Download Lateral gene transfer in prokaryotic genomes: which genes

Lateral gene transfer in
prokaryotic genomes
Uri Gophna
Dept. of Molecular Microbiology and Biotechnology, TAU
Lateral (or Horizontal) Gene Transfer :
A process in which an organism transfers genetic material
(i.e. DNA) to another cell that is not its offspring.
Outline of the talk
1. Molecular mechanisms of lateral gene
transfer (LGT) in microorganisms.
2. Genomic evidence for the importance of
LGT.
3. LGT and the tree of life.
4. LGT detection methods.
5. A final note – which transferred genes
are fixed in populations?
Molecular mechanisms of lateral
gene transfer (LGT)
• Uptake of naked DNA (transformation).
• Phages (transduction).
• Plasmids (conjugation).
• Integrative and transposable elements
(transposition).
• Cell fusion (in Archaea).
Transformation and competence
• Many microorganisms can
naturally take up DNA
fragments from broken cells.
• Inserted DNA can sometimes
be recombined into the
chromosome.
Phages - generalized transduction
Many phages mistakenly
package some host DNA.
Resulting particle often
cannot replicate, but does
inject the foreign DNA.
Homologous
recombination can lead to
integration of acquired
DNA.
Phages - specialized transduction
Some phages can lysogenize –
integrate their DNA into the host
chromosome. This integration is sitespecific.
This is often benficial to the host –
protects from related phages and
sometimes confers advantages (toxin
genes in phages of C. diphteriae).
The phage can later be induced to exit
the chromosome and replicate (lytic
cycle).
Rarely the phage packages
neighboring host genes, leaving some
of its DNA behind.
Thus, a phage can shuttle DNA
between prokaryotes, or “contribute”
phage genes to their genome.
Plasmids and conjugation
• Plasmids are genetic elements that replicate independently of
the host chromosome.
• Exist as free (usually circular) DNA.
• Generally do not encode essential genes.
• Are spread among cells by cell to cell contact – conjugation,
usually involving-plasmid encoded pili.
• Host range varies from narrow to broad depending on
replication machinery (and usually not the conjugation factors).
• Some plasmids can integrate into the chromosome and
subsequently their conjugation can mobilize parts of it.
Integrated plasmids (episomes) can sometimes recombine with
the host chromosome and exit with a few chromosomal genes.
Plasmids can confer many selective advantages
Transposable elements (IS elemens and transposons)
Genetic elements that can move within the
genome.
Contain a gene encoding a transposase
flanked by inverted repeats and in the case
of transposons also other genes.
Usually integrate at specific sites.
Are also found in phages and plasmids.
Can mediate recombination and
chromosome re-arrangement.
= Inverted repeat
Transposable elements can jump from
one microbe to another by either:
• Being
located on a mobile
element such as phage or
plasmid.
• Having their own conjugation
systems – Integrating
Conjugative Elements (ICEs).
Integrons: Chromosomal elements that recruit
gene cassettes by site-specific recombination
Genomic evidence for the
importance of LGT
Clinical importance of LGT:
Staphylococcus aureus as an example
•
Phage-encoded toxins:
1. Enterotoxin A - food poisoning.
2. Exfoliative toxin A - scalded skin syndrome.
3. Panton-Valentine leukocidin - severe skin
infections and necrotizing pneumonia in children
(mortality rate of 40%).
• Plasmids - Antiseptic and antibiotic resistances.
• Integron- Methicillin resistance.
• Transposon-encoded vancomycin resistance
(from plasmids of enterococci!).
Based on Lindsay and Holden, 2004, (Trends Microbiol. 12:378-85)
LGT - driving adaptation and speciation
From colitis to plague - genes acquired less than
20000 years ago “created” the species Yersinia
pestis
• Ymt – Toxin, also essential for flea
colonization.
• Plasminogen activator Pla, invasin
essential for virulence by the
subcutaneous route.
• Following the new lifestyle – major gene
loss and accelerated evolution formed a
new bacterial species.
Factors influencing success of LGT
• Evolutionary/Genetic distance between organisms.
• Physical proximity of organisms.
• Gene function:
Frequently transferred:
(Strong positive selection)
• Resistance genes – Antibiotics, heavy metals, arsenic...
• Virulence factors – Pathogenicity islands.
• Metabolic pathways – Metabolic islands/plasmids.
Rarely transferred:
• Genes that are part of essential complexes, such as the
translation machinery – “The complexity hypothesis”.
Acquisition of potentially useful genes
• A totally new function.
• A function already performed by a homolog –
quasi duplication – sometimes followed by
orthologous replacement.
• A function already performed by a nonhomologous gene –leading to either nonorthologous replacement or functional
divergence.
Comparative genomics : There is much LGT
but is it always adaptive ?
EVIDENCE FOR LGT: PROKARYOTIC GENOMES
AS MOSAICS
----
“backbone” or
“core” genes
with common
history
---
“island” of
genes
with alien origin
phage
gene
single
alien
genes
Typical stretch of prokaryotic chromosome sequence
LGT and the tree of life
estimating its evolutionary
impact
LGT and the Tree of Life
conflicting views of its role in evolution
Committed verticalists
• LGT is rare and generally has little impact
on evolutionary processes (Kurland).
• A relatively stable core of genes is very
rarely transferred, while most other genes
can undergo LGT (Woese).
• Since most if not all genes in a genome
have been transferred at least once, a tree
of life is meaningless (Doolittle).
Enthusiastic lateralists
The Universal Tree of Life
mitochondria
chloroplasts
LAST UNIVERSAL COMMON ANCESTOR (LUCA)
Adapted from Doolittle, 1999 (Science, 284:2124-2128)
A core of genes showing the same true tree
core
genes
LUCA
(Last Universal Common Ancestor)
A web of life - no true tree and no LUCA
(there are no species trees just gene trees)
Adapted from Doolittle, 1999 (Science, 284:2124-2128)
How can we accurately assess the impact of LGT?
.
Extent of LGT Differs between genomes
Lateral gene transfer and the nature of bacterial innovation.
Ochman, Lawrence, Groisman. Nature. 2000;405(6784):299-304
How can we detect LGT?
• Phylogenetic trees.
• Composition-based methods: G+C
content, codon usage.
• Phylogenetic discordance – atypical
patterns of similarity to different
organisms.
• Distributional profiles.
Detecting LGT
Tree based detection
Comparing species tree to gene trees
Caulobacter
Caulobacter
Brucella
Sinorhizobium
Yersinia
Sinorhizobium
Yersinia
Escherichia
Brucella
Escherichia
Salmonella
Species Tree (usually 16S)
Salmonella
Gene Tree
Detecting LGT
Trees are not always an option…
• Making trees for all genes in a genome
requires pipelines that are computationally
intensive and still require much human
intervention – Moore vs. Moore.
• Inferring LGT by tree reconstruction
requires at least four-five homologs.
Detecting LGT
Tree-free methods
• Composition-based methods: G+C
content, codon usage...
• Distributional profiles.
• Phylogenetic discordance – atypical
patterns of similarity to different
organisms.
Compositional methods fail to detect many ancient
events – ancient LGT is often underestimated
G+C Content
Fraction of LGT detected
Codon usage
(MM)
Phylogenetic
Discordance
Distributional
Profiles
Phylogenetic
of inferred
Phylogenetic
depth of depth
inferred
event event
(antiquity)
Ragan, Harlow and Beiko 2006, (Trends Microbiol. 14:4-8)
Which laterally acquired genes tend to be
fixed in a microbial population?
• Genes under strong positive selection.
• Genes that form a functional cluster (Selfish operon
theory…).
• Genes that are not part of essential complexes (see Alon
Wellner’s poster).
• Genes with compatible codon usage to the new host
(Medrano-Soto et al., 2004).
• Acquiring a gene by LGT is up to six times more likely if an
enzyme that catalyses a coupled metabolite flux is already present
in the genome (Pal et al., 2005).
Acknowledgements
W. Ford Doolittle
Alon Wellner (see poster!)
Mor Lurie
Amitai Or
Amir Kovacs
Funding
Research Networks Program in Bioinformatics (Israeli MOST/ Ministry of
Foreign Affairs and the Ministry of National Education and Research of
France.