. In this review we will focus on the structure of VirF, on its sophisticated regulation, and on its role as major player in the path leading from the non-invasive to the invasive phenotype of Shigella. We will address also the involvement of VirF in mechanisms aimed at withstanding adverse conditions inside the host, indicating that this protein is emerging as a global regulator whose action is not limited to virulence systems. Finally, we will discuss recent observations conferring VirF the potential of a novel antibacterial target for shigellosis.
Collapse
Affiliation(s)
- Maria Letizia Di Martino
- Dipartimento di Biologia e Biotecnologie C. Darwin, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma Roma, Italy
| | - Maurizio Falconi
- Laboratorio di Genetica Molecolare e dei Microrganismi, Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino Camerino, Italy
| | - Gioacchino Micheli
- Istituto di Biologia e Patologia Molecolari, Consilglio Nazionale Delle Richerche Roma, Italy
| | - Bianca Colonna
- Dipartimento di Biologia e Biotecnologie C. Darwin, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma Roma, Italy
| | - Gianni Prosseda
- Dipartimento di Biologia e Biotecnologie C. Darwin, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma Roma, Italy
| |
Collapse
|