Horizontal gene transfer and the history of life

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

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

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, 523-527(4 October 2001) doi:10.1038/35097083

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

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

Sequence patterns vary across species The genetic code is redundant

Sequence patterns vary across species Species vary in which codons they use REFERENCE: Modified from Maloy, S., V. Stewart, and R. Taylor. 1996. Genetic analysis of pathogenic bacteria. Cold Spring Harbor Laboratory Press, NY.

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.

Horizontal versus vertical gene transfer

Microbes gain complex traits via HGT

HGT obscures evolutionary history

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

Transformation Natural transformation Induced transformation in lab

Transduction (transfer by viruses) Generalized transduction Specialized transduction

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)

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

Specialized Transduction: Details in lambda

Conjugation Plasmids Or Plasmid + host genes

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

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

Conjugation: DNA transfer molecules Donor Recipient Donor Recipient

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

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

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

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

Generalized recombination process 3 4 5 6 RecA finds region of homology: Why region of homology?

Generalized recombination Holliday junction Molecule 6 viewed in different ways

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

Gene duplication and loss by recombination

Insertion sequences

Pseudogenes

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