Regulation of the Sre1 Hypoxic Transcription Factor by Oxygen-Dependent Control of DNA Binding

Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Molecular cell (Impact Factor: 14.02). 10/2011; 44(2):225-34. DOI: 10.1016/j.molcel.2011.08.031
Source: PubMed


Regulation of gene expression plays an integral role in adaptation of cells to hypoxic stress. In mammals, prolyl hydroxylases control levels of the central transcription factor hypoxia inducible factor (HIF) through regulation of HIFα subunit stability. Here, we report that the hydroxylase Ofd1 regulates the Sre1 hypoxic transcription factor in fission yeast by controlling DNA binding. Prolyl hydroxylases require oxygen as a substrate, and the activity of Ofd1 regulates Sre1-dependent transcription. In the presence of oxygen, Ofd1 binds the Sre1 N-terminal transcription factor domain (Sre1N) and inhibits Sre1-dependent transcription by blocking DNA binding. In the absence of oxygen, the inhibitor Nro1 binds Ofd1, thereby releasing Sre1N and leading to activation of genes required for hypoxic growth. In contrast to the HIF system, where proline hydroxylation is essential for regulation, Ofd1 inhibition of Sre1N does not require hydroxylation and, thus, defines a new mechanism for hypoxic gene regulation.

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    • "Conversely, only Ubr1 regulates the oxidative stress response and drug resistance by controlling the levels of active Pap1, a bZIP transcription factor (Kitamura et al., 2011). Ubr1 is also involved in various processes in Sz. pombe, such as nuclear localization of the proteasome (Takeda and Yanagida, 2005), invasive growth (Dodgson et al., 2009), stability of the Sre1 transcription factor under aerobic conditions (Lee et al., 2011) and meiosis and regulation of cell morphology (our unpublished observations). "
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    ABSTRACT: The N-end rule pathway degrades proteins bearing a destabilization-inducing amino acid at the N-terminus. In this proteolytic system, Ubr ubiquitin ligases recognize and ubiquitylate substrates intended for degradation. Schizosaccharomyces pombe has two similar Ubr proteins, Ubr1 and Ubr11. Both proteins have unique roles in various cellular processes, although the ubr1∆ strain shows more severe defects. However, their involvement in the N-end rule pathway is unclear, and even the N-end rule pathway-dependent proteolytic activity has not been demonstrated in Sz. pombe. Here, we show that: (a) Sz. pombe has the N-end rule pathway in which only Ubr11, but not Ubr1, is responsible; and (b) the C-terminal fragment of the meiotic cohesin Rec8 (denoted as Rec8c) generated by separase-mediated cleavage is an endogenous substrate of the N-end rule pathway. Forced overexpression of stable Rec8c was deleterious in mitosis and caused a loss of the mini-chromosome. In unperturbed mitosis without overexpression, the rate of mini-chromosome loss was five-fold higher in the ubr11∆ strain. Since Rec8 is normally produced in meiosis, we examined whether meiosis and sporulation were affected in the ubr11∆ strain. In unperturbed meiosis, chromosome segregation occurred almost normally and viable spores were produced in the ubr11∆ cells, irrespective of the presence of undegraded endogenous Rec8c peptides. Copyright © 2012 John Wiley & Sons, Ltd.
    Preview · Article · Jan 2013 · Yeast
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    • "The HIF system involves enzymes (FIH, PHDs) modifying substrates (HIFα, ARD proteins) and has been modeled as such (Kohn et al., 2004; Qutub and Popel, 2006, 2007; Dayan et al., 2009; Schmierer et al., 2010). In contrast, Ofd1 is known to bind both Sre1N and Nro1 (Lee et al., 2009, 2011) but is not known to enzymatically modify either, and Ofd1 enzyme activity is not required for it to inhibit DNA binding or accelerate degradation of Sre1N (Hughes and Espenshade, 2008; Lee et al., 2011). Accordingly , our model describes the binding and unbinding of Ofd1 without assuming enzymatic activity, and this is sufficient to replicate the observed behavior of the Sre1 pathway (Figure 2). "
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    ABSTRACT: Cells adapt to changes in ambient oxygen by changing their gene expression patterns. In fission yeast, the sterol regulatory element-binding protein Sre1 is proteolytically cleaved under low oxygen, and its N-terminal segment (Sre1N) serves as a hypoxic transcription factor. When oxygen is present, the prolyl hydroxylase Ofd1 down-regulates Sre1N activity in two ways: first, by inhibiting its binding to DNA, and second, by accelerating its degradation. Here we use a mathematical model to assess what each of these two regulatory functions contributes to the hypoxic response of the cell. By disabling individual regulatory functions in the model, which would be difficult in vivo, we found that the Ofd1 function of inhibiting Sre1N binding to DNA is essential for oxygen-dependent Sre1N regulation. The other Ofd1 function of accelerating Sre1N degradation is necessary for the yeast to quickly turn off its hypoxic response when oxygen is restored. In addition, the model predicts that increased Ofd1 production at low oxygen plays an important role in the hypoxic response, and the model indicates that the Ofd1 binding partner Nro1 tunes the response to oxygen. This model quantifies our understanding of a novel oxygen-sensing mechanism that is widely conserved.
    Preview · Article · Jul 2012 · Molecular biology of the cell
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    • "When this complex senses a decrease in ER ergosterol, Sre1 is activated (X A ), and Scp1 is recycled to its unbound state (Espenshade and Hughes, 2007). Active Sre1, in turn, promotes further production of its inactive precursor (Todd et al., 2006), and unbound inactive Sre1 and active Sre1 are degraded (Hughes et al., 2009; Lee et al., 2011). The state variables of N 2 are concentrations of these four chemical species. "
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    ABSTRACT: When part of a biological system cannot be investigated directly by experimentation, we face the problem of structure identification: how can we construct a model for an unknown part of a mostly known system using measurements gathered from its input and output? This problem is especially difficult to solve when the measurements available are noisy and sparse, i.e. widely and unevenly spaced in time, as is common when measuring biological quantities at the cellular level. Here we present a procedure to identify a static nonlinearity embedded between two dynamical systems using noisy, sparse measurements. To reduce the level of error caused by measurement noise, we introduce the concept of weighted-sum predictability. If we make the input and output subsystems weighted-sum predictable and normalize the measurements to their weighted sum, we achieve better noise reduction than through normalizing to a loading control. We then interpolate the normalized measurements to obtain continuous input and output signals, with which we solve directly for the input-output characteristics of the unknown static nonlinearity. We demonstrate the effectiveness of this structure identification procedure by applying it to identify a model for ergosterol sensing by the proteins Sre1 and Scp1 in fission yeast. Simulations with this model produced outputs consistent with experimental observations. The techniques introduced here will provide researchers with a new tool by which biological systems can be identified and characterized.
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