Skip to main content
Article thumbnail
Location of Repository

The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081

By Nicholas Robert Thomson, Sarah Howard, Brendan Wren, Matthew T. G. Holden, Lisa Crossman, Gregory L. Challis, Carol Churcher, Karen Mungall, Karen Brooks, Tracey Chillingworth, Theresa Feltwell, Zahra Abdellah, Heidi Hauser, Kay Jagels, Mark Maddison, Sharon Moule, Mandy Sanders, Sally Whitehead, Michael A. Quail, Gordon Dougan, Julian Parkhill and Michael B. Prentice

Abstract

The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending\ud from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the\ud genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8;\ud biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis\ud reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a\ud plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has\ud provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the\ud high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide\ud new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes\ud potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in\ud the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are\ud absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients\ud used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate\ud respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y.\ud enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into\ud the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations\ud looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution\ud of other human enteropathogens

Topics: QR
Publisher: Public Library of Science
Year: 2006
OAI identifier: oai:wrap.warwick.ac.uk:4431

Suggested articles

Citations

  1. (1997). A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system. doi
  2. (2000). A chromosomally encoded type III secretion pathway in Yersinia enterocolitica is important in virulence. doi
  3. (2005). A guild of 45 CRISPRassociated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. doi
  4. (2005). A nutritive view on the host–pathogen interplay. doi
  5. (2005). ACT: The Artemis Comparison Tool. doi
  6. (2004). Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle doi
  7. (2006). Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity. doi
  8. (2003). Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. doi
  9. (2004). Bacterial variations on the methionine salvage pathway. doi
  10. (2006). Bickerton A
  11. (1981). Characterization of plasmids and plasmid-associated determinants of Yersinia enterocolitica pathogenesis.
  12. (2002). Characterization of the ysa pathogenicity locus in the chromosome of Yersinia enterocolitica and phylogeny analysis of type III secretion systems. doi
  13. (1994). Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2.
  14. (1996). Cobalamin (coenzyme B12): Synthesis and biological significance. doi
  15. (2003). Cobalamin synthesis in Yersinia enterocolitica 8081. Functional aspects of a putative metabolic island. doi
  16. (2004). Colbeau A doi
  17. (2004). Comparison of the biotypes of Yersinia enterocolitica isolated from pigs, cattle and sheep at slaughter and from humans with yersiniosis in Great Britain during 1999–2000. doi
  18. (2001). Complete DNA sequence of Yersinia enterocolitica serotype 0:8 low-calcium-response plasmid reveals a new virulence plasmid-associated replicon. doi
  19. (2001). Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. doi
  20. (2004). Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. doi
  21. (2003). Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. doi
  22. (2005). CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. doi
  23. (2006). Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics. doi
  24. (1992). Epidemiology of Yersinia pseudotuberculosis and Y. enterocolitica infections in sheep in Australia.
  25. (1996). Evolution of coenzyme B12 synthesis among enteric bacteria: Evidence for loss and reacquisition of a multigene complex.
  26. (2002). Evolutionary genomics of Salmonella: Gene acquisitions revealed by microarray analysis. doi
  27. (2002). Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. doi
  28. (1991). Factors promoting acute and chronic diseases caused by yersiniae.
  29. (1999). Ferric enterochelin transport in Yersinia enterocolitica: Molecular and evolutionary aspects.
  30. (1984). Genetic manipulation of virulence of Yersinia enterocolitica and Yersinia pseudotuberculosis. Zentralbl Bakteriol Mikrobiol Hyg [A]
  31. (1984). Genetically manipulated virulence of Yersinia enterocolitica.
  32. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. doi
  33. (2004). Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. doi
  34. (2002). Genome sequence of Yersinia pestis KIM. doi
  35. (2001). Genome sequence of Yersinia pestis, the causative agent of plague. doi
  36. (2002). Identification of genes that are associated with DNA repeats in prokaryotes. doi
  37. (1997). Identification of novel chromosomal loci affecting Yersinia enterocolitica pathogenesis. doi
  38. (1999). Identification of Yersinia enterocolitica genes affecting survival in an animal host using signature-tagged transposon mutagenesis. doi
  39. (1988). Increased virulence of Yersinia pseudotuberculosis by two independent mutations. doi
  40. (2004). Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. doi
  41. (2004). Microevolution and history of the plague bacillus, Yersinia pestis. doi
  42. (2003). Molecular analysis of the copper-transporting efflux system CusCFBA of Escherichia coli. doi
  43. (2002). Molecular hydrogen as an energy source for Helicobacter pylori. doi
  44. (2000). Motility is required to initiate host cell invasion by Yersinia enterocolitica. doi
  45. (2000). Nonspecific adherence by Actinobacillus actinomycetemcomitans requires genes widespread in bacteria and archaea. doi
  46. (2003). Novel virulence-associated type II secretion system unique to high-pathogenicity Yersinia enterocolitica. doi
  47. (2003). Olczak A doi
  48. (2000). Osmoregulated periplasmic glucans in Proteobacteria. doi
  49. (2001). Pathoadaptive mutations that enhance virulence: Genetic organization of the cadA regions of Shigella spp. doi
  50. (2004). Phages and the evolution of bacterial pathogens: From genomic rearrangements to lysogenic conversion. doi
  51. (1983). Plasmid-mediated antigens of human pathogenic Yersinia enterocolitica strains. Zentralbl Bakteriol Mikrobiol Hyg [A]
  52. (2003). Rakin A doi
  53. (1982). Rapid isolation of Yersinia spp. from feces.
  54. (1995). Report of four cases of Yersinia pseudotuberculosis septicemia and a literature review. doi
  55. (2004). Respiratory hydrogen use by Salmonella enterica serovar Typhimurium is essential for virulence. doi
  56. (1987). Revised biogrouping scheme of Yersinia enterocolitica.
  57. (1995). The ars operon of Escherichia coli confers arsenical and antimonial resistance.
  58. (1991). The epidemiology of Yersinia enterocolitica infection in the British Isles 1983–1988.
  59. (1994). The Escherichia coli AlkB protein PLoS Genetics | www.plosgenetics.org
  60. (2005). The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli. doi
  61. (2000). The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.
  62. (1999). The mdoC gene of Escherichia coli encodes a membrane protein that is required for succinylation of osmoregulated periplasmic glucans. doi
  63. (1995). The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases.
  64. (2001). The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix. doi
  65. (2006). The nature and dynamics of bacterial genomes. doi
  66. (2004). The role of carbon monoxide in the gastrointestinal tract. doi
  67. (2004). The role of prophage-like elements in the diversity of Salmonella enterica serovars. doi
  68. (2005). The Shigella flexneri effector OspG interferes with innate immune responses by targeting ubiquitin-conjugating enzymes. doi
  69. (2003). The widespread colonization island of Actinobacillus actinomycetemcomitans.N a t doi
  70. (2004). The Yersinia high-pathogenicity island (HPI): Evolutionary and functional aspects. doi
  71. (2003). The yersiniae—A model genus to study the rapid evolution of bacterial pathogens. doi
  72. (2003). Tight-adherence genes of Actinobacillus actinomycetemcomitans are required for virulence in a rat model. doi
  73. (2004). Transferable antibiotic resistance elements in Haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands. doi
  74. (2005). Use of molecular hydrogen as an energy substrate by human pathogenic bacteria. doi
  75. (2003). Viewing and annotating sequence data with Artemis. doi
  76. (1997). Virulence and arsenic resistance in Yersiniae.
  77. (2004). YAPI, a new Yersinia pseudotuberculosis pathogenicity island. doi
  78. (1987). Yersinia enterocolitica, a primary model for bacterial invasiveness. doi
  79. (1981). Yersinia enterocolitica: Its isolation by cold enrichment from patients and healthy subjects. doi
  80. (1997). Yersinia pestis—Etiologic agent of plague.
  81. (1999). Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. doi
  82. (2002). Yersinia pseudotuberculosis harbors a type IV pilus gene cluster that contributes to pathogenicity. doi
  83. (2002). Yersinia type III secretion: Send in the effectors. doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.