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.
Histones are ubiquitinated in response to DNA double-strand breaks (DSB), promoting recruitment of repair proteins to chromatin. UBC13 (also known as UBE2N) is a ubiquitin-conjugating enzyme (E2) ...that heterodimerizes with UEV1A (also known as UBE2V1) and synthesizes K63-linked polyubiquitin (K63Ub) chains at DSB sites in concert with the ubiquitin ligase (E3), RNF168 (ref. 3). K63Ub synthesis is regulated in a non-canonical manner by the deubiquitinating enzyme, OTUB1 (OTU domain-containing ubiquitin aldehyde-binding protein 1), which binds preferentially to the UBC13∼Ub thiolester. Residues amino-terminal to the OTU domain, which had been implicated in ubiquitin binding, are required for binding to UBC13∼Ub and inhibition of K63Ub synthesis. Here we describe structural and biochemical studies elucidating how OTUB1 inhibits UBC13 and other E2 enzymes. We unexpectedly find that OTUB1 binding to UBC13∼Ub is allosterically regulated by free ubiquitin, which binds to a second site in OTUB1 and increases its affinity for UBC13∼Ub, while at the same time disrupting interactions with UEV1A in a manner that depends on the OTUB1 N terminus. Crystal structures of an OTUB1-UBC13 complex and of OTUB1 bound to ubiquitin aldehyde and a chemical UBC13∼Ub conjugate show that binding of free ubiquitin to OTUB1 triggers conformational changes in the OTU domain and formation of a ubiquitin-binding helix in the N terminus, thus promoting binding of the conjugated donor ubiquitin in UBC13∼Ub to OTUB1. The donor ubiquitin thus cannot interact with the E2 enzyme, which has been shown to be important for ubiquitin transfer. The N-terminal helix of OTUB1 is positioned to interfere with UEV1A binding to UBC13, as well as with attack on the thiolester by an acceptor ubiquitin, thereby inhibiting K63Ub synthesis. OTUB1 binding also occludes the RING E3 binding site on UBC13, thus providing a further component of inhibition. The general features of the inhibition mechanism explain how OTUB1 inhibits other E2 enzymes in a non-catalytic manner.
SAGA is a transcriptional coactivator complex that is conserved across eukaryotes and performs multiple functions during transcriptional activation and elongation. One role is deubiquitination of ...histone H2B, and this activity resides in a distinct subcomplex called the deubiquitinating module (DUBm), which contains the ubiquitin-specific protease Ubp8, bound to Sgf11, Sus1, and Sgf73. The deubiquitinating activity depends on the presence of all four DUBm proteins. We report here the 1.90 angstrom resolution crystal structure of the DUBm bound to ubiquitin aldehyde, as well as the 2.45 angstrom resolution structure of the uncomplexed DUBm. The structure reveals an arrangement of protein domains that gives rise to a highly interconnected complex, which is stabilized by eight structural zinc atoms that are critical for enzymatic activity. The structure suggests a model for how interactions with the other DUBm proteins activate Ubp8 and allows us to speculate about how the DUBm binds to monoubiquitinated histone H2B in nucleosomes.
Introducing band gap states to TiO2 photocatalysts is an efficient strategy for expanding the range of accessible energy available in the solar spectrum. However, few approaches are able to introduce ...band gap states and improve photocatalytic performance simultaneously. Introducing band gap states by creating surface disorder can incapacitate reactivity where unambiguous adsorption sites are a prerequisite. An alternative method for introduction of band gap states is demonstrated in which selected heteroatoms are implanted at preferred surface sites. Theoretical prediction and experimental verification reveal that the implanted heteroatoms not only introduce band gap states without creating surface disorder, but also function as active sites for the CrVI reduction reaction. This promising approach may be applicable to the surfaces of other solar harvesting materials where engineered band gap states could be used to tune photophysical and ‐catalytic properties.
Band gap state engineering: Band gap states are introduced to the surface electronic structure of rutile TiO2 by substituting the in‐plane oxygen atoms of the (110) facet with nitrogen atoms without creating surface disorder. The modified material is able to reduce CrVI, which suggests that adsorption and heteroatom sites create an active surface that promotes charge transfer.
Mycoplasma synoviae (M. synoviae) is an important pathogen in poultry industry and has led to major economic losses. Understanding the epidemiology is crucial to improve control and eradication ...program of M. synoviae. In this study, 487 samples suspected with M. synoviae infection were collected from August 2020 to June 2021 in China. Among 487 samples, 324 samples were MS positive, the positive rate was 66.53%, and 104 strains were isolated from 324 positive samples. The multilocus sequence typing (MLST) method based on seven housekeeping genes was used to conduct genotyping 104 M. synoviae strains isolated, and the 104 isolates belonged to 8 sequence types (STs) after MLST genotyping, and ST-34 had the highest proportion. After BURST analysis, all 104 isolates were divided into group 12 with other 56 strains isolated from China. Phylogenetic tree constructed by neighbor-joining method showed that nearly all of Chinese isolates (160 isolates) clustered together and separated from other reference isolates (217 isolates) in the PubMLST database. In conclusion, this study suggested that the M. synoviae strains in China were highly similar and independent of abroad strains.
Accurate estimations of the vertical leaf nitrogen (N) distribution within a rice canopy is helpful for understanding the nutrient supply and demand of various functional leaf layers of rice and for ...improving the predictions of rice productivity. A two-year field experiment using different rice varieties, N rates, and planting densities was performed to investigate the vertical distribution of the leaf nitrogen concentration (LNC, %) within the rice canopy, the relationship between the LNC in different leaf layers (LNC
, i = 1, 2, 3, 4), and the relationship between the LNC
and the LNC at the canopy level (LNC
). A vertical distribution model of the LNC was constructed based on the relative canopy height. Furthermore, the relationship between different vegetation indices (VIs) and the LNC
, the LNC
, and the LNC vertical distribution model parameters were studied. We also compared the following three methods for estimating the LNC in different leaf layers in rice canopy: (1) estimating the LNC
by VIs and then estimating the LNC
based on the relationship between the LNC
and LNC
; (2) estimating the LNC in any leaf layer of the rice canopy by VIs, inputting the result into the LNC vertical distribution model to obtain the parameters of the model, and then estimating the LNC
using the LNC vertical distribution model; (3) estimating the model parameters by using VIs directly and then estimating the LNC
by the LNC vertical distribution model. The results showed that the LNC in the bottom of rice canopy was more susceptible to different N rates, and changes in the LNC with the relative canopy height could be simulated by an exponential model. Vegetation indices could estimate the LNC at the top of rice canopy. R
/(R
+R
) (R
= 0.763) and the renormalized difference vegetation index (RDVI) (1340, 730) (R
= 0.747) were able to estimate the parameter "a" of the LNC vertical distribution model in indica rice and japonica rice, respectively. In addition, method (2) was the best choice for estimating the LNC
(R
= 0.768, 0.700, 0.623, and 0.549 for LNC
, LNC
, LNC
, and LNC
, respectively). These results provide technical support for the rapid, accurate, and non-destructive identification of the vertical distribution of nitrogen in rice canopies.
Rapid and accurate estimation of plant potassium accumulation (PKA) using hyperspectral remote sensing is of significance for the precise management of crop K fertilizer. This study focused on the ...separation of non-negative matrix factorization (NMF) for hyperspectral reflectance from the ground and unmanned aerial vehicle (UAV) platforms and its mitigation effect on the water and soil background. Pure vegetation spectra were extracted from the canopy mixed spectra using NMF, and then a partial least-squares regression (PLSR) model was established based on the extracted vegetation spectra and rice PKA to construct an estimation model of rice PKA. The results showed that the green light and red edge bands contributed significantly to the rice PKA estimation. NMF could effectively extract pure vegetation and water and soil spectra from mixed spectra, and enhance the green peak, red valley, and red edge information of the extracted vegetation spectra. Compared with spectral indices, the PLSR performed best for ground and UAV data. Besides, the R
2
of the PLSR model based on NMF-extracted vegetation spectra increased by 15.15% to 0.76%, and the verified RMSE and RE decreased by 16.93% and 16.77% to 3.19 g m
−2
and 45.07%, respectively. Hyperspectral dataset testing from different years, growth stages and varieties, and UAV platforms showed that NMF could improve the estimation accuracy of rice PKA. This study showed that NMF could be applied to both ground and UAV hyperspectral platforms to improve the estimation accuracy of rice K nutrition.
Nicotinamide phosphoribosyltransferase (Nampt) synthesizes nicotinamide mononucleotide (NMN) from nicotinamide in a mammalian NAD+ biosynthetic pathway and is required for SirT1 activity in vivo. ...Nampt has also been presumed to be a cytokine (PBEF) or a hormone (visfatin). The crystal structure of Nampt in the presence and absence of NMN shows that Nampt is a dimeric type II phosphoribosyltransferase and provides insights into the enzymatic mechanism.
Intracerebral hemorrhage (ICH) is the most devastating subtype of stroke, but effective prevention and treatment strategies are lacking. Recently, gut microbiome and its metabolitesis are considered ...to be an influencing factor of stroke. However, little is known about the effects of the gut microbiome on ICH and host metabolic activity. Therefore, we used 16S sequencing, macrogenomics sequencing and untargeted metabolomics to explore the differences in gut microbial-metabolome interactions between patients with intracerebral hemorrhage and healthy control populations. We found a significant decrease in the phylum of
and a significant increase of Bacteroidetes in ICH patients. At the genus level,
, and
were more abundant in ICH patients. Macrogenomic analysis revealed active glycosaminoglycan degradation, heme synthesis, galactose degradation, lipopolysaccharide core region synthesis, and beta-Lactam resistance in ICH patients. Serum untargeted metabolomic analysis combined with ROC curves showed that octanoylcarnitine, decanoylcarnitine, dodecanoylcarnitine, glyceric acid, pyruvic acid, aspartic acid, methylcysteine, pyroglutamic acid, 9E-tetradecenoic acid, N-Acetylneuraminic acid, and aconitic acid were the best markers for the diagnosis of ICH. Correlation analysis showed that microbiome enriched in the gut of ICH patients were significantly correlated with serum metabolites, revealing a close correlation between the gut microbiome of ICH patients and the host metabolome, and significant differences from the healthy population. microbiota-host co-metabolites including pyruvic acid and 9E-tetradecenoic acid is associated with the the National Institutes of Health Stroke Scale (NIHSS) scores. In conclusion, microbiome-related metabolites in ICH patients was associated with the severity of ICH, the microbiota-host co-metabolites may be a potential may be potential therapeutic targets.
Prostate alignment is subject to interobserver variability in cone-beam CT (CBCT)-based soft-tissue matching. This study aims to analyze the impact of possible interobserver variability in CBCT-based ...soft-tissue matching for prostate cancer radiotherapy.
Retrospective data, consisting of 156 CBCT images from twelve prostate cancer patients with elective nodal irradiation were analyzed in this study. To simulate possible interobserver variability, couch shifts of 2 mm relative to the resulting patient position of prostate alignment were assumed as potential patient positions (27 possibilities). For each CBCT, the doses of the potential patient positions were re-calculated using deformable image registration-based synthetic CT. The impact of the simulated interobserver variability was evaluated using tumor control probabilities (TCPs) and normal tissue complication probabilities (NTCPs).
No significant differences in TCPs were found between prostate alignment and potential patient positions (0.944 ± 0.003 vs 0.945 ± 0.003, P = 0.117). The average NTCPs of the rectum ranged from 5.16 to 7.29 (%) among the potential patient positions and were highly influenced by the couch shift in the anterior-posterior direction. In contrast, the average NTCPs of the bladder ranged from 0.75 to 1.12 (%) among the potential patient positions and were relatively negligible.
The NTCPs of the rectum, rather than the TCPs of the target, were highly influenced by the interobserver variability in CBCT-based soft-tissue matching. This study provides a theoretical explanation for daily CBCT-based image guidance and the prostate-rectum interface matching procedure.
Not applicable.
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