Glucose-induced CRL4COP1-p53 axis amplifies glycometabolism to drive tumorigenesis.

The diabetes-cancer association remains underexplained. Here, we describe a glucose-signaling axis that reinforces glucose uptake and glycolysis to consolidate the Warburg effect and overcome tumor suppression. Specifically, glucose-dependent CK2 O-GlcNAcylation impedes its phosphorylation of CSN2, a modification required for the deneddylase CSN to sequester Cullin RING ligase 4 (CRL4). Glucose, therefore, elicits CSN-CRL4 dissociation to assemble the CRL4COP1 E3 ligase, which targets p53 to derepress glycolytic enzymes. A genetic or pharmacologic disruption of the O-GlcNAc-CK2-CSN2-CRL4COP1 axis abrogates glucose-induced p53 degradation and cancer cell proliferation. Diet-induced overnutrition upregulates the CRL4COP1-p53 axis to promote PyMT-induced mammary tumorigenesis in wild type but not in mammary-gland-specific p53 knockout mice. These effects of overnutrition are reversed by P28, an investigational peptide inhibitor of COP1-p53 interaction. Thus, glycometabolism self-amplifies via a glucose-induced post-translational modification cascade culminating in CRL4COP1-mediated p53 degradation. Such mutation-independent p53 checkpoint bypass may represent the carcinogenic origin and targetable vulnerability of hyperglycemia-driven cancer.

Predicting drug-target binding affinity with cross-scale graph contrastive learning.

Identifying the binding affinity between a drug and its target is essential in drug discovery and repurposing. Numerous computational approaches have been proposed for understanding these interactions. However, most existing methods only utilize either the molecular structure information of drugs and targets or the interaction information of drug-target bipartite networks. They may fail to combine the molecule-scale and network-scale features to obtain high-quality representations. In this study, we propose CSCo-DTA, a novel cross-scale graph contrastive learning approach for drug-target binding affinity prediction. The proposed model combines features learned from the molecular scale and the network scale to capture information from both local and global perspectives. We conducted experiments on two benchmark datasets, and the proposed model outperformed existing state-of-art methods. The ablation experiment demonstrated the significance and efficacy of multi-scale features and cross-scale contrastive learning modules in improving the prediction performance. Moreover, we applied the CSCo-DTA to predict the novel potential targets for Erlotinib and validated the predicted targets with the molecular docking analysis.

Microbial behaviours inside alternating anaerobic-anoxic environment of a sulfur cycle-driven EBPR system: A metagenomic investigation.

Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) was recently developed for saline wastewater treatment. However, the main functional bacteria and the interrelationship of functional bacteria of the DS-EBPR have not been defined and identified so far. This study used metagenomics and multivariate statistics to deduce the functional microbial community and distribution of functional genes associated with the critical metabolic pathways of carbon (C), nitrogen (N), phosphorus (P) and sulfur (S), particularly regarding how they would behave under the alternating anaerobic-anoxic conditions inside a long-term DS-EBPR system. An analysis of the metagenomics and metabolic functions identified 11 major microbial species which were classifiable into four groups: sulfate reducing bacteria (SRB, 0.8-2.2%), sulfur oxidizing bacteria (SOB, 31.9-37.7%), denitrifying phosphate accumulating organisms (DPAOs, 10.0-15.8%) and glycogen accumulating organisms (GAOs, 3.7-7.7%). The four groups of microorganisms performed their respective metabolisms synergistically. In terms of distribution of functional genes, SRB (Desulfococcus and Desulfobacter) and SOB (Chromatiaceae and Thiobacillus) are not only encoded by the related sulfur conversion genes (sqr, dsrAB, aprAB and sat), but also encoded by the necessary ppx and ppk1 gene for P removal that they can be considered as the potential S-related PAOs. Between the anaerobic and anoxic conditions, the metagenome-based microbial community remained structurally similar, but the functional genes, which encode various key enzymes for the P, N, and S pathways, changed in abundance. This study contributes to our understanding on the interactions and competition between the SRB, SOB, DPAOs, and GAOs in a DS-EBPR system.

A General Method to Edit Histone H3 Modifications on Chromatin Via Sortase-Mediated Metathesis.

The post-translational modifications (PTMs) on the tail of histone H3 control chromatin structure and influence epigenetics and gene expression. The current chemical methods including unnatural amino acid incorporation and protein splicing enable preparations of the histone with diverse PTMs in cellular contexts, but they are not applicable to edit native chromatin. The manipulation of histone-modifying enzymes alter the endogenous histone PTMs but the lack of specificity of most histone-modifying enzymes prevents precise control of specific H3 tail PTM patterns. Here we report a new method to edit the N-tail of histone H3 via sortase mediated metathesis (SMM). The sortase can install desired PTM patterns into histone H3 on nucleosomes in vitro and in cellulo. This study expands the application scope of sortase from ligation to metathesis in live cells using cell-penetrating peptides (CPPs). In addition, it offers a strategy to edit PTMs of cellular histone H3 with potential for the development of precise epigenome editing.

Recombinant expression, biophysical and functional characterization of ClpS from Mycobacterium tuberculosis.

Intracellular proteolysis is attracting more and more attention for its unique and important character in Mycobacterium tuberculosis (Mt). The ClpS protein from Mt (MtClpS) plays a critical role in intracellular proteolysis by recognizing N-end rule substrates, which makes it become a potential target for antibacterial drugs. However, the molecular mechanism of MtClpS recognizing N-end rule substrates remains unclear. Preparation of highly concentrated and pure MtClpS protein is a prerequisite for further structural and functional studies. In the present work, we tried several fusion tags and various expression conditions to maximize the production of MtClpS in Escherichia coli. We established an efficient approach for preparing the MtClpS protein with a high yield of 24.7 mg/l and a high purity of 98%. After buffer screening, we obtained a stable MtClpS protein sample concentrated at 0.63 mM in the presence of glycerol, l-Arginine, and l-Glutamate. Moreover, circular dichroism characterization indicated that the secondary structure of MtClpS consists of 38% α-helix and 24% ß-sheet. The 2D 1H-15N HSQC nuclear magnetic resonance spectrum showed a good dispersion of resonance peaks with uniform intensity, indicating that the purified MtClpS protein was well folded and conformationally homogeneous. Isothermal titration calorimetry experiments revealed significant interactions of MtClpS with N-end rule peptides beginning with Leu, Tyr, Trp, or Phe. Furthermore, residues D34, D35, and H66 were confirmed as key residues for MtClpS recognizing the N-end rule peptide. The successful expression and biophysical characterization of MtClpS enabled us to gain insight into the molecular mechanism of MtClpS recognizing N-end rule substrates. The obtained stable and pure recombinant MtClpS will enable future inhibitor screening experiments.

New insights on ecological roles of waste activated sludge in nutrient-stressed co-digestion.

There have been extensive applications of waste activated sludge (WAS) in anaerobic co-digestion (AcoD). Nonetheless, mechanisms through which AcoD systems maintain stability, particularly under nutrient-stressed conditions, are under-appreciated. In this study, the role of WAS in a nutrient-stressed WAS-food waste AcoD system was re-evaluated. Our findings demonstrated that WAS-based co-digestion increased methane production (by 20-60%) as WAS bolsters such systems' resilience via establishing a core niche-based microbial balance. The carbon utilization investigation suggested a microbial niche balance is attainable if two conditions are satisfied: 1) hydrolysis efficiency is greater than 50%; and 2) both the acidogenesis-to-hydrolysis and acetogenesis-to-hydrolysis efficiencies surpass 0.5. Metagenomic assembly genome (MAG) analysis indicated that the versatile metabolic characteristics strengthened the microbial niche balance, rendering the system resilient and efficient through a syntrophic mode, contributing to both acidogenesis and acetogenesis. The findings of this study provide new insights into the ecological effects of WAS on AcoD.

Carbon fixation via volatile fatty acids recovery from sewage sludge through electrochemical-pretreatment-based anaerobic digestion.

Capturing the carbon in volatile fatty acids (VFA) produced from the anaerobic digestion (AD) of sewage sludge has the potential to not only provide economic benefits but also reduce greenhouse gas production. This study demonstrates a chemical-free method to collect VFA from an AD instead of methane that involves electrochemical pretreatment (EPT) of sludge. Experimental results show that applying 15 V EPT for 45 min enhances acidogenesis and selectively inhibits methanogenesis, leading to a substantial VFA accumulation (2563.1 ± 307.9 mg COD/L) and achieving 2.5 times more carbon fixation than via methane production. Interfacial thermodynamic analysis shows that EPT induces a decrease in both the repulsive electrostatic energy (from 152.9 kT to 12.2 kT) and the energy barrier (from 57.0 kT to 2.6 kT) in the sludge, leading to increased sludge aggregation and entrapment of microorganisms. Molecular docking sheds lights on how the methanogens interacts with the organic matter released from EPT (e.g., alanine-tRNA ligase), showing that these interactions potentially interfere with the proteins that are associated with the activities of the methanogens and the electron transfer pathways, thereby impeding methanogenesis. Integrating EPT into AD therefore facilitates the recovery of valuable VFA and the capture of carbon from freshwater sludge, providing notable economic and environmental benefits in sewage sludge treatment.

Disentangling microbial niche balance and intermediates' trade-offs for anaerobic digestion stability and regulation.

Anaerobic digestion (AD) is a key technology for converting organic matters to methane-rich biogas. However, nutrient imbalance can destabilize the whole digestion. To realize stable operation of AD and improve its efficiency, this work considers a new strategy to control the intermediate concentrations of poor AD under nutrient stress. For this purpose, long-term digestion under different nutrient conditions was investigated. Results showed that the feedstock with a low C/N ratio (= 6) caused VFA accumulation (2072 ± 632 mg/L), leading to the inhibition of methane production. Employing a substrate with a higher C/N ratio (= 11) and/or adding NH4HCO3 (200 mg NH4+-N/Ladd) could alleviate the VFA inhibition, but excessive dosage of NH4HCO3 would induce ammonia inhibition. Through the established digestion balance between free ammonia nitrogen (FAN) between 0 and 25 mg/L, volatile fatty acid (VFA) 510-2100 mg/L, and alkalinity (ALK) 3300-7800 mg/L, an efficient methane yield of 150-250 mL/g VS was achieved and stable operation of AD under nutrient stress (low C/N ratio) was realized. Metabolic reconstruction between Euryarchaeota sp. MAG162, Methanosarcina mazei MAG53 and Mesotoga infera MAG119 highlighted that microbial niche balance was developed as a result of digestion balance, which is beneficial for stable operation of AD. These findings improved our understanding of the interaction mechanism between intermediates and microbial niches for stability control in AD.

Sulfur bacteria-reinforced microbial electrochemical denitrification.

Two limiting factors of microbial electrochemical denitrification (MED) are the abundance and efficiency of the functional microorganisms. To supply these microorganisms, MED systems are inoculated with denitrifying sludge, but such method has much room for improvement. This study compared MED inoculated with autotrophic denitrifying inoculum (ADI) versus with heterotrophic denitrifying inoculum (HDI). ADI exhibited electroactivity for 50% less of timethan HDI. The denitrification efficiency of the ADI biocathode was42% higherthan that of the HDI biocathode. The HDI biocathode had high levels of polysaccharides while the ADI biocathode was rich in proteins, suggesting that two biocathodes may achieveMED but via differentpathways. Microbial communities of two biocathodes indicated MED of HDI biocathode may rely on interspecies electron transfer, whereas sulfur bacteria of ADI biocathode take electrons directly from the cathode to achieve MED. Utilizing autotrophic sulfur-oxidizing denitrifiers, this study offers a strategy for enhancing MED.

Innovative biomaterials for food packaging: Unlocking the potential of polyhydroxyalkanoate (PHA) biopolymers.

Polyhydroxyalkanoate (PHA) biopolyesters show a good balance between sustainability and performance, making them a competitive alternative to conventional plastics for ecofriendly food packaging. With an emphasis on developments over the last decade (2014-2024), this review examines the revolutionary potential of PHAs as a sustainable food packaging material option. It also delves into the current state of commercial development, competitiveness, and the carbon footprint associated with PHA-based products. First, a critical examination of the challenges experienced by PHAs in terms of food packaging requirements is undertaken, followed by an assessment of contemporary strategies addressing permeability, mechanical properties, and processing considerations. The various PHA packaging end-of-life options, including a comprehensive overview of the environmental impact and potential solutions will also be discussed. Finally, conclusions and future perspectives are elucidated with a view of prospecting PHAs as future green materials, with a blend of performance and sustainability of food packaging solutions.

From micro to macro: The role of seawater in maintaining structural integrity and bioactivity of granules in treating antibiotic-laden mariculture wastewater.

Granular sludge (GS) has superior antibiotic removal ability to flocs, due to GS's layered structure and rich extracellular polymeric substances. However, prolonged exposure to antibiotics degrades the performance and stability of GS. This study investigated how a seawater matrix might help maintain the structural integrity and bioactivity of granules. The results demonstrated that GS had better sulfadiazine (SDZ) removal efficiency in a seawater matrix (85.6 %) than in a freshwater matrix (57.6 %); the multiple ions in seawater enhanced boundary layer diffusion (kiR1 = 0.0805 mg·g-1·min-1/2 and kiR2 = 0.1112 mg·g-1·min-1/2) and improved adsorption performance by 15 % (0.123 mg/g-SS freshwater vs. 0.141 mg/g-SS seawater). Moreover, multiple hydrogen bonds (1-3) formed between each SDZ and lipid bilayer fortified the adsorption. Beyond S-N and S-C bond hydrolyses that took place in freshwater systems, there was an additional biodegradation pathway for GS to be cultivated in a saltwater system that involved sulfur dioxide extrusion. This additional pathway was attributable to the greater microbial diversity and larger presence of sulfadiazine-degrading bacteria containing SadAC genes, such as Leucobacter and Arthrobacter, in saltwater wastewater. The findings of this study elucidate how seawater influences GS properties and antibiotic removal ability.

Physicochemical changes in microplastics and formation of DBPs under ozonation.

Microplastics (MPs) are substances that pose a risk to both human life and the environment. Their types and production are increasing year on year, and their potential to cause environmental pollution is a worldwide concern. Conventional water treatment processes, particularly coagulation and sedimentation, are not effective at removing all MPs. It is therefore important to assess the morphological changes in the MPs, i.e., the thermoplastic polyurethane (TPU) and polyethylene (PE), during ozonation and the dissolved organic carbon leaching as well as chloroform formation in the subsequent chlorination. The results show that the appearance and surface chemistry of the MPs changed during the ozonation process, most notably for TPU. The trichloromethane (CHCl3) generation during chlorination was 0.168 and 0.152 µmol/L for TPU and PE, respectively, and the ozone pretreatment significantly increased the CHCl3 yield of TPU, while it had a weak effect on PE. Additional disinfection byproducts (DBPs), including CHCl2Br, CHClBr2, and CHBr3, were produced in the presence of bromide ions in the water column, and the total amount of DBPs produced by PE, PE-O, TPU, and TPU-O was significantly increased to 0.787, 0.814, 0.931, and 1.391 µmol/L, respectively. The study provides useful information for the environmental risk assessment of two representative MPs, i.e., TPU and MPs, in disinfection procedures for drinking water.

Structure of a SIN3-HDAC complex from budding yeast.

SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 Å. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.

Transiting from the inhibited steady-state to the steady-state through the ammonium bicarbonate mediation in the anaerobic digestion of low-C/N-ratio food wastes.

The current study aimed to determine the effects of NH4+ on anaerobic digestion (AD) metabolism and the feasibility of using NH4HCO3 to improve methane production in an AD system when treating a low-C/N-ratio food waste (FW). Increasing the ammonium concentration (500-1000 mg NH4Cl-N/L) added into the AD system did not limit the methane production but caused the volatile fatty acid (VFA) accumulation, forming an "inhibited steady-state" system. The addition of 200 mg NH4HCO3-N/L increased methane yield by 20% by aiding the microbial oxidation of VFAs. The high acetate content (65-85%) and abundance of acetoclastic methanogens (Methanosaeta and Methanosarcina) indicated an efficient acetoclastic methanogenesis process, which was facilitated by NH4HCO3. The long-term operation of the AD system demonstrated that NH4HCO3, at a concentration of 200 mg N/L, was capable of forming an active buffer system with NH4+ and VFAs, enhancing methane production (221 ± 86 mL/g VS).

Alleviating nutrient imbalance of low carbon-to-nitrogen ratio food waste in anaerobic digestion by controlling the inoculum-to-substrate ratio.

Food waste (FW) characterized by a low carbon/nitrogen (C/N) ratio ranging between 6 and 19 was used to investigate the feasibility and mechanism of maneuvering inoculum-to-substrate ratio (ISR) to alleviate the metabolic imbalance caused by imbalanced nutrients in the AD process, through biochemical methane potential tests and methanogenic pathway analysis. The maximum methane yield of 0.4 L/g of volatile solid (VS) was obtained at a C/N ratio of 11 and an ISR of 10:3. Increasing ISR from 1:2 to 10:3 promoted methane production by ∼20% via an enhancement in acetoclastic methanogenesis and the hydrolysis of carbohydrates and proteins. At lower ISR < 1, hydrogenotrophic methanogenic and syntrophic bacteria dominated, and methane production decreased by âˆ¼ 20% due to the energy disadvantages of syntrophic methanogenesis. Efficient digestion of FW with low C/N ratio FW could be achieved by using metabolic pathways to regulate it and increasing ISR from 1:1 to 10:3.

Investigating the response of electrogenic metabolism to salinity in saline wastewater treatment for optimal energy output via microbial fuel cells.

In the current study, MFCs treating saline wastewater with the different conductivities of 5.0 ± 0.2, 7.7 ± 0.6, 10.5 ± 0.9, 13.0 ± 1.0, 15.3 ± 1.0, and 16.0 ± 0.1 mS/cm were investigated. Increasing salinity drives a considerable shift of microbial communities, and it also affects metabolic pathways in MFCs. Overwhelming acetate oxidizing electron transfer with moderate conductivities between 7.7 and 13.0 mS/cm led to high energy outputs. Power generation at the low conductivities of less than 7.7 mS/cm was restricted by the competition between fermentative bacteria (e.g., Lactobacillus) and exoelectrogens (e.g., Pseudomonas and Shewanella) for substrate utilization. Increasing salinity beyond 13 mS/cm suppressed the fermentation of glucose to butyrate. It also induced sulfidogenesis; sulfide oxidizing bacteria Desulfovibrio (5.2%), Desulfuromonas (3.7%) and exoelectrogen Pseudomonas (1.1%) formed a sulfur-driven current production, thereby resulting in low energy outputs. The present study revealed the effects of ionic conductivity on electrical energy production and provided insights into the dynamics of the MFCs substrate utilization.

Pin-point denitrification for groundwater purification without direct chemical dosing: Demonstration of a two-chamber sulfide-driven denitrifying microbial electrochemical system.

The nitrate concentration in groundwater has been increasing over time due to the intensive use of nitrogen fertilizer. Current nitrate removal technologies are restricted by the high operational cost or the inevitable secondary contaminations. This study proposed a two-chamber sulfide-driven denitrifying microbial electrochemical system to denitrify nitrate in its cathode chamber. Instead of conventional organic substrates, sulfide is oxidized in the anode chamber to generate electrons for cathodic denitrification. Long-term performance of this novel system was evaluated over 200 days (100 cycles) of batch-fed operation. With the assistance of anodic microorganisms, sulfide can be directly oxidized to sulfate thus avoiding passivating the anode. Catalyzed by the cathodic microorganisms, complete denitrification was realized with neither nitrite nor nitrous oxide accumulation. Benefiting from the electroautotrophic behavior of the functional microorganisms, high electron utilization efficiencies were achieved, 80% and 85% for the anode (sulfide oxidation) and the cathode (denitrification) respectively. Both observed electrode potentials and microbial analyses revealed that cytochrome c is the crucial electron transfer mediator in the cathodic electron transfer for denitrification. Based on the analysis of planktonic and biofilm microbial samples, anodic and cathodic extracellular electron transfer bioprocesses are proposed, both the direct and mediated electron transfers involved, as were revealed by immobilized and planktonic functional microorganisms, respectively. This study demonstrates the feasibility of purifying nitrate-contaminated groundwater without sacrificing its water quality in a separate mode of treatment. This concept can be extended to a broader field, in which the water requires bio-polishing without introducing unwanted secondary pollution like the post-denitrification of wastewater effluents.