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N 6 -methyladenosine (m 6 A), the most prevalent internal RNA modification on mammalian messenger RNAs, regulates the fates and functions of modified transcripts through m 6 A-specific binding proteins 1 – 5 . In the nervous system, m 6 A is abundant and modulates various neural functions 6 – 11 . Whereas m 6 A marks groups of mRNAs for coordinated degradation in various physiological processes 12 – 15 , the relevance of m 6 A for mRNA translation in vivo remains largely unknown. Here we show that, through its binding protein YTHDF1, m 6 A promotes protein translation of target transcripts in response to neuronal stimuli in the adult mouse hippocampus, thereby facilitating learning and memory. Mice with genetic deletion of Ythdf1 show learning and memory defects as well as impaired hippocampal synaptic transmission and long-term potentiation. Re-expression of YTHDF1 in the hippocampus of adult Ythdf1 -knockout mice rescues the behavioural and synaptic defects, whereas hippocampus-specific acute knockdown of Ythdf1 or Mettl3 , which encodes the catalytic component of the m 6 A methyltransferase complex, recapitulates the hippocampal deficiency. Transcriptome-wide mapping of YTHDF1-binding sites and m 6 A sites on hippocampal mRNAs identified key neuronal genes. Nascent protein labelling and tether reporter assays in hippocampal neurons showed that YTHDF1 enhances protein synthesis in a neuronal-stimulus-dependent manner. In summary, YTHDF1 facilitates translation of m 6 A-methylated neuronal mRNAs in response to neuronal stimulation, and this process contributes to learning and memory. Neuronal stimulation induces protein translation of m 6 A-methylated neuronal mRNAs facilitated by YTHDF1, and this process contributes to learning and memory.

Lysine lactylation (Kla) has recently been reported to participate in regulating transcription in human cells. However, the characterization, regulatory mechanism and functional consequence of Kla in prokaryotes remain unclear. Here, we report that YiaC functions as a lysine lactylase and that CobB serves as a lysine delactylase in the regulation of metabolism. We demonstrate that YiaC catalyzes the addition of Kla, while CobB erases this PTM both in vitro and intracellularly. Moreover, we show that YdiF can catalyze the formation of a lactyl-coenzyme A, which donates lactyl group for Kla. Quantitative proteomic analysis further reveals 446 endogenous Kla sites targeted by CobB and 79 candidates targeted by YiaC in Escherichia coli ( E. coli ). Furthermore, we present that Kla can influence the functions of metabolic enzymes. Interestingly, we demonstrate that CobB can specifically modulate the activity of PykF by regulating K382la, promoting glycolysis and bacterial growth. Our study identifies the regulatory enzymes and functional network of Kla and reveals a Kla-mediated molecular mechanism catalyzed by CobB for glycolysis regulation in E. coli . The characterization of lysine lactylation (Kla) in prokaryotes remains unclear. Here, the authors identify the regulatory enzymes (YiaC as a lactylase and CobB as a delactylase) and functional network of Kla and reveal a Kla-mediated molecular mechanism for glycolysis regulation in Escherichia coli.

Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. We show that HBO1 catalyzes the addition of Kla in vitro and intracellularly, and E508 is a key site for the lactyltransferase activity of HBO1. Quantitative proteomic analysis further reveals 95 endogenous Kla sites targeted by HBO1, with the majority located on histones. Using site-specific antibodies, we find that HBO1 may preferentially catalyze histone H3K9la and scaffold proteins including JADE1 and BRPF2 can promote the enzymatic activity for histone Kla. Notably, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on transcription start sites (TSSs). Besides, the regulated Kla can promote key signaling pathways and tumorigenesis, which is further supported by evaluating the malignant behaviors of HBO1- knockout (KO) tumor cells, as well as the level of histone H3K9la in clinical tissues. Our study reveals HBO1 serves as a lactyltransferase to mediate a histone Kla-dependent gene transcription. The regulatory mechanism and functional consequence of lysine lactylation remain to be explored. Here, the authors identify HBO1 as a lysine lactyltransferase and suggest a potential role of HBO1 in tumorigenesis through H3K9la-mediated transcription regulation.

Mass-spectrometry (MS)-based proteomics has evolved into a powerful tool for comprehensively analysing biological systems. Recent technological advances have markedly increased sensitivity, enabling single-cell proteomics and spatial profiling of tissues. Simultaneously, improvements in throughput and robustness are facilitating clinical applications. In this Review, we present the latest developments in proteomics technology, including novel sample-preparation methods, advanced instrumentation and innovative data-acquisition strategies. We explore how these advances drive progress in key areas such as protein–protein interactions, post-translational modifications and structural proteomics. Integrating artificial intelligence into the proteomics workflow accelerates data analysis and biological interpretation. We discuss the application of proteomics to single-cell analysis and spatial profiling, which can provide unprecedented insights into cellular heterogeneity and tissue architecture. Finally, we examine the transition of proteomics from basic research to clinical practice, including biomarker discovery in body fluids and the promise and challenges of implementing proteomics-based diagnostics. This Review provides a broad and high-level overview of the current state of proteomics and its potential to revolutionize our understanding of biology and transform medical practice. This Review summarizes advances in mass-spectrometry-based proteomics and explores the potential applications of these technologies in the clinic.

Key Points Bacterial proteins can be damaged by oxidants that are present in the environment. Cys and Met residues are easily oxidized. Bacterial cells have a range of proteins that repair oxidized proteins. Thioredoxins (Trxs) and glutaredoxins (Grxs) repair oxidized cysteine residues. Methionine sulfoxide reductases (Msrs) repair oxidized methionine residues. Antioxidant defences are present in the bacterial cytoplasm and in extracytoplasmic compartments. Oxidative damage can have a devastating effect on the structure and activity of proteins, leading to cell death. This Review discusses how bacteria repair oxidized proteins and highlights the importance of these repair systems in physiology and virulence. Oxidative damage can have a devastating effect on the structure and activity of proteins, and may even lead to cell death. The sulfur-containing amino acids cysteine and methionine are particularly susceptible to reactive oxygen species (ROS) and reactive chlorine species (RCS), which can damage proteins. In this Review, we discuss our current understanding of the reducing systems that enable bacteria to repair oxidatively damaged cysteine and methionine residues in the cytoplasm and in the bacterial cell envelope. We highlight the importance of these repair systems in bacterial physiology and virulence, and we discuss several examples of proteins that become activated by oxidation and help bacteria to respond to oxidative stress.

Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes. A review of the recent developments in reprogramming the genetic code of cells and organisms to include non-canonical amino acids in precisely engineered proteins. Rewriting genetic guidelines In living organisms, proteins that are encoded by DNA are composed of 20 canonical amino acids, with some organisms using up to two additional derivatives. Theoretically, other molecules that are related to these amino acids could form a similar protein backbone and might confer new properties on the proteins. Jason Chin reviews the most recent studies on reprogramming the genetic code, where progress is being made in incorporating these non-canonical (that is, not naturally occurring) amino acids into proteins, even using the cell's own machinery to do so, and without disrupting overall protein function.

Covalent organic frameworks (COFs) as drug-delivery carriers have been mostly evaluated in vitro due to the lack of COFs nanocarriers that are suitable for in vivo studies. Here we develop a series of water-dispersible polymer-COF nanocomposites through the assembly of polyethylene-glycol-modified monofunctional curcumin derivatives (PEG-CCM) and amine-functionalized COFs (APTES-COF-1) for in vitro and in vivo drug delivery. The real-time fluorescence response shows efficient tracking of the COF-based materials upon cellular uptake and anticancer drug (doxorubicin (DOX)) release. Notably, in vitro and in vivo studies demonstrate that PEG-CCM@APTES-COF-1 is a smart carrier for drug delivery with superior stability, intrinsic biodegradability, high DOX loading capacity, strong and stable fluorescence, prolonged circulation time and improved drug accumulation in tumors. More intriguingly, PEG 350 -CCM@APTES-COF-1 presents an effective targeting strategy for brain research. We envisage that PEG-CCM@APTES-COF-1 nanocomposites represent a great promise toward the development of a multifunctional platform for cancer-targeted in vivo drug delivery. Despite their potential application as drug-delivery carriers, covalent organic frameworks (COF) have been only evaluated in vitro. Here the authors show by real time tracking in vivo the cell uptake of anticancer-drug loaded and water dispersible COFs.

Scrophularia striata , commonly known as figwort, is one of the most important medicinal plants that mainly grows in cold regions of the Zagros Mountains (West of Iran). Although the chemical composition of this plant species has not yet been explored, people living in Ilam province (W Iran) have used it for many years to treat different illnesses. The present study aims to analyze the effect of some ecological factors on the antioxidant potential and the amount of phenol present in this plant species, using a random factorial design with two factors (elevation and region) and three replicates. The fruits of the plant were gathered from three different elevations. They were collected from three regions of the Ilam province (Badreh, Dareshahr, and Dehloran) in June 2016, when the fruits appear. Moreover, to analyze different soil chemical and physical features, soil samples were gathered from a depth of 0.5 m under the shrubs. The antioxidant action of the methanol extract from the plant samples and the total amount of phenol compounds were measured using 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and the Folin-Ciocalteu method, respectively. The results showed that the effects of site and elevation, and the interaction between these factors, on the antioxidant potential and total phenol amount were significant with a probability of error of 1%. The maximum extract efficiency (19.37 ± 3.07%), antioxidant potential (126.5656 ± 0.96 µg/mL), and total amount of phenol (55.7689 ± 3.17 µg/mL) were obtained from Dareshahr at an elevation of 600 m above mean sea level. The minimum amount of total phenol (24.6544 ± 3.21 µg/ml) was recorded at the lowest elevation of Badreh, at which phosphorus, potassium, organic carbon, organic material, nitrogen, acidity, lime, and silt were present at the lowest amount. However, the antioxidant activity and total amount of phenol had a strong direct correlation in the two districts of Dareshahr and Badreh, but were reversely and strongly correlated in Dehloran. Therefore, it can be stated that Scrophularia striata has the potential for antioxidant activity, however, the complexity of the effect of ecological factors on one hand, and the emergence of different chemical processes in the plant under such effects on the other hand, has led to the synthesis of different compounds with antioxidant potential in the plant in different regions.

In the present paper, Graphene Oxide (GO) particles were prepared via Hummer method, and used in synthesis of composite membranes. Polyethersulfone (PES) nanocomposite membranes were synthesized via wet phase inversion technique, and using water as non-solvent. The membrane morphology was investigated using scanning electron microscopy (SEM). Change in the membrane surface hydrophilicity after modification was studied using contact angle measurements. The performance of fabricated PES nanocomposite membranes was measured by evaluating pure water flux, salt rejection, dye retention and heavy metals removal. The results indicated that by increasing the filler percentage up to 5 wt.%, the contact angle between the water droplet and the membrane surface was decreased and the droplet was more dispersed on the membrane surface which implies higher hydrophilicity of the prepared nanocomposite membranes. Moreover, the experimental results corroborated that addition of GO to the membrane significantly improved the pure water flux, salt rejection and heavy metals removal, and can be used as a novel methodology for preparation of high performance membranes in water treatment.

Butyrate and R-β-hydroxybutyrate are two related short chain fatty acids naturally found in mammals. Butyrate, produced by enteric butyric bacteria, is present at millimolar concentrations in the gastrointestinal tract and at lower levels in blood; R-β-hydroxybutyrate, the main ketone body, produced by the liver during fasting can reach millimolar concentrations in the circulation. Both molecules have been shown to be histone deacetylase (HDAC) inhibitors, and their administration has been associated to an improved metabolic profile and better cellular oxidative status, with butyrate inducing PGC1α and fatty acid oxidation and R-β-hydroxybutyrate upregulating oxidative stress resistance factors FOXO3A and MT2 in mouse kidney. Because of the chemical and functional similarity between the two molecules, we compared here their impact on multiple cell types, evaluating i) histone acetylation and hydroxybutyrylation levels by immunoblotting, ii) transcriptional regulation of metabolic and inflammatory genes by quantitative PCR and iii) cytokine secretion profiles using proteome profiling array analysis. We confirm that butyrate is a strong HDAC inhibitor, a characteristic we could not identify in R-β-hydroxybutyrate in vivo nor in vitro . Butyrate had an extensive impact on gene transcription in rat myotubes, upregulating PGC1α, CPT1b, mitochondrial sirtuins (SIRT3-5), and the mitochondrial anti-oxidative genes SOD2 and catalase. In endothelial cells, butyrate suppressed gene expression and LPS-induced secretion of several pro-inflammatory genes, while R-β-hydroxybutyrate acted as a slightly pro-inflammatory molecule. Our observations indicate that butyrate induces transcriptional changes to a higher extent than R-β-hydroxybutyrate in rat myotubes and endothelial cells, in keep with its HDAC inhibitory activity. Also, in contrast with previous reports, R-β-hydroxybutyrate, while inducing histone β-hydroxybutyrylation, did not display a readily detectable HDAC inhibitor activity and exerted a slight pro-inflammatory action on endothelial cells.