Download An Introduction to “Bioinformatics to predict bacterial

An Introduction to
“Bioinformatics to Predict
Bacterial Phenotypes”
Jerry H. Kavouras, Ph.D.
Lewis University
Romeoville, IL
Why study bioinformatics?
It’s a rapidly growing field in biology
and computer science that analyzes the
genetic information stored in DNA.
What are phenotypes?
Phenotypes are the observed manifestations
of genes, which are linear sequences of
nucleotides on chromosomes and plasmids.
Examples:
Cell shapes (bacillus, coccus)
Metabolic capacity (glucokinase)
Antibiotic resistance (b-lactamase)
How are phenotypes determined?
Traditionally, microbiologists determine
phenotypes by culture methods and
microscopic techniques.
Examples:
Test
Gram stain
Catalase test
Phenotype
Cell wall
Degrades H2O2
What phenotypes do you observe
in this Gram stain preparation?
Phenotypic observations
1mm
Coccus
Gram negative
Bacillus
Gram positive
Length is 3 mm
Homologous genes
Homologous genes share similar sequences
-- Related by evolution
-- Good chance have similar function
Similar sequences are likely to be versions of
the same gene, or at least similar genes,
meaning there is a very good chance the
PHENOTYPE is present.
Use bioinformatics to predict
cellular phenotypes!
Possible to predict cellular phenotypes
from a linear sequence of chromosomal or
plasmid DNA if the gene is already known.
Why is this important?
This means microbiologists can determine
the phenotypes for a microbe without
culture methods and microscopy.
Why use bioinformatics instead of
standard methods?
Microbiologists estimate the overwhelming
majority of bacteria in nature have not been
cultured (based on analyses of 16S rDNA
sequences)
Microbiologists can predict the phenotypes
of UNCULTURED bacteria!
-- Very powerful tool
Genomes & Bioinformatics
The number of complete genome sequences for
organisms is increasing steadily.
Someday microbiologists may rely on DNA
sequences for determining cell phenotypes.
This does not mean culture methods and
microscopy will not be important!
Real world applications
How can the same species of bacteria be
pathogenic and nonpathogenic?
Answer: Different strains!
Example:
Escherichia coli K-12 (nonpathogenic)
Escherichia coli O157:H7 (pathogen)
Real world applications (cont’d)
Because the chromosomal and plasmid
sequences are known for these strains,
bioinformatics can determine differences in
the set of genes (genome) for each organism.
Now use the Signature Genes tool at NMPDR to
actually answer this question.
Compare whole genomes
• Go to www.nmpdr.org
• Select the Signature
Genes tool from the
left navigation bar
• Choose E. coli O157:H7
as the reference
• Choose another strain
of the O157:H7
serotype, strain
EDL933, in set 1
• Choose two strains of
avirulent E. coli K12 in
the exclusion set 2
• Click Go
Find genes responsible for
virulence phenotype
• 847 genes common to two strains of
O157:H7 and absent from two lab strains
of E. coli
• Most of these are phage-associated
• Included are 6 toxin genes
• What might the remaining 841 genes be
doing?
How do you explore physical &
biological context of virulence
genes in E. coli?
1. Study phylogenetic profiles
-- evolutionary relationships
among genes
2. Study protein families
-- functional (analogous)
relationships among genes
Acknowledgements
Thanks to Leslie McNeil for her additions,
assistance, and comments in preparing this
exercise introduction.