Molecular basis for C-degron recognition by CRL2APPBP2 ubiquitin ligase.

E3 ubiquitin ligases determine the specificity of eukaryotic protein degradation by selective binding to destabilizing protein motifs, termed degrons, in substrates for ubiquitin-mediated proteolysis. The exposed C-terminal residues of proteins can act as C-degrons that are recognized by distinct substrate receptors (SRs) as part of dedicated cullin-RING E3 ubiquitin ligase (CRL) complexes. APPBP2, an SR of Cullin 2-RING ligase (CRL2), has been shown to recognize R-x-x-G/C-degron; however, the molecular mechanism of recognition remains elusive. By solving several cryogenic electron microscopy structures of active CRL2APPBP2 bound with different R-x-x-G/C-degrons, we unveiled the molecular mechanisms underlying the assembly of the CRL2APPBP2 dimer and tetramer, as well as C-degron recognition. The structural study, complemented by binding experiments and cell-based assays, demonstrates that APPBP2 specifically recognizes the R-x-x-G/C-degron via a bipartite mechanism; arginine and glycine, which play critical roles in C-degron recognition, accommodate distinct pockets that are spaced by two residues. In addition, the binding pocket is deep enough to enable the interaction of APPBP2 with the motif placed at or up to three residues upstream of the C-end. Overall, our study not only provides structural insight into CRL2APPBP2-mediated protein turnover but also serves as the basis for future structure-based chemical probe design.

Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif.

The Spalt-like 4 transcription factor (SALL4) plays an essential role in controlling the pluripotent property of embryonic stem cells via binding to AT-rich regions of genomic DNA, but structural details on this binding interaction have not been fully characterized. Here, we present crystal structures of the zinc finger cluster 4 (ZFC4) domain of SALL4 (SALL4ZFC4) bound with different dsDNAs containing a conserved AT-rich motif. In the structures, two zinc fingers of SALL4ZFC4 recognize an AATA tetranucleotide. We also solved the DNA-bound structures of SALL3ZFC4 and SALL4ZFC1. These structures illuminate a common preference for the AATA tetranucleotide shared by ZFC4 of SALL1, SALL3, and SALL4. Furthermore, our cell biology experiments demonstrate that the DNA-binding activity is essential for SALL4 function as DNA-binding defective mutants of mouse Sall4 failed to repress aberrant gene expression in Sall4-/- mESCs. Thus, these analyses provide new insights into the mechanisms of action underlying SALL family proteins in controlling cell fate via preferential targeting to AT-rich sites within genomic DNA during cell differentiation.

Structural insights into SMCR8 C-degron recognition by FEM1B.

C-degrons play critical roles in targeting the receptor proteins of Cullin-RING E3 ligase complexes to initiate protein degradation. FEM1 proteins, including FEM1A, FEM1B, and FEM1C, act as the receptors to specifically recognize Arg/C-degrons to enable CRL2-mediated protein turnover. Very few substrates have been identified for FEM1B, except CDK5R1. We found that CRL2FEM1B also recognizes the C-degron of an SMCR8 isoform, and uncovered the recognition of SMCR8 by FEM1B through presenting the structure of FEM1B bound to SMCR8. Our work provides insights into the role of CRL2FEM1B in regulating the lifetime of SMCR8, a critical autophagy regulator.

Safety and efficacy of side-to-end anastomosis versus colonic J-pouch anastomosis in sphincter-preserving resections: an updated meta-analysis of randomized controlled trials.

BACKGROUND: The application of side-to-end anastomosis (SEA) in sphincter-preserving resection (SPR) is controversial. We performed a meta-analysis to compare the safety and efficacy of SEA with colonic J-pouch (CJP) anastomosis, which had been proven effective in improving postoperative bowel function. METHODS: The protocol was registered in PROSPERO under number CRD42020206764. PubMed, Embase, Web of Science, and the Cochrane Register of Controlled Trials databases were searched. The inclusion criteria were randomized controlled trials (RCTs) that evaluated the safety or efficacy of SEA in comparison with CJP anastomosis. The outcomes included the pooled risk ratio (RR) for dichotomous variables and weighted mean differences (WMDs) for continuous variables. All outcomes were calculated with 95% confidence intervals (CI) by STATA software (Stata 14, Stata Corporation, TX, USA). RESULTS: A total of 864 patients from 10 RCTs were included in the meta-analysis. Patients undergoing SEA had a higher defecation frequency at 12 months after SPR (WMD = 0.20; 95% CI, 0.14-0.26; P < 0.01) than those undergoing CJP anastomosis with low heterogeneity (I2 = 0%, P = 0.54) and a lower incidence of incomplete defecation at 3 months after surgery (RR = 0.28; 95% CI, 0.09-0.86; P = 0.03). A shorter operating time (WMD = - 17.65; 95% CI, - 23.28 to - 12.02; P < 0.01) was also observed in the SEA group without significant heterogeneity (I2 = 0%, P = 0.54). A higher anorectal resting pressure (WMD = 6.25; 95% CI, 0.17-12.32; P = 0.04) was found in the SEA group but the heterogeneity was high (I2 = 84.5%, P = 0.84). No significant differences were observed between the groups in terms of efficacy outcomes including defecation frequency, the incidence of urgency, incomplete defecation, the use of pads, enema, medications, anorectal squeeze pressure and maximum rectal volume, or safety outcomes including operating time, blood loss, the use of protective stoma, postoperative complications, clinical outcomes, and oncological outcomes. CONCLUSIONS: The present evidence suggests that SEA is an effective anastomotic strategy to achieve similar postoperative bowel function without increasing the risk of complications compared with CJP anastomosis. The advantages of SEA include a shorter operating time, a lower incidence of incomplete defecation at 3 months after surgery, and better sphincter function. However, close attention should be paid to the long-term defecation frequency after SPR.

On the mechanism of acceptorless dehydrogenation of N-heterocycles catalyzed by tBuOK: a computational study.

The catalytic acceptorless dehydrogenation (ADH) of saturated N-heterocycles has recently gained considerable attention as a promising strategy for hydrogen release from liquid organic hydrogen carriers (LOHCs). Recently, a simple tBuOK base-promoted ADH of N-heterocycles was developed by Yu et al. (Adv. Synth. Catal. 2019, 361, 3958). However, it is still open as to how the tBuOK plays a catalytic role in the ADH process. Herein, our density functional study reveals that the tBuOK catalyzes the ADH of 1,2,3,4-tetrahydroquinoline (THQ) through a quasi-metal-ligand bifunctional catalytic channel or a base-catalyzed pathway with close energy barriers. The hydride transfer in the first dehydrogenation process is determined to be the rate determining step, and the second dehydrogenation can proceed directly from 34DHQ regulated by the tBuOK. In addition, the computational results show that the cooperation of a suitable alkali metal ion with the tBuO- group is so critical that the tBuOLi and the isolated tBuO- are both inferior to tBuOK as a dehydrogenation catalyst.

Photothermally driven decoupling of gas evolution at the solid-liquid interface for boosted photocatalytic hydrogen production.

The slow mass transfer, especially the gas evolution process at the solid-liquid interface in photocatalytic water splitting, restricts the overall efficiency of the hydrogen evolution reaction. Here, we report a novel gas-solid photocatalytic reaction system by decoupling hydrogen generation from a traditional solid-liquid interface. The success relies on annealing commercial melamine sponge (AMS) for effective photothermal conversion that leads to rapid water evaporation. The vapor flows towards the photocatalyst covering the surface of the AMS and is split by the catalyst therein. This liquid-gas/gas-solid coupling system avoids the formation of photocatalytic bubbles at the solid-liquid interface, leading to significantly improved mass transfer and conversion. Utilizing CdS nanorods anchored by highly dispersed nickel atoms/clusters as a model photocatalyst, the highest hydrogen evolution rate from water splitting reaches 686.39 µmol h-1, which is 5.31 times that of the traditional solid-liquid-gas triphase system. The solar-to-hydrogen (STH) efficiency can be up to 2.06%. This study provides a new idea for the design and construction of efficient practical photocatalytic systems.

Structural basis for Gemin5 decamer-mediated mRNA binding.

Gemin5 in the Survival Motor Neuron (SMN) complex serves as the RNA-binding protein to deliver small nuclear RNAs (snRNAs) to the small nuclear ribonucleoprotein Sm complex via its N-terminal WD40 domain. Additionally, the C-terminal region plays an important role in regulating RNA translation by directly binding to viral RNAs and cellular mRNAs. Here, we present the three-dimensional structure of the Gemin5 C-terminal region, which adopts a homodecamer architecture comprised of a dimer of pentamers. By structural analysis, mutagenesis, and RNA-binding assays, we find that the intact pentamer/decamer is critical for the Gemin5 C-terminal region to bind cognate RNA ligands and to regulate mRNA translation. The Gemin5 high-order architecture is assembled via pentamerization, allowing binding to RNA ligands in a coordinated manner. We propose a model depicting the regulatory role of Gemin5 in selective RNA binding and translation. Therefore, our work provides insights into the SMN complex-independent function of Gemin5.

An Asia-specific variant of human IgG1 represses colorectal tumorigenesis by shaping the tumor microenvironment.

Emerging studies have focused on ways to treat cancers by modulating T cell activation. However, whether B cell receptor signaling in the tumor microenvironment (TME) can be harnessed for immunotherapy is unclear. Here, we report that an Asia-specific variant of human IgG1 containing a Gly396 to Arg396 substitution (hIgG1-G396R) conferred improved survival of patients with colorectal cancer (CRC). Mice with knockin of the murine functional homolog mIgG2c-G400R recapitulated the alleviated tumorigenesis and progression in murine colon carcinoma models. Immune profiling of the TME revealed broad mobilizations of IgG1+ plasma cells, CD8+ T cells, CD103+ DCs, and active tertiary lymphoid structure formation, suggesting an effective antitumor microenvironment in hIgG1-G396R CRC patients. Mechanistically, this variant potentiated tumor-associated antigen-specific (TAA-specific) plasma cell differentiation and thus antibody production. These elevated TAA-specific IgG2c antibodies in turn efficiently boosted the antibody-dependent tumor cell phagocytosis and TAA presentation to effector CD8+ T cells. Notably, adoptive transfer of TAA-specific class-switched memory B cells harboring this variant exhibited therapeutic efficacy in murine tumor models, indicating their clinical potential. All these results prompted a prospective investigation of hIgG1-G396R in patients with CRC as a biomarker for clinical prognosis and demonstrated that manipulating the functionality of IgG1+ memory B cells in tumors could improve immunotherapy outcomes.

Mechanistic insights into the C-H activation of methane mediated by the unsupported and silica-supported VO2OH and CrOOH: a DFT study.

The direct activation and conversion of methane has been a topic of interest in both academia and industry for several decades. Deep understanding of the corresponding mechanism and reactivity mediated by diverse catalytic clusters, as well as the supporting materials, is still highly desired. In this work, the regulation mechanism of C-H bond activation of methane, mediated by the closed-shell VO2OH, the open-shell CrOOH, and their silica supported clusters, has been investigated by density functional theory (DFT) calculations. The hydrogen-atom transfer (HAT) reaction towards methane C-H bond activation is more feasible when mediated by the unsupported/silica-supported CrOOH clusters versus the VO2OH clusters, due to the intrinsic spin density located on the terminal Ot atom. The proton-coupled electron transfer (PCET) pathways are regulated by both the nucleophilicity of the Ot site and the electrophilicity of the metal center, which show no obvious difference in energy consumption among the four reactions examined. Moreover, the introduction of a silica support can lead to subtle influences on the intermolecular interaction between the CH4 molecule and the catalyst cluster, as well as the thermodynamics of the methane C-H activation.

Genetic mutations associated with sensitivity to neoadjuvant chemotherapy in metastatic colon cancer: A case report and review of literature.

BACKGROUND: Colorectal liver metastases (CLM) occur in 15%-30% of patients with colorectal cancer (CRC). Advancements in next generation sequencing (NGS) can provide more precise prognoses for cancer patients and help guide clinical treatment. However, the genetic variants that predict high sensitivity to neoadjuvant chemotherapy remain unclear, especially in patients with CLM. The aim of this study was to identify the relevant genetic variants in a single CLM patient and to summarize the current evidence on mutations and single nucleotide polymorphisms (SNPs) that objectively predict sensitivity to neoadjuvant chemotherapy. CASE SUMMARY: A 76-year-old male patient, who was diagnosed as stage IV colon cancer with liver metastases, was found to have APC/TP53/KRAS mutations. He showed a good therapeutic response to 12 courses of oxaliplatin regimens combined with Bevacizumab. Genetic analysis of the patient identified 5 genes with 7 detected SNPs that may be related to a better response to chemotherapy drugs. In addition, a critical literature review was performed based on a standardized appraisal form after selecting the articles. Ultimately, 21 eligible studies were appraised to assess the association between gene mutations and good prognosis. Mutations in KRAS, TP53, SMAD4, and APC were identified as being associated with a poor response to chemotherapy drugs, whereas mutations of CREBBP and POLD1 were associated with longer overall survival. CONCLUSION: NGS can identify precise predictors of response to neoadjuvant chemotherapy, leading to improved outcomes for CRC patients.

[Ecosystem approach: a new concept for ecosystem management].

Ecosystem approach (EA) was firstly proposed by ecologists in developed countries and then supported by a number of international institutions and NGOs, among which, CBD, IUCN and WWF played important roles. Ecosystem approach is an integrated strategy for the management of land, soil and bio-resources. The application of EA will help to reach a balance between conservation, sustainable use, and fair and equitable sharing of the benefits arising out of the utilization of biological resources. Ecosystem approach is a methodology of ecosystem management, focusing on the biological organisms and recognising that human beings, with their cultural diversity, are an integral component of many ecosystems. The decision V/6 adopted by the Conference of the Parties to the CBD at its fifth meeting in 2000 concretized the EA in the form of twelve principles and five operational guidelines. Our government has recently made a lot of efforts in ecosystem management at large scale with many important measures and obtained significant achievements, but the potential role of local governments, institutions and individuals has not been fully played. In the attempts of managing a specific ecosystem, there are many successful cases done by our ecologists, for example, the ecological management of Chinese fir plantation forest in central subtropical China. However, the whole ecosystem at national or regional level is confronted with a lot of serious problems, mainly because there is a lack of complete understanding of the significance of ecosystem management and a lack of guidelines or principles from an integrated scientific theory. The introduction and implementation of ecosystem approach will play an important role in improving the ecosystem management in China.

[Temporal and spatial change of land use in Horqin Desert and its outer area].

Based on two sets of land use data (1985 and 2000), the land use change in Horqin Desert and its outer area, in both spatial and temporal aspects, was studied with the tools of geographical information system (GIS) and statistics in this paper. Conclusions of this study are drawn as follows: From 1985 to 2000, the area order of individual land use changes was grassland > plough land > forestland > unused land > water body > residential and industrial land. As to the form of changes, the swapping area was greater than its quantitative change for forestland while the quantity change was greater, with different degree, than swap for the rest 5 land use types. As a whole, the quantity change was far greater than its swap. The analysis of land use dynamics showed that the speed of individual land use changes was in order of cultivated land > water body > grassland > forestland > unused land > residential and industrial land in sequence. Meanwhile, there was notable difference of land use change among counties in the region. For plough land change, Zhalute county was the greatest. Naiman the smallest. For forest change, Naiman was the greatest, Kalaqin the smallest. For grassland change, Tongliao city was the greatest, Alukerqin the smallest. For water change, Kezuozhongqi was the greatest, Balinzuoqi the smallest. For residential and industrial land change, Naiman was the greatest, Alukerqin the smallest. Finally, the change of unused land is more obvious in Chifeng city. As to the spatial change, 9 major land use change types were identified. Wherein, the change from grassland to plough land, expanding from the center of Horqin desert towards its outer counties, was still the most important land use change for the whole study area. In addition, the construction of protective forest for grassland in Naiman, the return from plough land to forestland in Kezuozhongqi, the return from plough land to grassland in Tongliao city, the deforestation for plough land in Kukun county, the degradation of grassland in Zhaluteqi, the exploit of river beach in Kailu, the reclamation of unused land in Kezuobouqi, and the regeneration of natural vegetation in Alukerqin were all important regional characteristics of land use change during the past 15 years.

[Carbon budget of ecosystem in Changbai Mountain Natural Reserve].

The study used EPPML, a biological geochemistry cycle model that was built, to simulate the carbon budget for ecosystems in Changbai Mountain Natural Reserve. The results indicated that the annual net primary productivity [NPP (carbon)] of the natural reserve was 1.332 x 10(6) t.a-1. The annual NPP of mixed broad-leaved and Korean pine forest and spruce-fir forest were maximal, 0.540 x 10(6) t.a-1 and 0.428 x 10(6) t.a-1 respectively. The area and productivity of the two stands were maximal in Changbai Mountain, therefore, the simulating productivity of the two stands most greatly affect carbon cycle and carbon budget of the natural reserve, and the veracity of the former decides the security of the latter. To sum up, not only did the simulations accord with routines in the relative comparisons between different vegetation belts and climate belts in the whole natural reserve, but also was exact in the absolute comparisons with very disperse data from field survey. Vegetations in the natural reserve had evident carbon sink functions, mainly exhibiting in the increasing of carbon, about 1.058 x 10(6) t.a-1. The annual carbon of mixed broad-leaved and Korean pine forest increased greatest (0.452 x 10(6) t.a-1), secondly spruce-fir forest (0.339 x 10(6) t.a-1). The two stands played crucial roles in the carbon sink for Changbai Mountain, others being Changbai larch forest, broad-leaved forest, meadow, shrub, alpine tundra, subalpine Betula ermanii forest and alpine grass. In 1995, the decomposing carbon of soil organic matter was 0.169 x 10(6) t.a-1 higher than the littering carbon in the natural reserve. There was accumulation of organic matter in the meadow soil and shrub soil. The decomposition and accumulation of soil organic matter was in the nearly balancing condition in the alpine tundra soil and alpine grass soil. The decomposition of organic matter was as one and a half time or double as litterfall in the arbor forest soil.

[Ecosystem productivity process model for landscape based on remote sensing and surface data].

In this paper, the a ecosystem productivity process model for landscape (EPPML) reflecting carbon and water cycles of system was described and discussed. In EPPML, leaf area index (LAI) that greatly influenced vegetation productivity was received from remote sensing images, the spatial distribution and temporal dynamics of net primary productivity (NPP) and evapotranspiration were simulated. Geographical information system (GIS) was used to process, analyze, and display spatial data. Thus, the studies on physiological ecology could be extended, and converted from small scale to larger scale. Using EPPML, the vegetation productivity in Changbai Mountain Natural Reserve in 1995 was simulated. EPPML could well and truly simulate the NPP of main vegetations in the natural reserve. NPP was estimated to be 0.680 kg Cm.-2.yr.-1, mostly ranging from 0.105 to 1.241 kg C.m-2.yr.-1, accounting for 82.1%. The highest NPP (1.084 kg C.m-2.yr-1) appeared in mixed broad-leaved and Korean pine forests. The total NPP was estimated to be 1.332 x 10(6) t C.yr-1. The highest total NPP appeared in mixed broad-leaved and Korean pine forests and spruce-fir forest, which were 0.540 x 10(6) t C.yr.-1 and 0.428 x 10(6) t C.yr.-1, respectively. The seasonal variation of NPP appeared obvious single peak with peak value in July (6.13 g C.m-2.d-1). The most NPP accumulated in the summer, which was 0.465 kg C.m-2, secondly in the spring, and least in the winter.

[Simulation of temporal-spatial variation characteristics of surface runoff in Changbai Mountain based on process model for landscape scale].

The seasonal dynamics and spatial distribution characteristics of surface runoff in Changbai Mountain simulated by the process model (EPPML), and the relationships between surface runoff and environmental conditions were analyzed. The results showed that the seasonal variation of surface runoff in Changbai Mountain presented obvious three-peak pattern, i.e., the lowest values in June and September, peak values in August (2.58 mm.d-1), similar to that of soil water content. Total trend of surface runoff for different vegetations in the growing season was in order of grass and shrub > coniferous forest > broad-leaved forest > mixed broad-leaved and Korean pine forest, highly correlated to LAI. Annual surface runoff in 1995 was estimated to be 0.203 m.yr.-1, mostly ranging from 0.0 to 0.246.m.yr.-1, accounting for 69.3%. The trend of spatially increasing annual surface runoff along with increasing altitude was obvious. The maximum annual surface runoff appeared in alpine grass (0.619 m.yr.-1), minimum in mixed broad-leaved and Korean pine (Pinus koraiensis) forest (0.081 m.yr.-1), others being alpine tundra, Betula ermanii forest, meadow, shrub, mixed spruce (Picea asperata) and fir (Abies nephrolepis) forest, Changbai larch (Larix olgensis) forest and broad-leaved forest. Vegetation and environmental conditions controlled the main trend of the spatial distribution of annual surface runoff in Changbai Mountain. There was very strong negative exponential correlativity between annual surface runoff and LAI (R2 = 0.857). The more LAI, the more literfall, the more precipitation intercepted by litter, thus, the less surface runoff. Annual surface runoff was highly negatively correlated with air temperature and total solar radiation (R2 being 0.965 and 0.836 respectively), however, it was highly positively correlated with precipitation, relative humidity and wind speed (R2 being more than 0.950). And annual surface runoff was also strongly correlated to soil characteristics.

[Analysis on factors affecting net primary productivity distribution in Changbai Mountain based on process model for landscape scale].

Based on the data received from remote sensing images, the spatial distribution of annual net primary productivity (NPP) was simulated by the process model (EPPML), and the relationships between annual NPP and environmental conditions were analyzed. The results showed that NPP in 1995 was 0.680 kg C.m-2.yr.-1, mostly ranging from 0.105 to 1.241 kg C.m-2.yr.-1, accounting for 82.1%. The highest NPP (1.084 kg C.m-2.yr.-1) appears in mixed broad-leaved and Korean pine forest. Environmental conditions decide the main trend of the spatial distribution of annual NPP (Carbon) in Changbai Mountain. Soil water content had a negative correlativity with NPP, and the correlation coefficient (R) was -0.65. Therefore, water was sufficient for the growth of plants in Changbai Mountain. NPP was highly correlated with LAI (R = 0.81). When LAI was greater than 4-5 m2.m-2, NPP became saturated. NPP was also highly correlated with canopy transpiration (R = 0.77). The response of NPP on environmental conditions, LAI and canopy transpiration in Betula ermanii and broad-leaved forests were different from those in other vegetation.