Transcript Single Nucleotide Polymorphisms in Industrial Yeasts

Single Nucleotide Polymorphisms in
Industrial Yeasts
Chris and Jarlath
Introduction
• Industrial yeasts are aneuploid
• Possess multigene families
• Reorganization events
• Selective process?
Hypothesis
• Low selective pressure leads to silent
single nucleotide polymorphisms (SNPs)
in multigene families that are important
to overall fermentation process
Methods
• Identify candidate genes
• Matrix-assisted laser desorption/
ionization time-of-flight mass
spectrometry
(MALDI-TOF MS)
• Design Primers
Genes Selected for
MALDI-TOF MS
• Degradation of starch
• Glucoamylase multigene family
• STA1 (chr.IV)
• STA2 (chr.II)
• STA3 (chr.XIV)
Information Base
Sequences producing significant alignments:
emb|X02649|SDSTA1 Yeast (S. diastaticus) STA1
gb|M60650|YSCSTA2A S.cerevisiae STA2
gb|M90490|YSCSTA2K Saccharomyces diastaticus
gb|U30626|SCU30626 Saccharomyces cerevisiae
gb|U95022|SCU95022 Saccharomyces cerevisiae Sta3
dbj|D00428|YSCSTA1A Yeast glucoamylase (STA1) gene.
Score E
(bits) Value
5118
5111
5073
1108
860
628
0.0
0.0
0.0
0.0
0.0
0.0
Expected Results
• Detection of SNPs
• Are SNPs random or restricted to hot spots?
• Implications for fermentation characteristics?
Conclusions
• Multicopy, multigene families likely to
contain SNPs
• Implications for overall fermentation
process
• Engineered industrial yeast strains
Other Applications
• Genome-wide SNP analysis in humans
e.g. BCRA1
• Pharmacogenomics
References
Hinchcliffe, E. (1992) Developing new strains of yeast. J. Inst. Brew.98:27-31.
Johnston, J. R. (1994) Molecular genetics of yeast. Oxford University Press, Oxford, UK.
Lambrechts, M.G., Pretorius, I.S., Marmur, J. and Sollitti, P. (1995) The S1, S2 and SGA1 ancestral
genes for the STA glucoamylase genes all map to chromosome IX in Saccharomyces cerevisiae. Yeast
30:783-787.
Lyness, C.A., Jones, C.R., and Meaden P.G. (1993) The STA2 and MEL1 genes of Saccharomyces
cerevisiae are idiomorphic. Curr Genet. 23:92-94.
Pretorius, I.S., Lambrechts, M.G., and Marmur, J. (1991) The glucoamylase multigene family in
Saccharomyces cerevisiae var. diastaticus: an overview.Crit. Rev. Biochem. Mol. Biol. 26:53-76.
Pugh, T.A., and Clancy, M.J. (1990) Differential regulation of STA genes of Saccharomyces cerevisiae.
Mol. Gen. Genet. 222:87-96.
Ross, P., Hall, L., Smirnov, I., and Haff, L. (1998) High level multiplex genotyping by MALDI-TOF
mass spectrometry. Nat. Biotech. 16:1347-1351.
http://www.proteome.com
http://morgat.ugs.es/microbsem/v1203-96/benitez.html