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Genome evolution II - other factors contributing to genome expansion

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.

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Genome evolution II - other factors contributing to genome expansion

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  1. Genome evolution II - other factors contributing to genome expansion Transposons & retrotransposons DNA-mediated transposition - mobile element encodes transposase Conservative Replicative Fig. 7.1

  2. 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

  3. 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…

  4. “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

  5. Bacterial genomes Possible explanations for species that are outliers? Fig. 8.1

  6. “Molecular archaeology of the E.coli genome” 4.6 Mbp Transposition events (IS elements) Horizontal gene transfer Lawrence & Ochman PNAS 95:9413, 1998

  7. “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

  8. 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

  9. 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

  10. Wide variation in GC content among bacterial genomes consequences for codon usage patterns? Fig.8.26 Fig. 8.29

  11. “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

  12. SPECULATIONS ON EVOLUTION OF EARLY LIFE-FORMS Joyce Nature 418:214, 2002

  13. “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)

  14. 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

  15. PCR RiNA GmbH “Experimental evolution” in vitro SELEX – iterated cycles of selection & amplification of sequences Bittker Curr Opin Chem Biol 6:367, 2002

  16. 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.” - after 9 rounds of selection & reproduction, 4 “mutations” (pink sites) predominant Freeman Fig. 16.5 Beaudry & Joyce Science 257:613, 1992

  17. “Experimental evolution” in vivo Comparison of positions of orthologous genes in Mycoplasma & Haemophilus Fig.8.22 Papdopoulos, PNAS 96:3807, 1999

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