Julius B. Lucks/Meetings and Notes/SMBE2007/extreme genomes 1

Patrick Keeling: Nuclear Genome Diversity

Background

• Botany: U British Columbia

Talk

• Keeling and Slamovits, 2005, Curr. Opin, Genet. Div.
• dynoflaggelites and ameoba have large genomes
• 2 small genome groups
  • microsporidia - related to fungi - obligate intracell parasites
    • huge tube that can peirce cell that they can travel into
  • nucleomorphs - organells found in algae: cryptomonads, chloracniophytes
    • have engulfed another algae and kept it as a symbiont
• Keeling 2005, Trends Ecol. Evol.

How genomes get small

• reduction - massive gene loss
  • host-dependance - loss of whole pathways
• compaction - 2x compaction of yeost
  • very short intergenic regions
  • reduced number and size of introns
  • genes shorter
• how does this affect how genomes work?
  • most eukaryotic - promoter upstream and terminator downstream
  • reduced genomes - transcripts overlap - opposite strands (transcriptional collision), or same strand (promoter occlusion)
    • like some viruses
  • Williams, PNAS, 2005
• keep all tRNAs and ribosomal RNAs - ribosomal RNAs at the telomeres

Comparison of Antonospora and Encephalitozoon

• promoter regions of a gene can be inside coding region upstream of it

Pygmy Introns (Nucleomorphs)

• cryptomonid - 17 introns of about 50 bases (Douglas, Nature, 2001)
  • lost many
• chloracachniophyte - 841 introns 18,19,29,21 bp (Gilson, 2006, PNAS)
  • retained all, but shrunk
  • GTnnnnAG - GT/AG boundaries - spliceosomal introns

Shrinking Proteins

• genes shorter - Katinka, 2003
  • 9% reduction compared to yeast
• want to reduce DNA that bad?
• reduction of complexity of the proteome?
• ostreococcus tauri - picoplankton - one of smallest organisms known
• 12.5 mbp, 8,166 proteins, gene density 1.54 genes/kbp (in between yeast and the extremes)

Questions

• intron loss by reverse transcriptase mediated gene replacement
• Koonin: any lifestyle differences between the cryptomonids and chloracachniophytes?

Jeffrey Palmer: Horizontal gene transfer gone wild in plant mitochondrial genes

Talk

• Amborella trichopoda mtDNA: 4 Mb - outside:native::5:1
• bacteria - maybe 1/2 of genome can be from outside sources
• Parkinson, Adams, Palmer, Curr. Biol, 9, 1481, 1999 - Amborella one of 1st angiosperms (flowing plants)
• Amborella contains foreign mitochondrial genes of moss and angiosperm origin
• grows only on new caledania (next to Australia) (80% of plants are endemic there (only live there))
• mtDNA:
  • Human 16 kb
  • Arabidobsis 367 kb
  • Zea 570 kb
  • Amborella 4,000 kb!
• does not have
  • foreign chloroplast DNA
  • foreign nuclear DNA
  • bacterial DNA
  • mtDNA from fungi and other 'not-green' plants
• Frequent fusion and fission fof plant mitochondria - PNAS
  • phylogenetic gulf in fusion mechanisms between (animals/fungi) & plants- Hoppins et al Ann Rev Biochem 76,751,2007
  • chloroplasts don't fuse like mitochondria
• mtDNA retains synteny of its foreign acquisitions

How does foreign mtDNA get into Amborella's mitochondria

• how do mitochondria get from one plant into cells of another
  • direct plant-to-plant contact
    • grows in wet env - lots of epiphytes, epaphylls - mosses, lichens
    • how get into germ line?
      • large tree that gets wounded and dies back - suckers grow off at sites of wounding
      • suckering - cellular dediffertiation - recreate meristems - promotes mitochondrial fusion
        • mascerate foreign substances in a wound to get foreign sources
      • other plants that grow like this have same mitochondrial size?
  • biological vectoring agents - viruses, bacteria, insects
  • illegitimate pollination
• of 250 forign mt genes - probably very few functional

Atsushi Nakabachi: Smallest cellular genome

Background

• RIKEN (Intitute of Physical and Chemical Research)

Words to Look Up

• Chromosome FISH

Talk

• Carsonella ruddii 160 kb genome
  • endocellular symbiotic bacterium of psyllids

• E. coli - 4000 genes (Human 23,000, Yeast 6,000)
• prokaryotes - simpler body plans and lifestyles
  • gene density high, no introns so gene #'s proportional to genome sizes
• endocellular prasites (prokaryotes) have smaller genomes
• insects - bacteriocytes (in body cavity) - host cells specialized to harbor symbionts
  • host live in nutrient poor environments
  • obligate mutualisw
• Host: Bacteriocyte : Symbiont
  • Carpenter Ant: midgut epithelium : Blochmannia floidanus
  • Tsetse flies: specialized epithelial cells : Wiggleswortha glossinidia
  • Aphids: body cavity: Buchnera aphidicula

General featurs of bacterial symbiont genomes

• massive reduction in genome sizes (420-800kb)
• AT-richness (20-30% GC-content)
• gene inactivation and deletion - relaxed selection, small pop size, mutational pressure due to loss of DNA repair genes
• general correlation between GC-content and Genome size

Corsonella

• hakcberry petiole gall psyllid - related to aphids - body cavity bacteriacyte
  • Pachypsylla venusta
  • Carsonella primary symbiont
• 16.5% GC-content, 0.16 Mb
  • 15.9% protein coding regieons
• single chromosome no plasmids
• 159,662 bp
  • < 1/2 of 2nd smallest genome
  • approx same as chloroplast genomes
• no insertion sequences, phages or transposons
• 182 predicted ORFs - 136 putative functions
  • avg length 826 bp (not shorter than in other bacteriocyte symbionts (981-1006 bp))
  • in bacteria approx 1 kb
• 97.3% protein and RNA coding regions (other bacteriocyte symbionts 77-80%)
  • due to numerous overlaping ORFs
  • majority are tandem out of frame overlaps on same strand
• COG classification of ORFs
  • mostly in translation (35%), and amino acid metabolism (18%)
• phyllids and aphids feed only on plant ploem sap - poor in essential AAs - need symbionts to synthesize some AAs
• apparently no genes for cell division
• no genes for cell envelope biogenesis (biosynthesis of fatty acid, phospholipid, lipopolysacharide)
• no genes for lipid or nucleotide metabolism
• many known genes necc for glycolysis and TCA cylle missing
• only 2 transporter genes retained
• few genes for DNA rep, recomb and repair - helicase (dnaB), primase (dnaG), alpha (dnaE) and epsilon (dnaQ) subunits of DNA pol III, and recA retained

How can Survive?

• biological processes shared by prokaryotes and metazoa
  • compensation for metazoa-like processes of host psyllids (synthesis of non-essential AAs)
• proteins gained multiple functions?
• genes transferred to host nuclear genome?
  • have happened to mitochondria and chloroplasts (endosymbiont to organelle)
  • transfer of genes, acquisition of promoters, evolution of protein translocation

Questions

• have you seen Carsonella divide?
  • tubular structure - have to be short before transfer to next generation of insect - cell div should happen before this
• biased nucleotide usage in leading and lagging strands - see this as well?
• does cell wall of Carsonella have peptidoglycan? - not known