Article

Growth Landscape Formed by Perception and Import of Glucose in Yeast

Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Nature (Impact Factor: 42.35). 12/2009; 462(7275):875-9. DOI: 10.1038/nature08653
Source: PubMed

ABSTRACT An important challenge in systems biology is to quantitatively describe microbial growth using a few measurable parameters that capture the essence of this complex phenomenon. Two key events at the cell membrane-extracellular glucose sensing and uptake-initiate the budding yeast's growth on glucose. However, conventional growth models focus almost exclusively on glucose uptake. Here we present results from growth-rate experiments that cannot be explained by focusing on glucose uptake alone. By imposing a glucose uptake rate independent of the sensed extracellular glucose level, we show that despite increasing both the sensed glucose concentration and uptake rate, the cell's growth rate can decrease or even approach zero. We resolve this puzzle by showing that the interaction between glucose perception and import, not their individual actions, determines the central features of growth, and characterize this interaction using a quantitative model. Disrupting this interaction by knocking out two key glucose sensors significantly changes the cell's growth rate, yet uptake rates are unchanged. This is due to a decrease in burden that glucose perception places on the cells. Our work shows that glucose perception and import are separate and pivotal modules of yeast growth, the interaction of which can be precisely tuned and measured.

Download full-text

Full-text

Available from: Alexander van Oudenaarden, Jul 30, 2015
0 Followers
 · 
92 Views
  • Source
    • "The presence of xylose and glucose greatly improved 158 anaerobic fermentation of xylodextrins ( Figure 5 and Figure 5—figure supplement 1 159 and Figure 5—figure supplement 2 ) , indicating that metabolic sensing in S . cerevisiae 160 with the complete xylodextrin pathway may require additional tuning ( Youk and van 161 Oudenaarden 2009 ) for optimal xylodextrin fermentation . Notably , we observed that the 162 XR / XDH pathway produced much less xylitol when xylodextrins were used in 163 fermentations than from xylose ( Figure 5 and Figure 5 – figure supplement 2B ) . "
    [Show abstract] [Hide abstract]
    ABSTRACT: eLife digest Plants can be used to make ‘biofuels’, which are more sustainable alternatives to traditional fuels made from petroleum. Unfortunately, most biofuels are currently made from simple sugars or starch extracted from parts of plants that we also use for food, such as the grains of cereal crops. Making biofuels from the parts of the plant that are not used for food—for example, the stems or leaves—would enable us to avoid a trade-off between food and fuel production. However, most of the sugars in these parts of the plant are locked away in the form of large, complex carbohydrates called cellulose and hemicellulose, which form the rigid cell wall surrounding each plant cell. Currently, the industrial processes that can be used to make biofuels from plant cell walls are expensive and use a lot of energy. They involve heating or chemically treating the plant material to release the cellulose and hemicellulose. Then, large quantities of enzymes are added to break these carbohydrates down into simple sugars that can then be converted into alcohol (a biofuel) by yeast. Fungi may be able to provide us with a better solution. Many species are able to grow on plants because they can break down cellulose and hemicellulose into simple sugars they can use for energy. If the genes involved in this process could be identified and inserted into yeast it may provide a new, cheaper method to make biofuels from plant cell walls. To address this challenge, Li et al. studied how the fungus Neurospora crassa breaks down hemicellulose. This study identified a protein that can transport molecules of xylodextrin—which is found in hemicellulose—into the cells of the fungus, and two enzymes that break down the xylodextrin to make simple sugars, using a previously unknown chemical intermediate. When Li et al. inserted the genes that make the transport protein and the enzymes into yeast, the yeast were able to use plant cell wall material to make simple sugars and convert these to alcohol. The yeast used more of the xylodextrin when they were grown with an additional source of energy, such as the sugars glucose or sucrose. Li et al.'s findings suggest that giving yeast the ability to break down hemicellulose has the potential to improve the efficiency of biofuel production. The next challenge will be to improve the process so that the yeast can convert the xylodextrin and simple sugars more rapidly. DOI: http://dx.doi.org/10.7554/eLife.05896.002
    eLife Sciences 02/2015; 4. DOI:10.7554/eLife.05896 · 8.52 Impact Factor
  • Source
    • "To our knowledge, all previous reports were confined either to nonexponentially growing cultures or to a single exogenous protein or to the last generation of batch growth when growth rate, to the extent it can estimated, was declining. In contrast, we observed pervasive dynamics during the whole span (including early and middle phases) of batch growth, including during phases that are considered to represent a single well-defined steady state (Newman et al., 2006; Belle et al., 2006; Pelechano and Pé rez-Ortín, 2010; Schwanhä usser et al., 2011; Heyland et al., 2009; Youk and van Oudenaarden, 2009; Boisvert et al., 2012). Our data demonstrate that, at least for two very different growth conditions, exponentially growing cultures can change their metabolism continuously, prompting the investigation of metabolic and cell-signaling dynamics even in conditions previously assumed to represent steady states (Silverman et al., 2010; Slavov et al., 2011, 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Fermentating glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting additional physiological roles for aerobic glycolysis. We investigated such roles in yeast batch cultures by quantifying O2 consumption, CO2 production, amino acids, mRNAs, proteins, posttranslational modifications, and stress sensitivity in the course of nine doublings at constant rate. During this course, the cells support a constant biomass-production rate with decreasing rates of respiration and ATP production but also decrease their stress resistance. As the respiration rate decreases, so do the levels of enzymes catalyzing rate-determining reactions of the tricarboxylic-acid cycle (providing NADH for respiration) and of mitochondrial folate-mediated NADPH production (required for oxidative defense). The findings demonstrate that exponential growth can represent not a single metabolic/physiological state but a continuum of changing states and that aerobic glycolysis can reduce the energy demands associated with respiratory metabolism and stress survival.
    Cell Reports 04/2014; 7(3). DOI:10.1016/j.celrep.2014.03.057 · 7.21 Impact Factor
  • Source
    • "In the budding yeast Saccharomyces cerevisiae, such a regulatory step takes place in the unbudded, G1 phase of the cell cycle, at a regulatory area termed START (Pringle and Hartwell, 1981). At START cellular parameters (i.e., the metabolic state) and environmental factors, including nutrient availability (Lord and Wheals, 1980; Vanoni et al., 1983; Searle and Sanchez, 2004; Youk and van Oudenaarden, 2009; Busti et al., 2010; Gutteridge et al., 2010) and mating pheromones (Cross and McKinney, 1992), are integrated and contribute to the cells decision to divide, or to differentiate in a resting state (Alberghina et al., 2012). In higher eukaryotes, the Restriction Point (Pardee, 1974) similarly integrates environmental signals, notably including growth factors, and its dysregulation results in abnormal cell cycle and development of proliferative disorders (Pardee, 1989; Sherr, 1996). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Cell growth and proliferation require a complex series of tight-regulated and well-orchestrated events. Accordingly, proteins governing such events are evolutionary conserved, even among distant organisms. By contrast, it is more singular the case of "core functions" exerted by functional analogous proteins that are not homologous and do not share any kind of structural similarity. This is the case of proteins regulating the G1/S transition in higher eukaryotes-i.e., the retinoblastoma (Rb) tumor suppressor Rb-and budding yeast, i.e., Whi5. The interaction landscape of Rb and Whi5 is quite large, with more than one hundred proteins interacting either genetically or physically with each protein. The Whi5 interactome has been used to construct a concept map of Whi5 function and regulation. Comparison of physical and genetic interactors of Rb and Whi5 allows highlighting a significant core of conserved, common functionalities associated with the interactors indicating that structure and function of the network-rather than individual proteins-are conserved during evolution. A combined bioinformatics and biochemical approach has shown that the whole Whi5 protein is highly disordered, except for a small region containing the protein family signature. The comparison with Whi5 homologs from Saccharomycetales has prompted the hypothesis of a modular organization of structural disorder, with most evolutionary conserved regions alternating with highly variable ones. The finding of a consensus sequence points to the conservation of a specific phosphorylation rhythm along with two disordered sequence motifs, probably acting as phosphorylation-dependent seeds in Whi5 folding/unfolding. Thus, the widely disordered Whi5 appears to act as a hierarchical, "date hub" that has evolutionary assayed an original way of modular organization before being supplanted by the globular, multi-domain structured Rb, more suitable to cover the role of a "party hub".
    Frontiers in Physiology 01/2013; 4:315. DOI:10.3389/fphys.2013.00315 · 3.50 Impact Factor
Show more