Oscillation patterns in negative feedback loops

Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein concentrations or gene expression levels are related to the presence of at least one negative feedback loop in the regulatory network. Here we study the dynamics of a very general class of negative feedback loops. Our main result is that in these systems the sequence of maxima and minima of the concentrations is uniquely determined by the topology of the loop and the activating/repressing nature of the interaction between pairs of variables. This allows us to devise an algorithm to reconstruct the topology of oscillating negative feedback loops from their time series; this method applies even when some variables are missing from the data set, or if the time series shows transients, like damped oscillations. We illustrate the relevance and the limits of validity of our method with three examples: p53-Mdm2 oscillations, circadian gene expression in cyanobacteria, and cyclic binding of cofactors at the estrogen-sensitive pS2 promoter.Comment: 10 pages, 8 figure

Delineation of a unique protein-protein interaction site on the surface of the estrogen receptor

Recent studies have identified a series of estrogen receptor (ER)interacting peptides that recognize sites that are distinct from the classic coregulator recruitment (AF2) region. Here, we report the structural and functional characterization of an ER alpha-specific peptide that binds to the liganded receptor in an AF2-independent manner. The 2-angstrom crystal structure of the ER/peptide complex reveals a binding site that is centered on a shallow depression on the beta-hairpin face of the ligand-binding domain. The peptide binds in an unusual extended conformation and makes multiple contacts with the ligand-binding domain. The location and architecture of the binding site provides an insight into the peptide's ER subtype specificity and ligand interaction preferences. In vivo, an engineered coactivator containing the peptide motif is able to strongly enhance the transcriptional activity of liganded ER alpha, particularly in the presence of 4-hydroxytamoxifen. Furthermore, disruption of this binding surface alters ER's response to the coregulator TIF2. Together, these results indicate that this previously unknown interaction site represents a bona fide control surface involved in regulating receptor activity

Coactivator AIB1 links estrogen receptor transcriptional activity and stability

Agonist-mediated degradation of estrogen receptor α (ERα) has been associated with its transcriptional activity. However, the mechanism by which ERα is targeted for degradation and whether there is a direct functional link between ERα stability and ERα-mediated transactivation have not been elucidated. Here we provide evidence that the p160 coactivator, AIB1, uniquely mediates agonist-induced, but not antagonist-induced, ERα degradation. We show that AIB1 recruitment by ERα is not only necessary but also sufficient to promote degradation. Suppression of AIB1 levels leads to ERα stabilization in the presence of 17β-estradiol and, despite increased ERα levels, reduced recruitment of ERα to endogenous target gene promoters. In addition, association of RNA polymerase II with ERα target promoters is lost when AIB1 is suppressed, leading to inhibition of target gene transcription. AIB1 thus plays a dual role in regulating ERα activity, one in recruiting transcription factors including other coactivators involved in gene activation and the other in regulating ERα protein degradation mediated by the ubiquitin–proteosome machinery

HSP90/70 chaperones are required for rapid nucleosome removal upon induction of the GAL genes of yeast

Induction of transcription of the GAL genes of yeast by galactose is a multistep process: Galactose frees the activator Gal4 of its inhibitor, Gal80, allowing Gal4 to recruit proteins required to transcribe the GAL genes. Here, we show that deletion of components of either the HSP90 or the HSP70 chaperone machinery delays this induction. This delay remains when the galactose-signaling pathway is bypassed, and it cannot be explained by a chaperone requirement for DNA binding by Gal4. Removal of promoter-bound nucleosomes is delayed in a chaperone mutant, and our findings suggest an involvement of HSP90 and HSP70 in this early step in gene induction