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.
l-arabinose
glucose
xylose
cultures
protein
evolutionary
yeast genome
alcoholic fermentation
chemostat
biotin-prototrophy
gene prediction
Author
J. F. Nijkamp
Delft University of Technology
Kluyver Centre for Genomics of Industrial Fermentation
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
Amyris, Inc.
Delft University of Technology
Kluyver Centre for Genomics of Industrial Fermentation
L. Bosman
Delft University of Technology
Kluyver Centre for Genomics of Industrial Fermentation
M. A. Luttik
Delft University of Technology
Kluyver Centre for Genomics of Industrial Fermentation
P. Daran-Lapujade
Kluyver Centre for Genomics of Industrial Fermentation
Delft University of Technology
Wanwipa Vongsangnak
Chalmers, Chemical and Biological Engineering, Life Sciences
Jens B Nielsen
Chalmers, Chemical and Biological Engineering, Life Sciences
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 Universitat Frankfurt am Main
R. C. van Ham
Centre for Biosystems Genomics, Wageningen
Wageningen University and Research Centre
Keygene N.V.
M. J. T. Reinders
Delft University of Technology
Kluyver Centre for Genomics of Industrial Fermentation
Netherlands Bioinformatics Center
J. Pronk
Delft University of Technology
Kluyver Centre for Genomics of Industrial Fermentation
D. De Ridder
Delft University of Technology
Netherlands Bioinformatics Center
Kluyver Centre for Genomics of Industrial Fermentation
Platform for Green Synthetic Biology
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- 36Subject Categories (SSIF 2011)
Industrial Biotechnology
Areas of Advance
Life Science Engineering (2010-2018)
DOI
10.1186/1475-2859-11-36