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

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

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

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