Transcript Diversity of Saccharomyces cerevisiae

Diversity of Saccharomyces
cerevisiae
Linda F. Bisson
Department of Viticulture and Enology
University of California, Davis
What Is a Yeast Strain?
Members of the same genus and species
Differ in a measurable way
Differences can be neutral or impact cell
phenotypes
What Is Strain Diversity?
Differences in information that is inherited
Differences in expression of inherited
information
What Causes Strain Diversity?
Differences in sequences of genes on nuclear
chromosomes
Differences in position of gene sequences on
chromosomes
Differences in organelle genomes or composition
Presence of extrachromosomal circular and linear
nucleic acids
Inherited transcriptional states
Inherited protein conformational states
Saccharomyces
Nucleus
Mitochondrion
Secretory
Pathway
Golgi
Vacuole
Endoplasmic reticulum
Daughter Cells Inherit
Full complement of mother cell’s
chromosomes
Organelles: structure and DNA
Proteins, plasmids and expression
patterns
Sources of Inherited Information
Parental lineage
Lateral gene transfer: pick up of genetic
information from environment
Hybrid formation with other related species
or strains
How Does Diversity Arise?
Change in DNA sequence
Change in position on chromosome
Development of prion state
Gene Expression
DNA
mRNA
Protein
Gene Differences: Alleles
If gene sequence differs then protein
sequence will differ
If protein sequence differs, activity may
differ:
– Amount of activity
– Regulation of activity
– Type of activity
– Stability of activity
How Are Gene Sequences Changed?
Oxidative damage of base pairs (reactive
oxygen species derived from normal
metabolism)
Misreading of base pairs (mistakes during
DNA synthesis)
UV light damage to base pairs (failure of
repair mechanisms)
Chemical agent damage (rare event)
How Are Gene Sequences Changed?
Failure of mutation to be recognized and
repaired
Makes cells more fit for their local
environment
No selection against change
How Does Diversity Arise?
Change in DNA sequence
Change in position on chromosome
Development of prion state
What Are Chromosomes?
 Linear pieces of DNA that carry genes, regulatory
regions and spacer regions (Saccharomyces has 16)
 Comprised of centromere (point of attachment to
spindles during division)
 Telomeres (ends) point of attachment to the nuclear
membrane
Centromere
Telomere
Chromosome
Why Is Chromosome Position Important?
Position influences presence/absence of
gene
Position influences level of expression
Position influences amplification of gene
(number of copies)
Impact of Position of Gene
In certain chromosomal areas basal level
of expression is elevated (away from steric
hindrance)
In certain chromosomal areas basal level
of expression is decreased (near
centromeres)
Gene adjacency can impact expression
(interference from nearby genes)
How Does Diversity Arise?
Change in DNA sequence
Change in position on chromosome
Development of prion state
What Are Prions?
Protein-based inheritance
Proteins exist in different conformations
Conformation confers information
Most are stress-induced
Provide molecular memory of stress
(Brown, Lindquist, 2009)
[gar-] Presence of Glucose recognized and signal transduced by Rgt2/Snf3 to Yck1/2 which phosphorylate Std1
and Mth1, thus marking them for degradation. Rgt1 remains free in the cytosol, Hxt3 is still expressed.
[GAR+] In absence of glucose or in [GAR+] Std1 interacts with Pma1, possibly altering Std1 affinity for Rgt1.
They associate as a complex and enter the nucleus, inhibit HXT3 expression, leading to a
36 fold down-regulation of Hxt3! This alternate pathway is maintained as a dominant, heritable prion shift.
Wine Yeast Strain Diversity
Significant diversity exists among wine
strains:
– Presence/absence of genes
– Allele differences (single nucleotide
polymorphisms)
– Chromosomal rearrangement is found
– Differences in prion state are found
What Does Wine Strain Diversity Mean?
Differences in fermentation parameters
Ability to dominate fermentation varies
Aroma compounds vary in type and
concentration
Mouth feel factors differ
Sensitivity to stress varies
First Flight: Saccharomyces
cerevisiae Strains
Glass 1: VL1
Glass 2: Rhone 4600
Glass 3: BC
Glass 4: CKS-102
Glass 5: M2
Glass 6: Zymaflore X16