Genome sequence of Yersinia pestis, the causative agent of plague

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Genome sequence of Yersinia pestis, the
causative agent of plague

• J. Parkhill, B.W. Wren, N. R. Thomson, R.W.
  Titball, M. T. G. Holden,
• M. B. Prentice, M. Sebaihia, K. D. James, C.
  Churcher, K. L. Mungall,
• S. Baker, D. Basham, S. D. Bentley, K. Brooks,
• A. M. Cerdeno-Tarraga, T. Chillingworth, A.
  Cronin, R. M. Davies,
• P. Davis, G. Dougank, T. Feltwell, N. Hamlin, S.
  Holroyd, K. Jagels,
• A. V. Karlyshev, S. Leather, S. Moule, P. C. F.
  Oyston, M. Quail,
• K. Rutherford, M. Simmonds, J. Skelton, K.
  Stevens, S. Whitehead
• B. G. Barrell

Sara Speckels Naomi Bogenschutz
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Yersinia pestis
Photos Centers for Disease Control Prevention
Public Health Image Library
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200 MILLION DEATHS
Justinian Plague 500-700 A.D.
Image courtesy of University of Michigan
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200 MILLION DEATHS
The Black Death (1347-1353) Killed 25 million
people in less than 6 years!
Image University of Kansas, Wichita
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WarningThe following slide contains graphic
pictures of Yersinia pestis wrath! Viewer
discretion is advised!
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200 MILLION DEATHS
Modern Plague
Centers for Disease Control Prevention Public
Health Image Library
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Centers for Disease Control Prevention Public
Health Image Library
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Centers for Disease Control Prevention Public
Health Image Library
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How is the plague transmitted?
Nature, Volume 413, 4 October 2001
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Biological Warfare Weapon
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Yikes!

• Why is Yersinia pestis so dangerous?

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Sequenced Genome in 2001
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Methods
Congo Red Agar
Broth
Sheered by sonication to create fragment inserts
for libraries
DNA extraction
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Libraries

• To generate whole genome sequence
• 1-2.5kb inserts-
• 94,881 end sequences
• (9.6X sequence coverage)
• To construct scaffolds
• 9-11kb inserts- 3.1X clone coverage
• 20-22kb inserts- 4.0X clone coverage

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Chromosome- 4.65Mb Three plasmids
96.2kb, 70.3kb, 9.6kb
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pseudogenes
GC content
Figure 1 Circular representation of the
Y. pestis genome.
Insertion sequences
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Plasmids

• 70.3kb pYV1/pCD1
• virulence plasmid found in all pathogenic
  Yersinia
• 9.6kb pPst/pPCP1
• codes for an invasin necessary for infection
  through the skin
• 96.2kb pFra/pMT1
• codes for a toxin and capsular protein
• homologous to Salmonella plasmid

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GC bias abnormalities

• Certain genomic regions deviated from the
  bacterial bias toward G on the leading strand.
• Deviations could signal recent DNA acquisition
• How did they test for this?

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Insertion sequences

• Figure 5-70. Alberts et. al. Molecular Biology of
  the Cell 4th edition. 2002.

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What did they find?
Supplement One Notable GC variable loci and
potential pathogenicity islands in the Y.pestis
genome.
Many pathogenicity genes appear to be insertions.
And many more
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• Figure 2A
• Chaperone-usher systems
• Aids in surface adherence and coagulation
• Contributes to bacterial pathogenicity

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Secretion Flagellar Systems

• Type III secretion systems, related to flagellar
  export systems

Figure 2b
Figure 2c
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Insecticidal toxins

• Homologs of genes from other insect pathogens,
  suggesting lateral transfer
• Some toxin genes are non-functional

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Pseudogenes

• Genes acquired through duplications and/or
  transpositions that have been inactivated by
  mutations.

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149 Pseudogenes

• Many code for genes involved in pathogenicity
• Frame-shift mutations and can easily revert back
  to functional form.

Supplement One Pseudogenes predicted in the
Yersinia pestis CO92 genome
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What does this mean?Are we all going to die?

• Yersinia pestis genome
• Fluidity contributes to organisms ability to
  evolve and remain highly virulent
• Insertion sequences indicate lateral transfer of
  genes from other organisms
• Resistance and virulence genes are easily
  acquired
• Antibiotics could become less effective to treat
  infection

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What can we do now?
Sara

• Understand mechanisms of virulence
• Develop novel treatments
• Combat threat of bioterrorism