MCB 502A 2015 Lecture 3 Genome Evolution DNA replication The two major types of genome evolution DNA replication The problem of helix unwinding Various explanations Following the fate of parental DNA in bacteriophages Equilibrium centrifugation The experiment of Meselson and Stahl The experiment of Taylor Break induced replication outside the S phase in eukaryotes The two major types of genome evolution 1 The cross hybridization studies revealed certain patterns that are easier to operate at the level of total DNA information content of the cell the differences between genomes of different species The two major types of genome evolution 2 For a long time genome evolution was thought to be driven by point mutations one nucleotide changes in the DNA sequence to gradually adapt to a stable environment with occasional genome scrambling by rearrangements to get a foothold in an entirely new habitat Environment Constant Changing Erratic Selection Stabilizing Adaptation to new or multiple conditions Mechanism of evolution Point mutations and small rearrangements Large scale intra genome rearrangements Genomes are expected to retain their common frames to be scrambled no common frame preserved The two major types of genome evolution 3 hybridization and wholegenome sequencing produced The bacterial genomes There is a significant flow of genes A picture of fishing in gene flow The two major types of genome evolution 4 Bacteria love to eat DNA but sometimes this food escapes You are what you eat http www deviantart com art Cell meets plasmid 151423037 The two major types of genome evolution 5 horizontal gene transfer mosaic genomes common frame interspersed with homeologous and completely heterologous patches remarkable stability of genomic frames The reason for this high synteny remains a mystery Bacillus genome comparison B cereus vs B thuringiensis The two major types of genome evolution 6 different from the classic mode that yields evolutionary trees continuous gene flow changes the mode of evolution from branching to festooning Horizontal gene transfer allows for a faster adaptation to a new environment The two major types of genome evolution 7 example the benign E coli genome size in the 4 2 4 7 Mbp range a minimal complete genome of 3 7 Mbp enteropathogenic relatives causing food poisoning with genome sizes up to 5 4 Mbp The two major types of genome evolution 8 mobilome the collection of genes on the extrachromosomal elements plasmids and phages and on mobile elements within the chromosome examples Bacillus cereus Bacillus antracis lethal differences in the resident plasmids and the Vibrio deadly lysogenic conversion by the XTS prophage The two major types of genome evolution 9 a bacterial genome can accommodate a lot of foreign DNA the circularity of bacterial chromosome disallows certain GCRs because mobile element movement stimulates rearrangements The two major types of genome evolution 10 The general patterns of archaeal genome evolution rapid gene loss and reacquisition via horizontal gene transfer intolerance for active mobile elements repeats high synteny between related archaeal genomes The two major types of genome evolution 11 In contrast to bacteria and archaea eukaryotic genome evolution HGT does not work in eukaryotes because their DNA is kept in the nucleus while their cytoplasmic routing of exogenous DNA so the exogenous DNA is degraded by cytoplasmic DNases The two major types of genome evolution 12 1 exogenous DNA that can get into the eukaryotic genome http velica deviantart com art Retrovirus remake 213910841 The two major types of genome evolution 12 2 Retroviruses are ssRNA viruses that replicate only in the nucleus Since retroviruses have to get to the nucleus to replicate while no other DNA can a unique biology makes retroviral infections a major driver of the eukaryotic genome evolution The two major types of genome evolution 13 1 The small sizes of the retroviral genomes 2 the one enzyme mechanism of retroviral cDNA formation and 3 the rampant recombination during cDNA synthesis breed ever changing families of simplistic mobile retroelements The two major types of genome evolution 14 These retroelements and the layers of their decaying remnants 50 90 Figure 3 The chromosomal distribution of the LTR retrotransposon composition of the B73 maize genome http www ploscollections org article info 3Adoi 2F10 1371 2Fjournal pgen 1000732 The two major types of genome evolution 15 eukaryotic genomes tolerate mobile element infestation because of split genes alternative splicing The two major types of genome evolution 16 repeat driven GCRs linear eukaryotic chromosomes tolerate exchange type rearrangements without copy number change inversions reciprocal translocations no problem The two major types of genome evolution 17 a peculiar level of karyotype fluidity eukaryotic chromosomes even evolutionarily closely related higher eukaryotes have different numbers of chromosomes and no common genome frame The two major types of genome evolution 18 For example while there is a single major inversion and a few minor ones that separates the common gene frame of E coli and Salmonella two related enteric bacteria separated by 150 Myr there are 245 major rearrangements and 3170 minor ones between human and mouse genomes essentially the same genome content separated by only 75 Myr http cinteny cchmc org doc wholegenome php http www uhnresearch ca labs tillier Xplots html The two major types of genome evolution 19 junk yards of eukaryotic genomes prokaryotic genomes are busy highways the genome size in prokaryotes is an accurate reflection of the gene content The two major types of genome evolution 20 prokaryotic introns are always big coding for selfish elements in contrast to eukaryotes prokaryotic genomes have a few tightly controlled active mobile elements The low activity of mobile elements evolutionarily stable common frames and a high degree of synteny in the prokaryotic genomes Location of 35 IS elements on the E coli B chromosome Schneider et al BMC Microbiology 2002 2 18 http www biomedcentral com 1471 2180 2 18 The two major types of genome evolution 21 prokaryotes strongly prefer to delete rather than insert DNA The nature of this unrelenting space crunch is not known http gbe oxfordjournals org content 1 145 long The two major types of genome evolution 22 Therefore we can list the following aspects of prokaryotic bacteria archaea VS eukaryotic cells as contributors
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