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

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

Talk

• 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

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

Talk

• 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

Talk

• 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

Questions

• 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

Talk

• 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

Talk

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