Julius B. Lucks/Meetings and Notes/SMBE2007/extreme genomes 2

From OpenWetWare
Jump to: navigation, search

Jean-Michel Claverie: Mimivirus and the origin of large DNA viruses infecting eukaryotes - reconciling incompatible scenarii

  • Institute de Biologie Structureale et Microbiologique

Words to Lookup

  • intein


  • 1.2 Mbp genome
  • in between Eukarya and the tri-vertex of Euk, Bac, Archea
  • 1992 Bradforcoccus
    • gram-positive cocci-like intracellular bacterium - Bradforcoccus
    • no 16S rRNA, no culture
  • A giant Virus in Amoeba, Science 299, 203, 2003
  • icosahedral virus-like particle
    • 750 nm - same size as U. urealyticum - almost a micron size
  • how prove is a virus
    • typical 'eclipse phase' during infection - not divide like bacteria
      • eclipse - disappear, then reappear when start to multiple
    • use confocal microscopy
  • The 1.2 Mb genome of Mimivirus. Sciene 206, 1344, 2004
  • linear, 72% AT, 911 predicted CDS (298 with putative function), 90.5% fraction coding, 6 tRNAs, 1 intein, Intron (Type 1b) $ + 2
  • J. Virol, 75, 11720, Koonin - Common origin of four diverse families of large eukaryotic DNA viruses
    • core genes of NCDLVs - Nucleo-Cytoplasmic Large DNA Viruses
    • all these genes are in Mimivirus
  • no transcription apparatus (RNA polymerase, etc.)
  • 1st virus to have genome bigger than cellular organism (parasytic bacteria)
    • bigger in complexity than some free-living bacteria
  • viruses and bacteria
    • v no translation app
    • v no energy metab
    • v no biosynthesis
    • v have capsid protein genes
    • v have core protein genes
  • Mimi - 8 components of translation
    • uses universal code
    • 4 tRNA synthetases
      • one does not recognize 3rd base of codon - Tyr tRNA synth, only competition is TAT or TAG - both stop codons
        • this could be viral optimization, or a relic of a long time ago
    • all translation factors to start, elongate and end translation
    • tRNA modification enzyme (U to T in a t-loop)
    • 6 tRNA (3 Leu, Trp, His, Cys)
    • does have some metabolism genes
    • all DNA repair enzymes
    • using these genes, can hang on the tree of life
    • only virus with MutS - mismatch repair
      • seems to be maybe on another branch of life, or at least a distant ancestor on the eukaryotic branch

Mimivirus predates the Eukaryotic radiation

  • falsifiable prediction
  • equidistant from all Eukaryotic kingdoms

Evolutionary hypotheses

  • viruses predate everything (d'Herelle, 1922)
  • viruses at origin of nucleus (Villareal)
  • nucleus at origin of viruses (Bell)
  • viruses invented DNA (Forterre)
  • see 'iterative virual eukaryogenesis & nuclear viriogenesis' - Forterre-lke - start with RNA cell
    • cell stores its own genes in viral DNA genome (virus invent DNA)
    • viruses revert to viral world - every time cycle produce a new lineage

Where genes coming from

  • not duplication
  • not accretion
  • reduction
    • reduction from a past NCLDV ancestor - have lineage specific losses
  • see GiantVirus.org
    • another NCDLV infect the xxx huxlei algae that occur in blooms - responsible for the loss of the bloom

A New way of Looking at Viruses

Martine Zilversmit: Low-complexity region in the human malaria parisite Plasmodium falciparum - missing links in the evolution of an extreme genome

  • collaborated with Mark DePristo!

Words to look Up

  • low complexity regions
    • regions selected from limited amount of AAs
    • simple repeats
    • aperiodic repeats
    • predominantly hydrophilic
    • very non-compact structure - flexible


  • not a monolithic type of sequence
    • 3 distinct families of sequence, with non-overlapping characteristics and evol mechanisms
  • pathology and public health intimately link with evolution of plasmodium
    • organism can adapt to human intervention
      • evades immune system, adapts to chemicals
  • eukaryotic parasite - protist
  • 14 chromosome karyotype
  • 81% AT
  • highly recombinogenic (1% per 17 kilobases - approx 60% more than human genome)
  • 87% proteins have low complex region
  • LCRs
    • adaptive smokescreens in surface antigens
    • polymorphic in terms of size
    • P. falciparum proteins longer than orthologs because of LCRs
    • elevated AT-content relative to flanking coding regions
    • coded for by low-complexity DNA sequence
  • comp genomics
    • LCRs abundant in AT-rich genomes, but not adaptive
    • extreme codon bias (due to AT and hydrophilic functional pressure) - proposed results in formation of random repeat regions
    • repeats initially groww by replication slyppage
    • evidence of elevated recombination rates

Christopher Lane: Impact of genome reduction on the eukaryotic proteome - nucleomorphs as a case study

  • DalHousie

Words to Look Up

  • ribosomal cistron


  • chryptomonads (engulphed red algae) and chloracniophytes (engulphed green algae)
  • similar functional categaries in nucleomorphs, but not a lot of overlap
  • no obvious barrier for NM-to-N gene transfer (Nucleomorph to Nuclear)
  • Gillardia theta nucleomarch (2001), letters to Nature, 'The highly reduced genome of an enslaved algal nucleus', Susan Douglas et. al.
  • Hemiselmis andersenii nucleomorh (chryptomonad) - sequenced
    • 60% conserved genes
    • all introns lost (also splicing machinery)
    • 94% conserved sequences with Gillardia are syntenic
  • genome compaction can significantly impact the structure and function of proteins


  • Koonin: spliceosomes coupled to nuclear transport - given that no introns, have looked at nuclear pore?

Christina Toft: Identifying candidate genes for non-functionalisation in endosymbiotic genomes

  • evol genet and bioinformatics, Murfit institute of genetics, Trinity College, Dublin

Words to Look Up

  • Muellers ratchet


  • phylogenetics of the eukaryotes. Mol Biol Evol, 10, 1093,2007, Pisani, Cotton, Mcinerney
  • endosymbiosis highly unstable system
    • very few bacteria transferred between hosts
    • bacteria are asexual - very low opportunity to recombine
    • small population
    • all lead to Muellers ratchet phenomenon
      • mutation load increases as goes through generations
      • can lead to non-functionalisation, disintegration, genome reduction
  • Genome Reduction Analysis Software Tool (GRAST) Toft and Fares, 2006, Bioinformatics, 22, 1551

Dinis Lavrov: Convergent evolution in animal mitochondrial DNA

  • Iowa state


Animal mtDNA

  • size and gene content - Buger, TIG, 2003
    • 22 tRNA (trnX)
    • 2 ribosomal RNA (rns, rnl)
    • 13 protein genes (nad1-6,4L,cob,cox1-3)
  • bizarre tRNA and rRNA structures
    • 3 diff tRNA structures - some have only D-arm, some only T-arm, some both ('normal')
  • multiple changes in the genetic code - Knight, TIG, 2003 (Trends in Genetics?)
    • TGA: Stop to Try
    • AGR: Arg to Ser
    • AUA: Ile to Met
    • last 2 allows animals to use 22 tRNAs instead of 24 as minimal set
  • mutation rate 15-34x10^-9 /site/year - up to 25 times faster
    • in plants 20 times slower
    • used in criminal and phylogeography study - can detect differences between individuals

Animal mtDNA evolution

  • porifera (sponges)
  • Lavrov, 2005, MBE: demosponges - extra genes (atp9, tRNAs) - minimally derived genetic code, conserved structuras of RNAs, multiple intergenic regions

Convergent evolution of animal mtDNA