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

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

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

Wed Jun 27 08:01:54 EDT 2007

• UMBI, NIST

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

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

Wed Jun 27 08:03:16 EDT 2007

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