Molecular responses of saccharomyces cerevisiae to near-zero

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Titel: Molecular responses of saccharomyces cerevisiae to near-zero growth rates
Auteur: M.M.M. Bisschops
ISBN: 9789461866011
Conditie: Als nieuw

General Introduction Saccharomyces cerevisiae: from industrial workhorse.… The application of yeast by humankind dates back millennta, as illustrated by ancient Egvphan drawings of leavening of bread and beer production (Fig. 1.1 A), and references in the Bible to the use of yeast (Exodus X11:34;39). Saccharomyces cerevístae is the most used veast m baking, hence rts common name baker's yeast. Leavening of dough is not the only application of yeast that dates back to ancient times, as indicated by its binomial name and other common name, brewer’s yeast. The excellent fermentative capacities of S, cerevisiae and other, closely related Saccharomyces species are also used for production of alcoholic beverages such as wine and beer. This longstanding relation between humans and yeast (Fig. 1.0 has, in recent years, expanded beyond food biotechnology. Nowadays, S. cerevisiae is extensively used in ‘industrìal biotechnology’: the industrial production of a wide variety of chemicals from renewable feedstock, with the aid of microbes and enzymes. Ethanol, a natural product of S. cerevisiae and an alternative transport fuel, is currently the single largest product in industrial biotechnology (85 billion liters in 2011,(Caspeta et al, 2013). However, ethanol is only one example of a large-scale product of industrial yeast biotechnology. Through metabolic engineering, S. cerevisiae strains have been constructed that can produce bulk-chemicals such as organic acids, glycerol and the hydrocarbon farnesene (Asadollahi et al, 2010; Cordier et al., 2007; Curran et al., 2013; Kirby and Keasling, 2008; Otero et al., 2013; Zelle et al., 2008), fine chemicals such as a key precursor for the anti-malaria drug artimisinin (Paddon et al., 2013) and medicinally or industrially relevant peptides and proteins, such as insulin and amylase (Liu et al., 2014; Nielsen, 2013; Thim et al., 1987). The long-standing relationship between yeast and man (A) Yeast was already employed in ancient times as demonstrated by drawings on the Mastaba Tomb of Ty depicting the production of bread and beer, dated ca. 2500 BC (Image courtesy of Dr. Benderitter, copyright by www.osirisnet.net). (B) Millennia later, in 1680, Anthonie van Leeuwenhoek was the first to observe yeast cells, although he was not aware of their true nature. A drawing from his observations in a letter to the Royal Society of London (van Leeuwenhoek, 1684). (C) Phase contrast-micrograph of budding yeast Saccharomyces cerevisiae, Scale bar represents 5 mu m. Due to the long use of S. cerevisiae in several biotechnological processes and tha ease of its cultivation, this unicellular fungus is now one of the mast and. best-st 1d er eukarotic organisms. Although its physiology under various conditions, including proces; | and laboratory conditions, such as different temperatures and levels of nutrients, has been subject of study already for decades (Eaton and Klein, 1954; McManus, 1954; Ster, 1933 a turning point in yeast research took place in 1996. In that year, the full genome sequence of the laboratory strain S288C, the first full eukaryotic genome sequence, was publisheg (Goffeau et al, 1996). This milestone initiated a new era of systematic annotation of gene functions, mostly by deletion and overexpression studies. Progress in this area required and stimulated the development of new tools for analyzing and ‘editing’ the yeast genome. Today, the already rìch tool-set for genetic modification of S. cerevisiae continues to expand at an enormous rate. Examples include the use of new, recyclable markers for gene deletion (Solis-Escalante et al., 2013) and cloning of large genetic constructs using a procedure called Gibson Assembly (Gibson, 2012) or improvements thereof (Kuijpers et al, 2013, While these techniques are being implemented, new and spectacular options, such as the CRISPR-CAS system, make an entry into yeast molecular biotechnology (DiCarlo et al, 2013). These developments have led some authors to propose that S. cerevisiae may soan take over the role of the bacterium Escherichia coli as the universal laboratory work horse in molecular genetics research (Curtis et al., 2013). In addition to this strong development of what nowadays is denoted as synthetic biology, i.e. the design or re-design of biological parts for useful purposes, the availability of the genome sequence also initiated the ‘omics’ era. A vast set of technologies has been developed to generate information on different levels of yeast biology, examples are genomics, transcriptomics, proteomics and metabolomics data (Kandpal et al., 2009). Integration of the resulting, sometimes large datasets, allows the dissection of the different regulatory levels and more thorough understanding of the entire system. This integral, model-based approach to biology has been defined as systems biology (Castrillo and Oliver, 2011; Kowald and Wierling, 2011; Snyder and Gallagher, 2009). Integration of synthetic and system biology approaches holds great potential for the optimization of existing industrial applications of S. cerevisiae. The aforementioned production of fuel ethanol forms a perfect example of this, as metabolic engineering has led to reduction of by-product formation (Guadalupe-Medina et al, 2014), improvement of product yield (Basso et al., 2011b) and expansion of the substrate range of S. cerevisiae to include C5-sugars (Farwick et al., 2014; Kuyper et al., 2005; Wisselink et al., 2007). The latter development was an important step in enabling the use of non-food agricultural residues as feedstock for bioethanol production, a process that is currently being implemented at full industrial scale (POET-DSM, 2014). In addition to improving its current industria! applications, the increasing genetic accessibility of S. cerevisiae has played a major role in expanding its product portfolio. to eukaryotic model organism The same characteristics - ease of cultivation and genetic manipulation - that contributed to its strong reputation as an industrial workhorse, have also firmly established 5. cerevisiae as a model eukaryote for fundamental research. Many cellular processes are strongly conserved among eukanotes, enabling the use of yeast as a model organism to study such processes. Strong functional homologies between 5. cerevisiae and metazoans have even led to situation in which the discovery of fundamental biological mechanisms in yeast was followed by their detection in higher eukaryotes. A clear example ís provided by the experiments with S. cerevisiae and the fission yeast Schizosaccharomyces pombe that led to elucidation of key regulators ìn the eukaryotic cell cycle (Fig. 1.2), the cascade of events that cells undergo prior to and during cell division (Nurse et al, 1998). In 2001, the importance of these discoveries was underlined with the Nobel Prize in Physiology or Medicine 2001 (Pulverer, 2001). In addition to cell cycle control, large parts of other signaling cascades are also conserved between yeast and mammals (Smets et al, 2010). Examples include the Target Of Rapamycin (TOR) signaling pathway (De Virgilio and Loewith, 2006), AMP-activated/Snf1 protein kinases (Hardie 2007) and cAMP-activated protein kinase A (PKA), and Sch9/PKB (Geyskens et al 2001). Although the actual inducing signals may differ between organisms (De Virgilio and Loewith, 2006), yeast has played and continues to play a central role in studies on eukaryotic signal transduction pathways (Smets et al., 2010). Not only the signaling pathways, but also many of the processes that they control are conserved. An example is autophagy, the process that turns over organelles and proteins. This strongly conserved pathway is controlled by TOR and PKA and plays an important role in tumor suppression and protein aggregate clearance in humans (Stephan et al, 2010). While several cellular processes in eukaryotes were first discovered and studied in yeast, programmed cell death or apoptosis forms a notable exception. Apoptosis was long considered a purely metazoan mechanism until, in 1997, a mutant yeast strain was described to exhibit several hallmarks of apoptosis during cell death (Madeo et af, 1997; Madeo et al., 2002). Since then, yeast orthologs of key proteins involved in metazoan apoptosis have been identified. Currently, several research groups use $. cerevisiae to study apoptotic processes and inducers (Côrte-Real and Madeo, 2013; Madeo et al., 2004). Not only programmed cell death, but also cell division control and DNA repair are crucial processes for maintenance of healthy human tissues and alterations. Alterations in these processes can lead to transformation of normal cells into malignant tumor cells, ie. carcinogenesis (Hanahan and Weinberg, 2000). Due to the homology of these processes between metazoans and 5. cerevisiae, the latter can be used as an inexpensive, easy-to-cultivate model organism for studying specific hallmarks of carcinogenesis. The ease of cultivation also allows for fast screening and studying of responses, i.e. sensitivity or resistance of specific mutants to anti-cancer treatments and novel compounds

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