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Genome evolution II - other factors contributing to genome expansion
DNA-mediated transposition - mobile element encodes transposase
Conservative Replicative
Fig. 7.1
Transposons & retrotransposons
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eg SINES, LINES
- in human genome, Alu repeats derived from 7SL RNA gene
Fig. 7.1
short & long interspersed repetitive elements
- also tRNA-derived (MIR repeats) …
- mobile retroelement encodes reverse transcriptase
RNA-mediated transposition
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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…
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“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
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Fig. 8.1
Bacterial genomes
Possible explanations for species that are outliers?
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“Molecular archaeology of the E.coli genome”
Lawrence & Ochman PNAS 95:9413, 1998
Horizontal gene transfer
Transposition events (IS elements)
4.6 Mbp
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Ochman Nature 405: 299, 2000
“Bacterial speciation is likely to be driven by a high rate of horizontaltransfer, which introduces novel genes, confers beneficial phenotypiccapabilities, and permits the rapid exploitation of competitive environments”.
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Parkhill Nature 413:523, 2001
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?
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Bacterial genomes have bias for G on leading strand ofbidirectional replication fork
- replication error differences between leading and lagging DNA strands
Fig. 8.27
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Fig.8.26Fig. 8.29
Wide variation in GC content among bacterial genomes
consequences for codon usage patterns?
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“Extensive gene gain associated with adaptive evolution of poxviruses”
McLysaght PNAS 100:15655, 2003
20 genomes compared(including smallpox & vaccinia)
“disproportionately highproportion of genes inorthopox clade are under positive selection”
eg. genes important for host-parasite co-evolution
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Joyce Nature 418:214, 2002
SPECULATIONS ON EVOLUTION OF EARLY LIFE-FORMS
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- codes for proteins
- produces proteins
- carries out replication
- can act as catalyst
BUT … DNA more stable for storing information (& DNA repair systems)
“RNA world” hypothesis
- first primitive “living” systems had RNA genome
Supported by multifunctional nature of present-day RNA
ribozymes - self-cleaving, self-slicing, self-elongation…
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Pre-Darwinian evolution
Without self-replication, no entities to evolve through natural selection
Progressive Darwinian evolution
Strong selective advantage if able to propagate info & efficient production of useful proteins
Replication, transcription & translationmachinery “similar” in all life-forms
Period of rapid mutation, increased accuracy & efficiency of info transfer – gene organization & regulation
Origin of cellular life, communal web-of-life?
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
Doolittle & Brown PNAS 91:6721, 1994
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Bittker Curr Opin Chem Biol 6:367, 2002
“Experimental evolution” in vitro
SELEX – iterated cycles of selection & amplification of sequences
PCR
RiNA GmbH
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Test-tube evolution of ribozyme
- pool of ~1013 molecules
- 140 nt (brown) randomly mutatedso “5% chance not wt sequence atany given position”
- after 9 rounds of selection & reproduction,4 “mutations” (pink sites) predominant
- selection for improved cleavageof DNA oligomer substrate
Freeman Fig. 16.5
“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
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Papdopoulos, PNAS 96:3807, 1999
“Experimental evolution” in vivo
Comparison of positions of orthologous genes in Mycoplasma & Haemophilus
Fig.8.22
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