Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes

Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, L3.124, Dallas, TX 75390, USA.
Science (Impact Factor: 31.48). 12/2005; 310(5751):1152-8. DOI: 10.1126/science.1120499
Source: PubMed

ABSTRACT Budding yeast grown under continuous, nutrient-limited conditions exhibit robust, highly periodic cycles in the form of respiratory bursts. Microarray studies reveal that over half of the yeast genome is expressed periodically during these metabolic cycles. Genes encoding proteins having a common function exhibit similar temporal expression patterns, and genes specifying functions associated with energy and metabolism tend to be expressed with exceptionally robust periodicity. Essential cellular and metabolic events occur in synchrony with the metabolic cycle, demonstrating that key processes in a simple eukaryotic cell are compartmentalized in time.

Download full-text


Available from: Andrzej Kudlicki, Jan 22, 2014
1 Follower
  • Source
    • ". NF-APIN (Xiao et al., 2013), APPIN (Wang et al., 2013), TC-PIN (Tang et al., 2011), TSN-PCD (Li et al., 2012) and PCD-GED methods comparison (considering their best parameter values) based on DIP(Xenarios, Salwinski et al., 2002), PPI network and GED1 (Tu, Kudlicki et al., 2005), gene expression data. Best parameters settings for PCD- GED are α ¼0.8, β ¼0.3. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Detection of protein complexes from protein-protein interaction (PPI) networks is essential to understand the function of cell machinery. However, available PPIs are static, and cannot reflect the dynamics inherent in real networks. Our method uses time series gene expression data in addition to PPI networks to detect protein complexes. The proposed method generates a series of time-sequenced subnetworks (TSN) according to the time that the interactions are activated. It finds, from each TSN, the protein complexes by employing the weighted clustering coefficient and maximal weighted density concepts. The final set of detected protein complexes are obtained from union of all complexes from different subnetworks. Our findings suggest that by employing these considerations can produce far better results in protein complex detection problem. Copyright © 2015. Published by Elsevier Ltd.
    Journal of Theoretical Biology 08/2015; 378:31-38. DOI:10.1016/j.jtbi.2015.04.020 · 2.30 Impact Factor
  • Source
    • "In some cases they are not observed, might be due to the fact that they were overlooked, or masked by large experimental errors or missed due to the inadequate range of variation of the variables being measured. Apart from these factors, oscillations are observed in different types of complex systems [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: In this communication, the approach of phenomenological universalities of growth are considered to describe the behaviour of a system showing oscillatory growth. Two phenomenological classes are proposed to consider the behaviour of a system in which oscillation of a property may be observed. One of them is showing oscillatory nature with constant amplitude and the other represents oscillatory nature with a change in amplitude. The term responsible for damping in the proposed class is also been identified. The variations in the nature of oscillation with dependent parameters are studied in detail. In this connection, the variation of a specific growth rate is also been considered. The significance of presence and absence of each term involved in phenomenological description are also taken into consideration in the present communication. These proposed classes might be useful for the experimentalists to extract characteristic features from the dataset and to develop a suitable model consistent with their data set.
  • Source
    • "The biological function of time-of-day-dependent stem cell proliferation remains unexplained (Gaddameedhi et al., 2011; Geyfman et al., 2012; Janich et al., 2013; Plikus et al., 2013). One hypothesis is that organisms have evolved to temporally separate DNA synthesis from metabolic functions such as oxidative phosphorylation as a protective mechanism, as has been suggested for metabolic cycles in yeast (Tu et al., 2005). Energy production through oxidative phosphorylation creates high levels of reactive oxygen species (ROS), which damage DNA, leading to cellular toxicity, cancer, and aging. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Through the use of bulk measurements in metabolic organs, the circadian clock was shown to play roles in organismal energy homeostasis. However, the relationship between metabolic and circadian oscillations has not been studied in vivo at a single-cell level. Also, it is unknown whether the circadian clock controls metabolism in stem cells. We used a sensitive, noninvasive method to detect metabolic oscillations and circadian phase within epidermal stem cells in live mice at the single-cell level. We observe a higher NADH/NAD+ ratio, reflecting an increased glycolysis/oxidative phosphorylation ratio during the night compared to the day. Furthermore, we demonstrate that single-cell metabolic heterogeneity within the basal cell layer correlates with the circadian clock and that diurnal fluctuations in NADH/NAD+ ratio are Bmal1 dependent. Our data show that, in proliferating stem cells, the circadian clock coordinates activities of oxidative phosphorylation and glycolysis with DNA synthesis, perhaps as a protective mechanism against genotoxicity. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Cell Reports 12/2014; 10(1). DOI:10.1016/j.celrep.2014.12.007 · 8.36 Impact Factor
Show more