1. Horizontal gene transfer and the history of life

2. Yersinia pestis
Diverged from Yersinia pseudotuberculosis 1500 – 20,000 years ago
Y. pseudotuberculosis – fecal/oral transmission, low mortality
Y. pestis – through blood or air, high mortality

3. Class discussion on the plague
How could such a deadly disease evolve from such a mild ancestor?

4. Genome of Yersinia pestis
1,2 genes color coded by function
3, 4 pseudogenes
5, 6 insertion sequences
7 G+C content
8 GC bias (G-C/G+C)
3 Plasmids
One Yersinia specific
One pestis specific
One came from S. typhi
Genome sequence of Yersinia pestis, the causative agent of plague. J. Parkhill, et al. Nature 413, (4 October 2001)
doi: /

5. Learning goals
Explain the difference between horizontal and vertical gene transfer
Be able to explain each mechanism for horizontal gene transfer (HGT): conjugation, transduction, transformation
Explain the process of recombination and its role in: acquisition of new genes, loss of genes
Explain how horizontal gene transfer(HGT)is detected
Describe the impact of horizontal gene transfer on microbial genomes and evolution
Describe insertion sequences and pseudogenes

6. Lecture outline (HGT)
Microorganisms sometimes transfer genes horizontally, affecting their evolution and ecology
There are three basic mechanisms of HGT
Transformation – naked DNA
Conjugation - plasmids
Transduction - viruses
Recombination facilitates integration of foreign DNA, gene gain, and gene loss
Insertion sequences and pseudogenes

7. Sequence patterns vary across species
The genetic code is redundant

8. Sequence patterns vary across species
Species vary in which codons they use
REFERENCE: Modified from Maloy, S., V. Stewart, and R. Taylor Genetic analysis of pathogenic bacteria. Cold Spring Harbor Laboratory Press, NY.

9. We can find foreign DNA in many genomes
GC content variation
Codon bias
DNA sequence of foreign gene has different history than all others in the genome.

10. Horizontal versus vertical gene transfer

11. Microbes gain complex traits via HGT

12. HGT obscures evolutionary history

13. Mechanisms of horizontal gene transfer
How the DNA gets in
Transformation
Conjugation
Transduction

14. Transformation
Natural transformation
Induced transformation in lab

15. Transduction (transfer by viruses)
Generalized transduction
Specialized transduction

16. Generalized transduction
Work with a partner to draw a picture showing how generalized transduction could occur during the lytic cycle(Hint: Host DNA may often become fragmented during a phage infection)

17. Specialized Transduction
Specialized transduction: Draw how specialized transduction could happen in lambda.

18. Specialized Transduction: Details in lambda

19. Conjugation
Plasmids Or
Plasmid + host genes

20. Mechanism of conjugation
Relaxosome
Donor
Recipient
First stage
Consider what you know about DNA replication (semi-conservative) and work with a partner to develop a hypothesis for how you go from having one ds plasmid in the donor, to having a second copy in the recipient.
Consider:
Do both strands travel through the relaxosome at once? Or just one strand?
Which cell replicates DNA: Donor, Recipient, or both?
Donor
Recipient
Last stage

21. Mechanism of conjugation
Relaxosome
Donor
Recipient
First stage
Donor
Recipient
Last stage

22. Conjugation: DNA transfer molecules
Donor
Recipient
Donor
Recipient

23. Potential fates of foreign DNA
Plasmids: replicate in host
DNA from: transduction or transformation
Most likely degraded by nucleases
Otherwise, incorporated by recombination

24. Homologous recombination
How DNA gets into chromosome, and how genes are lost or duplicated

25. Generalized recombination
Requires homology between sequences
Functions:
DNA repair
New DNA
Gene duplication
and deletion

26. Generalized recombination process
Chi site = short sequence interspersed in all genomes 1 2

27. Generalized recombination process3 4 5 6
RecA finds region of homology:
Why region of homology?

28. Generalized recombination Holliday junction
Molecule 6 viewed in different ways

29. Recombination: Resolving Holliday junction
What if we cut it here instead?

30. Gene duplication and loss by recombination

31. Insertion sequences

32. Pseudogenes

33. How could such a deadly disease evolve?
3, 4 pseudogenes
5, 6 insertion sequences
7 G+C content
8 GC bias (G-C/G+C)
1,2 genes color coded by function