De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
Journal article, 2012

Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN. PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN. PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN. PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN. PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.

yeast genome

protein

chemostat

gene prediction

alcoholic fermentation

l-arabinose

cultures

evolutionary

xylose

glucose

biotin-prototrophy

Author

J. F. Nijkamp

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

M. van den Broek

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

E. Datema

Wageningen University and Research

Centre for Biosystems Genomics, Wageningen

Keygene N.V.

S. de Kok

Amyris, Inc.

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

L. Bosman

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

M. A. Luttik

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

P. Daran-Lapujade

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

Wanwipa Vongsangnak

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Jens B Nielsen

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

W. H. M. Heijne

DSM Biotechnology Centre

P. Klaassen

DSM Biotechnology Centre

C. J. Paddon

Amyris, Inc.

D. Platt

Amyris, Inc.

P. Kotter

Goethe University Frankfurt

R. C. van Ham

Keygene N.V.

Wageningen University and Research

Centre for Biosystems Genomics, Wageningen

M. J. T. Reinders

Delft University of Technology

Netherlands Bioinformatics Centre - NBIC

Kluyver Centre for Genomics of Industrial Fermentation

J. Pronk

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

D. De Ridder

Netherlands Bioinformatics Centre - NBIC

Platform for Green Synthetic Biology

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

J. M. Daran

Delft University of Technology

Platform for Green Synthetic Biology

Kluyver Centre for Genomics of Industrial Fermentation

Microbial Cell Factories

1475-2859 (ISSN)

Vol. 11 Article Number: 36- 36

Subject Categories

Industrial Biotechnology

Areas of Advance

Life Science Engineering

DOI

10.1186/1475-2859-11-36

More information

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9/6/2018 2