1
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Seabaugh JA, Anderson DM. Pathogenicity and virulence of Yersinia. Virulence 2024; 15:2316439. [PMID: 38389313 PMCID: PMC10896167 DOI: 10.1080/21505594.2024.2316439] [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: 10/05/2023] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
The genus Yersinia includes human, animal, insect, and plant pathogens as well as many symbionts and harmless bacteria. Within this genus are Yersinia enterocolitica and the Yersinia pseudotuberculosis complex, with four human pathogenic species that are highly related at the genomic level including the causative agent of plague, Yersinia pestis. Extensive laboratory, field work, and clinical research have been conducted to understand the underlying pathogenesis and zoonotic transmission of these pathogens. There are presently more than 500 whole genome sequences from which an evolutionary footprint can be developed that details shared and unique virulence properties. Whereas the virulence of Y. pestis now seems in apparent homoeostasis within its flea transmission cycle, substantial evolutionary changes that affect transmission and disease severity continue to ndergo apparent selective pressure within the other Yersiniae that cause intestinal diseases. In this review, we will summarize the present understanding of the virulence and pathogenesis of Yersinia, highlighting shared mechanisms of virulence and the differences that determine the infection niche and disease severity.
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Affiliation(s)
- Jarett A. Seabaugh
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
| | - Deborah M. Anderson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
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2
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Van Hofwegen DJ, Hovde CJ, Minnich SA. Comparison of Yersinia enterocolitica DNA Methylation at Ambient and Host Temperatures. EPIGENOMES 2023; 7:30. [PMID: 38131902 PMCID: PMC10742451 DOI: 10.3390/epigenomes7040030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Pathogenic bacteria recognize environmental cues to vary gene expression for host adaptation. Moving from ambient to host temperature, Yersinia enterocolitica responds by immediately repressing flagella synthesis and inducing the virulence plasmid (pYV)-encoded type III secretion system. In contrast, shifting from host to ambient temperature requires 2.5 generations to restore motility, suggesting a link to the cell cycle. We hypothesized that differential DNA methylation contributes to temperature-regulated gene expression. We tested this hypothesis by comparing single-molecule real-time (SMRT) sequencing of Y. enterocolitica DNA from cells growing exponentially at 22 °C and 37 °C. The inter-pulse duration ratio rather than the traditional QV scoring was the kinetic metric to compare DNA from cells grown at each temperature. All 565 YenI restriction sites were fully methylated at both temperatures. Among the 27,118 DNA adenine methylase (Dam) sites, 42 had differential methylation patterns, while 17 remained unmethylated regardless of the temperature. A subset of the differentially methylated Dam sites localized to promoter regions of predicted regulatory genes including LysR-type and PadR-like transcriptional regulators and a cyclic-di-GMP phosphodiesterase. The unmethylated Dam sites localized with a bias to the replication terminus, suggesting they were protected from Dam methylase. No cytosine methylation was detected at Dcm sites.
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Affiliation(s)
| | | | - Scott A. Minnich
- Department of Animal Veterinary and Food Science, University of Idaho, Moscow, ID 83843, USA; (D.J.V.H.); (C.J.H.)
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3
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Abdulkadieva MM, Sysolyatina EV, Vasilieva EV, Litvinenko VV, Kalinin EV, Zhukhovitsky VG, Shevlyagina NV, Andreevskaya SG, Stanishevskyi YM, Vasiliev MM, Petrov OF, Ermolaeva SA. Motility provides specific adhesion patterns and improves Listeria monocytogenes invasion into human HEp-2 cells. PLoS One 2023; 18:e0290842. [PMID: 37651463 PMCID: PMC10470941 DOI: 10.1371/journal.pone.0290842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023] Open
Abstract
Listeria monocytogenes is motile at 22°C and non-motile at 37°C. In contrast, expression of L. monocytogenes virulence factors is low at 22°C and up-regulated at 37°C. Here, we studied a character of L. monocytogenes near surface swimming (NSS) motility and its effects on adhesion patterns and invasion into epithelial cells. L. monocytogenes and its saprophytic counterpart L. innocua both grown at 22°C showed similar NSS characteristics including individual velocities, trajectory lengths, residence times, and an asymmetric distribution of velocity directions. Similar NSS patterns correlated with similar adhesion patterns. Motile bacteria, including both pathogenic and saprophytic species, showed a preference for adhering to the periphery of epithelial HEp-2 cells. In contrast, non-motile bacteria were evenly distributed across the cell surface, including areas over the nucleus. However, the uneven distribution of motile bacteria did not enhance the invasion into HEp-2 cells unless virulence factor production was up-regulated by the transient shift of the culture to 37°C. Motile L. monocytogenes grown overnight at 22°C and then shifted to 37°C for 2 h expressed invasion factors at the same level and invaded human cells up to five times more efficiently comparatively with non-motile bacteria grown overnight at 37°C. Taken together, obtained results demonstrated that (i) NSS motility and correspondent peripheral location over the cell surface did not depend on L. monocytogenes virulence traits; (ii) motility improved L. monocytogenes invasion into human HEp-2 cells within a few hours after the transition from the ambient temperature to the human body temperature.
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Affiliation(s)
- Mariam M. Abdulkadieva
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
- Institute of Biochemical Technology and Nanotechnology, People’s Friendship University RUDN, Moscow, Russia
| | - Elena V. Sysolyatina
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
| | - Elena V. Vasilieva
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
| | - Veronika V. Litvinenko
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
| | - Egor V. Kalinin
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Institute of Biochemical Technology and Nanotechnology, People’s Friendship University RUDN, Moscow, Russia
| | - Vladimir G. Zhukhovitsky
- Department of Bacterial Infections, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Russian Medical Academy of Continuing Professional Education (RMANPO), Ministry of Public Health, Moscow, Russia
| | - Natalia V. Shevlyagina
- Department of Bacterial Infections, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
| | - Svetlana G. Andreevskaya
- Department of Bacterial Infections, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
| | - Yaroslav M. Stanishevskyi
- Institute of Biochemical Technology and Nanotechnology, People’s Friendship University RUDN, Moscow, Russia
| | - Mikhail M. Vasiliev
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
| | - Oleg F. Petrov
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
| | - Svetlana A. Ermolaeva
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
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4
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Swali P, Schulting R, Gilardet A, Kelly M, Anastasiadou K, Glocke I, McCabe J, Williams M, Audsley T, Loe L, Fernández-Crespo T, Ordoño J, Walker D, Clare T, Cook G, Hodkinson I, Simpson M, Read S, Davy T, Silva M, Hajdinjak M, Bergström A, Booth T, Skoglund P. Yersinia pestis genomes reveal plague in Britain 4000 years ago. Nat Commun 2023; 14:2930. [PMID: 37253742 DOI: 10.1038/s41467-023-38393-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Extinct lineages of Yersinia pestis, the causative agent of the plague, have been identified in several individuals from Eurasia between 5000 and 2500 years before present (BP). One of these, termed the 'LNBA lineage' (Late Neolithic and Bronze Age), has been suggested to have spread into Europe with human groups expanding from the Eurasian steppe. Here, we show that the LNBA plague was spread to Europe's northwestern periphery by sequencing three Yersinia pestis genomes from Britain, all dating to ~4000 cal BP. Two individuals were from an unusual mass burial context in Charterhouse Warren, Somerset, and one individual was from a single burial under a ring cairn monument in Levens, Cumbria. To our knowledge, this represents the earliest evidence of LNBA plague in Britain documented to date. All three British Yersinia pestis genomes belong to a sublineage previously observed in Bronze Age individuals from Central Europe that had lost the putative virulence factor yapC. This sublineage is later found in Eastern Asia ~3200 cal BP. While the severity of the disease is currently unclear, the wide geographic distribution within a few centuries suggests substantial transmissibility.
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Affiliation(s)
- Pooja Swali
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | | | | | - Monica Kelly
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | | | - Isabelle Glocke
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Jesse McCabe
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Mia Williams
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | | | - Louise Loe
- Oxford Archaeology, Osney Mead, Oxford, UK
| | - Teresa Fernández-Crespo
- School of Archaeology, University of Oxford, Oxford, UK
- Laboratoire Méditerranéen de Préhistoire Europe Afrique-UMR 7269, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
- Departamento de Prehistoria, Arqueología, Antropología Social y Ciencias y Técnicas Historiográficas, Universidad de Valladolid, Valladolid, Spain
| | - Javier Ordoño
- Department of Archaeology and New Technologies, Arkikus, Spain
| | | | - Tom Clare
- Levens Local History Group, Levens, Cumbria, UK
| | - Geoff Cook
- Levens Local History Group, Levens, Cumbria, UK
| | - Ian Hodkinson
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | | | | | - Tom Davy
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Marina Silva
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
- Department of Evolutionary Genetics and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Thomas Booth
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
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5
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Guo XP, Yan HQ, Yang W, Yin Z, Vadyvaloo V, Zhou D, Sun YC. A frameshift in Yersinia pestis rcsD alters canonical Rcs signalling to preserve flea-mammal plague transmission cycles. eLife 2023; 12:e83946. [PMID: 37010269 PMCID: PMC10191623 DOI: 10.7554/elife.83946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/02/2023] [Indexed: 04/04/2023] Open
Abstract
Multiple genetic changes in the enteric pathogen Yersinia pseudotuberculosis have driven the emergence of Yesinia pestis, the arthropod-borne, etiological agent of plague. These include developing the capacity for biofilm-dependent blockage of the flea foregut to enable transmission by flea bite. Previously, we showed that pseudogenization of rcsA, encoding a component of the Rcs signalling pathway, is an important evolutionary step facilitating Y. pestis flea-borne transmission. Additionally, rcsD, another important gene in the Rcs system, harbours a frameshift mutation. Here, we demonstrated that this rcsD mutation resulted in production of a small protein composing the C-terminal RcsD histidine-phosphotransferase domain (designated RcsD-Hpt) and full-length RcsD. Genetic analysis revealed that the rcsD frameshift mutation followed the emergence of rcsA pseudogenization. It further altered the canonical Rcs phosphorylation signal cascade, fine-tuning biofilm production to be conducive with retention of the pgm locus in modern lineages of Y. pestis. Taken together, our findings suggest that a frameshift mutation in rcsD is an important evolutionary step that fine-tuned biofilm production to ensure perpetuation of flea-mammal plague transmission cycles.
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Affiliation(s)
- Xiao-Peng Guo
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hai-Qin Yan
- Department of Basic Medical Sciences, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical CollegeBengbuChina
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Viveka Vadyvaloo
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yi-Cheng Sun
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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6
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Neumann GU, Skourtanioti E, Burri M, Nelson EA, Michel M, Hiss AN, McGeorge PJP, Betancourt PP, Spyrou MA, Krause J, Stockhammer PW. Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete. Curr Biol 2022; 32:3641-3649.e8. [PMID: 35882233 DOI: 10.1016/j.cub.2022.06.094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/25/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022]
Abstract
During the late 3rd millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained with a combination of social and climatic factors.1-4 However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories.5 The plague bacterium Yersinia pestis, which was involved in some of the most destructive historical pandemics,5-8 circulated across Eurasia at least from the onset of the 3rd millennium BCE,9-13 but the challenging preservation of ancient DNA in warmer climates has restricted the identification of Y.pestis from this period to temperate climatic regions. As such, evidence from culturally prominent regions such as the Eastern Mediterranean is currently lacking. Here, we present genetic evidence for the presence of Y. pestis and Salmonella enterica, the causative agent of typhoid/enteric fever, from this period of transformation in Crete, detected at the cave site Hagios Charalambos. We reconstructed one Y. pestis genome that forms part of a now-extinct lineage of Y. pestis strains from the Late Neolithic and Bronze Age that were likely not yet adapted for transmission via fleas. Furthermore, we reconstructed two ancient S. enterica genomes from the Para C lineage, which cluster with contemporary strains that were likely not yet fully host adapted to humans. The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and beyond.
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Affiliation(s)
- Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Marta Burri
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Department of Anthropology, University of Connecticut, 354 Mansfield Road, Storrs, CT 06269, USA
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Human Evolutionary Biology, Harvard University, 10 Divinity Avenue, Cambridge, MA 02138, USA
| | - Alina N Hiss
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | | | - Philip P Betancourt
- Department of Art History and Archaeology, Temple University, 2001 N. 13(th) St., Philadelphia, PA 19122, USA
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Hölderlinstr. 12, 72074 Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80799 München, Germany.
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Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague. Proc Natl Acad Sci U S A 2022; 119:e2116722119. [PMID: 35412864 PMCID: PMC9169917 DOI: 10.1073/pnas.2116722119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry. The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology.
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Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis. Microbiol Spectr 2022; 10:e0224221. [PMID: 35438532 PMCID: PMC9248902 DOI: 10.1128/spectrum.02242-21] [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] [Indexed: 11/20/2022] Open
Abstract
The life cycle of Yersinia pestis has changed a lot to adapt to flea-borne transmission since it evolved from an enteric pathogen, Yersinia pseudotuberculosis. Small insertions and deletions (indels), especially frameshift mutations, can have major effects on phenotypes and contribute to virulence and host adaptation through gene disruption and inactivation. Here, we analyzed 365 Y. pestis genomes and identified 2,092 genome-wide indels on the core genome. As recently reported in Mycobacterium tuberculosis, we also detected "indel pockets" in Y. pestis, with average complexity scores declining around indel positions, which we speculate might also exist in other prokaryotes. Phylogenic analysis showed that indel-based phylogenic tree could basically reflect the phylogenetic relationships of major phylogroups in Y. pestis, except some inconsistency around the Big Bang polytomy. We observed 83 indels arising in the trunk of the phylogeny, which played a role in accumulation of pseudogenes related to key metabolism and putatively pathogenicity. We also discovered 32 homoplasies at the level of phylogroups and 7 frameshift scars (i.e., disrupted reading frame being rescued by a second frameshift). Additionally, our analysis showed evidence of parallel evolution at the level of genes, with sspA, rpoS, rnd, and YPO0624, having enriched mutations in Brazilian isolates, which might be advantageous for Y. pestis to cope with fluctuating environments. The diversified selection signals observed here demonstrates that indels are important contributors to the adaptive evolution of Y. pestis. Meanwhile, we provide potential targets for further exploration, as some genes/pseudogenes with indels we focus on remain uncharacterized. IMPORTANCE Yersinia pestis, the causative agent of plague, is a highly pathogenic clone of Yersinia pseudotuberculosis. Previous genome-wide SNP analysis provided few adaptive signatures during its evolution. Here by investigating 365 public genomes of Y. pestis, we give a comprehensive overview of general features of genome-wide indels on the core genome and their roles in Y. pestis evolution. Detection of "indel pockets," with average complexity scores declining around indel positions, in both Mycobacterium tuberculosis and Y. pestis, gives us a clue that this phenomenon might appear in other bacterial genomes. Importantly, the identification of four different forms of selection signals in indels would improve our understanding on adaptive evolution of Y. pestis, and provide targets for further physiological mechanism researches of this pathogen. As evolutionary research based on genome-wide indels is still rare in bacteria, our study would be a helpful reference in deciphering the role of indels in other species.
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Choe Y, Lee D, Seong M, Yoon JB, Yang JH, Yang JY, Moon KH, Kang HY. Characterization of Edwardsiella piscicida CK108 flagellin genes and evaluation of their potential as vaccine targets in the zebrafish model. JOURNAL OF FISH DISEASES 2022; 45:249-259. [PMID: 34843109 DOI: 10.1111/jfd.13550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
The control of bacterial pathogens, including Edwardsiella piscicida, in the aquaculture industry has high economic importance. This study aimed to identify a potential live vaccine candidate against E. piscicida infection to minimize the side effects and elicit immunity in the host. This study evaluated the virulence factors of E. piscicida CK108, with a special focus on the flagella. E. piscicida has two important homologous flagellin genes, namely flagellin-associated protein (fap) and flagellin domain-containing protein (fdp). CK226 (Δfap), CK247 (Δfdp) and CK248 (Δfap, fdp) mutant strains were constructed. Both CK226 and CK247 displayed decreased length and thickness of flagellar filaments, resulting in reduced bacterial swimming motility, while CK248 was non-motile as it lacked flagella. The loss of flagella and decreased motility was expected to decrease the pathogenicity of CK248. However, the median lethal dose (LD50 ) of CK248 against zebrafish was lower than those of the wild-type, CK226 and CK247 strains. The protective immunity and cytokine gene expression levels in the CK248-infected zebrafish were lower than those in the wild type-infected zebrafish. In conclusion, Fap and Fdp are essential for flagella formation and motility, and for stimulating fish immune response, which can be utilized as a potential adjuvants for E. piscicida vaccination.
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Affiliation(s)
- Yunjeong Choe
- Department of Microbiology, Pusan National University, Busan, Korea
- Laboratory Animal Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Korea
| | - Donghee Lee
- Department of Microbiology, Pusan National University, Busan, Korea
- Department of Microbiology and Immunology, East Carolina University, Greenville, North Carolina, USA
| | - Minji Seong
- Department of Microbiology, Pusan National University, Busan, Korea
- Laboratory Animal Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Korea
- Mucosal Immunology Lab., Department of Biological Sciences, Pusan National University, Busan, Korea
| | - Ju Bin Yoon
- Department of Convergence Study on the Ocean Science and Technology, Korea Maritime & Ocean University, Busan, Korea
- Lab. of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime & Ocean University, Busan, Korea
| | - Jun Hyeok Yang
- Lab. of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime & Ocean University, Busan, Korea
- Department of Marine Bioscience and Environment, Korea Maritime & Ocean University, Busan, Korea
| | - Jin-Young Yang
- Mucosal Immunology Lab., Department of Biological Sciences, Pusan National University, Busan, Korea
| | - Ki Hwan Moon
- Department of Convergence Study on the Ocean Science and Technology, Korea Maritime & Ocean University, Busan, Korea
- Lab. of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime & Ocean University, Busan, Korea
- Department of Marine Bioscience and Environment, Korea Maritime & Ocean University, Busan, Korea
| | - Ho Young Kang
- Department of Microbiology, Pusan National University, Busan, Korea
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10
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Wen J, Xuan B, Liu Y, Wang L, He L, Meng X, Zhou T, Wang Y. Updating the NLRC4 Inflammasome: from Bacterial Infections to Autoimmunity and Cancer. Front Immunol 2021; 12:702527. [PMID: 34276697 PMCID: PMC8283967 DOI: 10.3389/fimmu.2021.702527] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 01/07/2023] Open
Abstract
Inflammasomes comprise a family of cytosolic multi-protein complexes that modulate the activation of cysteine-aspartate-specific protease 1 (caspase-1) and promote the maturation and secretion of interleukin (IL)-1β and IL-18, leading to an inflammatory response. Different types of inflammasomes are defined by their sensor protein which recognizes pathogenic ligands and then directs inflammasome assembly. Although the specific molecular mechanisms underlying the activation of most inflammasomes are still unclear, NLRC4 inflammasomes have emerged as multifaceted agents of the innate immune response, playing important roles in immune defense against a variety of pathogens. Other studies have also expanded the scope of NLRC4 inflammasomes to include a range of inherited human autoimmune diseases as well as proposed roles in cancer. In this review article, we provide an updated overview of NLRC4 inflammasomes, describing their composition, activation mechanisms and roles in both microbial infections and other disease conditions.
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Affiliation(s)
- Jiexia Wen
- Department of Central Laboratory, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
| | - Bin Xuan
- Department of General Surgery, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
| | - Yang Liu
- Department of General Surgery, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
| | - Liwei Wang
- Department of General Surgery, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
| | - Li He
- Department of General Surgery, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
| | - Xiangcai Meng
- Department of General Surgery, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
| | - Tao Zhou
- Department of General Surgery, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
| | - Yimin Wang
- Department of Central Laboratory, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China.,Department of General Surgery, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
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11
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Schubert KA, Xu Y, Shao F, Auerbuch V. The Yersinia Type III Secretion System as a Tool for Studying Cytosolic Innate Immune Surveillance. Annu Rev Microbiol 2020; 74:221-245. [PMID: 32660389 DOI: 10.1146/annurev-micro-020518-120221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial pathogens have evolved complex mechanisms to interface with host cells in order to evade host defenses and replicate. However, mammalian innate immune receptors detect the presence of molecules unique to the microbial world or sense the activity of virulence factors, activating antimicrobial and inflammatory pathways. We focus on how studies of the major virulence factor of one group of microbial pathogens, the type III secretion system (T3SS) of human pathogenic Yersinia, have shed light on these important innate immune responses. Yersinia are largely extracellular pathogens, yet they insert T3SS cargo into target host cells that modulate the activity of cytosolic innate immune receptors. This review covers both the host pathways that detect the Yersinia T3SS and the effector proteins used by Yersinia to manipulate innate immune signaling.
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Affiliation(s)
- Katherine Andrea Schubert
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, USA;
| | - Yue Xu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Feng Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Victoria Auerbuch
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, USA;
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12
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Andrade WA, Zamboni DS. NLRC4 biology in immunity and inflammation. J Leukoc Biol 2020; 108:1117-1127. [PMID: 32531834 DOI: 10.1002/jlb.3mr0420-573r] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Inflammasomes are cytosolic multiprotein complexes that sense microbial infections or host cell damage, triggering cytokine production and a proinflammatory form of cell death, called pyroptosis. Whereas pyroptosis and cytokine production may often promote host resistance to infections, uncontrolled inflammasome activation leads to autoinflammatory diseases in humans. Among the multiple inflammasomes described, the neuronal apoptosis inhibitory protein/nucleotide-binding domain leucine-rich repeat-containing protein family caspase activation and recruitment domain-containing protein 4 (NLRC4) inflammasome emerged as a critical component for the restriction of bacterial infections. Accordingly, our understanding of this inflammasome advanced remarkably over the last 10 yr, expanding our knowledge about ligand-receptor interaction; cryo-EM structure; and downstream effectors and substrates, such as gasdermin-D, caspase-1, caspase-8, and caspase-7. In this review, we discuss recent advances on the biology of the NLRC4 inflammasome, in terms of structure and activation mechanisms, importance in bacterial and nonbacterial diseases, and the identification of NLRC4 gain-of-function mutations leading to NLRC4-associated autoinflammatory diseases in humans.
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Affiliation(s)
- Warrison A Andrade
- Department of Cell Biology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Dario S Zamboni
- Department of Cell Biology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
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13
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Jozwick AKS, LaPatra SE, Graf J, Welch TJ. Flagellar regulation mediated by the Rcs pathway is required for virulence in the fish pathogen Yersinia ruckeri. FISH & SHELLFISH IMMUNOLOGY 2019; 91:306-314. [PMID: 31121291 DOI: 10.1016/j.fsi.2019.05.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
The flagellum is a complex surface structure necessary for a number of activities including motility, chemotaxis, biofilm formation and host attachment. Flagellin, the primary structural protein making up the flagellum, is an abundant and potent activator of innate and adaptive immunity and therefore expression of flagellin during infection could be deleterious to the infection process due to flagellin-mediated host recognition. Here, we use quantitative RT-PCR to demonstrate that expression of the flagellin locus fliC is repressed during the course of infection and subsequently up-regulated upon host mortality in a motile strain of Yersinia ruckeri. The kinetics of fliC repression during the infection process is relatively slow as full repression occurs 7-days after the initiation of infection and after approximately 3-logs of bacterial growth in vivo. These results suggests that Y. ruckeri possesses a regulatory system capable of sensing host and modulating the expression of motility in response. Examination of the master flagellar operon (flhDC) promoter region for evidence of transcriptional regulation and regulatory binding sites revealed potential interaction with the Rcs pathway through an Rcs(A)B Box. Deletion of rcsB (ΔrcsB) by marker-exchange mutagenesis resulted in overproduction of flagellin and unregulated motility, showing that the Rcs pathway negatively regulates biosynthesis of the flagellar apparatus. Experimental challenge with ΔrcsB and ΔrcsBΔfliC1ΔfliC2 mutants revealed that mutation of the Rcs pathway results in virulence attenuation which is dependent on presence of the flagellin gene. These results suggest that the inappropriate expression of flagellin during infection triggers host recognition and thus immune stimulation resulting in attenuation of virulence. In addition, RNAseq analyses of the ΔrcsB mutant strain verified the role of this gene as a negative regulator of the flagellar motility system and identified several additional genes regulated by the Rcs pathway.
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Affiliation(s)
| | | | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Timothy J Welch
- (d)National Center for Cool and Cold Water Aquaculture, Agricultural Research Service/U.S. Department of Agriculture, Kearneysville, West Virginia, USA.
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14
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Abstract
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.
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15
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Rudenko I, Ni B, Glatter T, Sourjik V. Inefficient Secretion of Anti-sigma Factor FlgM Inhibits Bacterial Motility at High Temperature. iScience 2019; 16:145-154. [PMID: 31170626 PMCID: PMC6551532 DOI: 10.1016/j.isci.2019.05.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/01/2019] [Accepted: 05/15/2019] [Indexed: 12/03/2022] Open
Abstract
Temperature is one of the key cues that enable microorganisms to adjust their physiology in response to environmental changes. Here we show that motility is the major cellular function of Escherichia coli that is differentially regulated between growth at normal host temperature of 37°C and the febrile temperature of 42°C. Expression of both class II and class III flagellar genes is reduced at 42°C because of lowered level of the upstream activator FlhD. Class III genes are additionally repressed because of the destabilization and malfunction of secretion apparatus at high temperature, which prevents secretion of the anti-sigma factor FlgM. This mechanism of repression apparently accelerates loss of motility at 42°C. We hypothesize that E. coli perceives high temperature as a sign of inflammation, downregulating flagella to escape detection by the immune system of the host. Secretion-dependent coupling of gene expression to the environmental temperature is likely common among many bacteria. E. coli motility is tightly turned off at febrile temperature (42°C) Repression of motility is achieved at two levels of hierarchical gene regulation Lowered FlhD level reduces expression of all flagellar genes Impaired FlgM secretion tightens repression of class III genes
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Affiliation(s)
- Iaroslav Rudenko
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Bin Ni
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Victor Sourjik
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany.
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16
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A Family of Small Intrinsically Disordered Proteins Involved in Flagellum-Dependent Motility in Salmonella enterica. J Bacteriol 2018; 201:JB.00415-18. [PMID: 30373755 DOI: 10.1128/jb.00415-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/21/2018] [Indexed: 02/08/2023] Open
Abstract
By screening a collection of Salmonella mutants deleted for genes encoding small proteins of ≤60 amino acids, we identified three paralogous small genes (ymdF, STM14_1829, and yciG) required for wild-type flagellum-dependent swimming and swarming motility. The ymdF, STM14_1829, and yciG genes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829 mutant due to the downregulation of the flhDC operon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829 strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829 mutant, suggesting the indirect repression of the flhDC operon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, including Escherichia coli and Pseudomonas aeruginosa We showed that the inactivation of STM14_1829 homologs in E. coli and P. aeruginosa also alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility.IMPORTANCE This study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility in Salmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.
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17
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Arifuzzaman M, Ang WXG, Choi HW, Nilles ML, St John AL, Abraham SN. Necroptosis of infiltrated macrophages drives Yersinia pestis dispersal within buboes. JCI Insight 2018; 3:122188. [PMID: 30232285 DOI: 10.1172/jci.insight.122188] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/07/2018] [Indexed: 12/18/2022] Open
Abstract
When draining lymph nodes become infected by Yersinia pestis (Y. pestis), a massive influx of phagocytic cells occurs, resulting in distended and necrotic structures known as buboes. The bubonic stage of the Y. pestis life cycle precedes septicemia, which is facilitated by trafficking of infected mononuclear phagocytes through these buboes. However, how Y. pestis convert these immunocytes recruited by host to contain the pathogen into vehicles for bacterial dispersal and the role of immune cell death in this context are unknown. We show that the lymphatic spread requires Yersinia outer protein J (YopJ), which triggers death of infected macrophages by downregulating a suppressor of receptor-interacting protein kinase 1-mediated (RIPK1-mediated) cell death programs. The YopJ-triggered cell death was identified as necroptotic, which released intracellular bacteria, allowing them to infect new neighboring cell targets. Dying macrophages also produced chemotactic sphingosine 1-phosphate, enhancing cell-to-cell contact, further promoting infection. This necroptosis-driven expansion of infected macrophages in buboes maximized the number of bacteria-bearing macrophages reaching secondary lymph nodes, leading to sepsis. In support, necrostatins confined bacteria within macrophages and protected mice from lethal infection. These findings define necrotization of buboes as a mechanism for bacterial spread and a potential target for therapeutic intervention.
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Affiliation(s)
| | | | - Hae Woong Choi
- Department of Pathology, Duke University, Durham, North Carolina, USA
| | - Matthew L Nilles
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - Ashley L St John
- Department of Pathology, Duke University, Durham, North Carolina, USA.,Program in Emerging Infectious Diseases, Duke-National University of Singapore, Singapore, Singapore
| | - Soman N Abraham
- Department of Molecular Genetics and Microbiology and.,Department of Pathology, Duke University, Durham, North Carolina, USA.,Program in Emerging Infectious Diseases, Duke-National University of Singapore, Singapore, Singapore.,Department of Immunology, Duke University, Durham, North Carolina, USA
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18
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Spyrou MA, Tukhbatova RI, Wang CC, Valtueña AA, Lankapalli AK, Kondrashin VV, Tsybin VA, Khokhlov A, Kühnert D, Herbig A, Bos KI, Krause J. Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague. Nat Commun 2018; 9:2234. [PMID: 29884871 PMCID: PMC5993720 DOI: 10.1038/s41467-018-04550-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 04/27/2018] [Indexed: 12/23/2022] Open
Abstract
The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics. Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000–3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear. Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia. We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested. Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day. Yersinia pestis has caused infections (plague) in humans since the Early Bronze Age (5000 years ago). Here, Spyrou et al. reconstruct Y. pestis genomes from Late Bronze Age individuals, and find genomic evidence compatible with flea-mediated transmission causing bubonic plague.
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Affiliation(s)
- Maria A Spyrou
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany.
| | - Rezeda I Tukhbatova
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Center of Excellence "Archaeometry", Kazan Federal University, Kazan, 420008, Russian Federation
| | - Chuan-Chao Wang
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Department of Anthropology and Ethnology, Xiamen University, 361005, Xiamen, China
| | - Aida Andrades Valtueña
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Aditya K Lankapalli
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | | | - Victor A Tsybin
- State Institute of Culture, Agency for Preservation of the Historical and Cultural Heritage of the Samara Region, Samara, 443010, Russia
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Maxim Gorky Str., Samara, 443090, Russia
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany.
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19
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Philip NH, Zwack EE, Brodsky IE. Activation and Evasion of Inflammasomes by Yersinia. Curr Top Microbiol Immunol 2017; 397:69-90. [PMID: 27460805 DOI: 10.1007/978-3-319-41171-2_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The innate immune system plays an essential role in initiating the early response against microbial infection, as well as instructing and shaping subsequent responses. Microbial pathogens are enormously diverse in terms of the niches they occupy, their metabolic properties and requirements, and the cellular pathways that they target. Nevertheless, innate sensing of pathogens triggers a relatively stereotyped set of responses that involve transcriptional induction of key inflammatory mediators, as well as post-translational assembly and activation of a multiprotein inflammatory complex termed 'the inflammasome.' Along with classical Pattern Recognition Receptors, the inflammasome activation pathway has emerged as a key regulator of tissue homeostasis and immune defense. Components of the inflammasome generally exist within the cell in a soluble, monomeric state, and oligomerize in response to diverse enzymatic activities associated with infection or cellular stress. Inflammasome assembly triggers activation of the pro-enzyme caspase-1, resulting in the cleavage of caspase-1 targets. The most extensively studied targets are the cytokines of the IL-1 family, but the recent discovery of Gasdermin D as a novel target of caspase-1 and the related inflammatory caspase, caspase-11, has begun to mechanistically define the links between caspase-1 activation and cell death. Cell death is a hallmark of macrophage infection by many pathogens, including the gram-negative bacterial pathogens of the genus Yersinia. Intriguingly, the activities of the Yersinia-secreted effector proteins and the type III secretion system (T3SS) itself have been linked to both inflammasome activation and evasion during infection. The balance between these activating and inhibitory activities shapes the outcome of Yersinia infection. Here, we describe the current state of knowledge on interactions between Yersinia and the inflammasome system, with the goal of integrating these findings within the general framework of inflammasome responses to microbial pathogens.
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Affiliation(s)
- Naomi H Philip
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19104, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.,Immunology Graduate Group, Philadelphia, PA, 19104, USA
| | - Erin E Zwack
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19104, USA.,Cell and Molecular Biology Graduate Group, Philadelphia, PA, 19104, USA
| | - Igor E Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19104, USA. .,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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20
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Barnes AC, Delamare-Deboutteville J, Gudkovs N, Brosnahan C, Morrison R, Carson J. Whole genome analysis of Yersinia ruckeri isolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection. Microb Genom 2016; 2:e000095. [PMID: 28348835 PMCID: PMC5320707 DOI: 10.1099/mgen.0.000095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 10/25/2016] [Indexed: 01/06/2023] Open
Abstract
Yersinia ruckeri is a salmonid pathogen with widespread distribution in cool-temperate waters including Australia and New Zealand, two isolated environments with recently developed salmonid farming industries. Phylogenetic comparison of 58 isolates from Australia, New Zealand, USA, Chile, Finland and China based on non-recombinant core genome SNPs revealed multiple deep-branching lineages, with a most recent common ancestor estimated at 18 500 years BP (12 355–24 757 95% HPD) and evidence of Australasian endemism. Evolution within the Tasmanian Atlantic salmon serotype O1b lineage has been slow, with 63 SNPs describing the variance over 27 years. Isolates from the prevailing lineage are poorly/non-motile compared to a lineage pre-vaccination, introduced in 1997, which is highly motile but has not been isolated since from epizootics. A non-motile phenotype has arisen independently in Tasmania compared to Europe and USA through a frameshift in fliI, encoding the ATPase of the flagella cluster. We report for the first time lipopolysaccharide O-antigen serotype O2 isolates in Tasmania. This phenotype results from deletion of the O-antigen cluster and consequent loss of high-molecular-weight O-antigen. This phenomenon has occurred independently on three occasions on three continents (Australasia, North America and Asia) as O2 isolates from the USA, China and Tasmania share the O-antigen deletion but occupy distant lineages. Despite the European and North American origins of the Australasian salmonid stocks, the lineages of Y. ruckeri in Australia and New Zealand are distinct from those of the northern hemisphere, suggesting they are pre-existing ancient strains that have emerged and evolved with the introduction of susceptible hosts following European colonization.
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Affiliation(s)
- Andrew C Barnes
- 1School of Biological Sciences, The University of Queensland, Gehrmann Laboratories (60), St Lucia, Brisbane, QL 4072, Australia
| | - Jerome Delamare-Deboutteville
- 1School of Biological Sciences, The University of Queensland, Gehrmann Laboratories (60), St Lucia, Brisbane, QL 4072, Australia
| | - Nicholas Gudkovs
- 2CSIRO Australian Animal Health Laboratory, Newcomb, VIC 3219, Australia
| | - Cara Brosnahan
- 3Ministry for Primary Industries, Animal Health Laboratory, Wallaceville, New Zealand
| | - Richard Morrison
- 4Department of Primary Industries Parks Water & Environment (DPIPWE), Kings Meadows, Launceston, TAS 7249, Australia
| | - Jeremy Carson
- 4Department of Primary Industries Parks Water & Environment (DPIPWE), Kings Meadows, Launceston, TAS 7249, Australia
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21
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Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CMO, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 2015; 163:571-82. [PMID: 26496604 PMCID: PMC4644222 DOI: 10.1016/j.cell.2015.10.009] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 11/25/2022]
Abstract
The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics. Yersinia pestis was common across Eurasia in the Bronze Age The most recent common ancestor of all Y. pestis was 5,783 years ago The ymt gene was acquired before 951 cal BC, giving rise to transmission via fleas Bronze Age Y. pestis was not capable of causing bubonic plague
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Affiliation(s)
- Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Morten Erik Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Kasper Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Anders Gorm Pedersen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alex Van Dam
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Christian Moliin Outzen Kapel
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Henrik Bjørn Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Pavel Avetisyan
- Division of Armenology and Social Sciences, Institute of Archaeology and Ethnography, National Academy of Sciences, 0025 Yerevan, Republic of Armenia
| | - Andrey Epimakhov
- Institute of History and Archaeology RAS (South Ural Department), South Ural State University, 454080 Chelyabinsk, Russia
| | | | - Artak Gnuni
- Department of Archaeology and Ethnography, Yerevan State University, 0025 Yerevan, Republic of Armenia
| | - Aivar Kriiska
- Department of Archaeology, University of Tartu, 51003 Tartu, Estonia
| | - Irena Lasak
- Institute of Archaeology, University of Wrocław, 50-139 Wrocław, Poland
| | - Mait Metspalu
- Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Andrei Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Dalia Pokutta
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Lehti Saag
- Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia
| | - Liivi Varul
- Department of Archaeology, University of Tartu, 51003 Tartu, Estonia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Rasmus Nielsen
- Center for Theoretical Evolutionary Genetics, University of California, Berkeley, California 94720-3140, USA
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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Shin S, Brodsky IE. The inflammasome: Learning from bacterial evasion strategies. Semin Immunol 2015; 27:102-10. [PMID: 25914126 DOI: 10.1016/j.smim.2015.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 01/01/2023]
Abstract
The innate immune system plays a critical role in defense against microbial infection and employs germline-encoded pattern recognition receptors to detect broadly conserved microbial structures or activities. Pattern recognition receptors of the nucleotide binding domain/leucine rich repeat (NLR) family respond to particular microbial products or disruption of cellular physiology, and mediate the activation of an arm of the innate immune response termed the inflammasome. Inflammasomes are multiprotein complexes that are inducibly assembled in response to the contamination of the host cell cytosol by microbial products. Individual NLRs sense the presence of their cognate stimuli, and initiate assembly of inflammasomes via the adaptor protein apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) and the effector pro-enzyme caspase-1. Inflammasome activation leads to rapid release of pro-inflammatory mediators of the IL-1 family as well as the release of intracellular alarmins due to a lytic form of programmed cell death termed pyroptosis. Over the past 15 years, a great deal has been learned about the mechanisms that drive inflammasome activation in response to infection by diverse pathogens. However, pathogens have also evolved mechanisms to evade or suppress host defenses, and the mechanisms by which pathogens evade inflammasome activation are not well-understood. Here, we will discuss emerging evidence on how diverse pathogens evade inflammasome activation, and what these studies have revealed about inflammasome biology. Deeper understanding of pathogen evasion of inflammasome activation has the potential to lead to development of novel classes of immunomodulatory factors that could be used in the context of human inflammatory diseases.
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Affiliation(s)
- Sunny Shin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Igor E Brodsky
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Transcriptomic Analysis of Yersinia enterocolitica Biovar 1B Infecting Murine Macrophages Reveals New Mechanisms of Extracellular and Intracellular Survival. Infect Immun 2015; 83:2672-85. [PMID: 25895974 DOI: 10.1128/iai.02922-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/10/2015] [Indexed: 11/20/2022] Open
Abstract
Yersinia enterocolitica is typically considered an extracellular pathogen; however, during the course of an infection, a significant number of bacteria are stably maintained within host cell vacuoles. Little is known about this population and the role it plays during an infection. To address this question and to elucidate the spatially and temporally dynamic gene expression patterns of Y. enterocolitica biovar 1B through the course of an in vitro infection, transcriptome sequencing and differential gene expression analysis of bacteria infecting murine macrophage cells were performed under four distinct conditions. Bacteria were first grown in a nutrient-rich medium at 26 °C to establish a baseline of gene expression that is unrelated to infection. The transcriptomes of these bacteria were then compared to bacteria grown in a conditioned cell culture medium at 37 °C to identify genes that were differentially expressed in response to the increased temperature and medium but not in response to host cells. Infections were then performed, and the transcriptomes of bacteria found on the extracellular surface and intracellular compartments were analyzed individually. The upregulated genes revealed potential roles for a variety of systems in promoting intracellular virulence, including the Ysa type III secretion system, the Yts2 type II secretion system, and the Tad pilus. It was further determined that mutants of each of these systems had decreased virulence while infecting macrophages. Overall, these results reveal the complete set of genes expressed by Y. enterocolitica in response to infection and provide the groundwork for future virulence studies.
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Inflammasome activation in response to the Yersinia type III secretion system requires hyperinjection of translocon proteins YopB and YopD. mBio 2015; 6:e02095-14. [PMID: 25691590 PMCID: PMC4337566 DOI: 10.1128/mbio.02095-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Type III secretion systems (T3SS) translocate effector proteins into target cells in order to disrupt or modulate host cell signaling pathways and establish replicative niches. However, recognition of T3SS activity by cytosolic pattern recognition receptors (PRRs) of the nucleotide-binding domain leucine rich repeat (NLR) family, either through detection of translocated products or membrane disruption, induces assembly of multiprotein complexes known as inflammasomes. Macrophages infected with Yersinia pseudotuberculosis strains lacking all known effectors or lacking the translocation regulator YopK induce rapid activation of both the canonical NLRP3 and noncanonical caspase-11 inflammasomes. While this inflammasome activation requires a functional T3SS, the precise signal that triggers inflammasome activation in response to Yersinia T3SS activity remains unclear. Effectorless strains of Yersinia as well as ΔyopK strains translocate elevated levels of T3SS substrates into infected cells. To dissect the contribution of pore formation and translocation to inflammasome activation, we took advantage of variants of YopD and LcrH that separate these functions of the T3SS. Notably, YopD variants that abrogated translocation but not pore-forming activity failed to induce inflammasome activation. Furthermore, analysis of individual infected cells revealed that inflammasome activation at the single-cell level correlated with translocated levels of YopB and YopD themselves. Intriguingly, LcrH mutants that are fully competent for effector translocation but produce and translocate lower levels of YopB and YopD also fail to trigger inflammasome activation. Our findings therefore suggest that hypertranslocation of YopD and YopB is linked to inflammasome activation in response to the Yersinia T3SS. The innate immune response is critical to effective clearance of pathogens. Recognition of conserved virulence structures and activities by innate immune receptors such as NLRs constitute one of the first steps in mounting the innate immune response. However, pathogens such as Yersinia actively evade or subvert components of host defense, such as inflammasomes. The T3SS-secreted protein YopK is an essential virulence factor that limits translocation of other Yops, thereby limiting T3SS-induced inflammasome activation. However, what triggers inflammasome activation in cells infected by YopK-deficient Yersinia is not clear. Our findings indicate that hypertranslocation of pore complex proteins promotes inflammasome activation and that YopK prevents inflammasome activation by the T3SS by limiting translocation of YopD and YopB themselves.
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25
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Xu T, Su Y, Xu Y, He Y, Wang B, Dong X, Li Y, Zhang XH. Mutations of flagellar genes fliC12, fliA and flhDC of Edwardsiella tarda attenuated bacterial motility, biofilm formation and virulence to fish. J Appl Microbiol 2013; 116:236-44. [PMID: 24118854 DOI: 10.1111/jam.12357] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 09/29/2013] [Accepted: 10/01/2013] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to investigate functions of flagellar genes fliC2, fliC12, fliA and flhDC in a bacterial fish pathogen Edwardsiella tarda. METHODS AND RESULTS In this study, functions of flagellar genes, fliC2, fliC12 (fliC1 + fliC2), fliA and flhDC (flhD + flhC) of Edw. tarda H1 were analysed by constructing in-frame deletion mutants respectively and complementary strains fliC2(+) and fliA(+) . Electron microscopy revealed that in-frame deletion of fliC12, fliA and flhDC significantly impaired the number and length of flagellar filaments, resulting in loss of both swimming and swarming motilities of the bacteria. In addition, compared to the wild-type strain and complementary strains, the flagellum-impaired mutants exhibited reduced biofilm formation ability, showed decreased ability in adherence and internalization to Epithelioma papulosum cyprini (EPC) cells and reduced pathogenicity to zebrafish. CONCLUSIONS These results indicated that fliC12, fliA and flhDC of Edw. tarda played essential roles in flagellar filaments structure, bacteria motility, biofilm formation, adherence, internalization and pathogenicity of this bacterium. SIGNIFICANCE AND IMPACT OF THE STUDY This study revealed that flagella function in facilitating virulence and it may provide a new target for vaccines against Edw. tarda infection.
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Affiliation(s)
- T Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Y Su
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Y Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Y He
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - B Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - X Dong
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Y Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - X-H Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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26
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Casson CN, Copenhaver AM, Zwack EE, Nguyen HT, Strowig T, Javdan B, Bradley WP, Fung TC, Flavell RA, Brodsky IE, Shin S. Caspase-11 activation in response to bacterial secretion systems that access the host cytosol. PLoS Pathog 2013; 9:e1003400. [PMID: 23762026 PMCID: PMC3675167 DOI: 10.1371/journal.ppat.1003400] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 04/19/2013] [Indexed: 01/13/2023] Open
Abstract
Inflammasome activation is important for antimicrobial defense because it induces cell death and regulates the secretion of IL-1 family cytokines, which play a critical role in inflammatory responses. The inflammasome activates caspase-1 to process and secrete IL-1β. However, the mechanisms governing IL-1α release are less clear. Recently, a non-canonical inflammasome was described that activates caspase-11 and mediates pyroptosis and release of IL-1α and IL-1β. Caspase-11 activation in response to Gram-negative bacteria requires Toll-like receptor 4 (TLR4) and TIR-domain-containing adaptor-inducing interferon-β (TRIF)-dependent interferon production. Whether additional bacterial signals trigger caspase-11 activation is unknown. Many bacterial pathogens use specialized secretion systems to translocate effector proteins into the cytosol of host cells. These secretion systems can also deliver flagellin into the cytosol, which triggers caspase-1 activation and pyroptosis. However, even in the absence of flagellin, these secretion systems induce inflammasome activation and the release of IL-1α and IL-1β, but the inflammasome pathways that mediate this response are unclear. We observe rapid IL-1α and IL-1β release and cell death in response to the type IV or type III secretion systems of Legionella pneumophila and Yersinia pseudotuberculosis. Unlike IL-1β, IL-1α secretion does not require caspase-1. Instead, caspase-11 activation is required for both IL-1α secretion and cell death in response to the activity of these secretion systems. Interestingly, whereas caspase-11 promotes IL-1β release in response to the type IV secretion system through the NLRP3/ASC inflammasome, caspase-11-dependent release of IL-1α is independent of both the NAIP5/NLRC4 and NLRP3/ASC inflammasomes as well as TRIF and type I interferon signaling. Furthermore, we find both overlapping and non-redundant roles for IL-1α and IL-1β in mediating neutrophil recruitment and bacterial clearance in response to pulmonary infection by L. pneumophila. Our findings demonstrate that virulent, but not avirulent, bacteria trigger a rapid caspase-11-dependent innate immune response important for host defense. The inflammasome, a multiprotein complex, is critical for host defense against bacterial infection. The inflammasome activates the host protease caspase-1 to process and secrete IL-1β. Another caspase, caspase-11, can cause cell death and IL-1α release. The bacterial signals that trigger caspase-11 activation are poorly understood. A common feature of many bacterial pathogens is the ability to inject virulence factors and other bacterial molecules into the host cell cytosol by means of a variety of virulence-associated secretion systems. These secretion systems can introduce bacterial flagellin into the host cytosol, which leads to caspase-1 activation and cell death. However, many bacteria lack or down-regulate flagellin yet still activate the inflammasome. Here, we show that the type IV secretion system of Legionella pneumophila and the type III secretion system of Yersinia pseudotuberculosis rapidly trigger caspase-11 activation in a flagellin-independent manner. Caspase-11 activation mediates two separate inflammasome pathways: one leading to IL-1β processing and secretion, and one leading to cell death and IL-1α release. Furthermore, we find these caspase-11-regulated cytokines are critical for neutrophil recruitment to the site of infection and clearance of non-flagellated Legionella in vivo. Overall, our findings show that virulent bacteria activate a rapid caspase-11-dependent immune response that plays a critical role in host defense.
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Affiliation(s)
- Cierra N Casson
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Scott CJW, Austin B, Austin DA, Morris PC. Non-adjuvanted flagellin elicits a non-specific protective immune response in rainbow trout (Oncorhynchus mykiss, Walbaum) towards bacterial infections. Vaccine 2013; 31:3262-7. [PMID: 23707165 DOI: 10.1016/j.vaccine.2013.05.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/15/2013] [Accepted: 05/08/2013] [Indexed: 11/28/2022]
Abstract
Enteric redmouth disease, caused by Yersinia ruckeri, may result in high mortalities in farmed salmonids. Prophylaxis has been achieved with an immersion vaccine comprised of inactivated serovar 1 biotype 1 (motile) Y. ruckeri cultures. However, there has been a growing number of enteric redmouth outbreaks in vaccinated livestock associated with serovar 1 biotype 2 (non-motile) Y. ruckeri strains which do not produce flagellin. It was the aim of this study to evaluate the protective role of flagellin in enteric redmouth vaccines. Results showed that flagellin in the inactivated whole-cell vaccine were not the main immunoprotective molecule in eliciting a protective immune response towards infection. However, use of non-adjuvanted flagellin as a sub-unit vaccine, both in the native and recombinant form, resulted in a potent non-specific protective function towards challenge with biotype 1 (flagellin-producing) and biotype 2 (flagellin-devoid) Y. ruckeri. This vaccine can also protect rainbow trout against other microbial fish pathogens, for example Aeromonas salmonicida. Thus non-adjuvanted flagellin may have potential as a non-specific vaccine for fish towards bacterial pathogens.
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Affiliation(s)
- Callum J W Scott
- School of Life Sciences, Heriot-Watt University, Riccarton, Edinburgh, Scotland EH14 4AS, UK
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28
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Abstract
A comprehensive TnphoA mutant library was constructed in Yersinia pestis KIM6 to identify surface proteins involved in Y. pestis host cell invasion and bacterial virulence. Insertion site analysis of the library repeatedly identified a 9,042-bp chromosomal gene (YPO3944), intimin/invasin-like protein (Ilp), similar to the Gram-negative intimin/invasin family of surface proteins. Deletion mutants of ilp were generated in Y. pestis strains KIM5(pCD1(+)) Pgm(-) (pigmentation negative)/, KIM6(pCD1(-)) Pgm(+), and CO92. Comparative analyses were done with the deletions and the parental wild type for bacterial adhesion to and internalization by HEp-2 cells in vitro, infectivity and maintenance in the flea vector, and lethality in murine models of systemic and pneumonic plague. Deletion of ilp had no effect on bacterial blockage of flea blood feeding or colonization. The Y. pestis KIM5 Δilp strain had reduced adhesion to and internalization by HEp-2 cells compared to the parental wild-type strain (P < 0.05). Following intravenous challenge with Y. pestis KIM5 Δilp, mice had a delayed time to death and reduced dissemination to the lungs, livers, and kidneys as monitored by in vivo imaging using a lux reporter system (in vivo imaging system [IVIS]) and bacterial counts. Intranasal challenge in mice with Y. pestis CO92 Δilp had a 55-fold increase in the 50% lethal dose ([LD(50)] 1.64 × 10(4) CFU) compared to the parental wild-type strain LD(50) (2.98 × 10(2) CFU). These findings identified Ilp as a novel virulence factor of Y. pestis.
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29
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Kupz A, Guarda G, Gebhardt T, Sander LE, Short KR, Diavatopoulos DA, Wijburg OLC, Cao H, Waithman JC, Chen W, Fernandez-Ruiz D, Whitney PG, Heath WR, Curtiss R, Tschopp J, Strugnell RA, Bedoui S. NLRC4 inflammasomes in dendritic cells regulate noncognate effector function by memory CD8⁺ T cells. Nat Immunol 2012; 13:162-9. [PMID: 22231517 DOI: 10.1038/ni.2195] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 11/28/2011] [Indexed: 12/13/2022]
Abstract
Memory T cells exert antigen-independent effector functions, but how these responses are regulated is unclear. We discovered an in vivo link between flagellin-induced NLRC4 inflammasome activation in splenic dendritic cells (DCs) and host protective interferon-γ (IFN-γ) secretion by noncognate memory CD8(+) T cells, which could be activated by Salmonella enterica serovar Typhimurium, Yersinia pseudotuberculosis and Pseudomonas aeruginosa. We show that CD8α(+) DCs were particularly efficient at sensing bacterial flagellin through NLRC4 inflammasomes. Although this activation released interleukin 18 (IL-18) and IL-1β, only IL-18 was required for IFN-γ production by memory CD8(+) T cells. Conversely, only the release of IL-1β, but not IL-18, depended on priming signals mediated by Toll-like receptors. These findings provide a comprehensive mechanistic framework for the regulation of noncognate memory T cell responses during bacterial immunity.
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Affiliation(s)
- Andreas Kupz
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
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Mutagenic analysis of the Clostridium difficile flagellar proteins, FliC and FliD, and their contribution to virulence in hamsters. Infect Immun 2011; 79:4061-7. [PMID: 21788384 DOI: 10.1128/iai.05305-11] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although toxins A and B are known to be important contributors to the acute phase of Clostridium difficile infection, the role of colonization and adherence to host tissues in the overall pathogenesis of these organisms remains unclear. Consequently, we used the recently introduced intron-based ClosTron gene interruption system to eliminate the expression of two reported C. difficile colonization factors, the major flagellar structural subunit (FliC) and the flagellar cap protein (FliD), to gain greater insight into how flagella and motility contribute to C. difficile's pathogenic strategy. The results demonstrate that interrupting either the fliC or the fliD gene results in a complete loss of flagella, as well as motility, in C. difficile. However, both the fliC and fliD mutant strains adhered better than the wild-type 630Δerm strain to human intestine-derived Caco-2 cells, suggesting that flagella and motility do not contribute to, or may even interfere with, C. difficile adherence to epithelial cell surfaces in vitro. Moreover, we found that the mutant strains were more virulent in hamsters, indicating either that flagella are unnecessary for virulence or that repression of motility may be a pathogenic strategy employed by C. difficile in hamsters.
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Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe. Appl Environ Microbiol 2011; 77:3493-9. [PMID: 21441334 DOI: 10.1128/aem.02997-10] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biotype 2 (BT2) variants of the bacterium Yersinia ruckeri are an increasing disease problem in U.S. and European aquaculture and have been characterized as serovar 1 isolates that lack both peritrichous flagella and secreted phospholipase activity. The emergence of this biotype has been associated with an increased frequency of enteric redmouth disease (ERM) outbreaks in previously vaccinated salmonid fish. In this study, four independent specific natural mutations that cause the loss of both motility and secreted lipase activity were identified in BT2 strains from the United States, United Kingdom, and mainland Europe. Each of these was a unique mutation in either fliR, flhA, or flhB, all of which are genes predicted to encode essential components of the flagellar secretion apparatus. Our results demonstrate the existence of independent mutations leading to the BT2 phenotype; thus, this phenotype has emerged separately at least four times. In addition, BT2 strains from the United Kingdom were shown to have the same mutant allele found in U.S. BT2 strains, suggesting a common origin of this BT2 lineage. This differentiation of distinct BT2 lineages is of critical importance for the development and validation of alternative vaccines or other treatment strategies intended for the control of BT2 strains.
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Raczkowska A, Skorek K, Bielecki J, Brzostek K. OmpR controls Yersinia enterocolitica motility by positive regulation of flhDC expression. Antonie van Leeuwenhoek 2010; 99:381-94. [PMID: 20830609 PMCID: PMC3032193 DOI: 10.1007/s10482-010-9503-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 08/25/2010] [Indexed: 11/26/2022]
Abstract
Flagella and invasin play important roles during the early stages of infection by the enteric pathogen Yersinia enterocolitica. Our previous study demonstrated that OmpR negatively regulates invasin gene expression at the transcriptional level. The present study focused on the role of OmpR in the regulation of flagella expression. Motility assays and microscopic observations revealed that an ompR mutant strain exhibits a non-motile phenotype due to the lack of flagella. An analysis of flhDC::lacZYA chromosomal fusions demonstrated a decrease in flhDC expression in ompR mutant cells, suggesting a role for OmpR in the positive control of flagellar master operon flhDC, which is in contrast to the negative role it plays in Escherichia coli. Moreover, high temperature or osmolarity and low pH decreased flhDC expression and OmpR was not required for the response to these factors. Evidence from an examination of the DNA binding properties of OmpR in vitro indicated that the mechanism by which OmpR regulates flhDC is direct. Electrophoretic mobility shift assays confirmed that OmpR binds specifically to the flhDC promoter region and suggested the presence of more than one OmpR-binding site. In addition, phosphorylation of OmpR by acetyl-P appeared to stimulate the binding abilities of OmpR. Together with the results of our previous studies revealing the negative role of OmpR in the regulation of invasin expression, these findings support a model in which invasion and motility might be reciprocally regulated by OmpR.
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Affiliation(s)
- Adrianna Raczkowska
- Department of Applied Microbiology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Karolina Skorek
- Department of Applied Microbiology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Jacek Bielecki
- Department of Applied Microbiology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Katarzyna Brzostek
- Department of Applied Microbiology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Winter SE, Winter MG, Godinez I, Yang HJ, Rüssmann H, Andrews-Polymenis HL, Bäumler AJ. A rapid change in virulence gene expression during the transition from the intestinal lumen into tissue promotes systemic dissemination of Salmonella. PLoS Pathog 2010; 6:e1001060. [PMID: 20808848 PMCID: PMC2924370 DOI: 10.1371/journal.ppat.1001060] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 07/22/2010] [Indexed: 12/12/2022] Open
Abstract
Bacterial pathogens causing systemic disease commonly evolve from organisms associated with localized infections but differ from their close relatives in their ability to overcome mucosal barriers by mechanisms that remain incompletely understood. Here we investigated whether acquisition of a regulatory gene, tviA, contributed to the ability of Salmonella enterica serotype Typhi to disseminate from the intestine to systemic sites of infection during typhoid fever. To study the consequences of acquiring a new regulator by horizontal gene transfer, tviA was introduced into the chromosome of S. enterica serotype Typhimurium, a closely related pathogen causing a localized gastrointestinal infection in immunocompetent individuals. TviA repressed expression of flagellin, a pathogen associated molecular pattern (PAMP), when bacteria were grown at osmotic conditions encountered in tissue, but not at higher osmolarity present in the intestinal lumen. TviA-mediated flagellin repression enabled bacteria to evade sentinel functions of human model epithelia and resulted in increased bacterial dissemination to the spleen in a chicken model. Collectively, our data point to PAMP repression as a novel pathogenic mechanism to overcome the mucosal barrier through innate immune evasion.
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Affiliation(s)
- Sebastian E. Winter
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United States of America
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, München, Germany
| | - Maria G. Winter
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United States of America
| | - Ivan Godinez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United States of America
| | - Hee-Jeong Yang
- Department of Microbial and Molecular Pathogenesis, College of Medicine, Texas A&M University System Health Science Center, College Station, Texas, United States of America
| | - Holger Rüssmann
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, München, Germany
- HELIOS Klinikum Emil von Behring, Institut für Mikrobiologie, Immunologie und Laboratoriumsmedizin, Berlin, Germany
| | - Helene L. Andrews-Polymenis
- Department of Microbial and Molecular Pathogenesis, College of Medicine, Texas A&M University System Health Science Center, College Station, Texas, United States of America
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United States of America
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Brodsky IE, Palm NW, Sadanand S, Ryndak MB, Sutterwala FS, Flavell RA, Bliska JB, Medzhitov R. A Yersinia effector protein promotes virulence by preventing inflammasome recognition of the type III secretion system. Cell Host Microbe 2010; 7:376-87. [PMID: 20478539 DOI: 10.1016/j.chom.2010.04.009] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/31/2010] [Accepted: 04/09/2010] [Indexed: 12/14/2022]
Abstract
Bacterial pathogens utilize pore-forming toxins or specialized secretion systems to deliver virulence factors to modulate host cell physiology and promote bacterial replication. Detection of these secretion systems or toxins, or their activities, by nucleotide-binding oligomerization domain leucine-rich repeat proteins (NLRs) triggers the assembly of inflammasomes, multiprotein complexes necessary for caspase-1 activation and host defense. Here we demonstrate that caspase-1 activation in response to the Yersinia type III secretion system (T3SS) requires the adaptor ASC and involves both NLRP3 and NLRC4 inflammasomes. Further, we identify a Yersinia type III secreted effector protein, YopK, which interacts with the T3SS translocon to prevent cellular recognition of the T3SS and inflammasome activation. In the absence of YopK, inflammasome sensing of the T3SS promotes bacterial clearance from infected tissues in vivo. These data demonstrate that a class of bacterial proteins interferes with cellular recognition of bacterial secretion systems and contributes to bacterial survival within host tissues.
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Affiliation(s)
- Igor E Brodsky
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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35
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Yersinia pestis two-component gene regulatory systems promote survival in human neutrophils. Infect Immun 2009; 78:773-82. [PMID: 19933831 DOI: 10.1128/iai.00718-09] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Human polymorphonuclear leukocytes (PMNs, or neutrophils) are the most abundant innate immune cell and kill most invading bacteria through combined activities of reactive oxygen species (ROS) and antimicrobial granule constituents. Pathogens such as Yersinia pestis resist destruction by the innate immune system and are able to survive in macrophages and neutrophils. The specific molecular mechanisms used by Y. pestis to survive following phagocytosis by human PMNs are incompletely defined. To gain insight into factors that govern Y. pestis intracellular survival in neutrophils, we inactivated 25 two-component gene regulatory systems (TCSs) with known or inferred function and assessed susceptibility of these mutant strains to human PMN granule extracts. Y. pestis strains deficient for PhoPQ, KdpED, CheY, CvgSY, and CpxRA TCSs were selected for further analysis, and all five strains were altered for survival following interaction with PMNs. Of these five strains, only Y. pestis DeltaphoPQ demonstrated global sensitivity to a panel of seven individual neutrophil antimicrobial peptides and serine proteases. Notably, Y. pestis DeltaphoPQ was deficient for intracellular survival in PMNs. Iterative analysis with Y. pestis strains lacking the PhoP-regulated genes ugd and pmrK indicated that the mechanism most likely responsible for increased resistance to killing is 4-amino-4-deoxy-l-arabinose modification of lipid A. Together, the data provide new information about Y. pestis evasion of the innate immune system.
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Abstract
Bacterial enteric infections are often associated with diarrhoea or vomiting, which are clinical presentations commonly referred to as gastroenteritis. However, some enteric pathogens, including typhoidal Salmonella serotypes, Brucella species and enteropathogenic Yersinia species are associated with a clinical syndrome that is characterized by abdominal pain and/or fever and is distinct from acute gastroenteritis. Recent insights into molecular mechanisms of the host-pathogen interaction show that these enteric pathogens share important characteristics that explain why the initial host responses associated with these agents more closely resemble host responses to viral or parasitic infections. Host responses contribute to the clinical presentation of disease and improved understanding of these responses in the laboratory is beginning to bridge the gap between bench and bedside.
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Airhart CL, Rohde HN, Bohach GA, Hovde CJ, Deobald CF, Lee SS, Minnich SA. Induction of innate immunity by lipid A mimetics increases survival from pneumonic plague. MICROBIOLOGY-SGM 2008; 154:2131-2138. [PMID: 18599840 DOI: 10.1099/mic.0.2008/017566-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This study analysed the effect of priming the innate immune system using synthetic lipid A mimetics in a Yersinia pestis murine pulmonary infection model. Two aminoalkyl glucosaminide 4-phosphate (AGP) Toll-like receptor 4 (TLR4) ligands, delivered intranasally, extended time to death or protected against a lethal Y. pestis CO92 challenge. The level of protection was dependent upon the challenge dose of Y. pestis and the timing of AGP therapy. Protection correlated with cytokine induction and a decreased bacterial burden in lung tissue. AGP protection was TLR4-dependent and was not evidenced in transgenic TLR4-deficient mice. AGP therapy augmented with subtherapeutic doses of gentamicin produced dramatically enhanced survival. Combined, these results indicated that AGPs may be useful in protection of immunologically naive individuals against plague and potentially other infectious agents, and that AGP therapy may be used synergistically with other therapies.
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Affiliation(s)
- Christina L Airhart
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID 83844-3052, USA
| | - Harold N Rohde
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID 83844-3052, USA
| | - Gregory A Bohach
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID 83844-3052, USA
| | - Carolyn J Hovde
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID 83844-3052, USA
| | - Claudia F Deobald
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID 83844-3052, USA
| | - Stephen S Lee
- Department of Statistics, University of Idaho, Moscow, ID 83844-3052, USA
| | - Scott A Minnich
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID 83844-3052, USA
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