Enzyme In Pathway Research Articles

RNAseq and targeted metabolomics implicate RIC8 in regulation of energy homeostasis, amino acid compartmentation, and asexual development in Neurospora crassa

ABSTRACT Heterotrimeric G protein signaling pathways control growth and development in eukaryotes. In the multicellular fungus Neurospora crassa , the guanine nucleotide exchange factor RIC8 regulates heterotrimeric Gα subunits. In this study, we used RNAseq and liquid chromatography-mass spectrometry (LC-MS) to profile the transcriptomes and metabolomes of N. crassa wild type, the Gα subunit mutants Δ gna-1 and Δ gna-3 , and Δ ric8 strains. These strains exhibit defects in growth and asexual development (conidiation), with wild-type and Δ gna-1 mutants producing hyphae in submerged cultures, while Δ gna-3 and Δ ric8 mutants develop conidiophores, particularly in the Δ ric8 mutant. RNAseq analysis showed that the Δ gna-1 mutant possesses 159 mis-regulated genes, while Δ gna-3 and Δ ric8 strains have more than 1,000 each. Many of the mis-regulated genes are involved in energy homeostasis, conidiation, or metabolism. LC-MS revealed changes in levels of primary metabolites in the mutants, with several arginine metabolic intermediates impacted in Δ ric8 strains. The differences in metabolite levels could not be fully explained by the expression or activity of pathway enzymes. However, transcript levels for two predicted vacuolar arginine transporters were affected in Δ ric8 mutants. Analysis of arginine and ornithine levels in transporter mutants yielded support for altered compartmentation of arginine and ornithine between the cytosol and vacuole in Δ ric8 strains. Furthermore, we validated previous reports that arginine and ornithine levels are low in wild-type conidia. Our results suggest that RIC8 regulates asexual sporulation in N. crassa at least in part through altered expression of vacuolar transporter genes and the resultant mis-compartmentation of arginine and ornithine. IMPORTANCE Resistance to inhibitors of cholinesterase-8 (RIC8) is an important regulator of heterotrimeric Gα proteins in eukaryotes. In the filamentous fungus Neurospora crassa , mutants lacking ric8 undergo inappropriate asexual development (macroconidiation) during submerged growth. Our work identifies a role for RIC8 in regulating expression of transporter genes that retain arginine and ornithine in the vacuole (equivalent of the animal lysosome) and relates this function to the developmental defect. Arginine is a critical cellular metabolite, both as an amino acid for protein synthesis and as a precursor for an array of compounds, including proline, ornithine, citrulline, polyamines, creatine phosphate, and nitric oxide. These results have broad relevance to human physiology and disease, as arginine modulates immune, vascular, hormonal, and other functions in humans.

Studies on the Oxidative Damage of the Wobble 5-Methylcarboxymethyl-2-Thiouridine in the tRNA of Eukaryotic Cells with Disturbed Homeostasis of the Antioxidant System

We have previously shown that 2-thiouridine (S2U), either as a single nucleoside or as an element of RNA chain, is effectively desulfurized under applied in vitro oxidative conditions. The chemically induced desulfuration of S2U resulted in two products: 4-pyrimidinone nucleoside (H2U) and uridine (U). Recently, we investigated whether the desulfuration of S2U is a natural process that also occurs in the cells exposed to oxidative stress or whether it only occurs in the test tube during chemical reactions with oxidants at high concentrations. Using different types of eukaryotic cells, such as baker’s yeast, human cancer cells, or modified HEK293 cells with an impaired antioxidant system, we confirmed that 5-substituted 2-thiouridines are oxidatively desulfurized in the wobble position of the anticodon of some tRNAs. The quantitative LC-MS/MS-MRMhr analysis of the nucleoside mixtures obtained from the hydrolyzed tRNA revealed the presence of the desulfuration products of mcm5S2U: mcm5H2U and mcm5U modifications. We also observed some amounts of immature cm5S2U, cm5H2U and cm5U products, which may have indicated a disruption of the enzymatic modification pathway at the C5 position of 2-thiouridine. The observed process, which was triggered by oxidative stress in the living cells, could impair the function of 2-thiouridine-containing tRNAs and alter the translation of genetic information.

Targeting Candida albicans O-acetyl-L-homoserine sulfhydrylase (Met15p) in antifungal treatment.

Fungal infections are a serious threat to public health as they are becoming increasingly frequent. A major problem stems also from a rising fungal resistance to currently available antifungal therapies, therefore novel molecular targets are highly desirable. Exploration of enzymes participating in the biosynthesis pathways of essential amino acids such as L-methionine (L-Met) may provide new insights into pharmaceutical development. The MET15 gene from Candida albicans, encoding O-acetyl-L-homoserine sulfhydrylase (Met15p), an enzyme catalyzing the second step in that pathway, was cloned and expressed in two versions: as N and C-terminal oligo-His-tagged fusion proteins. The recombinant enzymes revealed appropriate activity, and catalyzed conversion of O-acetyl-L-homoserine and a sulfide ion to produce L-homocysteine. A new RP-HPLC-DAD method, using the enzymatic reaction product pre-column derivatization with 5,5'-dithio-bis-(2-nitrobenzoic acid) was developed and used by us to determine Met15p activity. Newly synthesized compounds as well as two commercially available exhibited a Met15p inhibitory effect which was related to antifungal activity. Fungal cells' sensitivity to inhibitors depending on the presence or absence of L-Met in the medium clearly indicated Met15p targeting. Moreover, the synergistic effect of the first methionine biosynthetic enzyme affecting inhibitor and Met15p inhibitors indicate that methionine biosynthesis pathway enzymes are promising molecular targets.

The Impact of Soil Dry–Wet Cycles on the Mineralization of Soil Organic Carbon and Total Nitrogen in Check Dams of the Loess Plateau

Frequent soil drying and wetting cycles significantly affect the mineralization processes of soil organic carbon (SOC) and total nitrogen (STN), impacting soil quality and contributing to nutrient loss. However, the effects of these dry–wet cycles on SOC and STN mineralization in dam soil are not well understood. This study simulated four consecutive wet–dry cycles under five soil moisture gradients of 0% (CK), 5%, 10%, 15%, and 100%, and 100%, across four cycles of 7, 14, 21, and 28 days, to investigate the effects on soil aggregates, enzyme activities, and the mineralization of SOC and STN. The results indicated that soil enzyme activity peaked after two dry–wet cycles and then began to decline. The dry–wet cycles reduced the proportion of soil macro-aggregates while also decreasing the proportions of small and micro-aggregates. In contrast, the 100% treatment conditions exhibited the opposite effect. Dry–wet cycles enhanced the mineralization rates of SOC and STN, with the average mineralization rates under the 10% soil moisture content being the highest—1.78 and 2.38 times greater than the CK treatment for SOC and STN, respectively. The impact of dry–wet cycles on SOC and STN mineralization through the enzyme pathway was greater than through the aggregate pathway. These research findings provide theoretical insights and scientific references for the efficient operation and ecological protection of sedimentation dams in the Loess Plateau.

Effects of Melatonin Pre- and Post-Drought Treatment on Oxidative Stress Markers and Expression of Proline-Related Transcripts in Young Wheat Plants

Wheat can tolerate a mild water deficit, but prolonged drought causes a number of detrimental physiological changes resulting in a substantial decrease in productivity. The present study evaluates the potential of the natural plant growth regulator melatonin to alleviate the negative effects of moderate drought in two Bulgarian winter wheat cultivars at the early vegetative stage. Melatonin doses of 75 µM were root-supplemented 24 h before or after the stress period. The levels of several biometric parameters, osmolyte content and stress indicators as well as the expression of genes coding for key enzymes of the proline biosynthesis pathway were analyzed in leaves at the end of the drought stress and after two and four days of recovery. Applied alone, melatonin did not exert significant effects on most of the monitored parameters. Water deprivation negatively affected seedlings’ fresh weight and water content and increased the stress markers and osmolyte levels. These were accompanied by a high accumulation of TaP5CS and TaP5CR transcripts coding for the enzymes Δ-pyrroline-5-carboxylate synthase and Δ-pyrroline-5-carboxylate reductase, respectively. The effect of melatonin in reducing drought stress was similar whether applied before or after exposure, though slightly more effective when used as a pre-treatment.

Structural, biophysical, and biochemical insights into C–S bond cleavage by dimethylsulfone monooxygenase

Sulfur is an essential element for life. Bacteria can obtain sulfur from inorganic sulfate; but in the sulfur starvation-induced response, Pseudomonads employ two-component flavin-dependent monooxygenases (TC-FMOs) from the msu and sfn operons to assimilate sulfur from environmental compounds including alkanesulfonates and dialkylsulfones. Here, we report binding studies of oxidized FMN to enzymes involved within the P. fluorescens enzymatic pathway responsible for converting dimethylsulfone (DMSO2) to sulfite. In this catabolic pathway, SfnG serves as the initial TC-FMO for sulfur assimilation, which is investigated in detail by solving the 2.6-Å resolution crystal structure of unliganded SfnG and the 1.75-Å resolution crystal structure of the SfnG ternary complex containing FMN and DMSO2. We find that SfnG adopts a (β/α)8 barrel fold with a distinct quaternary configuration from other tetrameric class C TC-FMOs. To probe the unexpected tetramer arrangement, structural heterogeneity is assessed by chromatography and light scattering to confirm ligand binding correlates with a tetramer. Binding of FMN and DMSO2 accompanies ordering of the active site, with DMSO2 bound on the si-face of the flavin. A previously unobserved protein backbone conformation is found within the oxygen-binding site on the re-face of the flavin. Functional assays and the positioning of ligands with respect to the oxygen-binding site are consistent with use of an N5-(hydro)peroxyflavin pathway. Biochemical endpoint assays and docking studies reveal SfnG breaks the C-S bond of a range of dialkylsulfones.

IMMU-58. BCAT1 TARGETED METABOLIC REPROGRAMMING PLAYS CRITICAL ROLES IN MODULATING MYELOID DERIVED SUPPRESSOR CELL FUNCTION IN GLIOBLASTOMA

Abstract A key component that has limited the efficacy of immunotherapy in glioblastoma (GBM) is the significant infiltration of immunosuppressive myeloid cells. Our previous work characterized myeloid derived suppressor cells (MDSCs) unique to GBM that drive tumor growth and immune suppression. Transcriptomic and flow cytometric analyses demonstrated that the most induced programs in these MDSCs are dominated by metabolic and mTOR pathways. Therefore, we aimed to understand the role of metabolic reprogramming in MDSC differentiation and immunosuppressive function. Using single cell RNA sequencing, we identified overexpression of enzymes and transporters involved in branched-chain amino acid (BCAA) metabolism, notably branched chain aminotransferase 1 (BCAT1), the first enzyme in the metabolic pathway. Intriguingly, this was only found in specific populations of early and monocytic MDSCs (E-MDSCs, M-MDSCs), and not polymorphonuclear MDSCs (PMN-MDSCs). Using established MDSC modeling systems, we found that M-MDSC differentiation and T cell suppressive function are dependent on BCAAs and can be hindered by pharmacological inhibition of BCAT1 activity or genetic knockout of BCAT1. We also establish that the influence of BCAA on M-MDSC function is specifically reliant on the BCAT1-mediated step of BCAA metabolism. To determine the underlying mechanism driving BCAT1’s impact on M-MDSC function, we evaluated the activity of signaling pathways known to be critical to M-MDSCs including the mTORC1 pathway. We found that the impact of BCAA and BCAT1 activity on M-MDSC function is abrogated by inhibition of mTORC1 pathway with reduction in M-MDSC differentiation and activity. Consistent with our single cell RNA sequencing analysis, modulation of BCAA levels and BCAT1 activity had no impact on PMN-MDSCs. Our results underscore the critical role of BCAT1 in preferentially modulating M-MDSC activity through mTORC1 signaling. Our finding paves the way for discovery of a targetable therapeutic approach to harness immunometabolism in myeloid cells to develop novel immune therapies.

Comparative transcriptomic analysis provides insights into the regulation of root-specific saponin production in Panax japonicus.

Panax japonicus, a traditional medicinal plant from the Araliaceae family, produces bioactive triterpenes with health benefits. In Traditional Chinese Medicine, its roots have been used, but the chemical basis of its medicinal use is unclear, particularly regarding the metabolism and regulation of triterpene saponin biosynthesis. This study employed an integrative approach using Ultra Performance Liquid Chromatography (UPLC) and transcriptome analysis. Our UPLC analysis showed that ginsenoside Ro and chikusetsusaponin IVa were mainly detected in P. japonicus root. Subsequently, a comparative transcriptome analysis of four P. japonicus tissues (roots, leaves, flowers and fruits) was conducted using Illumina sequencing. As a result, 90,985 unigenes were functionally annotated from a total of 211,650 assembled non-redundant transcripts. Among these, 42,829 unigenes were annotated in NR database. Tissue-specific gene analysis revealed that roots had the highest number of specifically expressed unigenes (11,832). The majority of these unigenes were associated with metabolic processes. Additionally, tissue expression patterns analysis for three common transcription factor families indicated that WRKY family genes showed a significantly root-specific expression pattern, potentially playing a role in triterpene saponin biosynthesis. Notably, we investigated the expression profiles of genes related to the biosynthesis of triterpene saponins and found that four genes, ACCT, HMGS, HMGR and SS, encoding key enzymes in triterpene saponins biosynthesis pathway, were primarily expressed in the root. Overall, our study provides a set of P. japonicus tissue transcriptome data, which will aid in the discovery of triterpene saponin biosynthetic genes and offers valuable genetic information for this medical plant.

Exploring the Reactivity of High Valent Iron Intermediates in Water

The exceptional reactivity observed in non‐heme iron enzymes can be attributed to their capability to access high‐valent iron oxygen species in their active site. Numerous inorganic model complexes have been reported to date, providing insights into the intricate structural and spectroscopic features of many iron‐containing enzymes and advancing our understanding of their enzymatic reaction pathways. While the reactivities of synthetic iron complexes have been evaluated using various oxidants, the investigation into the formation of reactive intermediates has primarily focused on acetonitrile. However, water, which serves as the medium in biological systems, has been less frequently employed in these studies. Motivated by this, we conducted a comprehensive study on the generation of key reactive species using various oxidants with a model complex, [(BnTPEN)Fe(II)(OTf)]+ (1) (where BnTPEN = N‐benzyl‐N,N,N‐tris(2‐pyridylmethyl)‐1,2‐diaminoethane) in water, which yielded important findings. In water, a quantitative yield of Fe(IV)=O species was achieved with the oxidant NaIO4. Additionally, we observed an equilibrium between side‐on Fe(III)‐OO and Fe(III)‐OOH, with the latter eventually converting to Fe(IV)=O. The insights gained from this study are likely to be relevant in the chemistry of other Fe(II) complexes with polypyridyl pentadentate ligands.

CNSC-68. SEX DIFFERENCES IN GLYCINE BIOSYNTHESIS DRIVE RESPONSES TO COMBINED NUTRIENT DEPRIVATION AND PHARMACOLOGICAL INHIBITION IN PEDIATRIC HGG

Abstract In children and adults, high-grade gliomas (HGGs) are the most common and deadly primary brain malignancies. Generally, male HGGs occur at higher incidence and demonstrate more rapid proliferation, resulting in shorter overall male survival. Obscurity of molecular mechanisms driving this phenomenon prevents implementation of clinically effective treatments. Recently, a positive correlation between HGG cellular proliferation and metabolic reprogramming toward glycine biosynthesis was identified. By analyzing pediatric and adult HGG patient data, we discovered significantly worse outcomes unique to pediatric males bearing upregulation of serine and glycine biosynthesis transcripts. Previously, we have identified differential flux of glucose into serine and glycine biosynthesis drives sex differences in lung cancer. Therefore, we sought to confirm and target this paradigm in our NF1-/- DNp53 model of HGG. By performing metabolic tracing with [13C]-labeled glucose in male and female cells, we identified higher enrichment of [13C]-labeled serine and glycine in male cells relative to female cells. Through Western blotting, we identify male-specific upregulation of serine and glycine biosynthetic pathway enzymes in transformed cells, supporting our labelling results. Next, we sought to determine if inhibition of de-novo serine and glycine biosynthesis was similarly sex-biased. Utilizing serine-and-glycine-deprived media conditions, we identified a male-biased decrease in proliferation following pharmacological inhibition of de-novo serine and glycine biosynthesis. More precisely, in the absence of exogenous glycine, we discovered that inhibition of de-novo synthesis of glycine from serine drove male-specific decreases in proliferation. Additionally, we identified that transformed female cell robustness against inhibition of glycine biosynthesis is driven by the uptake of exogenous nucleotide precursors. These data confirm that sex differences in de-novo glycine biosynthesis drive sex differences in HGG cellular proliferation. As well, our work suggests that dietary restriction of serine and glycine, in-combination with pharmacological inhibition of de-novo glycine biosynthesis, represents a novel treatment paradigm.

Mevalonate pathway inhibition reduces bladder cancer metastasis by modulating RhoB protein stability and integrin β1 localization

The progression and outcome of bladder cancer (BLCA) are critically affected by the propensity of tumor metastasis. Our previous study revealed that activation of the mevalonate (MVA) pathway promoted migration of BLCA cells; however, the exact mechanism is unclear. Here we show that elevated expression of MVA pathway enzymes in BLCA cells, correlating with poorer patient prognosis by analyzing single-cell and bulk-transcriptomic datasets. Inhibition of the MVA pathway, either through knockdown of farnesyl diphosphate synthase (FDPS) or using inhibitors such as zoledronic acid or simvastatin, led to a marked reduction in BLCA cell migration. Notably, this effect was reversed by administering geranylgeranyl pyrophosphate (GGPP), not farnesyl pyrophosphate (FPP) or cholesterol, indicating the specificity of geranylgeranylation for cell motility. Moreover, we found that RhoB, a Rho GTPase family member, was identified as a key effector of the impact of the MVA pathway on BLCA metastasis. The post-translational modification of RhoB by GGPP-mediated geranylgeranylation influenced its protein stability through the ubiquitin-proteasome pathway. Additionally, overexpression of RhoB was found to block the membrane translocation of integrin β1 in BLCA cells. In summary, our findings underscore the role of the MVA pathway in BLCA metastasis, providing insights into potential therapeutic targets of this malignancy.

PAMK Ameliorates Non-Alcoholic Steatohepatitis and Associated Anxiety/Depression-like Behaviors Through Restoring Gut Microbiota and Metabolites in Mice

Objectives: Long-term Western diet-induced non-alcoholic steatohepatitis (NASH) can lead to liver cirrhosis and NASH-associated hepatocellular carcinoma, which are end-stage liver diseases. Meanwhile, NASH is associated with mental burden and worsens as the disease progresses. Atractylodes Macrocephala Koidz (AMK) is one of the main ingredients of Shenling Baizhu San, and the effect of Polysaccharide from AMK ameliorates (PAMK), as an important medicinal ingredient of AMK, on NASH and associated anxiety/depression-like behaviors is still unclear. Methods: This study investigated the protective effect of PAMK on NASH and associated anxiety/depression-like behaviors through a Western diet-induced NASH mice model. Results: showed that PAMK decreased the concentrations of liver TC, TG, and serum AST and ALT, improving glucose tolerance, and reducing liver steatosis and fibrosis. Moreover, the expression of liver IL-6, IL-1β, TNF-α, IL-18 and MCP-1 could be reduced by PAMK significantly. Additionally, PAMK decreased anxiety/depression-like behaviors and expression of IL-6, IL-1β, TNF-α, and MCP-1 in the hippocampus. 16S rRNA gene sequencing revealed that PAMK diminished the Firmicutes/Bacteroidetes ratio and abundance of Faecalibaculum_rodentium, and increased the abundance of Muribaculaceae. This might be related to gene abundance of Pentose, the glucuronate interconversions pathway and carbohydrate enzymes (GH1, GH4). Serum metabolomics suggested that PC (18:5e/2:0), PC (16:2e/2:0), Lysopc 20:4, PC (16:0/2:0), and LPC 19:0 upregulated significantly after PAMK intervention, together with the enrichment of carbon metabolism and Citrate cycle pathways specially. Conclusions: PAMK as a potential prebiotic ameliorated NASH and associated anxiety/depression-like behaviors in mice, probably by regulating Faecalibaculum_rodentium, carbohydrate enzymes and lipid metabolites.

Biosynthetic Origin of the Methoxy Group in Quinine and RelatedAlkaloids.

a methoxy group that has been assumed to be incorporated at a late pathway stage. Here we show that the methoxy group in quinine and related alkaloids is introduced onto the starting substrate tryptamine. Feeding studies definitively show that 5-methoxytryptamine is utilized as a quinine biosynthetic intermediate in planta. We discover the biosynthetic genes that encode the responsible oxidase and methyltransferase, and we use these genes to reconstitute the early steps of the alkaloid biosynthetic pathway in Nicotiana benthamiana to produce a mixture of methoxylated and non-methoxylated alkaloid intermediates. Importantly, we show that the co-occurrence of both tryptamine and 5-methoxytryptamine substrates, along with the substrate promiscuity of downstream pathway enzymes, enable parallel formation of both methoxylated and non-methoxylated alkaloids.

Molecular and Functional Characterization of the Key Proanthocyanidin Pathway Enzymes Anthocyanidin Reductases and Leucoanthocyanidin Reductases in Litchi chinensis.

The litchi genome has five anthocyanidin reductase (LcANR) and two leucoanthocyanidin reductase (LcLAR) members. The high expression of LcANR1a/2a and LcLAR1/2 is significantly positively correlated with the abundant proanthocyanidins and (-)-epicatechin (EC) in the pericarp, leaf, root, etc. The recombinant LcANR1a/2a converts cyanidin to both EC and (+)-catechin (CT) (EC:CT ≈ 1:1) and converts delphindin to (+)-gallocatechin and (-)-epigallocatechin; the recombinant LcLAR1/2 converts leucocyanidin to CT. The enzymatic kinetics of the four enzymes are presented, with the respective Km of LcLAR1/2 to leucocyanidin, 19 and 34 μM, and the Vmax, 7 and 5 nmol min-1 mg-1, which are rarely reported for other plants. Overexpression of LcANR1a/2a and LcLAR1/2 in Arabidopsis ban mutant recovered EC and CT biosynthesis respectively in the seeds; however, the EC-only recovery by LcANR1a/2a is inconsistent with their in vitro activity, indicating that the ANR/LAR function is dependent on characteristic molecular contexts in plants and correlated to the distinct PA profiles in litchi.

Optimizing HMG-CoA Synthase Expression for Enhanced Limonene Production in Escherichia coli through Temporal Transcription Modulation Using Optogenetics.

Overexpression of a single enzyme in a multigene heterologous pathway may be out of balance with the other enzymes in the pathway, leading to accumulated toxic intermediates, imbalanced carbon flux, reduced productivity of the pathway, or an inhibited growth phenotype. Therefore, optimal, balanced, and synchronized expression levels of enzymes in a particular metabolic pathway is critical to maximize production of desired compounds while maintaining cell fitness in a growing culture. Furthermore, the optimal intracellular concentration of an enzyme is determined by the expression strength, specific timing/duration, and degradation rate of the enzyme. Here, we modulated the intracellular concentration of a key enzyme, namely HMG-CoA synthase (HMGS), in the heterologous mevalonate pathway by tuning its expression level and period of transcription to enhance limonene production in Escherichia coli. Facilitated by the tuned blue-light inducible BLADE/pBad system, we observed that limonene production was highest (160 mg/L) with an intermediate transcription level of HMGS from moderate light illumination (41 au, 150 s ON/150 s OFF) throughout the growth. Owing to the easy penetration and removal of blue-light illumination from the growing culture which is hard to obtain using conventional chemical-based induction, we further explored different induction patterns of HMGS under strong light illumination (2047 au, 300 s ON) for different durations along the growth phases. We identified a specific timing of HMGS expression in the log phase (3-9 h) that led to optimal limonene production (200 mg/L). This is further supported by a mathematical model that predicts several periods of blue-light illumination (3-9 h, 0-9 h, 3-12 h, 0-12 h) to achieve an optimal expression level of HMGS that maximizes limonene production and maintains cell fitness. Compared to moderate and prolonged transcription (41 au, 150 s ON/150 s OFF, 0-73 h), strong but time-limited transcription (2047 au, 300 s ON, 3-9 h) of HMGS could maintain its optimal intracellular concentration and further increased limonene production up to 92% (250 mg/L) in the longer incubation (up to 73 h) without impacting cell fitness. This work has provided new insight into the "right amount" and "just-in-time" expression of a critical metabolite enzyme in the upper module of the mevalonate pathway using optogenetics. This study would complement previous findings in modulating HMGS expression and potentially be applicable to heterologous production of other terpenoids in E. coli.

Amelioration of fructose-induced hepatic lipid accumulation by vitamin D3 supplementation and high-intensity interval training in male Sprague‒Dawley rats

BackgroundIntrahepatic lipid accumulation (IHL), a hallmark of metabolic disorders, is closely associated with de novo lipogenesis (DNL). Notably, fructose feeding increased the DNL. Lifestyle modifications resulting from dietary changes and increased physical activity/exercise can decrease the IHL content. We examined the effects of vitamin D3 supplementation (VDS), high-intensity interval training (HIIT), and their combination on the transcription factors and enzymes of the DNL pathway in male Sprague‒Dawley rats fed a high-fructose diet (HFrD).MethodsForty male rats were assigned to 5 groups (n = 8): CS (the control group had a standard diet); CF (the control group had HFrD (10% (w/v) fructose solution in tap water)); and FT (HFrD + HIIT: 10 bouts of 4 min of high-intensity running, corresponding to 85–90% of the maximal speed with 2 min active rest periods of 50% maximal speed, 5 days per week); FD (HFrD + intervention of intraperitoneal injection of 10000 IU/kg/week VDS); FTD (HFrD + HIIT + VDS) that were maintained for 12 weeks. ELISA, the GOD-POD assay, folch, western blotting, and oil red O staining were used to determine insulin, fasting blood glucose (FBG), hepatic triglyceride (TG) and cholesterol levels; SREBP1c, ChREBP-β, ACC1, FASN, p-ACC1, AMPK, p-AMPK, and PKA protein expression; and IHL content, respectively.ResultsBoth HIIT and VDS led to significant increases in the levels of PKA, AMPK, p-AMPK, and p-ACC1, as well as significant decreases in the levels of SREBP1c, ChREBP-β, ACC1, FASN, insulin, FBG, liver TG, liver cholesterol, and IHL. HIIT exhibited superior efficacy over VDS in reducing ChREBP-β, ACC1, insulin, FBG, liver TG and cholesterol, as well as increasing p-ACC1 and PKA. Notably, the combined intervention of HIIT and VDS yielded the most substantial improvements across all the parameters.ConclusionsHFrD causes IHL accumulation and the onset of diabetes, whereas VDS and HIIT, along with their combined effects, prevent the consequences of HFrD.

Genome-wide comparative analysis of photosynthetic enzymatic genes provides novel insights into foxtail millet and other cereals

C4 crops have more efficient photosynthetic pathways that enable their higher photosynthetic capacities as well as nitrogen and water use efficiencies than C3 crops. Previous research has demonstrated that the genomes of C3 species include and express every gene needed for the C4 photosynthesis pathway. However, very little is known about the dynamics and evolutionary history of such genetic evolution in C4 plants. In this study, the genes encoding five key photosynthetic pathway enzymes in the genomes of C3 (rice), C4 (maize, sorghum, and foxtail millet), and CAM (pineapple) crops were identified and compared systematically. The numbers of genes in these photosynthetic enzymes were highest in the C4 crops like sorghum and foxtail millet, while only eight genes were identified in the CAM plant. However, 16 genes were identified in the C3 crop rice. Furthermore, we performed physical, chemical, gene structure and, cis-element analyses to obtain complete insights into these key genes. Tissue-specific expressions showed that most of the photosynthetic genes are expressed in the leaf tissues. Comparisons of the expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among the species, while the C4 gene copies in the C4 species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that could affect C4 gene expressions and subcellular localization were found in the coding and promoter regions. Our research also highlights the variations in how different genes have evolved within the C4 photosynthetic pathway, and we confirmed that specific high expressions in the leaves and right distribution within the cells were crucial for the development of the C4 photosynthetic abilities. The findings of this study are expected to aid in understanding the evolutionary process of the C4 photosynthetic pathway in grasses as well as offer insights for modifying the C4 photosynthetic pathways in wheat, rice, and other significant C3 cereal crops.

PHGDH Induction by MAPK is Essential for Melanoma Formation and Creates an Actionable Metabolic Vulnerability.

Overexpression of PHGDH, the rate-limiting enzyme in the serine synthesis pathway, promotes melanomagenesis, melanoma cell proliferation, and survival of metastases in serine-low environments such as the brain. Here, we found that PHGDH is universally increased in melanoma cells and required for melanomagenesis. While PHGDH amplification explained PHGDH overexpression in a subset of melanomas, oncogenic BRAFV600E also promoted PHGDH transcription through mTORC1-mediated translation of ATF4. Importantly, depletion of PHGDH in genetic mouse melanoma models blocked tumor formation. In addition to BRAFV600E-mediated upregulation, PHGDH was further induced by exogenous serine restriction. Surprisingly, BRAFV600E inhibition diminished serine restriction-mediated PHGDH expression by preventing ATF4 induction. Consequently, melanoma cells could be specifically starved of serine by combining BRAFV600E inhibition with exogenous serine restriction, which promoted cell death in vitro and attenuated melanoma growth in vivo. In summary, this study identified that PHGDH is essential for melanomagenesis and regulated by BRAFV600E, revealing a targetable vulnerability in BRAFV600E-mutant melanoma.

Decoding eggplant fruit: Multi-omics profiling of caffeoyl-CoA-3-OMT expression

Eggplant (Solanum melongena L.) is a rich source of health-promoting phenolic acids, mainly chlorogenic acid (CGA), and trace elements. CGA has been shown to have antioxidant, anti-inflammatory, neuroprotective, cardioprotective, anticancer, and antidiabetic properties. The natural genome of eggplants contains essential genes for beneficial traits like drought tolerance, disease resistance, and high concentrations of medicinal substances. Transcriptomic analysis of eggplant overexpressing the hydroxycinnamoyl CoA quinate hydroxycinnamoyl transferase (HQT) gene revealed upregulation of 2165 genes, including three similar to HQT and cinnamate-4-hydroxylase (C4H). Sequence similarity analysis showed homology to caffeoyl-CoA O-methyltransferases, key enzymes in the phenylpropanoid pathway leading to CGA biosynthesis. Gene ontology and KEGG pathway analysis identified 5 highly upregulated glycosyltransferase family 43 genes (650.3-fold change). Glycosyltransferases like UDP-glucose:cinnamate glucosyltransferase and cinnamate-glucose 4′-O-glucosyltransferase are crucial for CGA production in eggplant. qRT-PCR validated the potential upregulation of HQT and C4H in transgenic eggplants. Comparative analysis revealed eggplant has the highest CGA content (5–8.1 g/kg dry weight) among vegetables, with foliar CGA acting as a natural insecticide. CGA offers antioxidant, hypoglycemic, antiviral, and hepatoprotective benefits to humans. This study highlights the role of HQT and C4H in elevating the medicinal properties of eggplant through CGA biosynthesis pathway engineering.

Genome-wide identification of SAP family genes and characterization of TaSAP6-A1 to improve Cd tolerance in Triticum aestivum L.

Stress Associated Proteins (SAPs) contain A20/AN1 zinc finger domains and, have been proposed to function in various physiological processes such as cold, salinity, drought, heavy metals, damage, and flooding resistance in plants. Here, a total of 131 SAP genes were identified, including T. aestivum (60), T. urartu (10), Ae. Tauschii (16), T. dicoccoides (13), O. sativa (18), and Arabidopsis (14). A phylogenetic analysis revealed that the SAPs are clustered into two subfamilies. The TaSAP genes in the collinear region comprised 34 pairs of duplicated genes formed through segmental duplication events. Overexpressing TaSAP6-A1 in wheat enhanced Cd tolerance, whereas knock-down of this gene increased Cd sensitivity. Yeast two-hybrid (Y2H) and bimolecular fluorescent complementation assays (BiFC) demonstrated interaction between TaSAP6-A1 and phenylalanine ammonia-lyase (TaPAL), the first enzyme in the phenylpropanoid pathway. This study provides a valuable reference for further investigations into the functional and molecular mechanisms of the SAP gene family.