Download MAT - Unifr

The mating
type locus
Chr. III
The MAT locus information
• The MAT locus can encode three regulatory peptides:
- a1 is encoded by the MATa allele
- 1 and 2 are encoded by the MAT allele
• Three regulatory activities: 1, 2, and a1-2.
Sterile mutants can monitor the MAT status
• Mutations have been identified at several loci that produce
a non-mating phenotype, called sterile (STE).
• The sterile mutations fall into three classes:
1. sterility only in a cells
- STE2, the a pheromone receptor
2. sterility only in  cells
- STE3, the  pheromone receptor
3. sterility in both a and  cells
- STE12, the general pheromone-responsive transcription factor
Saccharomyces as a model system
• How do cells generate a mitotically stable, complex,
specific cell type?
 same DNA, but different gene expression states.
• How do cells respond to environmental change or
information from other cells?
 decision-making algorithms.
• How do cells maintain an undifferentiated state “stem cell”?
 non-equivalence of daughter cells at mitosis.
Sterile mutants can monitor the MAT status
• The STE genes can be used to track the effects of
mutations at other loci, such as MAT.
• STE response be measured as fertility/sterility (mating).
• Or, reporter gene constructs made with the
transcriptional response elements from STE genes can
drive the E. coli -galactosidase gene.
• The reporter gene is visualized on screens by the ability
to metabolize XGAL to a blue color, giving blue (gene
active) or white (gene inactive) colonies.
STE12 response
-galactosidase
MAT regulation in  cells
• When the  allele is present at MAT, two genes are
expressed: MAT1 and MAT2,
• Mutations in 1 affect only -specific genes, such as STE3.
• MAT1 mutants prevent normal expression of STE3.
• They do not affect other haploid specific genes or a-specific
genes.
 1 is a positive regulator of -specific genes
• Mutations in 2 allow the expression of a-specific genes,
even in a MAT cell.
 2 is a negative regulator of a-specific genes
• Consequently, in a MAT cell the  genes are expressed
while the a genes are not.
Genetic elements of yeast
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First eukaryotic genome sequenced, April 1996
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Consortium effort, US / EU
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16 well characterized chromosomes
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PFGE separation of chromosomes
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Chr. I (230 kb) <-> chr. IV (1532 kb)
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13 Mb (3.5 x coli)
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6183 ORFs > 99 aa
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72% coding ! (<2% human)
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Average ORF 1450 bp
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Few introns (<4% of ORFs)
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1/3 of ORFs characterized
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1/3 of ORFs have homologies, motifs
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1/3 of ORFs have unknown function
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120 rRNA copies of 9137 bp on chr. XII
–
262 tRNAs
The yeast
genome
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
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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
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No overlap of divergently transcribed ORFs
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Close shared promoters of divergently transcribed ORFs
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Most DNA is ORF

Few and small introns

Genes close to the centromer
chromosome III (cont.)
 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
Genetic nomenclature
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3 letter name with digit, eg. CDC33, CMD1
Italic = genes
Uppercase = wild-type
Loss of function, cdc33
cdc33-1, known allele
Cdc33 protein, Cdc33p
Phenotypes TS+, tsarg2∆, arg2::LEU2
Dominant / recessive
ORF designation YCR49w
The genome duplication
• whole genome duplication 100 mio years ago (polyploidy; Ohno’s
hypothesis, shark)
 Tetraploid -> diploid + many deletions and reciprocal translocations
 55 duplicate regions, 13% of all ORFs, 50% of the genome !
 functions in anaerobiosis ?
Genetic elements of yeast