The sterol regulatory element binding protein (SREBP) family of transcription activators are critical regulators of cholesterol and fatty acid homeostasis. We previously demonstrated that human SREBPs bind the CREB-binding protein (CBP)/p300 acetyltransferase KIX domain and recruit activator-recruited co-factor (ARC)/Mediator co-activator complexes through unknown mechanisms. Here we show that SREBPs use the evolutionarily conserved ARC105 (also called MED15) subunit to activate target genes. Structural analysis of the SREBP-binding domain in ARC105 by NMR revealed a three-helix bundle with marked similarity to the CBP/p300 KIX domain. In contrast to SREBPs, the CREB and c-Myb activators do not bind the ARC105 KIX domain, although they interact with the CBP KIX domain, revealing a surprising specificity among structurally related activator-binding domains. The Caenorhabditis elegans SREBP homologue SBP-1 promotes fatty acid homeostasis by regulating the expression of lipogenic enzymes. We found that, like SBP-1, the C. elegans ARC105 homologue MDT-15 is required for fatty acid homeostasis, and show that both SBP-1 and MDT-15 control transcription of genes governing desaturation of stearic acid to oleic acid. Notably, dietary addition of oleic acid significantly rescued various defects of nematodes targeted with RNA interference against sbp-1 and mdt-15, including impaired intestinal fat storage, infertility, decreased size and slow locomotion, suggesting that regulation of oleic acid levels represents a physiologically critical function of SBP-1 and MDT-15. Taken together, our findings demonstrate that ARC105 is a key effector of SREBP-dependent gene regulation and control of lipid homeostasis in metazoans.
The fast Fourier transformation has been the gold standard for transforming data from time to frequency domain in many spectroscopic methods, including NMR. While reliable, it has as a drawback that it requires a grid of uniformly sampled data points. This needs very long measuring times for sampling in multidimensional experiments in all indirect dimensions uniformly and even does not allow reaching optimal evolution times that would match the resolution power of modern high-field instruments. Thus, many alternative sampling and transformation schemes have been proposed. Their common challenges are the suppression of the artifacts due to the non-uniformity of the sampling schedules, the preservation of the relative signal amplitudes, and the computing time needed for spectra reconstruction. Here we present a fast implementation of the Iterative Soft Thresholding approach that can reconstruct high-resolution non-uniformly sampled NMR data up to four dimensions within a few hours and make routine reconstruction of high-resolution NUS 3D and 4D spectra convenient. We include a graphical user interface for generating sampling schedules with the Poisson-Gap method and an estimation of optimal evolution times based on molecular properties. The performance of the approach is demonstrated with the reconstruction of non-uniformly sampled medium and high-resolution 3D and 4D protein spectra acquired with sampling densities as low as 0.8%. The method presented here facilitates acquisition, reconstruction and use of multidimensional NMR spectra at otherwise unreachable spectral resolution in indirect dimensions.
The Fourier transform has been the gold standard to transform data from time to frequency domain in many spectroscopic methods, including NMR. While reliable, it has as a drawback that it requires a grid of uniformely sampled data points, which is not efficient for decaying signals, while it also suffers from artifacts when dealing with non-decaying signals. Over several decades many alternative sampling and transformation schemes have been proposed. Their common problem is that relative signal amplitudes are not well preserved. Here we demonstrate superior performance of a sineweighted Poisson gap distribution sparse sampling scheme, combined with FM reconstruction. While the relative signal amplitudes are well preserved, we also find that the signal-to-noise ratio is enhanced up to four fold per unit of data acquisition time as compared to the traditional linear sampling.The capabilities of modern NMR spectrometers have recently improved dramatically due to higher magnetic field instruments. To utilize the potential resolution of these spectrometers in multi-dimensional experiments various forms of sparse or non-uniform sampling (NUS) were proposed1 , 2. For optimal processing of such spectra we have recently developed the Forward Maximum entropy (FM) reconstruction method3, which was improved and combined with a distillation procedure4.The quality of spectra obtained form NUS depends crucially on the sampling schedules. In the past we have examined various forms of random sampling and realized that the quality of data retrieval depended significantly on the choice of the seed number when using standard Unix random number generators (e.g. drand48). We realized that (1) big gaps in the sampling Gerhard_Wagner@hms.harvard.edu. Supporting Information Available: Four figures comparing signal to peak-noise ratio, effect of order parameters in linear prediction, resolution between linear prediction with Poisson-gap sampling and a graphical representation of the used SPS schedule as well as a source code for C-program generating SPS schedule are available at http://pubs.acs.org/paragonplus/submission/jacsat/. schedule are generally unfavorable, and (2) gaps at the beginning or end of the sampling are worse than in the middle. A third, crucial criterion is: (3) the sampling requires suitably random variation to prevent violation of the Nyquist theorem. NIH Public AccessTo cope with this we have evaluated a sinusoidal weighted Poisson distribution of the gap lengths between sampling points followed by FM reconstruction. To achieve this distribution, we assume an average gap length of λ in the common Fourier grid and a specific gap size k between two acquired data points. Thus, a λ of 0.0 yields uniform sampling, a λ of 1.0, for example, creates a non-uniform schedule of 50% overall sampling density.The overall probability f for a specific gap size k ≥ 0 is assumed by the Poisson distribution:. This would satisfy the criteria (1) and (3). Obviously, no integer values k less than zero is allowed as no negative ga...
A high-precision solution structure of the elastase inhibitor eglin c was determined by NMR and distance geometry calculations. A large set of 947 nuclear Overhauser (NOE) distance constraints was identified, 417 of which were quantified from two-dimensional NOE spectra at short mixing times. In addition, a large number of homonuclear 'H-'H and heteronuclear 'H-"N vicinal coupling constants were used, and constraints on 42 x' and 38 q5 angles were obtained. Structure calculations were carried out using the distance geometry program DG-11. These calculations had a high convergence rate, in that 66 out of 75 calculations converged with maximum residual NOE violations ranging from 0.17 A to 0.47 A. The spread of the structures was characterized with average root mean square deviations ((rmsd)) between the structures and a mean structure. To calculate the (rmsd) unbiased toward any single structure, a new procedure was used for structure alignment. A canonical structure was calculated from the mean distances, and all structures were aligned relative to that. Furthermore, an angular order parameter S was defined and used to characterize the spread of structures in torsion angle space. To obtain an accurate estimate of the precision of the structure, the number of calculations was increased until the (rmsd) and the angular order parameters stabilized. This was achieved after approximately 40 calculations. The structure consists of a well-defined core whose backbone deviates from the canonical structure ca. 0.4 A, a disordered N-terminal heptapeptide whose backbone deviates by 0.8-12 A, and a proteinase-binding loop whose backbone deviates up to 3.0 A. Analysis of the angular order parameters and inspection of the structures indicates that a hinge-bending motion of the binding loop may occur in solution. Secondary structures were analyzed by comparison of dihedral angle patterns. The high precision of the structure allows one to identify subtle differences with four crystal structures of eglin c determined in complexes with proteinases.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
customersupport@researchsolutions.com
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
This site is protected by reCAPTCHA and the Google Privacy Policy and Terms of Service apply.
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.