Bacterial Comparative Genomics and Bioinformatics

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Bacterial Comparative Genomics and Bioinformatics
Research Seminar

• Yair Motro
• Center for Bioinformatics and Biological
  Computing
• http//cbbc.murdoch.edu.au

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An Introduction to CBBC

• Integrated Systems
• YABI client/server system for project
  management, hypothesis driven bioinformatics
  analysis, pipeline creation, audit trails,
  comparative analysis
• MASV and Multiblast genome viewer
• ERIC interactive genome viewer
• GRENDEL resource management
• MUMSDB Microsatellite database (allele
  assignment)
• UTILITIES (EST clustering, mirroring data, custom
  database formatting)
• Bioinformatics Analysis Audit trails and
  Ontologies

• Comparative Genomic Analysis
• Mammalian species
• Human full-length cDNA annotation
• Cereal genome analysis
• Legume species analysis
• Bacterial genome annotation (Bacterial
  Bioinformatics Group)
• Genomics Based Vaccine Design and Development
  (Bacterial Bioinformatics Group)

• Computation
• Sequence alignment (SANKOFF)
• Feature-based Sequence Alignment

• Other
• Protein profile classification (Neural Networks)
• DNA fingerprint profiling
• Microarray data analysis

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Bacterial Bioinformatics Group

• Collaboration between CBBC (Head Professor
  Matthew Bellgard) and the Murdoch University
  Bacteriology group (Head Professor David
  Hampson)
• Currently involved in
• Annotation of two bacterial genomes
• Analysis of these two bacterial genomes
  (Comparative Genomics)
• Genomics based vaccine design and development
  (Reverse Vaccinology)

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Bacterial Genomics

• Genomics is the study of all the nucleotide
  sequences, including structural genes, regulatory
  sequences, and non-coding DNA segments, in the
  chromosomes of an organism.
• Comparative Bacterial Genomics is the analysis
  of multiple bacterial genomes.

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Arising Issues and Focus of PhD Research

• The discussed bioinformatics analysis pipeline
  relies heavily on comparative analyses, the
  essence of my research
• The research focuses on the use of comparative
  genomics in answering the question
• What makes a good potential drug/vaccine
  candidate?
• Focus on key areas in bioinformatics
• Development of software solutions for general
  problems, with particular focus on visualisation
  issues
• Methodological limitations in comparative
  genomics-based analysis

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Research Questions

• What species should be compared to generate
  clusters?
• From these clusters, what genes would be
  considered unique/conserved?
• Is visualisation the limiting factor in such
  comparative analysis?
• Is it valid to find unique genes by comparing
  genomes of
• Related species?
• Unrelated species?
• Conservative evolution of genes, metabolic
  pathways, etc
• Why are some proteins, pathways and
  characteristics conserved in some species (even
  those that are not taxonomically closely
  related)?
• Visualisations of these conservations?
• Hierarchy of conservation and uniqueness
• By using different types of comparisons,
  different levels/aspects of gene uniqueness and
  conservation is observed
• To what extent can the reverse vaccinology
  process be automated?

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Bacterial Genome Statistics

• First complete genome sequence available in 1995
• Now, more than 190 completely sequenced genomes
  publicly available
• Provides extensive data for comparative analysis
• All available statistics of completely sequenced
  bacterial genomes to date, have been compiled
  into a single table (present study)
• Allowing for an initial comparative genomics
  analysis

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Bacterial Genome Statistics
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Comparative genomics of C. tetani, C. perfringens
and C. acetobutylicum, identifies 1506 ORFs that
are homologous in all three genomes and 516 ORFs
that are unique to C. tetani.(Bruggemann et al.,
2003)This type of comparative work can lead to
the identification of particular ORFs that are
unique to the microbe, and could thus become a
drug target or vaccine candidate.
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Gene conservation among related species can be
depicted through complete genome sequence
alignments, such as this one between C. tetani
and C. botulinum (causative agents of tetanus and
botulism respectively) .(Bruggemann et al.,
2003)This is a powerful comparative analysis
tool, as particular segments of conservation can
be visually picked out and further analysed.
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From the genomic analysis, the ori (origin of
replication) for C. tetani was predicted. 81
of all ORFs are transcribed in same direction as
replication proceeds (termed co-directionality),
which was also found in other Gram positive
bacteria (in contrast to Gram negative bacteria).
This comparative analysis demonstrates that both
specific characteristics of the chromosome can be
determined (i.e. ori elucidation) along with
general characteristics (i.e. co-directionality).
(Bruggemann et al., 2003)
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The diagram demonstrates the use of comparative
genomics on the collagenase protein (involved in
the hydrolysis of collagen, thus potentially
contributing to the loss of tissue integrity in
the infected host). Part A diagrammatically
presents a segment comparison of collagenases
from a number of species of the
Clostridium/Bacillus group. This is useful in
determining insertions and deletions between
species, which can be used to predict
phylogenetic relationships among the species
(Part B).(Bruggemann et al., 2003)
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Genome annotation can lead to the identification
of metabolic pathways, which may be essential to
the microbes existence, and may also
differentiate it from its host.C. tetani has a
great number of genes that encode for sodium
ion-dependant systems, which may be the reason
for the organisms successful invasion of
infected tissue. (Bruggemann et al., 2003)
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References

• Bruggemann, H., et al., The genome sequence of
  Clostridium tetani, the causative agent of
  tetanus disease. Proc Natl Acad Sci U S A, 2003.
  100(3) p. 1316-21.
• Bruggemann, H. and G. Gottschalk, Insights in
  metabolism and toxin production from the complete
  genome sequence of Clostridium tetani. Anaerobe,
  2003. in press.
• Adu-Bobie, J., et al., Two years into reverse
  vaccinology. Vaccine, 2003. 21(7-8) p. 605-10.
• Motro, Y., Dunn, D., La, T., Hampson, D.,
  Bellgard, M. (2004). A decade of bacterial genome
  sequencing. in progress.