Julius B. Lucks/Meetings and Notes/SMBE2007/introns early introns late

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Scott Roy : Simplification and embellishment of eukaryotic gene structures - creeping intron loss and lineage specific evolution of (alternative) splicing.

Wed Jun 27 08:00:37 EDT 2007

Words to Look Up

  • Fugu

Talk

  • introns-middle
  • spliceosomal introns
    • specific ansecstral (not universal)
    • interrupt coding genes
    • cannot self-splice
    • need spliceosome
  • group II introns
    • bacterial/endosymbiotic genomes
    • interrupt RNA genes ...
    • self-splice
  • Donor(GU)-BranchPoint(A)-Acceptor(AG)
    • BP attacks donor
    • donor attacks the acceptor
  • 1978
    • discov 1977
    • Wally Gilbert - News and Views - Genes and Pieces
    • named introns
    • predicted alternative splicing
    • predicted domain shuffling
    • role in increasing recomb
  • Ford Doolittle (N&V 3 months later)
    • 'like to argue that eukaryotic genome as genes in pieces is primitive form'
    • argued introns early
  • introns-early predictions
    • intron positions correspond to protein structure
    • exons are 3n basepairss
      • if add new exon in middle - causes frameshift
  • introns late prediction
    • spliceosomal system derived from group II introns (transferred from mitochondrion)
  • data
    • protein gene-structure corr p ~ 10^-10
    • p-value exon length ~ 10^-10 (Arlin Stoltzfus group)
    • similarity between spliceosome and type II introns - convinced of introns-late
  • intron loss and gain
    • no clear phylogenetic trend in intron contents
      • could be lots of intron gain, or loss - can't tell direction
  • Coulomb-Huntigton, Majewski, PNAS, 2006
  • 10-15% intron positions shared across fungi, animals and plants

Questions

Arlin Stoltzfus : The relationship of intron position to protein structural features

Wed Jun 27 08:01:54 EDT 2007

  • UMBI, NIST

Words to Look Up

Talk

  • functional interpretations
    • 'speed evolution' (Gilbert, 1978)
    • mediate chromatin structure
    • facilitate exon shuffling (Gilbert, 1986)
  • prevent homogenization of orthologs
    • represent a nexus of gene regulation
    • facilitate nonsense-mediated decay (Lynch)
  • Disruptive vs. Formative
    • Disruptive: some point whole protein coding genes
      • some time introns split these
    • Formative
      • assembly of exon coding mini-genes
    • to distinguish, need homology in intron sequences
      • intron seq evolve rapidly
      • exon shuffling creates new chimeric genes
  • generating predictions from the disruptive (insertional) model
    • introns gained non-randomly wrt nucleotide sequence

Conclusions

  • intron positions exhibit substantial corr with structural features
    • sec struct, solvent acc strongest
  • nucleotide model accounts for most of non-randomness
  • sig deviations remained

Questions

Eugene Koonin : Evolutionary dynamics of introns and their role in eukaryogenesis

Wed Jun 27 08:03:16 EDT 2007

Words to Look Up

Talk

  • outline
    • evol dynamics of introns - brief summary
    • adaptive intron gain?
    • glimpse of the pre-intron phase of eukaryotic evol
    • role of introns in eukaryogenesis
    • post-mortem on 'introns-early vs introns-late'
  • intron pos highly conserved
  • Carmel, Koonin, Gen. Res, 2007, 'Evolutionary conserved genes preferentially accumulate introns.'
  • chloroplast-derived genes in plants - intronless when entered eukaryotic genome
    • intron density lower than ancestral euk genes, but only by a little bit
  • hypothesis - nucleus evolved as defense device against massive intron invasion
    • why have nucleus - decouples transcription and translation, complicated export, ...
  • prokaryotes have introns too (very few)
  • bacteria - group II introns are retroelements that are deleterious when inserted into important protein-coding genes
    • selfish elements
  • alpha-proteobacterio - rich in group II introns
  • speculation - in wake of mitochon endosymb - symbionts group II introns went on a rampage
    • evol of the nucleus
  • indep compl evidence of mitochond triggering nucleogenesis - unleashed group II introns, but also supplied essential building blocks
    • Mans, Cell Cycle, 2004, 3, 1612 - com genomics, evol and origins of nucl envelope and nucl pore complex
  • Martin, Koonin, Nature, 440, 41, 2006
    • chain of causation for origin of nucleus
  • origin of spliceosome
    • inactivation of RT in invading group II introns - loss of mob - prevention of further damage
  • Koonin, Biol Direct, 2006, 14, 1 - origin of introns and their role in eukaryogenesis: compromise solution ...
  • no introns in protein-coding genes or spliceosome in prokaryotes
  • no support for introns-early from intron phase distribution
  • no support for introns-early from intron-domain correspondence

Questions