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.

gene prediction

chemostat

cultures

xylose

glucose

yeast genome

evolutionary

protein

l-arabinose

biotin-prototrophy

alcoholic fermentation

Författare

J. F. Nijkamp

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

M. van den Broek

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

E. Datema

Wageningen University and Research Centre

Centre for Biosystems Genomics, Wageningen

Keygene N.V.

S. de Kok

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

Amyris, Inc.

L. Bosman

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

M. A. Luttik

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

P. Daran-Lapujade

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

Wanwipa Vongsangnak

Kemi- och bioteknik, Livsvetenskaper, Systembiologi

Jens B Nielsen

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

Keygene N.V.

Wageningen University and Research Centre

Centre for Biosystems Genomics, Wageningen

M. J. T. Reinders

Netherlands Bioinformatics Center

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

J. Pronk

Kluyver Centre for Genomics of Industrial Fermentation

Delft University of Technology

D. De Ridder

Platform for Green Synthetic Biology

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

Netherlands Bioinformatics Center

J. M. Daran

Platform for Green Synthetic Biology

Delft University of Technology

Kluyver Centre for Genomics of Industrial Fermentation

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