Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is ...conserved from yeast to humans. We report here cryo-EM structures of Dot1L bound to ubiquitinated nucleosome that show how H2B-Ub stimulates Dot1L activity and reveal a role for the histone H4 tail in positioning Dot1L. We find that contacts mediated by Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to insert into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.
Display omitted
•Cryo-EM structures of Dot1L methyltransferase bound to H2B-ubiquitinated nucleosomes•Dot1L bound in poised and active states contacts the ubiquitin I36 hydrophobic patch•The tail of histone H4 binds in a cleft in Dot1L.•A conformational change is induced in histone H3 that enables Dot1L to access H3K79
Unanticipated conformational plasticity in the globular core of histone H3 underlies cross-talk between histone modifications.
Atmospheric carbon monoxide (CO) distributions are controlled by anthropogenic emissions, biomass burning, transport and oxidation by reaction with the hydroxyl radical (OH). Quantifying trends in CO ...is therefore important for understanding changes related to all of these contributions. Here we present a comprehensive record of satellite observations from 2000 through 2011 of total column CO using the available measurements from nadir-viewing thermal infrared instruments: MOPITT, AIRS, TES and IASI. We examine trends for CO in the Northern and Southern Hemispheres along with regional trends for Eastern China, Eastern USA, Europe and India. We find that all the satellite observations are consistent with a modest decreasing trend similar to -1 % yr super(-1) in total column CO over the Northern Hemisphere for this time period and a less significant, but still decreasing trend in the Southern Hemisphere. Although decreasing trends in the United States and Europe have been observed from surface CO measurements, we also find a decrease in CO over E. China that, to our knowledge, has not been reported previously. Some of the interannual variability in the observations can be explained by global fire emissions, but the overall decrease needs further study to understand the implications for changes in anthropogenic emissions.
Polyubiquitin chains target protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 to allow efficient substrate degradation. Despite Rpn11's essential function ...during substrate processing, its detailed structural and biochemical characterization has been hindered by difficulties in purifying the isolated enzyme. Here we report the 2.0-Å crystal structures of Zn(2+)-free and Zn(2+)-bound Saccharomyces cerevisiae Rpn11 in an MPN-domain heterodimer with Rpn8. The Rpn11-Rpn8 interaction occurs via two distinct interfaces that may be conserved in related MPN-domain complexes. Our structural and mutational studies reveal that Rpn11 lacks a conserved surface to bind the ubiquitin Ile44 patch, does not interact with the moiety on the proximal side of the scissile isopeptide bond and exhibits no linkage specificity for ubiquitin cleavage. These findings explain how Rpn11 functions as a promiscuous deubiquitinase for cotranslocational substrate deubiquitination during proteasomal degradation.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Poly-ubiquitin chains direct protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 during ATP-dependent substrate degradation. Rapid deubiquitination is ...required for efficient degradation but must be restricted to committed substrates that are engaged with the ATPase motor to prevent premature ubiquitin chain removal and substrate escape. Here we reveal the ubiquitin-bound structure of Rpn11 from S. cerevisiae and the mechanisms for mechanochemical coupling of substrate degradation and deubiquitination. Ubiquitin binding induces a conformational switch of Rpn11’s Insert-1 loop from an inactive closed state to an active β hairpin. This switch is rate-limiting for deubiquitination and strongly accelerated by mechanical substrate translocation into the AAA+ motor. Deubiquitination by Rpn11 and ubiquitin unfolding by the ATPases are in direct competition. The AAA+ motor-driven acceleration of Rpn11 is therefore important to ensure that poly-ubiquitin chains are removed only from committed substrates and fast enough to prevent their co-degradation.
Display omitted
•Proteasomal substrate degradation and deubiquitination are mechanochemically coupled•Ubiquitin binding to the proteasomal DUB Rpn11 induces a conformational switch•This switch is rate-limiting for ubiquitin chain removal from a substrate•Substrate translocation by the AAA ATPase motor accelerates the Rpn11 switch
Poly-ubiquitin modifications target protein substrates for degradation to the 26S proteasome, where they need to be removed for efficient substrate processing. Worden et al. reveal how degradation and deubiquitination are mechanochemically coupled through a conformational switch in the de-ubiquitinating subunit Rpn11, which is driven by the mechanical pulling of substrate into the proteasomal ATPase motor.
Methylation of histone H3K4 is a hallmark of actively transcribed genes that depends on mono-ubiquitination of histone H2B (H2B-Ub). H3K4 methylation in yeast is catalyzed by Set1, the ...methyltransferase subunit of COMPASS. We report here the cryo-EM structure of a six-protein core COMPASS subcomplex, which can methylate H3K4 and be stimulated by H2B-Ub, bound to a ubiquitinated nucleosome. Our structure shows that COMPASS spans the face of the nucleosome, recognizing ubiquitin on one face of the nucleosome and methylating H3 on the opposing face. As compared to the structure of the isolated core complex, Set1 undergoes multiple structural rearrangements to cement interactions with the nucleosome and with ubiquitin. The critical Set1 RxxxRR motif adopts a helix that mediates bridging contacts between the nucleosome, ubiquitin and COMPASS. The structure provides a framework for understanding mechanisms of trans-histone cross-talk and the dynamic role of H2B ubiquitination in stimulating histone methylation.
The 26S proteasome is the major eukaryotic ATP-dependent protease, yet the detailed mechanisms used by the proteasomal heterohexameric AAA+ unfoldase to drive substrate degradation remain poorly ...understood. To perform systematic mutational analyses of individual ATPase subunits, we heterologously expressed the unfoldase subcomplex from Saccharomyces cerevisiae in Escherichia coli and reconstituted the proteasome in vitro. Our studies demonstrate that the six ATPases have distinct roles in degradation, corresponding to their positions in the spiral staircases adopted by the AAA+ domains in the absence or presence of substrate. ATP hydrolysis in subunits at the top of the staircases is critical for substrate engagement and translocation. Whereas the unfoldase relies on this vertical asymmetry for substrate processing, interaction with the peptidase exhibits three-fold symmetry with contributions from alternate subunits. These diverse functional asymmetries highlight how the 26S proteasome deviates from simpler, homomeric AAA+ proteases.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
The version 6 cloud products of the Atmospheric Infrared Sounder (AIRS) and Advanced Microwave Sounding Unit (AMSU) instrument suite are described. The cloud top temperature, pressure, and height and ...effective cloud fraction are now reported at the AIRS field-of-view (FOV) resolution. Significant improvements in cloud height assignment over version 5 are shown with FOV-scale comparisons to cloud vertical structure observed by the CloudSat 94 GHz radar and the Cloud-Aerosol LIdar with Orthogonal Polarization (CALIOP). Cloud thermodynamic phase (ice, liquid, and unknown phase), ice cloud effective diameter (De), and ice cloud optical thickness (τ) are derived using an optimal estimation methodology for AIRS FOVs, and global distributions for 2007 are presented. The largest values of τ are found in the storm tracks and near convection in the tropics, while De is largest on the equatorial side of the midlatitude storm tracks in both hemispheres, and lowest in tropical thin cirrus and the winter polar atmosphere. Over the Maritime Continent the diurnal variability of τ is significantly larger than for the total cloud fraction, ice cloud frequency, and De, and is anchored to the island archipelago morphology. Important differences are described between northern and southern hemispheric midlatitude cyclones using storm center composites. The infrared-based cloud retrievals of AIRS provide unique, decadal-scale and global observations of clouds over portions of the diurnal and annual cycles, and capture variability within the mesoscale and synoptic scales at all latitudes.
Chemical transport models (CTMs) driven with high-resolution meteorological fields can better resolve small-scale processes, such as frontal lifting or deep convection, and thus improve the ...simulation and emission estimates of tropospheric trace gases. In this work, we explore the use of the GEOS-Chem four-dimensional variational (4D-Var) data assimilation system with the nested high-resolution version of the model (0.5 degree 0.67 degree ) to quantify North American CO emissions during the period of June 2004-May 2005. With optimized lateral boundary conditions, regional inversion analyses can reduce the sensitivity of the CO source estimates to errors in long-range transport and in the distributions of the hydroxyl radical (OH), the main sink for CO. To further limit the potential impact of discrepancies in chemical aging of air in the free troposphere, associated with errors in OH, we use surface-level multispectral MOPITT (Measurement of Pollution in The Troposphere) CO retrievals, which have greater sensitivity to CO near the surface and reduced sensitivity in the free troposphere, compared to previous versions of the retrievals. We estimate that the annual total anthropogenic CO emission from the contiguous US 48 states was 97 Tg CO, a 14 % increase from the 85 Tg CO in the a priori. This increase is mainly due to enhanced emissions around the Great Lakes region and along the west coast, relative to the a priori. Sensitivity analyses using different OH fields and lateral boundary conditions suggest a possible error, associated with local North American OH distribution, in these emission estimates of 20 % during summer 2004, when the CO lifetime is short. This 20 % OH-related error is 50 % smaller than the OH-related error previously estimated for North American CO emissions using a global inversion analysis. We believe that reducing this OH-related error further will require integrating additional observations to provide a strong constraint on the CO distribution across the domain. Despite these limitations, our results show the potential advantages of combining high-resolution regional inversion analyses with global analyses to better quantify regional CO source estimates.
We present satellite based ozone profile estimates derived by combining radiances measured at thermal infrared (TIR) wavelengths from the Aura Tropospheric Emission Spectrometer (TES) and ultraviolet ...(UV) wavelengths measured by the Aura Ozone Monitoring Instrument (OMI). The advantage of using these combined wavelengths and instruments for sounding ozone over either instrument alone is improved sensitivity near the surface as well as the capability to consistently resolve the lower troposphere, upper troposphere, and lower stratosphere for scenes with varying geophysical states. For example, the vertical resolution of ozone estimates from either TES or OMI varies strongly by surface albedo and temperature. Typically, TES provides 1.6 degrees of freedom for signal (DOFS) and OMI provides less than 1 DOFS in the troposphere. The combination provides 2 DOFS in the troposphere with approximately 0.4 DOFS for near surface ozone (surface to 700 hPa). We evaluated these new ozone profile estimates with ozonesonde measurements and found that calculated errors for the joint TES and OMI ozone profile estimates are in reasonable agreement with actual errors as derived by the root-mean-square (RMS) difference between the ozonesondes and the joint TES/OMI ozone estimates. We also used a common a priori profile in the retrievals in order to evaluate the capability of different retrieval approaches on capturing near-surface ozone variability. We found that the vertical resolution of the joint TES/OMI ozone profile estimates shows significant improvements on quantifying variations in near-surface ozone with RMS differences of 49.9% and correlation coefficient of R = 0.58 for the TES/OMI near-surface estimates as compared to 67.2% RMS difference and R = 0.33 for TES and 115.8% RMS difference and R = 0.09 for OMI. This comparison removes the impacts of using the climatological a priori in the retrievals. However, it results in artificially large sonde/retrieval differences. The TES/OMI ozone profiles from the production code of joint retrievals will use climatological a priori and therefore will have more realistic ozone estimates than those from using a common a priori volume mixing ratio profile.
The Tropospheric Emission Spectrometer (TES) on the Earth Observing System (EOS)‐Aura spacecraft measures global profiles of atmospheric ozone with vertical resolution of 6–7 km in the troposphere ...for the nadir view. For a first validation of TES ozone measurements we have compared TES‐retrieved ozone profiles to ozonesondes from fall, 2004. In some cases the ozonesonde data are from dedicated launches timed to match the Aura overpass, while other comparisons are performed with routine data available from the Southern Hemisphere Additional Ozonesonde (SHADOZ) archive and World Ozone and Ultraviolet Data Center (WOUDC) data archives. We account for TES measurement sensitivity and vertical resolution by applying the TES‐averaging kernel and constraint to the ozonesonde data before differencing the profiles. Overall, for V001 data, TES ozone profiles are systematically higher than sondes in the upper troposphere but compare well in the lower troposphere, with respect to estimated errors. These comparisons show that TES is able to detect relative variations in the coarse vertical structure of tropospheric ozone.
PDF
