Microbial pathogens

1
MICROBIAL FUNCTIONAL GENOMICS AND METABOLOMICS
physiological control
INPUT
transcriptome proteome metabolome
THE VIRTUAL CELL
data integration informatics
OUTPUT
2
Complexity and microbes

• Microbes have the smallest genomes 0.5 9Mbases
  with 500 few thousand genes.
• In a genome of n genes, the number of possible
  intra-gene binary interactions increases as
  n(n-1)/2.
• Number of possible binary states of system of n
  genes is 2n
• Modelling of eukaryotic cells with tens of
  thousands of genes is far beyond existing
  computing power.
• Modelling of simpler microbial cells may soon be
  a tractable problem.

3
Frazier et al 2003
4
The burden of infectious Diseases
5
Tuberculosis

• One third of the worlds population infected
• Responsible for 3-4 millions deaths per year
• Biggest cause of adult death in the developing
  world

6
Meningitis

• Caused by bacteria, viruses, funghi and protozoa
• About 1.2 million cases of bacterial meningitis
  occur each year and about 10 of them are fatal
• Major epidemics of meningitis are caused by the
  meningococcus
• Outbreak in Burkina Faso has reported a total of
  7146 cases including 1058 deaths since January
  2003
• 2-3,000 cases in the UK mostly group B

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Diarrhoeal Disease

• Biggest cause of infant mortality worldwide
• Responsible for about 1.5 million deaths each
  year
• Caused mainly by bacteria and viruses

8
Emerging and re-emerging infections

• SARS
• HIV
• TB
• West Nile Virus
• W135 meningococcus
• Bioterrorism

9
Microbial genomes

• Genomes of all major pathogens have now been
  sequenced
• Viruses
• TB bacillus
• Meningococcus
• Campylobacter

10
Functional Genomic capability in the Group/School

• Advanced robotics for microarray production and
  analysis
• Microarray scanners
• MALDI-tof
• Automated sequencer
• Confocal microscope
• FACS scanner
• Additional mass specs for metabolomics (eg. ion
  trap)

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Functional Genomics of Microbial Pathogens at
Surrey

• Bacteria
• Meningococcus
• Tubercle bacillus
• Campylobacter
• Viruses
• Astroviruses, caliciviruses
• Control of viral translation

• Drug targets
• Vaccines
• Diagnostics
• Vectors

12
Continuous Culture to Study Bacterial Pathogens

• Transcriptome
• Proteome
• Metabolome
• But, problems
• Physiological Control
• Reproducibility
• Continuous Culture

RPM
O2
0C
pH
13
Continuous culture of bacterial pathogens
P3 Chemostat Facility
transcriptome
MALDI-tof
RPM
O2
0C
pH
proteome
metabolome
Mass spec NMR
14
Identification of metabolic pathways that are
active during persistence in M. tuberculosis
New Drug Targets

• M. tuberculosis can persist in the host for many
  years
• Drug regimes have to be maintained for at least 6
  months
• Chemostat ? populations of cell growing at
  different rates.
• Proteome and transcriptome analysis of fast and
  slow-growing cells ? identify metabolic pathways
  active during persistence
• NEW DRUG TARGETS

15
Functional genomics to identify virulence genes
in the meningococcus
regulated virulence genes
a)
New Vaccine Candidate antigens
b)

16
Microbial Functional Genomics

• Bacteria
• Viruses
• Protozoa
• Funghi
• Algae

• Microbial Products
• Microbial Pathogenicity
• Microbial Ecology