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Guo XP, Yan HQ, Yang W, Yin Z, Vadyvaloo V, Zhou D, Sun YC. A frameshift in Yersinia pestis rcsD alters canonical Rcs signalling to preserve flea-mammal plague transmission cycles. eLife 2023; 12:e83946. [PMID: 37010269 PMCID: PMC10191623 DOI: 10.7554/elife.83946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/02/2023] [Indexed: 04/04/2023] Open
Abstract
Multiple genetic changes in the enteric pathogen Yersinia pseudotuberculosis have driven the emergence of Yesinia pestis, the arthropod-borne, etiological agent of plague. These include developing the capacity for biofilm-dependent blockage of the flea foregut to enable transmission by flea bite. Previously, we showed that pseudogenization of rcsA, encoding a component of the Rcs signalling pathway, is an important evolutionary step facilitating Y. pestis flea-borne transmission. Additionally, rcsD, another important gene in the Rcs system, harbours a frameshift mutation. Here, we demonstrated that this rcsD mutation resulted in production of a small protein composing the C-terminal RcsD histidine-phosphotransferase domain (designated RcsD-Hpt) and full-length RcsD. Genetic analysis revealed that the rcsD frameshift mutation followed the emergence of rcsA pseudogenization. It further altered the canonical Rcs phosphorylation signal cascade, fine-tuning biofilm production to be conducive with retention of the pgm locus in modern lineages of Y. pestis. Taken together, our findings suggest that a frameshift mutation in rcsD is an important evolutionary step that fine-tuned biofilm production to ensure perpetuation of flea-mammal plague transmission cycles.
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Affiliation(s)
- Xiao-Peng Guo
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hai-Qin Yan
- Department of Basic Medical Sciences, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical CollegeBengbuChina
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Viveka Vadyvaloo
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yi-Cheng Sun
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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2
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Pisarenko SV, Evchenko AY, Kovalev DA, Evchenko YМ, Bobrysheva OV, Shapakov NA, Volynkina AS, Kulichenko AN. Yersinia pestis strains isolated in natural plague foci of Caucasus and Transcaucasia in the context of the global evolution of species. Genomics 2021; 113:1952-1961. [PMID: 33862185 DOI: 10.1016/j.ygeno.2021.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/31/2021] [Accepted: 04/11/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Plague is a highly dangerous vector-borne infectious disease that has left a significant mark on history of humankind. There are 13 natural plague foci in the Caucasus, located on the territory of the Russian Federation, Azerbaijan, Armenia and Georgia. We performed whole-genome sequencing of Y. pestis strains, isolated in the natural foci of the Caucasus and Transcaucasia. Using the data of whole-genome SNP analysis and Bayesian phylogeny methods, we carried out an evolutionary-phylogeographic analysis of modern population of the plague pathogen in order to determine the phylogenetic relationships of Y. pestis strains from the Caucasus with the strains from other countries. RESULTS We used 345 Y. pestis genomes to construct a global evolutionary phylogenetic reconstruction of species based on whole-genome SNP analysis. The genomes of 16 isolates were sequenced in this study, the remaining 329 genomes were obtained from the GenBank database. Analysis of the core genome revealed 3315 SNPs that allow differentiation of strains. The evolutionary phylogeographic analysis showed that the studied Y. pestis strains belong to the genetic lineages 0.PE2, 2.MED0, and 2.MED1. It was shown that the Y. pestis strains isolated on the territory of the East Caucasian high-mountain, the Transcaucasian high-mountain and the Priaraksinsky low-mountain plague foci belong to the most ancient of all existing genetic lineages - 0.PE2. CONCLUSIONS On the basis of the whole-genome SNP analysis of 345 Y. pestis strains, we describe the modern population structure of the plague pathogen and specify the place of the strains isolated in the natural foci of the Caucasus and Transcaucasia in the structure of the global population of Y. pestis. As a result of the retrospective evolutionary-phylogeographic analysis of the current population of the pathogen, we determined the probable time frame of the divergence of the genetic lineages of Y. pestis, as well as suggested the possible paths of the historical spread of the plague pathogen.
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Affiliation(s)
- Sergey V Pisarenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
| | - Anna Yu Evchenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Dmitry A Kovalev
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Yuri М Evchenko
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Olga V Bobrysheva
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Nikolay A Shapakov
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
| | - Anna S Volynkina
- Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation
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3
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Spyrou MA, Tukhbatova RI, Wang CC, Valtueña AA, Lankapalli AK, Kondrashin VV, Tsybin VA, Khokhlov A, Kühnert D, Herbig A, Bos KI, Krause J. Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague. Nat Commun 2018; 9:2234. [PMID: 29884871 PMCID: PMC5993720 DOI: 10.1038/s41467-018-04550-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 04/27/2018] [Indexed: 12/23/2022] Open
Abstract
The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics. Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000–3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear. Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia. We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested. Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day. Yersinia pestis has caused infections (plague) in humans since the Early Bronze Age (5000 years ago). Here, Spyrou et al. reconstruct Y. pestis genomes from Late Bronze Age individuals, and find genomic evidence compatible with flea-mediated transmission causing bubonic plague.
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Affiliation(s)
- Maria A Spyrou
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany.
| | - Rezeda I Tukhbatova
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Center of Excellence "Archaeometry", Kazan Federal University, Kazan, 420008, Russian Federation
| | - Chuan-Chao Wang
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Department of Anthropology and Ethnology, Xiamen University, 361005, Xiamen, China
| | - Aida Andrades Valtueña
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Aditya K Lankapalli
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | | | - Victor A Tsybin
- State Institute of Culture, Agency for Preservation of the Historical and Cultural Heritage of the Samara Region, Samara, 443010, Russia
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Maxim Gorky Str., Samara, 443090, Russia
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany.
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4
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Abstract
This chapter summarizes researches on genome and evolution features of Yersinia pestis, the young pathogen that evolved from Y. pseudotuberculosis at least 5000 years ago. Y. pestis is a highly clonal bacterial species with closed pan-genome. Comparative genomic analysis revealed that genome of Y. pestis experienced highly frequent rearrangement and genome decay events during the evolution. The genealogy of Y. pestis includes five major branches, and four of them seemed raised from a "big bang" node that is associated with the Black Death. Although whole genome-wide variation of Y. pestis reflected a neutral evolutionary process, the branch length in the genealogical tree revealed over dispersion, which was supposedly caused by varied historical molecular clock that is associated with demographical effect by alternate cycles of enzootic disease and epizootic disease in sylvatic plague foci. In recent years, palaeomicrobiology researches on victims of the Black Death, and Justinian's plague verified that two historical pandemics were indeed caused by Y. pestis, but the etiological lineages might be extinct today.
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5
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Zimbler DL, Schroeder JA, Eddy JL, Lathem WW. Early emergence of Yersinia pestis as a severe respiratory pathogen. Nat Commun 2015; 6:7487. [PMID: 26123398 PMCID: PMC4491175 DOI: 10.1038/ncomms8487] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/12/2015] [Indexed: 11/09/2022] Open
Abstract
Yersinia pestis causes the fatal respiratory disease pneumonic plague. Y. pestis recently evolved from the gastrointestinal pathogen Y. pseudotuberculosis; however, it is not known at what point Y. pestis gained the ability to induce a fulminant pneumonia. Here we show that the acquisition of a single gene encoding the protease Pla was sufficient for the most ancestral, deeply rooted strains of Y. pestis to cause pneumonic plague, indicating that Y. pestis was primed to infect the lungs at a very early stage in its evolution. As Y. pestis further evolved, modern strains acquired a single amino-acid modification within Pla that optimizes protease activity. While this modification is unnecessary to cause pneumonic plague, the substitution is instead needed to efficiently induce the invasive infection associated with bubonic plague. These findings indicate that Y. pestis was capable of causing pneumonic plague before it evolved to optimally cause invasive infections in mammals.
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Affiliation(s)
- Daniel L Zimbler
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Jay A Schroeder
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Justin L Eddy
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Wyndham W Lathem
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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6
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Platonov ME, Evseeva VV, Efremenko DV, Afanas’ev MV, Verzhutski DB, Kuznetsova IV, Shestopalov MY, Dentovskaya SV, Kulichenko AN, Balakhonov SV, Anisimov AP. Intraspecies classification of rhamnose-positive Yersinia pestis strains from natural plague foci of Mongolia. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2015. [DOI: 10.3103/s0891416815010073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Sun YC, Jarrett CO, Bosio CF, Hinnebusch BJ. Retracing the evolutionary path that led to flea-borne transmission of Yersinia pestis. Cell Host Microbe 2015; 15:578-86. [PMID: 24832452 DOI: 10.1016/j.chom.2014.04.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 03/07/2014] [Accepted: 03/25/2014] [Indexed: 11/18/2022]
Abstract
Yersinia pestis is an arthropod-borne bacterial pathogen that evolved recently from Yersinia pseudotuberculosis, an enteric pathogen transmitted via the fecal-oral route. This radical ecological transition can be attributed to a few discrete genetic changes from a still-extant recent ancestor, thus providing a tractable case study in pathogen evolution and emergence. Here, we determined the genetic and mechanistic basis of the evolutionary adaptation of Y. pestis to flea-borne transmission. Remarkably, only four minor changes in the bacterial progenitor, representing one gene gain and three gene losses, enabled transmission by flea vectors. All three loss-of-function mutations enhanced cyclic-di-GMP-mediated bacterial biofilm formation in the flea foregut, which greatly increased transmissibility. Our results suggest a step-wise evolutionary model in which Y. pestis emerged as a flea-borne clone, with each genetic change incrementally reinforcing the transmission cycle. The model conforms well to the ecological theory of adaptive radiation.
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Affiliation(s)
- Yi-Cheng Sun
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4(th) Street, Hamilton, MT 59840, USA
| | - Clayton O Jarrett
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4(th) Street, Hamilton, MT 59840, USA
| | - Christopher F Bosio
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4(th) Street, Hamilton, MT 59840, USA
| | - B Joseph Hinnebusch
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4(th) Street, Hamilton, MT 59840, USA.
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8
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Wilharm G, Heider C. Interrelationship between type three secretion system and metabolism in pathogenic bacteria. Front Cell Infect Microbiol 2014; 4:150. [PMID: 25386411 PMCID: PMC4209828 DOI: 10.3389/fcimb.2014.00150] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/07/2014] [Indexed: 11/13/2022] Open
Abstract
Before the advent of molecular biology methods, studies of pathogens were dominated by analyses of their metabolism. Development of molecular biology techniques then enabled the identification and functional characterisation of the fascinating toolbox of virulence factors. Increasing, genomic and proteomic approaches form the basis for a more systemic view on pathogens' functions in the context of infection. Re-emerging interest in the metabolism of pathogens and hosts further expands our view of infections. There is increasing evidence that virulence functions and metabolism of pathogens are extremely intertwined. Type three secretion systems (T3SSs) are major virulence determinants of many Gram-negative pathogens and it is the objective of this review to illustrate the intertwined relationship between T3SSs and the metabolism of the pathogens deploying them.
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9
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Bobrov AG, Kirillina O, Vadyvaloo V, Koestler BJ, Hinz AK, Mack D, Waters CM, Perry RD. The Yersinia pestis HmsCDE regulatory system is essential for blockage of the oriental rat flea (Xenopsylla cheopis), a classic plague vector. Environ Microbiol 2014; 17:947-59. [PMID: 25586342 DOI: 10.1111/1462-2920.12419] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 01/22/2014] [Accepted: 01/29/2014] [Indexed: 01/04/2023]
Abstract
The second messenger molecule cyclic diguanylate is essential for Yersinia pestis biofilm formation that is important for blockage-dependent plague transmission from fleas to mammals. Two diguanylate cyclases (DGCs) HmsT and Y3730 (HmsD) are responsible for biofilm formation in vitro and biofilm-dependent blockage in the oriental rat flea Xenopsylla cheopis respectively. Here, we have identified a tripartite signalling system encoded by the y3729-y3731 operon that is responsible for regulation of biofilm formation in different environments. We present genetic evidence that a putative inner membrane-anchored protein with a large periplasmic domain Y3729 (HmsC) inhibits HmsD DGC activity in vitro while an outer membrane Pal-like putative lipoprotein Y3731 (HmsE) counteracts HmsC to activate HmsD in the gut of X. cheopis. We propose that HmsE is a critical element in the transduction of environmental signal(s) required for HmsD-dependent biofilm formation.
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Affiliation(s)
- Alexander G Bobrov
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, USA
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10
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Gilbert SE, Rose LJ, Howard M, Bradley MD, Shah S, Silvestri E, Schaefer FW, Noble-Wang J. Evaluation of swabs and transport media for the recovery of Yersinia pestis. J Microbiol Methods 2014; 96:35-41. [DOI: 10.1016/j.mimet.2013.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 10/22/2013] [Accepted: 10/23/2013] [Indexed: 11/30/2022]
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11
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Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A 2012; 110:577-82. [PMID: 23271803 DOI: 10.1073/pnas.1205750110] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The genetic diversity of Yersinia pestis, the etiologic agent of plague, is extremely limited because of its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes of Y. pestis strains that were isolated in China and elsewhere. These SNPs define the genealogy of Y. pestis since its most recent common ancestor. All but 28 of these SNPs represented mutations that happened only once within the genealogy, and they were distributed essentially at random among individual genes. Only seven genes contained a significant excess of nonsynonymous SNP, suggesting that the fixation of SNPs mainly arises via neutral processes, such as genetic drift, rather than Darwinian selection. However, the rate of fixation varies dramatically over the genealogy: the number of SNPs accumulated by different lineages was highly variable and the genealogy contains multiple polytomies, one of which resulted in four branches near the time of the Black Death. We suggest that demographic changes can affect the speed of evolution in epidemic pathogens even in the absence of natural selection, and hypothesize that neutral SNPs are fixed rapidly during intermittent epidemics and outbreaks.
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12
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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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13
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Platonov ME, Evseeva VV, Svetoch TE, Efremenko DV, Kuznetsova IV, Dentovskaya SV, Kulichenko AN, Anisimov AP. Phylogeography of Yersinia pestis vole strains isolated from natural foci of the Caucasus and South Caucasus. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2012. [DOI: 10.3103/s089141681203007x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Brubaker RR. Consequences of missense mutations in Yersinia pestis: efficient flow of metabolic carbon versus virulence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 954:31-8. [PMID: 22782743 DOI: 10.1007/978-1-4614-3561-7_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Affiliation(s)
- Robert R Brubaker
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, USA.
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15
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Gibbons HS, Krepps MD, Ouellette G, Karavis M, Onischuk L, Leonard P, Broomall S, Sickler T, Betters JL, McGregor P, Donarum G, Liem A, Fochler E, McNew L, Rosenzweig CN, Skowronski E. Comparative genomics of 2009 seasonal plague (Yersinia pestis) in New Mexico. PLoS One 2012; 7:e31604. [PMID: 22359605 PMCID: PMC3281092 DOI: 10.1371/journal.pone.0031604] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/10/2012] [Indexed: 02/07/2023] Open
Abstract
Plague disease caused by the Gram-negative bacterium Yersinia pestis routinely affects animals and occasionally humans, in the western United States. The strains native to the North American continent are thought to be derived from a single introduction in the late 19th century. The degree to which these isolates have diverged genetically since their introduction is not clear, and new genomic markers to assay the diversity of North American plague are highly desired. To assay genetic diversity of plague isolates within confined geographic areas, draft genome sequences were generated by 454 pyrosequencing from nine environmental and clinical plague isolates. In silico assemblies of Variable Number Tandem Repeat (VNTR) loci were compared to laboratory-generated profiles for seven markers. High-confidence SNPs and small Insertion/Deletions (Indels) were compared to previously sequenced Y. pestis isolates. The resulting panel of mutations allowed clustering of the strains and tracing of the most likely evolutionary trajectory of the plague strains. The sequences also allowed the identification of new putative SNPs that differentiate the 2009 isolates from previously sequenced plague strains and from each other. In addition, new insertion points for the abundant insertion sequences (IS) of Y. pestis are present that allow additional discrimination of strains; several of these new insertions potentially inactivate genes implicated in virulence. These sequences enable whole-genome phylogenetic analysis and allow the unbiased comparison of closely related isolates of a genetically monomorphic pathogen.
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Affiliation(s)
- Henry S Gibbons
- United States Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, United States of America.
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16
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Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC SYSTEMS BIOLOGY 2011; 5:163. [PMID: 21995956 PMCID: PMC3220653 DOI: 10.1186/1752-0509-5-163] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/13/2011] [Indexed: 11/20/2022]
Abstract
Background Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas. Results Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain. Conclusions Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, provides an in silico platform with which to investigate the metabolism of this important human pathogen.
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Affiliation(s)
- Pep Charusanti
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
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17
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Bobrov AG, Kirillina O, Ryjenkov DA, Waters CM, Price PA, Fetherston JD, Mack D, Goldman WE, Gomelsky M, Perry RD. Systematic analysis of cyclic di-GMP signalling enzymes and their role in biofilm formation and virulence in Yersinia pestis. Mol Microbiol 2010; 79:533-51. [PMID: 21219468 DOI: 10.1111/j.1365-2958.2010.07470.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cyclic di-GMP (c-di-GMP) is a signalling molecule that governs the transition between planktonic and biofilm states. Previously, we showed that the diguanylate cyclase HmsT and the putative c-di-GMP phosphodiesterase HmsP inversely regulate biofilm formation through control of HmsHFRS-dependent poly-β-1,6-N-acetylglucosamine synthesis. Here, we systematically examine the functionality of the genes encoding putative c-di-GMP metabolic enzymes in Yersinia pestis. We determine that, in addition to hmsT and hmsP, only the gene y3730 encodes a functional enzyme capable of synthesizing c-di-GMP. The seven remaining genes are pseudogenes or encode proteins that do not function catalytically or are not expressed. Furthermore, we show that HmsP has c-di-GMP-specific phosphodiesterase activity. We report that a mutant incapable of c-di-GMP synthesis is unaffected in virulence in plague mouse models. Conversely, an hmsP mutant, unable to degrade c-di-GMP, is defective in virulence by a subcutaneous route of infection due to poly-β-1,6-N-acetylglucosamine overproduction. This suggests that c-di-GMP signalling is not only dispensable but deleterious for Y. pestis virulence. Our results show that a key event in the evolution of Y. pestis from the ancestral Yersinia pseudotuberculosis was a significant reduction in the complexity of its c-di-GMP signalling network likely resulting from the different disease cycles of these human pathogens.
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Affiliation(s)
- Alexander G Bobrov
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA.
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The importance of the small RNA chaperone Hfq for growth of epidemic Yersinia pestis, but not Yersinia pseudotuberculosis, with implications for plague biology. J Bacteriol 2010; 192:4239-45. [PMID: 20543069 DOI: 10.1128/jb.00504-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Yersinia pestis, the etiologic agent of plague, has only recently evolved from Yersinia pseudotuberculosis. hfq deletion caused severe growth restriction at 37 degrees C in Y. pestis but not in Y. pseudotuberculosis. Strains from all epidemic plague biovars were similarly affected, implicating Hfq, and likely small RNAs (sRNAs), in the unique biology of the plague bacillus.
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Eppinger M, Worsham PL, Nikolich MP, Riley DR, Sebastian Y, Mou S, Achtman M, Lindler LE, Ravel J. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J Bacteriol 2010; 192:1685-99. [PMID: 20061468 PMCID: PMC2832528 DOI: 10.1128/jb.01518-09] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 12/25/2009] [Indexed: 11/20/2022] Open
Abstract
To gain insights into the origin and genome evolution of the plague bacterium Yersinia pestis, we have sequenced the deep-rooted strain Angola, a virulent Pestoides isolate. Its ancient nature makes this atypical isolate of particular importance in understanding the evolution of plague pathogenicity. Its chromosome features a unique genetic make-up intermediate between modern Y. pestis isolates and its evolutionary ancestor, Y. pseudotuberculosis. Our genotypic and phenotypic analyses led us to conclude that Angola belongs to one of the most ancient Y. pestis lineages thus far sequenced. The mobilome carries the first reported chimeric plasmid combining the two species-specific virulence plasmids. Genomic findings were validated in virulence assays demonstrating that its pathogenic potential is distinct from modern Y. pestis isolates. Human infection with this particular isolate would not be diagnosed by the standard clinical tests, as Angola lacks the plasmid-borne capsule, and a possible emergence of this genotype raises major public health concerns. To assess the genomic plasticity in Y. pestis, we investigated the global gene reservoir and estimated the pangenome at 4,844 unique protein-coding genes. As shown by the genomic analysis of this evolutionary key isolate, we found that the genomic plasticity within Y. pestis clearly was not as limited as previously thought, which is strengthened by the detection of the largest number of isolate-specific single-nucleotide polymorphisms (SNPs) currently reported in the species. This study identified numerous novel genetic signatures, some of which seem to be intimately associated with plague virulence. These markers are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies.
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Affiliation(s)
- Mark Eppinger
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Patricia L. Worsham
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Mikeljon P. Nikolich
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - David R. Riley
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Yinong Sebastian
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Sherry Mou
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Mark Achtman
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Luther E. Lindler
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Jacques Ravel
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
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Kutyrev VV, Eroshenko GA, Popov NV, Vidyaeva NA, Konnov NP. Molecular mechanisms of interactions of plague causative agents with invertebrates. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2010. [DOI: 10.3103/s0891416809040028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bearden SW, Brubaker RR. Recent findings regarding maintenance of enzootic variants of Yersinia pestis in sylvatic reservoirs and their significance in the evolution of epidemic plague. Vector Borne Zoonotic Dis 2010; 10:85-92. [PMID: 20158336 PMCID: PMC2945867 DOI: 10.1089/vbz.2009.0043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite the widespread presence of bubonic plague in sylvatic reservoirs throughout the world, the causative agent (Yersinia pestis) evolved in its present form within the last 20,000 years from enteropathogenic Yersinia pseudotuberculosis. Comparison of the genomes from the two species revealed that Y. pestis possesses only a few unique plasmid-encoded genes that contribute to acute disease, whereas this organism has lost about 13% of the chromosomal genes that remain active in Y. pseudotuberculosis. These losses reflect readily detectable additions, deletions, transpositions, inversions, and acquisition of about 70 insertion sequence (IS) inserts, none of which are likely to promote increased virulence. In contrast, major enzymes of intermediary metabolism, including glucose 6-phosphate dehydrogenase (Zwf ) and aspartase, are present but not catalytically functional due to the presence of missense mutations. The latter are generally not detectable by the technology of bioinformatics and, in the case of Y. pestis, result in radical changes in the metabolic flow of carbon. As an important consequence, plague bacilli exhibit a stringent low-calcium response characterized by conversion of L-glutamate (and metabolically related amino acids) to L-aspartate with secretion of the latter into supernatant fluid at 37 degrees C in culture media containing Na(+) but lacking added Ca(2+). This phenomenon also occurs in vivo and likely adversely affects the bioenergetics of host amino acid pools. Curiously, aspartase is functional in all tested enzootic (pestoides) strains of Y. pestis. These isolates are typically restricted to the ancient plague reservoirs of Central Asia and Africa and are fully virulent in members of the rodent Superfamily Muroidea but avirulent in guinea pigs and man. The implications of these findings for the distribution and ecology of Y. pestis could be significant.
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Affiliation(s)
- Scott W Bearden
- Division of Vector-Borne Infectious Diseases, Bacterial Diseases Branch, Centers for Disease Control and Prevention, Foothills Campus, Fort Collins, Colorado 80521, USA.
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Variability of the <i>aspA</i> Genes in <i>Yersinia pestis</i> Strains of the Main and Non-Main Subspecies. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2009. [DOI: 10.21055/0370-1069-2009-1(99)-52-54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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