Single Nucleotide Polymorphisms in Industrial Yeasts Chris and Jarlath

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 Score ESequences producing significant alignments: (bits) Value

emb|X02649|SDSTA1 Yeast (S. diastaticus) STA1 5118 0.0gb|M60650|YSCSTA2A S.cerevisiae STA2 5111 0.0gb|M90490|YSCSTA2K Saccharomyces diastaticus 5073 0.0gb|U30626|SCU30626 Saccharomyces cerevisiae 1108 0.0gb|U95022|SCU95022 Saccharomyces cerevisiae Sta3 860 0.0dbj|D00428|YSCSTA1A Yeast glucoamylase (STA1) gene. 628 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

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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.

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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

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