Strain Engineering Methods and Protocols
Classical methods for microbial strain engineering, used to improve the production of bioproducts, have serious drawbacks and have been found to be unsuitable for complex strain development applications. In Strain Engineering: Methods and Protocols, power
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1. Introduction The yeast Saccharomyces cerevisiae is an attractive organism for design-based strain engineering. This organism, commonly known as baker’s or budding yeast, is an industrially important organism. For example, it is used in the food industry for brewing, winemaking, and production of bread and in the bioenergy industry for production of ethanol. As a consequence, there are well-established large-scale production methods utilizing this organism. In addition, it is also a model eukaryotic genetic organism. Its genome was the first eukaryotic genome completely sequenced and assembled. The yeast genome is also well annotated. The genome sequence is available from the Saccharomyces Genome Database (SGD) (1). SGD also provides information about the genes and their biological functions, and resources and tools for exploring this data (2). In addition, there is substantial knowledge of yeast gene expression from experimental studies. For example, many yeast transcription factors and their binding James A. Williams (ed.), Strain Engineering: Methods and Protocols, Methods in Molecular Biology, vol. 765, DOI 10.1007/978-1-61779-197-0_11, © Springer Science+Business Media, LLC 2011
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sites are known. There is also information about mRNA sequence from a number of genome-wide studies. Integration of information from SGD with data from gene expression studies is a powerful tool for modeling gene expression. The bioinformatics resources for S. cerevisiae are complemented by simple and reliable genetic methods for manipulation of its genome (3–5). There is an extensive collection of genetic resources available for experiments using yeast. These resources include strain collections, plasmids, and antibodies. Together, this combination of tools, resources, and knowledge makes S. cerevisiae a powerful resource for rationale-based strain engineering. This chapter describes how to search for and analyze S. cerevisiae genes using the Saccharomyces Genome Database (SGD), how to identify homologs, tools and strategies for integration of data on gene expression, and the genetic resources available for doing experiments using S. cerevisiae.
2. Materials Broadband Internet connection and Web browser software such as Safari 3.0, Firefox 3.0, Internet Explorer 7, or higher ones.
3. Methods 3.1. Search and Analysis of S. cerevisiae Genes Using the Saccharomyces Genome Database
The Saccharomyces Genome Database (SGD; http://www. yeastgenome.org/) is a public resource with a collection of data and tools for genetic and proteomic analyses of S. cerevisiae. This database provides access to the sequences and annotations for S. cerevisiae. Annotated S. cerevisiae genes can be found using the known standard name, an alias, or systematic name for particular genes to search the database. Alternatively, the database can be queried with keywords such as function, mutant phenotype, and interactions. Yeast homologs for proteins or genes of interest can be found by BLAST searches of S. cerevisiae sequence datasets. Thi
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