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