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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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Nair S, Barker CR, Bird M, Greig DR, Collins C, Painset A, Chattaway M, Pickard D, Larkin L, Gharbia S, Didelot X, Ribeca P. Presence of phage-plasmids in multiple serovars of Salmonella enterica. Microb Genom 2024; 10:001247. [PMID: 38717818 PMCID: PMC11165635 DOI: 10.1099/mgen.0.001247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a bla CTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.
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Affiliation(s)
| | - Clare R. Barker
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
| | - Matthew Bird
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - David R. Greig
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Caitlin Collins
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Marie Chattaway
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
| | - Derek Pickard
- The Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | | | - Saheer Gharbia
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Xavier Didelot
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- School of Public Health and Department of Statistics, University of Warwick, Warwick, UK
| | - Paolo Ribeca
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- Biomathematics and Statistics Scotland, The James Hutton Institute, Edinburgh, UK
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3
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Puentes-Rodriguez SG, Norcross J, Mera PE. To let go or not to let go: how ParA can impact the release of the chromosomal anchoring in Caulobacter crescentus. Nucleic Acids Res 2023; 51:12275-12287. [PMID: 37933842 PMCID: PMC10711552 DOI: 10.1093/nar/gkad982] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
Chromosomal maintenance is vital for the survival of bacteria. In Caulobacter crescentus, chromosome replication initiates at ori and segregation is delayed until the nearby centromere-like region parS is replicated. Our understanding of how this sequence of events is regulated remains limited. The segregation of parS has been shown to involve multiple steps including polar release from anchoring protein PopZ, slow movement and fast ParA-dependent movement to the opposite cell pole. In this study, we demonstrate that ParA's competing attractions from PopZ and from DNA are critical for segregation of parS. Interfering with this balance of attractions-by expressing a variant ParA-R195E unable to bind DNA and thus favoring interactions exclusively between ParA-PopZ-results in cell death. Our data revealed that ParA-R195E's sole interactions with PopZ obstruct PopZ's ability to release the polar anchoring of parS, resulting in cells with multiple parS loci fixed at one cell pole. We show that the inability to separate and segregate multiple parS loci from the pole is specifically dependent on the interaction between ParA and PopZ. Collectively, our results reveal that the initial steps in chromosome segregation are highly regulated.
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Affiliation(s)
| | - John D Norcross
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paola E Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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4
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Puentes-Rodriguez SG, Norcross J, Mera PE. To let go or not to let go: how ParA can impact the release of the chromosomal anchoring in Caulobacter crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536610. [PMID: 37090538 PMCID: PMC10120649 DOI: 10.1101/2023.04.12.536610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Chromosomal maintenance is vital for the survival of bacteria. In Caulobacter crescentus, chromosome replication initiates at ori and segregation is delayed until the nearby centromere-like region parS is replicated. Our understanding of how this sequence of events is regulated remains limited. The segregation of parS has been shown to involve multiple steps including polar release from anchoring protein PopZ, slow movement, and fast ParA-dependent movement to opposite cell pole. In this study, we demonstrate that ParA's competing attractions from PopZ and from DNA are critical for segregation of parS. Interfering with this balance of attractions - by expressing a variant ParA-R195E unable to bind DNA and thus favoring interactions exclusively between ParA-PopZ - results in cell death. Our data revealed that ParA-R195E's sole interactions with PopZ obstruct PopZ's ability to release the polar anchoring of parS resulting in cells with multiple parS loci fixed at one cell pole. We show that the inability to separate and segregate multiple parS loci from the pole is specifically dependent on the interaction between ParA and PopZ. Interfering with interactions between PopZ and the partitioning protein ParB, which is the interaction that anchors parS at the cell pole, does not rescue the ability of cells to separate the fixed parS loci when expressing parA-R195E. Thus, ParA and PopZ appear to have a distinct conversation from ParB yet can impact the release of ParB-parS from the anchoring at the cell pole. Collectively, our results reveal that the initial steps in chromosome segregation are highly regulated.
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Affiliation(s)
| | - J.D. Norcross
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paola E. Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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5
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Exploring and Mitigating Plague for One Health Purposes. CURRENT TROPICAL MEDICINE REPORTS 2022. [DOI: 10.1007/s40475-022-00265-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Hau D, Wade B, Lovejoy C, Pandit SG, Reed DE, DeMers HL, Green HR, Hannah EE, McLarty ME, Creek CJ, Chokapirat C, Arias-Umana J, Cecchini GF, Nualnoi T, Gates-Hollingsworth MA, Thorkildson PN, Pflughoeft KJ, AuCoin DP. Development of a dual antigen lateral flow immunoassay for detecting Yersinia pestis. PLoS Negl Trop Dis 2022; 16:e0010287. [PMID: 35320275 PMCID: PMC8979426 DOI: 10.1371/journal.pntd.0010287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/04/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Background
Yersinia pestis is the causative agent of plague, a zoonosis associated with small mammals. Plague is a severe disease, especially in the pneumonic and septicemic forms, where fatality rates approach 100% if left untreated. The bacterium is primarily transmitted via flea bite or through direct contact with an infected host. The 2017 plague outbreak in Madagascar resulted in more than 2,400 cases and was highlighted by an increased number of pneumonic infections. Standard diagnostics for plague include laboratory-based assays such as bacterial culture and serology, which are inadequate for administering immediate patient care for pneumonic and septicemic plague.
Principal findings
The goal of this study was to develop a sensitive rapid plague prototype that can detect all virulent strains of Y. pestis. Monoclonal antibodies (mAbs) were produced against two Y. pestis antigens, low-calcium response V (LcrV) and capsular fraction-1 (F1), and prototype lateral flow immunoassays (LFI) and enzyme-linked immunosorbent assays (ELISA) were constructed. The LFIs developed for the detection of LcrV and F1 had limits of detection (LOD) of roughly 1–2 ng/mL in surrogate clinical samples (antigens spiked into normal human sera). The optimized antigen-capture ELISAs produced LODs of 74 pg/mL for LcrV and 61 pg/mL for F1 when these antigens were spiked into buffer. A dual antigen LFI prototype comprised of two test lines was evaluated for the detection of both antigens in Y. pestis lysates. The dual format was also evaluated for specificity using a small panel of clinical near-neighbors and other Tier 1 bacterial Select Agents.
Conclusions
LcrV is expressed by all virulent Y. pestis strains, but homologs produced by other Yersinia species can confound assay specificity. F1 is specific to Y. pestis but is not expressed by all virulent strains. Utilizing highly reactive mAbs, a dual-antigen detection (multiplexed) LFI was developed to capitalize on the diagnostic strengths of each target.
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Affiliation(s)
- Derrick Hau
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Brian Wade
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Chris Lovejoy
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Sujata G. Pandit
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Dana E. Reed
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Haley L. DeMers
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Heather R. Green
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Emily E. Hannah
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Megan E. McLarty
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Cameron J. Creek
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Chonnikarn Chokapirat
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Jose Arias-Umana
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Garett F. Cecchini
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Teerapat Nualnoi
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | | | - Peter N. Thorkildson
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Kathryn J. Pflughoeft
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - David P. AuCoin
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
- * E-mail:
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Mekasha S, Linke D. Secretion Systems in Gram-Negative Bacterial Fish Pathogens. Front Microbiol 2022; 12:782673. [PMID: 34975803 PMCID: PMC8714846 DOI: 10.3389/fmicb.2021.782673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.
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Affiliation(s)
- Sophanit Mekasha
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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8
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Acquisition of yersinia murine toxin enabled Yersinia pestis to expand the range of mammalian hosts that sustain flea-borne plague. PLoS Pathog 2021; 17:e1009995. [PMID: 34648607 PMCID: PMC8547695 DOI: 10.1371/journal.ppat.1009995] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/26/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Yersinia murine toxin (Ymt) is a phospholipase D encoded on a plasmid acquired by Yersinia pestis after its recent divergence from a Yersinia pseudotuberculosis progenitor. Despite its name, Ymt is not required for virulence but acts to enhance bacterial survival in the flea digestive tract. Certain Y. pestis strains circulating in the Bronze Age lacked Ymt, suggesting that they were not transmitted by fleas. However, we show that the importance of Ymt varies with host blood source. In accordance with the original description, Ymt greatly enhanced Y. pestis survival in fleas infected with bacteremic mouse, human, or black rat blood. In contrast, Ymt was much less important when fleas were infected using brown rat blood. A Y. pestis Ymt- mutant infected fleas nearly as well as the Ymt+ parent strain after feeding on bacteremic brown rat blood, and the mutant was transmitted efficiently by flea bite during the first weeks after infection. The protective function of Ymt correlated with red blood cell digestion kinetics in the flea gut. Thus, early Y. pestis strains that lacked Ymt could have been maintained in flea-brown rat transmission cycles, and perhaps in other hosts with similar blood characteristics. Acquisition of Ymt, however, served to greatly expand the range of hosts that could support flea-borne plague.
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9
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Drew GC, Stevens EJ, King KC. Microbial evolution and transitions along the parasite-mutualist continuum. Nat Rev Microbiol 2021; 19:623-638. [PMID: 33875863 PMCID: PMC8054256 DOI: 10.1038/s41579-021-00550-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Virtually all plants and animals, including humans, are home to symbiotic microorganisms. Symbiotic interactions can be neutral, harmful or have beneficial effects on the host organism. However, growing evidence suggests that microbial symbionts can evolve rapidly, resulting in drastic transitions along the parasite-mutualist continuum. In this Review, we integrate theoretical and empirical findings to discuss the mechanisms underpinning these evolutionary shifts, as well as the ecological drivers and why some host-microorganism interactions may be stuck at the end of the continuum. In addition to having biomedical consequences, understanding the dynamic life of microorganisms reveals how symbioses can shape an organism's biology and the entire community, particularly in a changing world.
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Affiliation(s)
| | | | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, UK.
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10
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Pfeifer E, Moura de Sousa JA, Touchon M, Rocha EPC. Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires. Nucleic Acids Res 2021; 49:2655-2673. [PMID: 33590101 PMCID: PMC7969092 DOI: 10.1093/nar/gkab064] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 01/16/2023] Open
Abstract
Plasmids and temperate phages are key contributors to bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage–plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage–plasmids are poorly known. Here, we screened for these elements among ca. 2500 phages and 12000 plasmids and identified 780 phage–plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to eight defined groups and 18 other broader communities of elements. The existence of these large groups suggests that phage–plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage–plasmids and found the key phage genes to be conserved and co-localized within distinct groups, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage–plasmids are a sizeable fraction of the sequenced plasmids (∼7%) and phages (∼5%), and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.
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Affiliation(s)
- Eugen Pfeifer
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris 75015, France
| | | | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris 75015, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris 75015, France
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11
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Meléndez AB, Menikpurage IP, Mera PE. Chromosome Dynamics in Bacteria: Triggering Replication at the Opposite Location and Segregation in the Opposite Direction. mBio 2019; 10:e01002-19. [PMID: 31363028 PMCID: PMC6667618 DOI: 10.1128/mbio.01002-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
Maintaining the integrity of the genome is essential to cell survival. In the bacterium Caulobacter crescentus, the single circular chromosome exhibits a specific orientation in the cell, with the replication origin (ori) residing at the pole of the cell bearing a stalk. Upon initiation of replication, the duplicated centromere-like region parS and ori move rapidly to the opposite pole where parS is captured by a microdomain hosting a unique set of proteins that contribute to the identity of progeny cells. Many questions remain as to how this organization is maintained. In this study, we constructed strains of Caulobacter in which ori and the parS centromere can be induced to move to the opposite cell pole in the absence of chromosome replication, allowing us to ask whether once these chromosomal foci were positioned at the wrong pole, replication initiation and chromosome segregation can proceed in the opposite orientation. Our data reveal that DnaA can initiate replication and ParA can orchestrate segregation from either cell pole. The cell reconstructs the organization of its ParA gradient in the opposite orientation to segregate one replicated centromere from the new pole toward the stalked pole (i.e., opposite direction), while displaying no detectable viability defects. Thus, the unique polar microdomains exhibit remarkable flexibility in serving as a platform for directional chromosome segregation along the long axis of the cell.IMPORTANCE Bacteria can accomplish surprising levels of organization in the absence of membrane organelles by constructing subcellular asymmetric protein gradients. These gradients are composed of regulators that can either trigger or inhibit cell cycle events from distinct cell poles. In Caulobacter crescentus, the onset of chromosome replication and segregation from the stalked pole are regulated by asymmetric protein gradients. We show that the activators of chromosome replication and segregation are not restricted to the stalked pole and that their organization and directionality can be flipped in orientation. Our results also indicate that the subcellular location of key chromosomal loci play important roles in the establishment of the asymmetric organization of cell cycle regulators.
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Affiliation(s)
- Ady B Meléndez
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA
| | - Inoka P Menikpurage
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA
| | - Paola E Mera
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA
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12
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Al-Jawdah AD, Ivanova IG, Waller H, Perkins ND, Lakey JH, Peters DT. Induction of the immunoprotective coat of Yersinia pestis at body temperature is mediated by the Caf1R transcription factor. BMC Microbiol 2019; 19:68. [PMID: 30922226 PMCID: PMC6440114 DOI: 10.1186/s12866-019-1444-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thermal regulation of gene expression occurs in many microorganisms, and is mediated via several typical mechanisms. Yersinia pestis is the causative agent of the plague and spreads by zoonotic transfer from fleas to mammalian blood with a concomitant rapid temperature change, from ambient to 37 °C, which induces the expression of capsular antigen (Caf1) that inhibits phagocytosis. Caf1 is formed into long polymeric fimbriae by a periplasmic chaperone (Caf1M) and outer membrane usher (Caf1A). All three are encoded on an operon regulated by an AraC-type transcription factor Caf1R. The aim of this study was to determine the role of Caf1R in the thermal control of caf1 operon gene expression. RESULTS PCR analysis of cDNA demonstrated that the genes of the operon are transcribed as a single polycistronic mRNA. Bioinformatic analysis, supported by deletion mutagenesis, then revealed a region containing the promoter of this polycistronic transcript that was critical for Caf1 protein expression. Caf1R was found to be essential for Caf1 protein production. Finally, RT-PCR analysis and western blot experiments showed large, Caf1R dependent increases in caf1 operon transcripts upon a shift in temperature from 25 °C to 35 °C. CONCLUSIONS The results show that thermal control of Caf1 polymer production is established at the transcriptional level, in a Caf1R dependent manner. This gives us new insights into how a virulent pathogen evades destruction by the immune system by detecting and responding to environmental changes.
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Affiliation(s)
- Abdulmajeed D Al-Jawdah
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Iglika G Ivanova
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Helen Waller
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Neil D Perkins
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel T Peters
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.
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13
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Rabaan AA, Al-Ahmed SH, Alsuliman SA, Aldrazi FA, Alfouzan WA, Haque S. The rise of pneumonic plague in Madagascar: current plague outbreak breaks usual seasonal mould. J Med Microbiol 2019; 68:292-302. [PMID: 30632956 DOI: 10.1099/jmm.0.000915] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Madagascar has just emerged from the grip of an acute urban pneumonic plague outbreak, which began in August 2017, before the usual plague season of October-April and outside the traditional plague foci in the northern and central highlands. The World Health Organization reported a total of 2417 confirmed, probable and suspected cases, including 209 deaths between 1 August and 26 November 2017. The severity and scope of this outbreak, which has affected those in higher socioeconomic groups as well as those living in poverty, along with factors including the potential for use of multi-drug-resistant strains of plague in bioterrorism, highlights the ongoing threat posed by this ancient disease. Factors likely to have contributed to transmission include human behaviour, including burial practices and movement of people, poor urban planning leading to overcrowding and ready transmission by airborne droplets, climatic factors and genomic subtypes. The outbreak demonstrates the importance of identifying targeted pneumonic plague therapies and of developing vaccines that can be administered in planned programmes in developing countries such as Madagascar where plague is endemic. The dominance of pneumonic plague in this outbreak suggests that we need to focus more urgently on the danger of person-to-person transmission, as well as the problem of transmission of plague from zoonotic sources.
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Affiliation(s)
- Ali A Rabaan
- 1Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- 2Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Shahab A Alsuliman
- 3Internal Medicine and Infectious Disease Department, Dammam Medical Complex, Dammam, Saudi Arabia
| | - Fatimah A Aldrazi
- 4Infection Control Department, Dammam Medical Complex, Dammam, Saudi Arabia
| | - Wadha A Alfouzan
- 5Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Shafiul Haque
- 6Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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14
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Döhlemann J, Wagner M, Happel C, Carrillo M, Sobetzko P, Erb TJ, Thanbichler M, Becker A. A Family of Single Copy repABC-Type Shuttle Vectors Stably Maintained in the Alpha-Proteobacterium Sinorhizobium meliloti. ACS Synth Biol 2017; 6:968-984. [PMID: 28264559 PMCID: PMC7610768 DOI: 10.1021/acssynbio.6b00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
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A considerable
share of bacterial species maintains segmented genomes.
Plant symbiotic α-proteobacterial rhizobia contain up to six repABC-type replicons in addition to the primary chromosome.
These low or unit-copy replicons, classified as secondary chromosomes,
chromids, or megaplasmids, are exclusively found in α-proteobacteria.
Replication and faithful partitioning of these replicons to the daughter
cells is mediated by the repABC region. The importance
of α-rhizobial symbiotic nitrogen fixation for sustainable agriculture
and Agrobacterium-mediated plant transformation as
a tool in plant sciences has increasingly moved biological engineering
of these organisms into focus. Plasmids are ideal DNA-carrying vectors
for these engineering efforts. On the basis of repABC regions collected from α-rhizobial secondary replicons, and
origins of replication derived from traditional cloning vectors, we
devised the versatile family of pABC shuttle vectors propagating in Sinorhizobium meliloti, related members of the Rhizobiales, and Escherichia coli. A modular plasmid library
providing the elemental parts for pABC vector assembly was founded.
The standardized design of these vectors involves five basic modules:
(1) repABC cassette, (2) plasmid-derived origin of
replication, (3) RK2/RP4 mobilization site (optional), (4) antibiotic
resistance gene, and (5) multiple cloning site flanked by transcription
terminators. In S. meliloti, pABC vectors showed
high propagation stability and unit-copy number. We demonstrated stable
coexistence of three pABC vectors in addition to the two indigenous
megaplasmids in S. meliloti, suggesting combinability
of multiple compatible pABC plasmids. We further devised an in vivo cloning strategy involving Cre/lox-mediated translocation of large DNA fragments to an autonomously
replicating repABC-based vector, followed by conjugation-mediated
transfer either to compatible rhizobia or E. coli.
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Affiliation(s)
- Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Marcel Wagner
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Carina Happel
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Martina Carrillo
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
| | - Tobias J. Erb
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Martin Thanbichler
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
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15
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AnCo3, a New Member of the Emerging Family of Phage-Like Plasmids. GENOME ANNOUNCEMENTS 2017; 5:5/19/e00110-17. [PMID: 28495760 PMCID: PMC5427195 DOI: 10.1128/genomea.00110-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A phage-like plasmid isolated from a clinical isolate of Salmonella enterica serovar Derby has strong nucleotide sequence identity to the phage-like plasmids pSTM_phi isolated from Salmonella enterica serovar Typhimurium L495, AnCo1 and AnCo2 from Escherichia coli 243 and Escherichia coli 244, and the virulent Salmonella-specific SSU5 bacteriophage.
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16
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Fernandez-Lopez R, de Toro M, Moncalian G, Garcillan-Barcia MP, de la Cruz F. Comparative Genomics of the Conjugation Region of F-like Plasmids: Five Shades of F. Front Mol Biosci 2016; 3:71. [PMID: 27891505 PMCID: PMC5102898 DOI: 10.3389/fmolb.2016.00071] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/18/2016] [Indexed: 11/29/2022] Open
Abstract
The F plasmid is the foremost representative of a large group of conjugative plasmids, prevalent in Escherichia coli, and widely distributed among the Enterobacteriaceae. These plasmids are of clinical relevance, given their frequent association with virulence determinants, colicins, and antibiotic resistance genes. Originally defined by their sensitivity to certain male-specific phages, IncF plasmids share a conserved conjugative system and regulatory circuits. In order to determine whether the genetic architecture and regulation circuits are preserved among these plasmids, we analyzed the natural diversity of F-like plasmids. Using the relaxase as a phylogenetic marker, we identified 256 plasmids belonging to the IncF/ MOBF12group, present as complete DNA sequences in the NCBI database. By comparative genomics, we identified five major groups of F-like plasmids. Each shows a particular operon structure and alternate regulatory systems. Results show that the IncF/MOBF12 conjugation gene cluster conforms a diverse and ancient group, which evolved alternative regulatory schemes in its adaptation to different environments and bacterial hosts.
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Affiliation(s)
| | - Maria de Toro
- Centro de Investigacion Biomedica de la Rioja Logroño, Spain
| | - Gabriel Moncalian
- Instituto de Biomedicina y Biotecnologia de Cantabria Santander, Spain
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17
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Phipps ML, Lillo AM, Shou Y, Schmidt EN, Paavola CD, Naranjo L, Bemdich S, Swanson BI, Bradbury ARM, Martinez JS. Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands. PLoS One 2016; 11:e0160940. [PMID: 27626637 PMCID: PMC5023105 DOI: 10.1371/journal.pone.0160940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 07/27/2016] [Indexed: 12/16/2022] Open
Abstract
Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report on the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.
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Affiliation(s)
- M. Lisa Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Antoinetta M. Lillo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Yulin Shou
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Emily N. Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Chad D. Paavola
- Space Biosciences Division, National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA 94035, United States of America
| | - Leslie Naranjo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Sara Bemdich
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Basil I. Swanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Andrew R. M. Bradbury
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Jennifer S. Martinez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
- Institute for Materials Science, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
- * E-mail:
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18
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Nelson-Sathi S, Martin WF. The Origin of a Killer Revealed by Bronze Age Yersinia Genomes. Cell Host Microbe 2016; 18:513-4. [PMID: 26567502 DOI: 10.1016/j.chom.2015.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bubonic plaque is caused by Yersinia pestis, a deadly pathogen that left deep scars in human history. Rasmussen et al. (2015) have now retrieved Y. pestis genomes from 2,800- to 5,000-year-old human teeth, shedding new light on origins of the strain that brought Black Death to Europe 670 years ago.
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Affiliation(s)
- Shijulal Nelson-Sathi
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
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19
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Oyston PCF, Williamson ED. Modern Advances against Plague. ADVANCES IN APPLIED MICROBIOLOGY 2016; 81:209-41. [PMID: 22958531 DOI: 10.1016/b978-0-12-394382-8.00006-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Plague has been a scourge of humanity, responsible for the deaths of millions. The etiological agent, Yersinia pestis, has evolved relatively recently from an enteropathogen, Yersinia pseudotuberculosis. The evolution of the plague pathogen has involved a complex series of genetic acquisitions, deletions, and rearrangements in its transition from an enteric niche to becoming a systemic, flea-vectored pathogen. With the advent of modern molecular biology techniques, we are starting to understand how the organism adapts to the diverse niches it encounters and how to combat the threat it poses.
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20
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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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21
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Liu Z, Wang H, Wang H, Wang J, Bi Y, Wang X, Yang R, Han Y. Intrinsic plasmids influence MicF-mediated translational repression of ompF in Yersinia pestis. Front Microbiol 2015; 6:862. [PMID: 26347736 PMCID: PMC4543863 DOI: 10.3389/fmicb.2015.00862] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/07/2015] [Indexed: 12/15/2022] Open
Abstract
Yersinia pestis, which is the causative agent of plague, has acquired exceptional pathogenicity potential during its evolution from Y. pseudotuberculosis. Two laterally acquired plasmids, namely, pMT1 and pPCP1, are specific to Y. pestis and are critical for pathogenesis and flea transmission. Small regulatory RNAs (sRNAs) commonly function as regulators of gene expression in bacteria. MicF, is a paradigmatic sRNA that acts as a post-transcriptional repressor through imperfect base pairing with the 5′-UTR of its target mRNA, ompF, in Escherichia coli. The high sequence conservation and minor variation in the RNA duplex of MicF-ompF has been reported in Yersinia. In this study, we utilized super-folder GFP reporter gene fusion to validate the post-transcriptional MicF-mediated regulation of target mRNA ompF in Y. pestis. Unexpectedly, upon MicF overexpression, the slightly upregulated expression of OmpF were found in the wild-type strain, which contradicted the previously established model. Interestingly, the translational repression of ompF target fusions was restored in the intrinsic plasmids-cured Y. pestis strain, suggesting intrinsic plasmids influence the MicF-mediated translational repression of ompF in Y. pestis. Further examination showed that plasmid pPCP1 is likely the main contributor to the abolishment of MicF-mediated translational repression of endogenous or plasmid-borne ompF. It represents that the possible roles of intrinsic plasmids should be considered upon investigating sRNA-mediated gene regulation, at least in Y. pestis, even if the exact mechanism is not fully understood.
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Affiliation(s)
- Zizhong Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Haili Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Hongduo Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China ; Animal Husbandry Base Teaching and Research Section, College of Animal Science and Technology, Hebei North University Zhangjiakou, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Xiaoyi Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
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22
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Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst 2015; 1:72-87. [PMID: 26594662 PMCID: PMC4651444 DOI: 10.1016/j.cels.2015.01.001] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
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Affiliation(s)
- Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shanin Chowdhury
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Hunter College, New York, NY 10065, USA
| | - Dyala Jaroudi
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Collin Boyer
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nick Bernstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Julia M Maritz
- Center for Genomics, New York University, New York, NY 10003, USA
| | - Darryl Reeves
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sagar Chhangawala
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Amber Simmons
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | - Nell Kirchberger
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Isaac Garcia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sean Dhanraj
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Tanzina Nawrin
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Yogesh Saletore
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Priyanka Vijay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Elizabeth M Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael Walsh
- State University of New York, Downstate, Brooklyn, NY 11203, USA
| | - Gregory D O'Mullan
- School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT 05405, USA
| | - Joel T Dudley
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anya Dunaif
- Rockefeller University, New York, NY 10065, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Eoghan O'Halloran
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland
| | - Tiago R Magalhaes
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Theodore R Muth
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | | | | | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Jane M Carlton
- Center for Genomics, New York University, New York, NY 10003, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; The Feil Family Brain and Mind Research Institute, New York, NY 10065, USA
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Abstract
Gram-positive bacteria are leading causes of many types of human infection, including pneumonia, skin and nasopharyngeal infections, as well as urinary tract and surgical wound infections among hospitalized patients. These infections have become particularly problematic because many of the species causing them have become highly resistant to antibiotics. The role of mobile genetic elements, such as plasmids, in the dissemination of antibiotic resistance among Gram-positive bacteria has been well studied; less well understood is the role of mobile elements in the evolution and spread of virulence traits among these pathogens. While these organisms are leading agents of infection, they are also prominent members of the human commensal ecology. It appears that these bacteria are able to take advantage of the intimate association between host and commensal, via virulence traits that exacerbate infection and cause disease. However, evolution into an obligate pathogen has not occurred, presumably because it would lead to rejection of pathogenic organisms from the host ecology. Instead, in organisms that exist as both commensal and pathogen, selection has favored the development of mechanisms for variability. As a result, many virulence traits are localized on mobile genetic elements, such as virulence plasmids and pathogenicity islands. Virulence traits may occur within a minority of isolates of a given species, but these minority populations have nonetheless emerged as a leading problem in infectious disease. This chapter reviews virulence plasmids in nonsporulating Gram-positive bacteria, and examines their contribution to disease pathogenesis.
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Host specificity and clade dependent distribution of putative virulence genes in Moritella viscosa. Microb Pathog 2014; 77:53-65. [PMID: 25277600 DOI: 10.1016/j.micpath.2014.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/25/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Moritella viscosa is the aetiological agent of winter-ulcer disease in farmed salmonids in the North Atlantic. Previously, two major (typical and variant) genetic clades have been demonstrated within this bacterial species, one of which is almost solely related to disease in Atlantic salmon (Salmo salar). In the present study infection trials demonstrated that 'typical' M. viscosa isolated from Norwegian Atlantic salmon was highly virulent in this fish species but resulted in lower levels of mortality in rainbow trout. 'Variant' M. viscosa isolated from rainbow trout resulted in modest mortality levels in both Atlantic salmon and rainbow trout. To investigate the possible genetic background for inter-strain virulence differences, 38 M. viscosa isolates of diverse geographical origin and host species and a number of other Moritella spp. were investigated for the presence/absence of putative virulence related homologs. All isolates were positive for DNA sequences coding for; the Type VI secretion ATPase (clpV), hemolysin co-regulated protein (hcp), bacterioferritins (bfrA and bfrB), lectin (hemG), phospholipase D (pld), multifunctional autoprocessing repeats-in-toxin (martxA), aerolysin (aer), invasin (inv), and cytotoxic necrotizing factor (cnf), with the exception of one isolate in which cnf could not be confirmed. The product of an ABC transporter metal-binding lipoprotein (mat) was consistently detected although 11 isolates, all phylogenetically related, appear to produce a truncated version. A putative insecticidal toxin complex (mitABC) was detected almost exclusively in 'typical' Atlantic salmon isolates, and our data indicate that this complex of genes is expressed and co-transcribed. Transmission electron microscopy investigation revealed pili and flagella surface structures on nine M. viscosa representing both typical and variant isolates. Our results provide strong support for the existence of host specificity/high virulence in 'typical' M. viscosa related to Atlantic salmon. The gene distribution also provides further support for the genetic division within M. viscosa, and constitutes a basis for further study of the importance of the mitABC complex in winter-ulcer pathogenesis.
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25
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Identification and characterization of the insecticidal toxin "makes caterpillars floppy" in Photorhabdus temperata M1021 using a cosmid library. Toxins (Basel) 2014; 6:2024-40. [PMID: 25014195 PMCID: PMC4113739 DOI: 10.3390/toxins6072024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/20/2014] [Accepted: 07/02/2014] [Indexed: 01/24/2023] Open
Abstract
Photorhabdus temperata is an entomopathogenic enterobacterium; it is a nematode symbiont that possesses pathogenicity islands involved in insect virulence. Herein, we constructed a P. temperata M1021 cosmid library in Escherichia coli XL1-Blue MRF` and obtained 7.14 × 105 clones. However, only 1020 physiologically active clones were screened for insect virulence factors by injection of each E. coli cosmid clone into Galleria mellonella and Tenebrio molitor larvae. A single cosmid clone, PtC1015, was consequently selected due to its characteristic virulent properties, e.g., loss of body turgor followed by death of larvae when the clone was injected into the hemocoel. The sequence alignment against the available sequences in Swiss-Prot and NCBI databases, confirmed the presence of the mcf gene homolog in the genome of P. temperata M1021 showing 85% homology and 98% query coverage with the P. luminescens counterpart. Furthermore, a 2932 amino acid long Mcf protein revealed limited similarity with three protein domains. The N-terminus of the Mcf encompassed consensus sequence for a BH3 domain, the central region revealed similarity to toxin B, and the C-terminus of Mcf revealed similarity to the bacterial export domain of ApxIVA, an RTX-like toxin. In short, the Mcf toxin is likely to play a role in the elimination of insect pests, making it a promising model for use in the agricultural field.
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26
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Abstract
Plague has been a scourge of mankind for centuries, and outbreaks continue to the present day. The virulence mechanisms employed by the etiological agent Yersinia pestis are reviewed in the context of the available prophylactic and therapeutic strategies for plague. Although antibiotics are available, resistance is emerging in this dangerous pathogen. Therapeutics used in the clinic are discussed and innovative approaches to the design and development of new therapeutic compounds are reviewed. Currently there is no licensed vaccine available for prevention of plague in the USA or western Europe, although both live attenuated strains and killed whole-cell extracts have been used historically. Live strains are still approved for human use in some parts of the world, such as the former Soviet Union, but poor safety profiles render them unacceptable to many countries. The development of safe, effective next-generation vaccines, including the recombinant subunit vaccine currently used in clinical trials is discussed.
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Affiliation(s)
- Petra C F Oyston
- Biomedical Sciences, Dstl Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
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27
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Williamson ED, Oyston PCF. Protecting against plague: towards a next-generation vaccine. Clin Exp Immunol 2013; 172:1-8. [PMID: 23480179 PMCID: PMC3719925 DOI: 10.1111/cei.12044] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2012] [Indexed: 01/22/2023] Open
Abstract
The causative organism of plague is the bacterium Yersinia pestis. Advances in understanding the complex pathogenesis of plague infection have led to the identification of the F1- and V-antigens as key components of a next-generation vaccine for plague, which have the potential to be effective against all forms of the disease. Here we review the roles of F1- and V-antigens in the context of the range of virulence mechanisms deployed by Y. pestis, in order to develop a greater understanding of the protective immune responses required to protect against plague.
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Affiliation(s)
- E D Williamson
- Biomedical Sciences Department, Defence Science and Technology Laboratory, Salisbury, Wilts, UK.
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28
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Yang R, Du Z, Han Y, Zhou L, Song Y, Zhou D, Cui Y. Omics strategies for revealing Yersinia pestis virulence. Front Cell Infect Microbiol 2012; 2:157. [PMID: 23248778 PMCID: PMC3521224 DOI: 10.3389/fcimb.2012.00157] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/27/2012] [Indexed: 01/12/2023] Open
Abstract
Omics has remarkably changed the way we investigate and understand life. Omics differs from traditional hypothesis-driven research because it is a discovery-driven approach. Mass datasets produced from omics-based studies require experts from different fields to reveal the salient features behind these data. In this review, we summarize omics-driven studies to reveal the virulence features of Yersinia pestis through genomics, trascriptomics, proteomics, interactomics, etc. These studies serve as foundations for further hypothesis-driven research and help us gain insight into Y. pestis pathogenesis.
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Affiliation(s)
- Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology Beijing, China.
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29
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Williamson ED, Oyston PCF. The natural history and incidence of Yersinia pestis and prospects for vaccination. J Med Microbiol 2012; 61:911-918. [PMID: 22442294 DOI: 10.1099/jmm.0.037960-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Plague is an ancient, serious, infectious disease which is still endemic in regions of the modern world and is a potential biothreat agent. This paper discusses the natural history of the bacterium and its evolution into a flea-vectored bacterium able to transmit bubonic plague. It reviews the incidence of plague in the modern world and charts the history of vaccines which have been used to protect against the flea-vectored disease, which erupts as bubonic plague. Current approaches to vaccine development to protect against pneumonic, as well as bubonic, plague are also reviewed. The considerable challenges in achieving a vaccine which is licensed for human use and which will comprehensively protect against this serious human pathogen are assessed.
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Affiliation(s)
- E D Williamson
- Biomedical Sciences, Dstl Porton Down, Salisbury SP4 0JQ, UK
| | - P C F Oyston
- Biomedical Sciences, Dstl Porton Down, Salisbury SP4 0JQ, UK
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30
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Lillo AM, Ayriss JE, Shou Y, Graves SW, Bradbury ARM. Development of phage-based single chain Fv antibody reagents for detection of Yersinia pestis. PLoS One 2011; 6:e27756. [PMID: 22174746 PMCID: PMC3234238 DOI: 10.1371/journal.pone.0027756] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 10/24/2011] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Most Yersinia pestis strains are known to express a capsule-like antigen, fraction 1 (F1)(.) F1 is encoded by the caf1 gene located on the large 100-kb pFra plasmid, which is found in Y. pestis but not in closely related species such as Yersinia enterocolytica and Yersinia pseudotuberculosis. In order to find antibodies specifically binding to Y. pestis we screened a large single chain Fv antibody fragment (scFv) phage display library using purified F1 antigen as a selection target. Different forms of the selected antibodies were used to establish assays for recombinant F1 antigen and Y. pestis detection. METHODS Phage antibody panning was performed against F1 in an automated fashion using the Kingfisher magnetic bead system. Selected scFvs were screened for F1-binding specificity by one-step alkaline phosphatase enzyme linked immunosorbant assay (ELISA), and assayed for binding to recombinant antigen and/or Y. pestis by flow cytometry and whole-cell ELISA. RESULTS Seven of the eight selected scFvs were shown to specifically bind both recombinant F1 and a panel of F1-positive Yersinia cells. The majority of the soluble scFvs were found to be difficult to purify, unstable and prone to cross-reactivity with F1-negative Yersinia strains, whereas phage displayed scFvs were found to be easy to purify/label and remarkably stable. Furthermore direct fluorescent labeling of phage displaying scFv allowed for an easy one-step flow cytometry assay. Slight cross-reactivity was observed when fixed cells were used in ELISA. CONCLUSIONS Our high throughput methods of selection and screening allowed for time and cost effective discovery of seven scFvs specifically binding Y. pestis F1 antigen. We describe implementation of different methods for phage-based immunoassay. Based on the success of these methods and the proven stability of phage, we indicate that the use of phage-displayed, rather than phage-free proteins, might generally overcome the shortcomings of scFv antibodies.
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Affiliation(s)
- Antonietta M. Lillo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Joanne E. Ayriss
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Yulin Shou
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Steven W. Graves
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Andrew R. M. Bradbury
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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31
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Selvy PE, Lavieri RR, Lindsley CW, Brown HA. Phospholipase D: enzymology, functionality, and chemical modulation. Chem Rev 2011; 111:6064-119. [PMID: 21936578 PMCID: PMC3233269 DOI: 10.1021/cr200296t] [Citation(s) in RCA: 267] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paige E Selvy
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37064, USA
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32
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Plague: Infections of Companion Animals and Opportunities for Intervention. Animals (Basel) 2011; 1:242-55. [PMID: 26486314 DOI: 10.3390/ani1020242] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/20/2011] [Accepted: 06/20/2011] [Indexed: 11/17/2022] Open
Abstract
Plague is a zoonotic disease, normally circulating in rodent populations, transmitted to humans most commonly through the bite of an infected flea vector. Secondary infection of the lungs results in generation of infectious aerosols, which pose a significant hazard to close contacts. In enzootic areas, plague infections have been reported in owners and veterinarians who come into contact with infected pets. Dogs are relatively resistant, but can import infected fleas into the home. Cats are acutely susceptible, and can present a direct hazard to health. Reducing roaming and hunting behaviours, combined with flea control measures go some way to reducing the risk to humans. Various vaccine formulations have been developed which may be suitable to protect companion animals from contracting plague, and thus preventing onward transmission to man. Since transmission has resulted in a number of fatal cases of plague, the vaccination of domestic animals such as cats would seem a low cost strategy for reducing the risk of infection by this serious disease in enzootic regions.
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33
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Plague: Infections of Companion Animals and Opportunities for Intervention. Animals (Basel) 2011. [PMID: 26486314 PMCID: PMC4513460 DOI: 10.3390/anil020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plague is a zoonotic disease, normally circulating in rodent populations, transmitted to humans most commonly through the bite of an infected flea vector. Secondary infection of the lungs results in generation of infectious aerosols, which pose a significant hazard to close contacts. In enzootic areas, plague infections have been reported in owners and veterinarians who come into contact with infected pets. Dogs are relatively resistant, but can import infected fleas into the home. Cats are acutely susceptible, and can present a direct hazard to health. Reducing roaming and hunting behaviours, combined with flea control measures go some way to reducing the risk to humans. Various vaccine formulations have been developed which may be suitable to protect companion animals from contracting plague, and thus preventing onward transmission to man. Since transmission has resulted in a number of fatal cases of plague, the vaccination of domestic animals such as cats would seem a low cost strategy for reducing the risk of infection by this serious disease in enzootic regions.
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34
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Prevalence and significance of plasmid maintenance functions in the virulence plasmids of pathogenic bacteria. Infect Immun 2011; 79:2502-9. [PMID: 21555398 DOI: 10.1128/iai.00127-11] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virulence functions of pathogenic bacteria are often encoded on large extrachromosomal plasmids. These plasmids are maintained at low copy number to reduce the metabolic burden on their host. Low-copy-number plasmids risk loss during cell division. This is countered by plasmid-encoded systems that ensure that each cell receives at least one plasmid copy. Plasmid replication and recombination can produce plasmid multimers that hinder plasmid segregation. These are removed by multimer resolution systems. Equitable distribution of the resulting monomers to daughter cells is ensured by plasmid partition systems that actively segregate plasmid copies to daughter cells in a process akin to mitosis in higher organisms. Any plasmid-free cells that still arise due to occasional failures of replication, multimer resolution, or partition are eliminated by plasmid-encoded postsegregational killing systems. Here we argue that all of these three systems are essential for the stable maintenance of large low-copy-number plasmids. Thus, they should be found on all large virulence plasmids. Where available, well-annotated sequences of virulence plasmids confirm this. Indeed, virulence plasmids often appear to contain more than one example conforming to each of the three system classes. Since these systems are essential for virulence, they can be regarded as ubiquitous virulence factors. As such, they should be informative in the search for new antibacterial agents and drug targets.
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35
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Antigen engineering can play a critical role in the protective immunity elicited by Yersinia pestis DNA vaccines. Vaccine 2010; 28:2011-9. [PMID: 20188257 DOI: 10.1016/j.vaccine.2009.10.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of a DNA immunization approach to deliver protective antigens against Yersinia pestis (Y. pestis) has been successful in previously reported studies. In the current study, the gene designs for V and F1, two well-studied virulent factors serving as main targets for vaccine development, were altered to explore additional options in hopes of improving the protective immunity of DNA vaccines expressing these two antigens. Compared to the wild type V gene DNA vaccines, the use of codon optimized V gene sequences was effective in improving the antigen expression, titers of anti-V antibody responses, and survival against a mucosal lethal challenge. For the F1 DNA vaccine, removal of the N-terminal hydrophobic region was able to improve protective immunity. However, adding a mammalian signal peptide sequence to F1 actually led to reduced protection despite it inducing slightly higher anti-F1 antibody responses. The F1 gene can be fused with a gene coding for YscF, a newly confirmed partial protective antigen for Y. pestis, to produce DNA vaccines that express fused F1 and YscF antigens. One design, in particular, that had YscF fused to the downstream sequence of F1, produced better protection than separate F1 or YscF DNA vaccines, suggesting a potential synergistic effect between these two antigens. Findings from the above studies indicated that there are multiple approaches to optimize the protective immunity for plague DNA vaccines. Most importantly, proper antigen engineering to produce optimal antigen gene inserts in DNA vaccines can clearly play a major role in the future designs of a wide range of DNA vaccines.
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36
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Pieper R, Huang ST, Parmar PP, Clark DJ, Alami H, Fleischmann RD, Perry RD, Peterson SN. Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation. BMC Microbiol 2010; 10:30. [PMID: 20113483 PMCID: PMC2835676 DOI: 10.1186/1471-2180-10-30] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 01/29/2010] [Indexed: 11/29/2022] Open
Abstract
Background The Gram-negative bacterium Yersinia pestis is the causative agent of the bubonic plague. Efficient iron acquisition systems are critical to the ability of Y. pestis to infect, spread and grow in mammalian hosts, because iron is sequestered and is considered part of the innate host immune defence against invading pathogens. We used a proteomic approach to determine expression changes of iron uptake systems and intracellular consequences of iron deficiency in the Y. pestis strain KIM6+ at two physiologically relevant temperatures (26°C and 37°C). Results Differential protein display was performed for three Y. pestis subcellular fractions. Five characterized Y. pestis iron/siderophore acquisition systems (Ybt, Yfe, Yfu, Yiu and Hmu) and a putative iron/chelate outer membrane receptor (Y0850) were increased in abundance in iron-starved cells. The iron-sulfur (Fe-S) cluster assembly system Suf, adapted to oxidative stress and iron starvation in E. coli, was also more abundant, suggesting functional activity of Suf in Y. pestis under iron-limiting conditions. Metabolic and reactive oxygen-deactivating enzymes dependent on Fe-S clusters or other iron cofactors were decreased in abundance in iron-depleted cells. This data was consistent with lower activities of aconitase and catalase in iron-starved vs. iron-rich cells. In contrast, pyruvate oxidase B which metabolizes pyruvate via electron transfer to ubiquinone-8 for direct utilization in the respiratory chain was strongly increased in abundance and activity in iron-depleted cells. Conclusions Many protein abundance differences were indicative of the important regulatory role of the ferric uptake regulator Fur. Iron deficiency seems to result in a coordinated shift from iron-utilizing to iron-independent biochemical pathways in the cytoplasm of Y. pestis. With growth temperature as an additional variable in proteomic comparisons of the Y. pestis fractions (26°C and 37°C), there was little evidence for temperature-specific adaptation processes to iron starvation.
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Affiliation(s)
- Rembert Pieper
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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37
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Yersinia ironomics: comparison of iron transporters among Yersinia pestis biotypes and its nearest neighbor, Yersinia pseudotuberculosis. Biometals 2010; 23:275-94. [DOI: 10.1007/s10534-009-9286-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 12/17/2009] [Indexed: 01/20/2023]
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38
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DiMezzo TL, Ruthel G, Brueggemann EE, Hines HB, Ribot WJ, Chapman CE, Powell BS, Welkos SL. In vitro intracellular trafficking of virulence antigen during infection by Yersinia pestis. PLoS One 2009; 4:e6281. [PMID: 19609450 PMCID: PMC2707630 DOI: 10.1371/journal.pone.0006281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Accepted: 06/03/2009] [Indexed: 11/27/2022] Open
Abstract
Yersinia pestis, the causative agent of plague, encodes several essential virulence factors on a 70 kb plasmid, including the Yersinia outer proteins (Yops) and a multifunctional virulence antigen (V). V is uniquely able to inhibit the host immune response; aid in the expression, secretion, and injection of the cytotoxic Yops via a type III secretion system (T3SS)-dependent mechanism; be secreted extracellularly; and enter the host cell by a T3SS-independent mechanism, where its activity is unknown. To elucidate the intracellular trafficking and target(s) of V, time-course experiments were performed with macrophages (MΦs) infected with Y. pestis or Y. pseudotuberculosis at intervals from 5 min to 6 h. The trafficking pattern was discerned from results of parallel microscopy, immunoblotting, and flow cytometry experiments. The MΦs were incubated with fluorescent or gold conjugated primary or secondary anti-V (antibodies [Abs]) in conjunction with organelle-associated Abs or dyes. The samples were observed for co-localization by immuno-fluorescence and electron microscopy. For fractionation studies, uninfected and infected MΦs were lysed and subjected to density gradient centrifugation coupled with immunoblotting with Abs to V or to organelles. Samples were also analyzed by flow cytometry after lysis and dual-staining with anti-V and anti-organelle Abs. Our findings indicate a co-localization of V with (1) endosomal proteins between 10–45 min of infection, (2) lysosomal protein(s) between 1–2 h of infection, (3) mitochondrial proteins between 2.5–3 h infection, and (4) Golgi protein(s) between 4–6 h of infection. Further studies are being performed to determine the specific intracellular interactions and role in pathogenesis of intracellularly localized V.
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Affiliation(s)
- Tracy L. DiMezzo
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Gordon Ruthel
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Ernst E. Brueggemann
- Integrated Toxicology, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Harry B. Hines
- Integrated Toxicology, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Wilson J. Ribot
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Carol E. Chapman
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Bradford S. Powell
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Susan L. Welkos
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
- * E-mail:
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Agar SL, Sha J, Baze WB, Erova TE, Foltz SM, Suarez G, Wang S, Chopra AK. Deletion of Braun lipoprotein gene (lpp) and curing of plasmid pPCP1 dramatically alter the virulence of Yersinia pestis CO92 in a mouse model of pneumonic plague. MICROBIOLOGY-SGM 2009; 155:3247-3259. [PMID: 19589835 DOI: 10.1099/mic.0.029124-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Deletion of the murein (Braun) lipoprotein gene, lpp, attenuates the Yersinia pestis CO92 strain in mouse models of bubonic and pneumonic plague. In this report, we characterized the virulence of strains from which the plasminogen activating protease (pla)-encoding pPCP1 plasmid was cured from either the wild-type (WT) or the Deltalpp mutant strain of Y. pestis CO92 in the mouse model of pneumonic infection. We noted a significantly increased survival rate in mice infected with the Y. pestis pPCP(-)/Deltalpp mutant strain up to a dose of 5000 LD(50). Additionally, mice challenged with the pPCP(-)/Deltalpp strain had substantially less tissue injury and a strong decrease in the levels of most cytokines and chemokines in tissue homogenates and sera when compared with the WT-infected group. Importantly, the Y. pestis pPCP(-)/Deltalpp mutant strain was detectable in high numbers in the livers and spleens of some of the infected mice. In the lungs of pPCP(-)/Deltalpp mutant-challenged animals, however, bacterial numbers dropped at 48 h after infection when compared with tissue homogenates from 1 h post-infection. Similarly, we noted that this mutant was unable to survive within murine macrophages in an in vitro assay, whereas survivability of the pPCP(-) mutant within the macrophage environment was similar to that of the WT. Taken together, our data indicated that a significant and possibly synergistic attenuation in bacterial virulence occurred in a mouse model of pneumonic plague when both the lpp gene and the virulence plasmid pPCP1 encoding the pla gene were deleted from Y. pestis.
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Affiliation(s)
- Stacy L Agar
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Jian Sha
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Wallace B Baze
- Department of Veterinary Sciences, University of Texas M. D. Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Tatiana E Erova
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Sheri M Foltz
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Giovanni Suarez
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Shaofei Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Ashok K Chopra
- Center for Biodefense and Emerging Infectious Diseases, UTMB, Galveston, TX 77555, USA.,Sealy Center for Vaccine Development, UTMB, Galveston, TX 77555, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
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40
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Ni B, Du Z, Guo Z, Zhang Y, Yang R. Curing of four different plasmids in Yersinia pestis using plasmid incompatibility. Lett Appl Microbiol 2009; 47:235-40. [PMID: 19241516 DOI: 10.1111/j.1472-765x.2008.02426.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Plasmids are critical for the pathogenicity of Yersinia pestis. In order to carry out a systematic investigation of their role in pathogenesis, we cured plasmids from Y. pestis. METHODS AND RESULTS Each plasmid's replicon of Y. pestis was cloned into plasmid pEX18Gm containing a counter-selectable sacB gene, and was then introduced into Y. pestis strain 201 by electroporation. Strains containing recombinant plasmids were cultivated under antibiotic selection. The resultant plasmid-curing colonies, identified by specific polymerase chain reactions, were then cured off pEX18Gm under sucrose pressure. This method was used to successfully cure all four plasmids of Y. pestis, singly or in different combinations. CONCLUSIONS Naturally evolving plasmids in Y. pestis are difficult to remove by conventional curing methods. We employed a method based on plasmid incompatibility to cure the plasmids from Y. pestis, which confirmed the efficacy of this method for curing plasmids with different types of replicons from one bacterium. SIGNIFICANCE AND IMPACT OF THE STUDY There have been no reports on the curing of multiple plasmids by using replication mechanisms from one bacterium with this technique. In the present study, we were able to successfully apply this methodology to cure four plasmids from Y. pestis, confirming its feasibility.
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Affiliation(s)
- B Ni
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, PR China
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41
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Yersinia pestis IS1541 transposition provides for escape from plague immunity. Infect Immun 2009; 77:1807-16. [PMID: 19237527 DOI: 10.1128/iai.01162-08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yersinia pestis is perhaps the most feared infectious agent due to its ability to cause epidemic outbreaks of plague disease in animals and humans with high mortality. Plague infections elicit strong humoral immune responses against the capsular antigen (fraction 1 [F1]) of Y. pestis, and F1-specific antibodies provide protective immunity. Here we asked whether Y. pestis generates mutations that enable bacterial escape from protective immunity and isolated a variant with an IS1541 insertion in caf1A encoding the F1 outer membrane usher. The caf1A::IS1541 insertion prevented assembly of F1 pili and provided escape from plague immunity via F1-specific antibodies without a reduction in virulence in mouse models of bubonic or pneumonic plague. F1-specific antibodies interfere with Y. pestis type III transport of effector proteins into host cells, an inhibitory effect that was overcome by the caf1A::IS1541 insertion. These findings suggest a model in which IS1541 insertion into caf1A provides for reversible changes in envelope structure, enabling Y. pestis to escape from adaptive immune responses and plague immunity.
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42
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Pieper R, Huang ST, Clark DJ, Robinson JM, Alami H, Parmar PP, Suh MJ, Kuntumalla S, Bunai CL, Perry RD, Fleischmann RD, Peterson SN. Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranes. Proteome Sci 2009; 7:5. [PMID: 19228400 PMCID: PMC2663777 DOI: 10.1186/1477-5956-7-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 02/19/2009] [Indexed: 11/28/2022] Open
Abstract
Yersinia pestis proteins were sequentially extracted from crude membranes with a high salt buffer (2.5 M NaBr), an alkaline solution (180 mM Na2CO3, pH 11.3) and membrane denaturants (8 M urea, 2 M thiourea and 1% amidosulfobetaine-14). Separation of proteins by 2D gel electrophoresis was followed by identification of more than 600 gene products by MS. Data from differential 2D gel display experiments, comparing protein abundances in cytoplasmic, periplasmic and all three membrane fractions, were used to assign proteins found in the membrane fractions to three protein categories: (i) integral membrane proteins and peripheral membrane proteins with low solubility in aqueous solutions (220 entries); (ii) peripheral membrane proteins with moderate to high solubility in aqueous solutions (127 entries); (iii) cytoplasmic or ribosomal membrane-contaminating proteins (80 entries). Thirty-one proteins were experimentally associated with the outer membrane (OM). Circa 50 proteins thought to be part of membrane-localized, multi-subunit complexes were identified in high Mr fractions of membrane extracts via size exclusion chromatography. This data supported biologically meaningful assignments of many proteins to the membrane periphery. Since only 32 inner membrane (IM) proteins with two or more predicted transmembrane domains (TMDs) were profiled in 2D gels, we resorted to a proteomic analysis by 2D-LC-MS/MS. Ninety-four additional IM proteins with two or more TMDs were identified. The total number of proteins associated with Y. pestis membranes increased to 456 and included representatives of all six β-barrel OM protein families and 25 distinct IM transporter families.
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Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis. Microbiology (Reading) 2009; 155:498-512. [DOI: 10.1099/mic.0.022160-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Yersinia pestis cells were grown in vitro at 26 and 37 °C, the ambient temperatures of its flea vector and its mammalian hosts, respectively, and subjected to subcellular fractionation. Abundance changes at 26 vs 37 °C were observed for many outer-membrane (OM) proteins. The cell adhesion protein Ail (y1324) and three putative small β-barrel OM proteins (y1795, y2167 and y4083) were strongly increased at 37 °C. The Ail/Lom family protein y1682 (OmpX) was strongly increased at 26 °C. Several porins and TonB-dependent receptors, which control small molecule transport through the OM, were also altered in abundance in a temperature-dependent manner. These marked differences in the composition of the OM proteome are probably important for the adaptation of Y. pestis to its in vivo life stages. Thirteen proteins that appear to be part of an intact type VI secretion system (T6SS) were identified in membrane fractions of stationary-phase cells grown at 26 °C, but not at 37 °C. The corresponding genes are clustered in the Y. pestis KIM gene locus y3658–y3677. The proteins y3674 and y3675 were particularly abundant and co-fractionated in a M
r range indicative of participation in a multi-subunit complex. The soluble haemolysin-coregulated protein y3673 was even more abundant. Its release into the extracellular medium was triggered by treatment of Y. pestis cells with trypsin. Proteases and other stress-response-inducing factors may constitute environmental cues resulting in the activation of the T6SS in Y. pestis.
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The Three Bears and Virulence-Associated Plasmids in the Genus Yersinia. MICROBIAL MEGAPLASMIDS 2009. [DOI: 10.1007/978-3-540-85467-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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The Yersinia pestis caf1M1A1 fimbrial capsule operon promotes transmission by flea bite in a mouse model of bubonic plague. Infect Immun 2008; 77:1222-9. [PMID: 19103769 DOI: 10.1128/iai.00950-08] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plague is a zoonosis transmitted by fleas and caused by the gram-negative bacterium Yersinia pestis. During infection, the plasmidic caf1M1A1 operon that encodes the Y. pestis F1 protein capsule is highly expressed, and anti-F1 antibodies are protective. Surprisingly, the capsule is not required for virulence after injection of cultured bacteria, even though it is an antiphagocytic factor and capsule-deficient Y. pestis strains are rarely isolated. We found that a caf-negative Y. pestis mutant was not impaired in either flea colonization or virulence in mice after intradermal inoculation of cultured bacteria. In contrast, absence of the caf operon decreased bubonic plague incidence after a flea bite. Successful development of plague in mice infected by flea bite with the caf-negative mutant required a higher number of infective bites per challenge. In addition, the mutant displayed a highly autoaggregative phenotype in infected liver and spleen. The results suggest that acquisition of the caf locus via horizontal transfer by an ancestral Y. pestis strain increased transmissibility and the potential for epidemic spread. In addition, our data support a model in which atypical caf-negative strains could emerge during climatic conditions that favor a high flea burden. Human infection with such strains would not be diagnosed by the standard clinical tests that detect F1 antibody or antigen, suggesting that more comprehensive surveillance for atypical Y. pestis strains in plague foci may be necessary. The results also highlight the importance of studying Y. pestis pathogenesis in the natural context of arthropod-borne transmission.
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Kenny JH, Zhou Y, Schriefer ME, Bearden SW. Detection of viable Yersinia pestis by fluorescence in situ hybridization using peptide nucleic acid probes. J Microbiol Methods 2008; 75:293-301. [PMID: 18655809 DOI: 10.1016/j.mimet.2008.06.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 06/19/2008] [Accepted: 06/24/2008] [Indexed: 11/28/2022]
Abstract
A successful method has been developed for the detection of live Yersinia pestis, the plague bacillus, which incorporates nascent RNA synthesis. A fluorescent in situ hybridization (FISH) assay using peptide nucleic acid (PNA) probes was developed specifically to differentiate Y. pestis strains from closely related bacteria. PNA probes were chosen to target high copy mRNA of the Y. pestis caf1 gene, encoding the Fraction 1 (F1) antigen, and 16S ribosomal RNA. Among Yersinia strains tested, PNA probes Yp-16S-426 and Yp-F1-55 exhibited binding specificities of 100% and 98%, respectively. Y. pestis grown in the presence of competing bacteria, as might be encountered when recovering Y. pestis from environmental surfaces in a post-release bioterrorism event, was recognized by PNA probes and neither hybridization nor fluorescence was inhibited by competing bacterial strains which exhibited faster growth rates. Using fluorescence microscopy, individual Y. pestis bacteria were clearly differentiated from competing bacteria with an average detection sensitivity of 7.9x10(3) cells by fluorescence microscopy. In the current system, this would require an average of 2.56x10(5) viable Y. pestis organisms be recovered from a post-release environmental sample in order to achieve the minimum threshold for detection. The PNA-FISH assays described in this study allow for the sensitive and specific detection of viable Y. pestis bacteria in a timely manner.
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Affiliation(s)
- John H Kenny
- Bacterial Diseases Branch, Division of Vector-Borne Infectious Diseases, National Center for Zoonotic, Vector-Borne and Enteric Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, United States
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Pieper R, Huang ST, Clark DJ, Robinson JM, Parmar PP, Alami H, Bunai CL, Perry RD, Fleischmann RD, Peterson SN. Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change. Proteomics 2008; 8:1442-58. [PMID: 18383009 DOI: 10.1002/pmic.200700923] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The periplasmic proteome of Yersinia pestis strain KIM6+ was characterized using differential 2-DE display of proteins isolated from several subcellular fractions. Circa 160 proteins were designated as periplasmic, including 62 (putative) solute-binding proteins of ATP-binding cassette (ABC) transporters (SBPs) and 46 (putative) metabolic enzymes. More than 30 SBPs were significantly increased in abundance during stationary phase cell growth, compared to the exponential phase. The data suggest that nutrient exhaustion in the stationary phase triggers cellular responses resulting in the induced expression of numerous ABC transporters, which are responsible for the import of solutes/nutrients. Limited availability of inorganic phosphate (P(i)) also caused dramatic proteomic changes. Nine proteins were functionally linked to the mobilization and import of three small molecules (P(i), phosphonate and glycerol-3-phosphate) and accounted for nearly half of the total protein mass in the periplasm of P(i)-starved cells. When cells were grown at 26 degrees C versus 37 degrees C, corresponding to ambient temperatures in the flea vector and mammalian hosts, respectively, several periplasmic proteins with no known roles in the Y. pestis life cycle were strongly altered in abundance. This included a putative nitrate/sulfonate/bicarbonate-specific SBP (Y1004), encoded by the virulence-associated plasmid pMT1 and increased in abundance at 37 degrees C.
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Abstract
Yersinia pestis, the highly virulent agent of plague, is a biological weapon. Strategies that prevent plague have been sought for centuries, and immunization with live, attenuated (nonpigmented) strains or subunit vaccines with F1 (Caf1) antigen is considered effective. We show here that immunization with live, attenuated strains generates plague-protective immunity and humoral immune responses against F1 pilus antigen and LcrV. Y. pestis variants lacking caf1 (F1 pili) are not only fully virulent in animal models of bubonic and pneumonic plague but also break through immune responses generated with live, attenuated strains or F1 subunit vaccines. In contrast, immunization with purified LcrV, a protein at the tip of type III needles, generates protective immunity against the wild-type and the fully virulent caf1 mutant strain, in agreement with the notion that LcrV can elicit vaccine protection against both types of virulent plague strains.
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Resistance of Yersinia pestis to complement-dependent killing is mediated by the Ail outer membrane protein. Infect Immun 2007; 76:612-22. [PMID: 18025094 DOI: 10.1128/iai.01125-07] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Yersinia pestis, the causative agent of plague, must survive in blood in order to cause disease and to be transmitted from host to host by fleas. Members of the Ail/Lom family of outer membrane proteins provide protection from complement-dependent killing for a number of pathogenic bacteria. The Y. pestis KIM genome is predicted to encode four Ail/Lom family proteins. Y. pestis mutants specifically deficient in expression of each of these proteins were constructed using lambda Red-mediated recombination. The Ail outer membrane protein was essential for Y. pestis to resist complement-mediated killing at 26 and 37 degrees C. Ail was expressed at high levels at both 26 and 37 degrees C, but not at 6 degrees C. Expression of Ail in Escherichia coli provided protection from the bactericidal activity of complement. High-level expression of the three other Y. pestis Ail/Lom family proteins (the y1682, y2034, and y2446 proteins) provided no protection against complement-mediated bacterial killing. A Y. pestis ail deletion mutant was rapidly killed by sera obtained from all mammals tested except mouse serum. The role of Ail in infection of mice, Caenorhabditis elegans, and fleas was investigated.
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Han Y, Qiu J, Guo Z, Gao H, Song Y, Zhou D, Yang R. Comparative transcriptomics in Yersinia pestis: a global view of environmental modulation of gene expression. BMC Microbiol 2007; 7:96. [PMID: 17963531 PMCID: PMC2231364 DOI: 10.1186/1471-2180-7-96] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Accepted: 10/29/2007] [Indexed: 12/22/2022] Open
Abstract
Background Environmental modulation of gene expression in Yersinia pestis is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions in vitro. Results To provide us with a comprehensive view of environmental modulation of global gene expression in Y. pestis, we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of Y. pestis were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). Conclusion The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in Y. pestis, it also serves as a basis for integrating increasing volumes of microarray data using existing methods.
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Affiliation(s)
- Yanping Han
- State Key laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 20, Dongdajie, Fengtai, Beijing 100071, China.
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