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Comparative genomics and structural biology of the molecular innovations of eukaryotes

Comparative genomics and structural biology of the molecular innovations of eukaryotes. L Aravind, LM Iyer, EV Koonin Presentation by Ruben Valas. LECA. Eukaryotes are very different than archaea and bacteria There are no extant organisms that are pre-eukaryote like

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Comparative genomics and structural biology of the molecular innovations of eukaryotes

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  1. Comparative genomics and structural biology of the molecular innovations of eukaryotes L Aravind, LM Iyer, EV Koonin Presentation by Ruben Valas

  2. LECA • Eukaryotes are very different than archaea and bacteria • There are no extant organisms that are pre-eukaryote like • This review paper examines some of the structures that are unique to eukaryotes

  3. Mixing of archaea and bacteria Lopez-Garcia and David Moreira, 2006

  4. Eukaryotes are very unique • Nucleus with linear chromosomes • Regulated cell cycle • Cytoskeleton system • Spliceosomal Introns • Distinct posttranslational regulation (ubiquitin) • Organelles such as mitochondria

  5. All of this happened fast • Since all eukaryotes have these traits they must have evolved in a very short period of time • Cavalier-Smith says this is quantum evolution triggered by the mitochondrial symbiosis

  6. Structure changed 3 ways • Ancient domains gained new functions • Ancient folds were tweaked to form new superfamilies • New folds emerged • This is a review paper, so this data comes from looking at the structures other papers identified

  7. Innovations

  8. Modification of Preexisting Domains

  9. Their conclusions • They conclude most innovations are α-helical or chelation-supported • α-helical and metal-supported structures depend less on hydrogen bonding between distant residues • These structures can change rapidly

  10. α-helical and metal-chelation-supported domains

  11. My Data • I can’t directly compare what we have because they aren’t only using SCOP FSFs • There are 60 SCOP FSFs that are only in eukaryotes and are in at least 58 of the 61 eukaryotes in Superfamily • If I use Dollo parsimony there are 123 or 145 FSFs in LECA depending on the tree

  12. FSFs in LECA

  13. Its not all alpha • Their data is based on novel functions in eukaryotes, some new structures take on old functions • I find more beta and alpha+beta than metal binding, how these evolve rapidly still needs to be established • If alpha proteins can evolve so fast why aren’t these folds seen earlier?

  14. Duplications • Many novel structures come from families of paralogs • These duplications appear to have happened before LECA • The mitchondrial symbiosis would act like a gene duplication for many genes

  15. Duplications predating LECA

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