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Genome evolution II
- other factors contributing to genome expansion
Transposons & retrotransposons
DNA-mediated transposition
- mobile element encodes transposase
Conservative
Replicative
Fig. 7.1
RNA-mediated transposition
- mobile retroelement encodes reverse transcriptase
eg SINES, LINES
short & long interspersed repetitive elements
- in human genome, Alu repeats derived from 7SL RNA gene
- also tRNA-derived (MIR repeats) …
Fig. 7.1
Possible evolutionary consequences of transposition events
(p.349-353)
1. Increase in genome size
2. Promotes major DNA rearrangements
– may affect gene structure or expression
- region between 2 TEs may be moved during transposition
- impact on synteny?
3. Increased mutation rate may improve survival under
adverse conditions?
eg. antibiotic resistance genes on TEs in bacteria, genomic
reorganization events in plants under environmental stress…
“Selfish DNA” - especially in eukaryotic genomes
- “playground for evolution”
- creation of new genes, reshuffling existing ones
- rich source of paleontological info
- tools (markers) for medical genetic & population studies
Fig. 8.15
Bacterial genomes
Possible explanations for species that are outliers?
Fig. 8.1
“Molecular archaeology of the E.coli genome”
4.6 Mbp
Transposition events (IS elements)
Horizontal gene transfer
Lawrence & Ochman PNAS 95:9413, 1998
“Bacterial speciation is likely to be driven by a high rate of horizontal
transfer, which introduces novel genes, confers beneficial phenotypic
capabilities, and permits the rapid exploitation of competitive environments”.
Ochman Nature 405: 299, 2000
Yersinia pestis
“The genome of the bacterium that
causes plague is highly dynamic and
scarred by genes acquired from other
organisms”.
Genome fluidity
- inversion/translocation of chromosomal segments
- intragenomic recombination at IS element sites
Gene acquisition and decay
- lateral transfer of genes from other bacteria & viruses
eg surface antigens, virulence factors involved in pathogenicity
vs. both mammals and insects
“reductive evolution” during colonization of new niche?
Parkhill Nature 413:523, 2001
Bacterial genomes have bias for G on leading strand of
bidirectional replication fork
- replication error differences between leading and
lagging DNA strands
Fig. 8.27
Wide variation in GC content among bacterial genomes
consequences for codon usage
patterns?
Fig.8.26
Fig. 8.29
“Extensive gene gain associated with adaptive evolution of poxviruses”
20 genomes compared
(including smallpox & vaccinia)
“disproportionately high
proportion of genes in
orthopox clade are under
positive selection”
eg. genes important for
host-parasite co-evolution
McLysaght PNAS 100:15655, 2003
SPECULATIONS ON EVOLUTION OF EARLY LIFE-FORMS
Joyce Nature 418:214, 2002
“RNA world” hypothesis
- first primitive “living” systems had RNA genome
Supported by multifunctional nature of present-day RNA
- codes for proteins
- produces proteins
- carries out replication
- can act as catalyst
ribozymes - self-cleaving, self-slicing, self-elongation…
BUT … DNA more stable for storing information (& DNA repair systems)
Post-progressive Darwinian evolution
- origin of multicellular life & environment driven
diversification
- most (but not all) mutations neutral
- those fixed by selection improve fitness only
for specific environmental conditions
Progressive Darwinian evolution
Origin of cellular life, communal web-of-life?
Strong selective advantage if able to propagate
info & efficient production of useful proteins
Replication, transcription & translation
machinery “similar” in all life-forms
Period of rapid mutation, increased
accuracy & efficiency of info transfer
– gene organization & regulation
Pre-Darwinian evolution
Without self-replication, no entities to
evolve through natural selection
Doolittle & Brown PNAS 91:6721, 1994
“Experimental evolution” in vitro
SELEX – iterated cycles of selection & amplification of sequences
PCR
RiNA GmbH
Bittker Curr Opin Chem Biol 6:367, 2002
Test-tube evolution of ribozyme
- selection for improved cleavage
of DNA oligomer substrate
- pool of ~1013 molecules
- 140 nt (brown) randomly mutated
so “5% chance not wt sequence at
any given position”
“The pool of variants was challenged
such that only those molecules that
could catalyze the cleavage of a DNA
oligomer substrate (black box) would
be allowed to reproduce.”
Beaudry & Joyce Science 257:613, 1992
- after 9 rounds of selection & reproduction,
4 “mutations” (pink sites) predominant
Freeman Fig. 16.5
“Experimental evolution” in vivo
Comparison of positions of orthologous
genes in Mycoplasma & Haemophilus
Papdopoulos, PNAS 96:3807, 1999
Fig.8.22