integrated bioinformatics nature of research articles comparison of genomes – scenario regular...
TRANSCRIPT
Integrated Bioinformatics
• Nature of research articles
• Comparison of genomes – Scenario
• Regular expressions in Python
• Installing and running Blast
• How to find differences
E. coli: What makes it kill?
Escherichia coli . . .
. . . very small lab rats
Courtesy of Kent State University Microbiology
E. coli: What makes it kill?
Escherichia coli . . .
• Shiga toxin-producing a.k.a. enterohemorrhagic E. coli (EHEC).
• Enterotoxigenic E. coli
• Enteropathogenic E. coli (EPEC)
• Enteroaggregative E. coli (EAEC)
• Enteroinvasive E. coli (EIEC)
• Diffusely adherent E. coli (DAEC)
At least six different dirarrheal "pathotypes" of E. coli !
http://www.cdc.gov/ecoli/general
E. coli: What makes it kill?
E. coli O157:H7 . . . The classic baddie!!
• Shiga toxin-producing (STEC)a.k.a. enterohemorrhagic E. coli (EHEC)
• First described as a pathogen in 1982
• The most prevalent in foodborne outbreaks
• Most self-resolving diarrhea and vomiting
• Hemolytic urinary syndrome a serious complication
Easily the most extensively studied pathogenic E. coli
E. coli: What makes it kill?
E. coli O104:H4 . . . The up-and-comer
• Enteroaggregative E. coli (EAEC)…but with acquired Shiga toxin genes!
• First described as a pathogen in 2005 (only one case!), but caused a huge outbreak in Germany in 2011
• German outbreak traced back to sprouts!
• 3,950 people affected, with 53 deaths, and 800 cases of hemolytic urinary syndrome
Good example of how "new" pathogens can suddenly emerge
Research papersPerna, N. T., G. Plunkett, 3rd, et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409(6819): 529-33
Hayashi, T., K. Makino, et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 8(1): 11-22
Loman, et al. (2013). A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4 JAMA 309(14): 1502-10
Hauser, et al. (2013). Phylogenetic and molecular analysis of food-borne shiga toxin-producing Escherichia coli. Appl Environ Microbiol. 79(8): 2731-40
E. coli: What makes it kill?
E. coli K12 E. coli O157:H7
Gene finder Gene finder
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA
E. coli: What makes it kill?
E. coli K12 E. coli O157:H7
Gene finder Gene finder
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA
E. coli: What makes it kill?
Similarity finder
Killer protein
Membrane protein, sodium transporter
Iron responsive transcriptional regulator
Calcium-dependent protein kinase
Unknown protein
Unknown protein
Unknown protein
. . .
Killer functions
Suggests therapeutic interventions
How do these differences arise?
Point mutation
organism 1 TTT TCT GAA TCC GTA GAC GTT organism 2 TTT TCT GAA TCA GCA GAC GTG
What kind of mutations arise?
How do genomic differences arise?
Can these explain the difference between K12 and O157:H7??
DNA mutation has multiple causes!
• Errors during DNA replication• base mis-incorporation• polymerase slippage / repeat amplification
• Errors during recombination or cell division• chromosome loss or rearrangement• large insertions or deletions
• Environmental factors – mutagens:• radiation – UV or ionizing radiation• chemical – many mechanism of action
• Spontaneous events:• tautomerisation• depurination• deamination
• Viral infection or transposons
Addition/deletion of DNA
How to distinguish from ?
Where do they come from?
– GC-content?
How do genomic differences arise?
InfectionPhage
Bacterial chromosome
Phage genome
Lysogenicpathway
LyticpathwayPhage genome
Lytic pathway = cell death!
General transductionHow do genomic differences arise?
InfectionPhage
Bacterial chromosome
Phage genome
Lysogenicpathway
LyticpathwayPhage genome
How do genomic differences arise?General transduction
Lysogenic pathway = Life!
How do genomic differences arise?
InfectionPhage
Bacterial chromosome
Phage genome
Lysogenicpathway
LyticpathwayPhage genome
General transduction
Lysogenic pathway = Life!
Specialized transduction
Occurs at defined sites
Specialized transduction
Occurs at defined sites
The gene encoding diphtheria toxin (tox) is carried on corynephage
Lysogenic conversion by corynephage confers toxogenicity!!
tox–C.d.
tox+C.d.