De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
Artikel i vetenskaplig tidskrift, 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.

biotin-prototrophy

yeast genome

xylose

l-arabinose

protein

glucose

evolutionary

alcoholic fermentation

cultures

gene prediction

chemostat

Författare

J. F. Nijkamp

Kluyver Centre for Genomics of Industrial Fermentation

Technische Universiteit Delft

M. van den Broek

Kluyver Centre for Genomics of Industrial Fermentation

Technische Universiteit Delft

E. Datema

Keygene N.V.

Centre for Biosystems Genomics, Wageningen

Wageningen University and Research Centre

S. de Kok

Amyris, Inc.

Kluyver Centre for Genomics of Industrial Fermentation

Technische Universiteit Delft

L. Bosman

Technische Universiteit Delft

Kluyver Centre for Genomics of Industrial Fermentation

M. A. Luttik

Technische Universiteit Delft

Kluyver Centre for Genomics of Industrial Fermentation

P. Daran-Lapujade

Technische Universiteit Delft

Kluyver Centre for Genomics of Industrial Fermentation

Wanwipa Vongsangnak

Chalmers, Kemi- och bioteknik, Livsvetenskaper, Systembiologi

Jens B Nielsen

Chalmers, Kemi- och bioteknik, Livsvetenskaper, Systembiologi

W. H. M. Heijne

DSM Biotechnology Center

P. Klaassen

DSM Biotechnology Center

C. J. Paddon

Amyris, Inc.

D. Platt

Amyris, Inc.

P. Kotter

Johann Wolfgang Goethe Universität Frankfurt am Main

R. C. van Ham

Wageningen University and Research Centre

Centre for Biosystems Genomics, Wageningen

Keygene N.V.

M. J. T. Reinders

Technische Universiteit Delft

Kluyver Centre for Genomics of Industrial Fermentation

Netherlands Bioinformatics Center

J. Pronk

Technische Universiteit Delft

Kluyver Centre for Genomics of Industrial Fermentation

D. De Ridder

Netherlands Bioinformatics Center

Platform for Green Synthetic Biology

Kluyver Centre for Genomics of Industrial Fermentation

Technische Universiteit Delft

J. M. Daran

Kluyver Centre for Genomics of Industrial Fermentation

Platform for Green Synthetic Biology

Technische Universiteit Delft

Microbial Cell Factories

1475-2859 (ISSN)

Vol. 11 Article Number: 36- 36

Ämneskategorier

Industriell bioteknik

Styrkeområden

Livsvetenskaper och teknik

DOI

10.1186/1475-2859-11-36