Download Genetic elements of yeast

Genetic elements of yeast
Yeast - Genome Overview
Chromosome number
Total length (kb)
XVI
13,392
ORFs (n)
6317
Known Proteins
3289
Introns (n)
231
tRNA genes (n)
276
snRNA genes (n)
80
Yeast genes and functions
Subcellular localization of proteins
Yeast genes and functions
–  First eukaryotic genome sequenced, April 1996
–  Consortium effort, US / EU
–  16 well characterized chromosomes
–  PFGE separation of chromosomes
–  Chr. I (230 kb) <-> chr. IV (1532 kb)
–  13 Mb (3.5 x coli)
–  6183 ORFs > 99 aa
–  72% coding ! (<2% human)
–  Average ORF 1450 bp
–  Few introns (<4% of ORFs)
–  1/3 of ORFs characterized
–  1/3 of ORFs have homologies, motifs
–  1/3 of ORFs have unknown function
–  120 rRNA copies of 9137 bp on chr. XII
–  262 tRNAs
The yeast
genome
Only a very small percentage of
genes are essential
•  50% of all genes have no DETECTABLE
phenotype when disrupted.
•  Possible reasons?
Essential genes
•  About 1000 of the 6100 ORF are essential genes
•  Test for essential gene:
–  Gene disruption in diploid
–  Sporulation and tetrad dissection
–  2 viable 2 dead spores
•  Many genes would be essential in nature that are
dispensable on laboratory rich media
–  eg. carbon source
–  Temperature
–  Salts...
The genetic and physical map of
chromosome III
•  Both strands contain about the same number of ORFs
•  Often several ORFs on one strand not interrupted by
ORFs on the other strand
•  Very few overlapping ORFs on the same strand
•  No overlap of divergently transcribed ORFs
•  Close shared promoters of divergently transcribed ORFs
•  Most DNA is ORF
•  Few and small introns
•  Genes close to the centromer
•  Dispersed tRNAs (270 / genome)
•  Ty elements and there remnants are 5’ to tRNAs
•  Dispersed snRNAs and snoRNAs
•  3kb / cM (200x less than in humans)
•  rRNA on Chr XII, no recombination, nucleolus
remains associated with the chromosome during
meiosis
•  Moderate suppression of recombination around
centromeres
•  Genome 4300 cM -> 45 x 2 crossovers per meiosis
The genome duplication
•  whole genome duplication 100 mio years ago
(polyploidy; Ohno’s hypothesis / 2R, shark)
•  Tetraploid -> diploid + many deletions and
reciprocal translocations
•  55 duplicate regions, 13% of all ORFs, 50% of
the genome !
•  functions in anaerobiosis ?
The mitochondrial genome
•  Nucleoid, 75kb, 10 proteins, tRNA, rRNA, „optional“ introns
•  Relaxed codon usage
•  Variation in the code, trp, met, thr
Mitochondrial genes
•  Mitochondrial function required to grow on nonfermentable carbon sources, lactate, glycerol, ethanol
•  Mutations in nuclear genes that affect mito function: PET
+ -> pet•  Mutations in mitochondrial DNA
•  Wild-type, ρ+
•  Large deletions, ρ•  Loss of mito genome, ρ°
•  Single site mutations, ρ+, mit- (normal translation)
•  Single site mutations, ρ+, syn- (deficient in translation)
•  Mito mutations give 4:0 segregation
Segregation of
mitochondrial
genes
Mitochondrial
fusion and fission
Non-Mendelian Determinants
•  2 µm plasmid, mitochondrial genes, RNA viruses,
•  + prions, cytoplasmatic inheritance
–  ψ+ (Psi+), ψ -, Sup35p (functions as translational
terminator)
–  [URE3], [ure3], Ure2p, deficiency in ureidosuccinate
utilization
Mammalian Prion Diseases
•  Mad cow disease, Creutzfeldt-Jacob Disease,
Scrapie
•  Aggregated (prion forms of PrPC -> PrPSc)
Prion propagation in yeast
Figure 1- Monitoring the [PSI+] prion by a simple colour assay. The
presence of the prion allows translation readthrough of an aberrant stop
codon in the ADE2 gene. The consequence of this is the prion containing
cells are white and cells lacking prions are red.
Prion propagation in yeast