Metabolic Genes Research Articles

Genome-wide identification of hormone biosynthetic and metabolism genes in the 2OGD family of tobacco and JOX genes silencing enhances drought tolerance in plants

Phytohormones play crucial roles in regulation of plant growth and tolerance to abiotic stresses. The 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily responds to hormone biosynthesis and metabolism in plants. However, the Nt2OGD family in tobacco has not been fully explored. In this study, we identify 126 members of the Nt2OGD family, and 60 of them are involved in hormone biosynthesis and metabolism process (Nt2OGD-Hs), including 1-aminocyclopropane-1-carboxylic acid oxidases (ACO), dioxygenases for auxin oxidation (DAO), gibberellin (GA) 20-oxidases and 3-oxidases (GA20ox and GA3ox), carbon-19 and carbon-20 GA 2-oxidases (C19-GA2ox and C20-GA2ox), lateral branching oxidoreductases (LBO), jasmonate-induced oxygenases (JOX), downy mildew resistant 6, and DMR6-like oxygenases (DMR6/DLO). Gene duplication analysis suggests the segmental duplication and whole genome duplication (WGD) might be a potential mechanism for the expansion of this family. Expression analysis reveals that most of Nt2OGD-Hs show tissue-specific expression patterns, and some of them respond to environmental conditions. Of Nt2OGD-Hs, the expression of NtJOX3 and NtJOX5, which are involved in JA metabolism, exhibits remarkable changes during drought treatments. Silencing of NtJOX3 or NtJOX5 increases tobacco tolerance to drought stress. Furthermore, knocking out OsJOX3 and OsJOX4, respectively in rice, result in high tolerance to drought. Taken together, our work comprehensively identifies the Nt2OGD family in tobacco and provides new insights into roles of the JA pathway in drought tolerance in plants.

Bibliometric Insights into Research Hotspots and Trends in Obesity and Asthma from 2013 to 2023

Introduction: Obesity and asthma are closely linked, but the current state of research on this topic and future research directions have yet to be comprehensively explored. This study aims to provide an up-to-date overview of the research landscape in the field of obesity and asthma. Methods: A bibliometric analysis was conducted using the Web of Science Core Collection database to identify papers published on obesity and asthma between 2013 and 2023. VOSviewer software was utilized for statistical analysis and visualization of collaborative networks, research trends, literature sources, citation analysis, co-citation analysis, and keyword analysis. Results: A total of 3,406 records from 1,010 journals authored by 17,347 researchers affiliated with 4,573 institutes across 117 countries and regions were retrieved. The number of publications and citations increased annually. The USA and China contributed the majority of records. Major nodes in the collaboration network map included Harvard Medical School, Johns Hopkins University, University of Newcastle, Karolinska Institution, University of Toronto, and Seoul National University. Prolific authors included Anne E. Dixon, Erick Forno, Lisa G. Wood, Deepa Rastogi, and Fernando Holguin. Research trends and hotspots focused on metabolism studies, Mendelian randomization, gut microbiome, inflammation response, gene, biomarker research, and comorbidities were identified as potential future research frontiers. Conclusion: This study provides a comprehensive overview of the current research status and trends in the field of obesity and asthma. Our findings highlight the importance of understanding collaboration patterns, research hotspots, and emerging frontiers to guide future research in this area.

Targeting SNRNP200-induced splicing dysregulation offers an immunotherapy opportunity for glycolytic triple-negative breast cancer

Metabolic dysregulation is prominent in triple-negative breast cancer (TNBC), yet therapeutic strategies targeting cancer metabolism are limited. Here, utilizing multiomics data from our TNBC cohort (n = 465), we demonstrated widespread splicing deregulation and increased spliceosome abundance in the glycolytic TNBC subtype. We identified SNRNP200 as a crucial mediator of glucose-driven metabolic reprogramming. Mechanistically, glucose induces acetylation at SNRNP200 K1610, preventing its proteasomal degradation. Augmented SNRNP200 then facilitates splicing key metabolic enzyme-encoding genes (GAPDH, ALDOA, and GSS), leading to increased lactic acid and glutathione production. Targeting SNRNP200 with antisense oligonucleotide therapy impedes tumor metabolism and enhances the efficacy of anti-PD-1 therapy by activating intratumoral CD8+ T cells while suppressing regulatory T cells. Clinically, higher SNRNP200 levels indicate an inferior response to immunotherapy in glycolytic TNBCs. Overall, our study revealed the intricate interplay between RNA splicing and metabolic dysregulation, suggesting an innovative combination strategy for immunotherapy in glycolytic TNBCs.

Standardization and application of ARMS TaqMan real-time PCR for screening of folate metabolism genes in Han Chinese.

Folate has antioxidant properties, and low concentration in seminal plasma may be associated with increased DNA damage in sperm. Mutations of the methylenetetrahydrofolate reductase (MTHFR) and methionine synthase reductase (MTRR) genes, including MTHFR C677T (rs1801133), MTHFR A1298C (rs1801131), and MTRR A66G (rs1801394), can lead to decreased activity of the encoded folate metabolic enzymes, thereby affecting male reproduction. The current SNP detection methods commonly used in clinical practice have some shortcomings, such as long time-consuming, complex detection steps, or high cost. The purpose of this study was to establish a simple, time-saving, sensitive, accurate, and easy to clinical popularization method for folate metabolism gene detection. We combined ARMS-PCR with TaqMan fluorescent probe to establish an ARMS TaqMan real-time PCR detection method. According to the variation of rs1801131, rs1801133, and rs1801394, two specific primers (one wild type and one mutant) were designed. Mismatched nucleotides were introduced at the penultimate or third position to improve the specificity of the primer. Specific TaqMan probe was introduced to detect PCR products to improve the sensitivity of the method. The results showed that the sensitivity of ARMS TaqMan real-time PCR in SNP genotyping was 1ng, and the accuracy was 100%. A total of 249 clinical samples were detected by the established method, and the correlation between three SNPs and semen quality was analyzed. We found that individuals carrying the AG+GG genotype of rs1801394 had a lower risk of abnormal semen quality. In conclusion, we developed a highly sensitive, accurate, rapid, and easy to be popularized method for detecting SNPs of rs1801394, rs1801131, and rs1801133. ARMS TaqMan real-time PCR is a reliable SNP genotyping method in folate metabolism genes.

Arsenic redox disequilibrium in geogenic contaminated groundwater: Bioenergetic insights from organic molecular characterization and gene-informed modeling

Biotransformation of arsenic (As) influences its speciation and mobility, obscuring mechanistic comprehension on spatiotemporal variation of As concentration in geogenic contaminated groundwater. In particular, unresolved processes underlying As redox disequilibrium in comparison to major redox couples discourage practical efforts to rehabilitate the As-contaminated groundwater. Here, quantitative metagenomic sequencing and ultrahigh-resolution mass spectrometry (FT-ICR-MS) were jointly applied to reveal the links between vertical distribution of As metabolic gene assemblages and that of free energy density of dissolved organic matter (DOM) in As-contaminated groundwater of Datong Basin. Observed small excess of Gibbs free energy available by DOM relative to that required for As(V)-to-As(III) reduction exerts thermodynamic constraint on metabolism-mediated redox transformation of As. Accordingly, the vertical distribution of dissolved As(V)/As(III) ratio correlated significantly with that of ars+acr3 and arr encoding As(V) reduction and aio encoding As(III) oxidation in the moderately/strongly reducing groundwater. Further gene-informed biogeochemical modeling suggests that a net effect of these kinetics-restricted bidirectional metabolic pathways leads to co-preservation of As(V) and As(III) even at relatively high rates of ars+acr3 encoded As(V) reduction. This study therefore provides new insights into bioenergetic constraints on As hydrobiogeochemical behavior, with implications for other redox-sensitive contaminants in the groundwater systems.

Genome-Wide Mapping of Main Histone Modifications and Coordination Regulation of Metabolic Genes under Salt Stress in Pea (Pisum sativum L)

Abstract Pea occupy a key position in modern biogenetics, playing a multifaceted roles as food, vegetable, fodder, and green manure. However, due to the complex nature of its genome and the prolonged unveiling of high-quality genetic maps, research into the molecular mechanisms underlying pea development and stress responses has been significantly delayed. Furthermore, the exploration of its epigenetic modification profiles and associated regulatory mechanisms remains uncharted. This research conducted a comprehensive investigation of four specific histone marks, namely H3K4me3, H3K27me3, H3K9ac, and H3K9me2 and the transcriptome in pea under normal condition, and established a global map of genome-wide regulatory elements, chromatin states, and dynamics based on these major modifications. Our analysis identified epigenomic signals across approximately 82.6% of the genome. Each modification exhibits distinct enrichment patterns: H3K4me3 is predominantly associated with the gibberellin response pathway, H3K27me3 is primarily associated with auxin and ethylene responses, and H3K9ac is primarily associated with negative regulatory stimulus responses. We also identified a novel bivalent chromatin state (H3K9ac-H3K27me3) in pea, which is related to their development and stress response. Additionally, we unveil that these histone modifications synergistically regulate metabolic-related genes, influencing metabolite production under salt stress conditions. Our findings offer a panoramic view of the major histone modifications in pea, elucidate their interplay, and highlight their transcriptional regulatory roles during salt stress.

Phosphorus Metabolism-Related Genes Serve as Novel Biomarkers for Predicting Prognosis in Bladder Cancer: A Bioinformatics Analysis.

Phosphorus metabolism might be associated with tumor initiation and progression. We aimed to screen out the phosphorus metabolism genes related to bladder cancer and construct a clinical prognosis model. The dataset used for the analysis was obtained from TCGA database. GO and KEGG enrichment analyses were subsequently applied to differentially expressed genes. Consensus clustering was utilized, and different clusters of the tumor immune microenvironment and other features were compared. The phosphorus metabolism-related genes involved in prognosis were screened out by univariate Cox regression, LASSO regression and multivariate Cox regression analysis, and a nomogram was constructed. The performance of the nomogram was validated using TCGA dataset and the GEO dataset, respectively. Overall, 405 phosphorus metabolism-related differentially expressed genes from TCGA database were identified, which were associated with phosphorylation, cell proliferation, leukocyte activation, and signaling pathways. Two clusters were obtained by consistent clustering. After tumor immune microenvironment analysis, significant differences in immune cell infiltration between cluster 1 and cluster 2 were found. Four phosphorus metabolism-related genes (LIME1, LRP8, SPDYA, and MST1R) were associated with the prognosis of bladder cancer (BLCA) patients. We built a prognostic model and visualized the model as a nomogram. Calibration curves demonstrated the performance of this nomogram, in agreement with that shown by the ROC curves. We successfully identified four phosphorus metabolism-related genes associated with prognosis, providing potential targets for biomarkers and therapeutics. A nomogram based on these genes was developed. Nevertheless, this study is based on bioinformatics, and experimental validation remains essential.

The Drosophila Estrogen-Related Receptor promotes triglyceride storage within the larval fat body.

The Estrogen-Related Receptor (ERR) family of nuclear receptors (NRs) serve key roles in coordinating triglyceride (TAG) accumulation with juvenile growth and development. In both insects and mammals, ERR activity promotes TAG storage during the post-embryonic growth phase, with loss-of-function mutations in mouse Esrra and Drosophila melanogaster dERR inducing a lean phenotype. However, the role of insect ERRs in controlling TAG accumulation within adipose tissue remains poorly understood, as previous transcriptomic and metabolomic studies relied on whole animal analyses. Here we address this shortcoming by using tissue-specific approaches to examine the role of dERR in regulating lipid metabolism within the Drosophila larval fat body. We find that dERR autonomously promotes TAG accumulation within fat body cells and regulates expression of genes involved in glycolysis, β-oxidation, and mevalonate metabolism. As an extension of these results, we not only discovered that dERR mutant fat bodies exhibit decreased expression of known dHNF4 target genes but also found that dHNF4 activity is decreased in dERR mutants. Overall, our findings indicate that dERR plays a multifaceted role in the larval fat body to coordinate lipid storage with developmental growth and hint at a conserved mechanism by which ERR and HNF4 homologs coordinately regulate metabolic gene expression.

Enhanced indigenous bacteria-mediated bioremediation of aged petroleum-contaminated soil by Fenton pretreatment: Synergistic effect of soil environmental improvement and microbial community response

Due to the harsh soil environment and low microbial activity, the efficacy of indigenous bacteria-mediated bioremediation is often limited in aged petroleum-contaminated soils. In this study, Fenton pretreatment (H2O2: 200 ∼ 600 mmol/kg, H2O2: Fe2+ = 100: 1) was applied to improve the aged soil environment and rebuild the microbial community to enhance subsequent bioremediation. After pretreated by 400 mmol/kg H2O2 and 4 mmol/kg Fe2+ (T2), the removal efficiency of total petroleum hydrocarbons (TPHs) was elevated to 93.27 %, equivalent to 1.96-fold of the natural attenuation (CK). Additionally, the half-life of biodegradation was shorted to 45.57 d, representing a decrease to 0.29-fold that of CK. Correlation analysis revealed a radar plot comprising five indicators, including bacterial quantification (BQ), dehydrogenase (DHA), polyphenol oxidase (PPO), permeability coefficient (K), and bulk density coefficient (γ), all of which exhibited positive correlations with TPHs degradation. Compared to CK, Fenton pretreatment increased the richness and evenness of the microbial community during incubation, thus facilitating TPHs biodegradation. Moreover, Fenton pretreatment accelerated the shift of the dominant genus in T2 from Pseudomonas (0.599) to Pseudomonas (0.258), Nocardioides (0.109), Dietzia (0.157), and Stenotrophomonas (0.120) throughout the incubation. Based on the analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG), the metabolism and enzymatic functional genes related to the biodegradation of petroleum hydrocarbons in T2 were enhanced during incubation, accounting for the high removal efficiency of TPHs. These findings demonstrated that moderate Fenton pretreatment was an effective approach to stimulate indigenous bacteria for the enhanced biodegradation of aged petroleum-contaminated soil.

429 Maternal rate of gain and one-carbon metabolites supplementation alters the gene expression profile of fetal brain during early gestation in beef heifers

Abstract Maternal nutritional plane during pregnancy may leave lifelong impacts on offspring in beef cattle. Given that, we hypothesized that the supplementation of one-carbon metabolites (OCM) during pregnancy would mitigate the negative effects of maternal rate of gain through brain gene expression regulation in early developing bovine fetuses. The objective of this study was to evaluate the effects of OCM supplementation and maternal rate of gain on gene expression in the developing fetal brain in gestating beef heifers. Herein, Angus crossbred heifers (n = 72, body weight = 406 ± 33 kg) were randomly assigned to 2 × 2 factorial arrangement of treatments with two levels of maternal rate of gain (CON, 0.60 kg/d; and RES, -0.23 kg/d) each with or without OCM supplementation (+OCM, and -OCM). Heifers were fed individually and were bred using female-sexed semen from a single sire. The OCM supplementation included rumen-protected choline (44.4 g/d) and methionine (7.4 g/d) in corn carrier fed daily and weekly injections of folate (320 mg) and vitamin B12 (20 mg). The -OCM heifers received the corn carrier and saline injections. The treatments started at the time of breeding and continued until d 63 of gestation when pregnant heifers (n = 29) were slaughtered to collect fetal brain tissues for RNA sequencing. The fetal brain phenotypic data were analyzed using MIXED procedures of SAS, indicating that restricted nutrition affected the fetal right hemisphere weight (P < 0.05), and there was a strong tendency for overall fetal brain weight (0.05 < P < 0.1) to be affected as well. Brain transcriptomics data were analyzed using STAR aligner and a total of 177 differentially expressed genes (DEGs, FDR < 0.05) were identified across all treatment comparisons using DESeq2. Most of the DEGs were either isoforms of spliceosomal non-coding RNAs or micro-RNAs (miRNAs) associated with biological processes (FDR < 0.1) like mRNA processing, cellular nitrogen metabolism, lipid metabolism, and post-transcriptional gene silencing. The key miRNAs upregulated in the brain tissue of restricted fetuses without OCM supplementation, bta-mir-2375, bta-mir-876, and bta-mir-196a-1, were found to be associated with early embryogenesis and essential cellular regulatory processes. Conversely, in restricted fetuses with OCM supplementation, upregulated miRNAs such as bta-mir-216b, bta-mir-2285dd, and bta-mir-1298 were linked to early embryonic development, muscular development, and lipid metabolism in cattle. Both phenotypic and transcriptomics data here revealed that the maternal rate of gain altered fetal brain development, with differences seemingly compensated by OCM supplementation. USDA is an equal opportunity provider and employer.

An abnormal metabolism-related gene, ALG3, is a potential diagnostic and prognostic biomarker for lung adenocarcinoma.

To explore the abnormal metabolism-related genes that affect the prognosis of patients with lung adenocarcinoma (LUAD), and analyze the relationship with immune infiltration and competing endogenous RNA (ceRNA) network. Transcriptome data of LUAD were downloaded from the Cancer Genome Atlas database. Abnormal metabolism-related differentially expressed genes in LUAD were screened by the R language. Cox analysis was used to construct LUAD prognostic risk model. Kaplan-Meier test, ROC curve and nomograms were used to evaluate the predictive ability of metabolic related gene prognostic model. CIBERSORT algorithm was used to analyze the relationship between risk score and immune infiltration. The starBase database constructed a regulatory network consistent with the ceRNA hypothesis. IHC experiments were performed to verify the differential expression of ALG3 in LUAD and paracancerous samples. In this study, 42 abnormal metabolism-related differential genes were screened. After survival analysis, the final 5 metabolism-related genes were used as the construction of prognosis model, including ALG3, COL7A1, KL, MST1, and SLC52A1. In the model, the survival rate of LUAD patients in the high-risk subgroup was lower than that in the low-risk group. In addition, the risk score of the constructed LUAD prognostic model can be used as an independent prognostic factor for patients. According to the analysis of CIBERSORT algorithm, the risk score is related to the infiltration of multiple immune cells. The potential ceRNA network of model genes in LUAD was constructed through the starBase database. IHC experiments revealed that ALG3 expression was upregulated in LUAD. The prognostic model of LUAD reveals the relationship between metabolism and prognosis of LUAD, and provides a novel perspective for diagnosis and research of LUAD.

Mechanistic insights to Paenibacillus lentimorbus mediated biocontrol of Alternaria solani in Solanum lycopersicum L. through carbohydrate reallocation and sweet immunity suppression

Researchers envisaged that PGPR (plant growth promoting rhizobacteria) has vast possibilities as a bioinoculant that will lead to revolution. However, it's still very far from becoming commercially successful. Here, the information regarding the root colonization of PGPR in host plants and plant response towards PGPR is inadequate. It can provide valuable information for developing successful biofertilizers and biocontrol agents. PGPR (Paenibacillus lentimorbus NRRL B-30488 or CHM12) has been previously reported as a successful commercial biofertilizer and biocontrol agent. However, the exact mechanism of plant growth promotion and biocontrol is poorly studied. So, CHM12 was appraised for biotic stress amelioration of pathogen Alternaria solani in Tomato (Solanum lycopersicum L.) var. S-22 plants. PGPR CHM12 was assessed for various plant growth parameters such as proline, sugar content, etc. in pathogen A. solani (AS) challenged plants and compared with the CHM12 treated plants in a greenhouse study. Then, the metabolomics tool (GC-MS) was used to identify metabolites and their respective genes playing pivotal roles in colonization tactics availed by PGPR. Further, gene expression analysis was done to affirm the involvement of various genes related to metabolites providing biotic stress tolerance in Tomato plants. The current research discerned that PGPR CHM12 revealed significant differences in different plant growth parameters studied. There were 33 distinct metabolites identified, which stipulated the involvement of carbohydrate metabolism mainly in combating biotic stress in this study. Thus, our study reconfirmed very few reported previous results through gene expression analysis, suggesting the downregulation of carbohydrate metabolism genes in PGPR-treated plants. This downregulation of carbohydrate genes might be the critical factor for suppressing the plant's immune response to gaining entry inside the host plant. This also helps in retaining and reallocating carbohydrates in plant cells to reduce pathogen proliferation.

Transcriptomic profiling reveals potential regulatory genes and molecular mechanisms of residual feed intake in Jian carp (Cyprinus carpio var. Jian)

Feed efficiency is one of the most important economic traits in animal production. Improving feed efficiency through genetic selection or other approaches will reduce production costs and mitigate environmental impacts. Residual feed intake (RFI) has some advantages over traditional feed efficiency metrics as a selection criterion for improving feed efficiency, because it is not a ratio and unrelated to growth. In this study, high RFI (HRFI) and low RFI (LRFI) Jian carp (Cyprinus carpio var. Jian) were tested for feed efficiency traits and serum biochemical indices. No significant differences were observed in the growth rates between HRFI and LRFI group, but daily feed intake of LRFI was significantly lower than that of the HRFI group. The results indicated that significantly higher content of triglyceride (TG) and total cholesterol (T-CHO) in the LRFI group was significantly correlated with RFI. We also selected HRFI and LRFI carp for transcriptomic analysis to determine differentially expressed genes (DEGs) in the liver tissues of 12 individuals. A total of 830 DEGs were identified between HRFI and LRFI group, of which 486 genes were up-regulated and 344 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were mainly enriched in fatty acid metabolism, ErbB signaling pathway, phosphatidylinositol signaling system, and autophagy. Lipid metabolism and autophagy-related genes, were considered candidate genes that played a crucial role in regulating feed efficiency. Taken together, these results indicated that differences in RFI affect Jian carp metabolism and cell fate, and that alterations in fatty acid metabolism and autophagy are key physiological modes of regulation in low RFI Jian carp. Our data provide valuable candidate genes and candidate pathways, which will help to study the molecular mechanisms of feed efficiency in carp.

Multi-omics study on the mixed culture of Trichoderma reesei and Aspergillus niger with improved lignocellulase production

The mixed culture of Trichoderma reesei and Aspergillus niger were found to improve lignocellulase production and ameliorate the composition (Fang et al., 2010; Fang et al., 2013; Zhao et al., 2018) [1-3]. However, the mechanism behind remained unclear. Here we conducted multi-omics study of the mixed culture to elucidate the mechanism comprehensively, including proteomics of the secretomes, metabolomics of the fermentation broths and transcriptomics. The mechanisms at transcriptional, proteomic and metabolomic levels were clarified. Proteomics show many proteins in the secretomes were up-regulated by the mix culture of T. reesei and A. niger, and lignocellulase production and the composition were improved, but the protein numbers and abundances of the lignocellulases were reduced. Transcriptomics demonstrate that lignocellulase gene expressions, stress responses and anti-stress were co-regulated in T. reesei, and that most lignocellulase genes in T. reesei were up-regulated and most A. niger lignocellulase genes were down-regulated. Metabolomics reveal the chemicals and the mechanism of the communication between T. reesei and A. niger in the mixed culture for improved lignocellulase production. The secondary metabolites such as p-cresol, nodularin and tolazoline could play important roles. Integrative analyses indicate that the secondary metabolites, stress-response, anti-stress, starch and sucrose metabolism and lignocellulase gene expressions were orchestrated. As a result, the roles of T. reesei and A. niger in the mixed culture were defined. The mechanism of the mixed culture for improved lignocellulase production was obtained, in short T. reesei was the major role and A. niger the minor. This work provides theory and targets as basis to obtain complete understanding of the mechanism and guide engineering of the microbial consortium of T. reesei and A. niger for further improvements.

Viral diversity within marine biofilms and interactions with corrosive microbes

In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This means that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.

Tendril length is determined by gibberellin deactivation during thigmo response in cucumber.

Changes in plant morphology due to mechanical stimulation are known as thigmo responses. As climbing organs in plants, tendrils can sense mechanical stimulation after attaching to a support and then change their morphology within a short time. Here, the thigmo responses of cucumber tendril were investigated. Our results showed that mechanical stimulation stopped tendril elongation and that tendril length was determined by the distance from the support in cucumber. The mimicry touch treatment indicated that mechanical stimulation stopped tendril elongation by inhibiting cell expansion. RNA-seq data showed that three gibberellin (GA) metabolic genes (CsGA2ox3, CsCYP714A2, and CsCYP714A3) were upregulated in mechanically stimulated tendrils, and a major endogenous bio-active GA (GA4) was reduced in mechanically stimulated tendrils. The roles of CsGA2ox3, CsCYP714A2, and CsCYP714A3 in GA deactivation were confirmed by their overexpression in transgenic Arabidopsis. Moreover, exogenous GA treatment recovered tendril elongation under mechanical stimulation, whereas exogenous uniconazole treatment inhibited tendril elongation without mechanical stimulation, suggesting that mechanical stimulation stopped tendril elongation, depending on GA deactivation. In summary, our results suggest that GA deactivation plays an important role in tendril thigmo response, ensuring that tendrils obtain a suitable final length according to their distance from the support in cucumber.

The sucrose signalling route controls Flavescence dorée phytoplasma load in grapevine leaves.

Flavescence dorée (FD) is a phytoplasma disease transmitted by insects, causing severe damage to vineyards across Europe. Infected plants cannot be cured and must be removed to prevent further spread. Different grapevine cultivars show varying susceptibility to FD, and some exhibit symptom remission, known as recovery, although the mechanisms behind this are unclear. Diseased plants accumulate soluble sugars, including sucrose, which influences the concentration of trehalose-6P (T6P), a signalling molecule affecting plant growth and stress responses. It is hypothesized that sucrose-mediated signalling via T6P could trigger defence mechanisms, reducing FD pathogen load and increasing plant recovery. Testing this, two grapevine genotypes with different susceptibility to FD were compared, revealing increased sucrose level and TPS activity in the more tolerant cultivar. However, FD-infected plants showed inhibited sucrose-cleaving enzymes and no activation of TPS expression. Attempts to enhance sucrose levels through trunk infusion and girdling promoted sucrose metabolism, T6P biosynthesis, and defence gene expression, facilitating symptom recovery. Girdling particularly enhanced T6P biosynthesis and defence genes above the treatment point, reducing FD pathogen presence and promoting recovery. These findings suggest that elevated sucrose levels, possibly signalling through T6P, may limit FD pathogen spread, aiding in plant recovery.

Genome-guided bioprospecting for industrially important enzymes from a thermophilic Bacillus subtilis strain SR-7, an isolate from hot spring of Madhya Pradesh, India

The study focused on isolating thermophilic bacteria from the hot springs of Madhya Pradesh, India, with the aim of identifying strains capable of producing industrially valuable enzymes. Among the 15 isolated strains, SR-7 identified as Bacillus subtilis exhibited significant enzyme activity, leading to its selection for further investigation. Genomic analysis revealed key characteristics of SR-7, including a 3,593,163 base pair chromosome with a GC content of 44.14 %. The genome was found to contain 55 tRNA genes, four rRNA clusters, and 3744 protein-coding genes. These genes encompass essential metabolic pathways and genes responsible for thermophilic adaptation, highlighting the potential for industrial applications. Further experimentation demonstrated SR-7 have the ability to produce various enzymes of industrial significance, such as amylase, lipase, cellulase, protease, lecithinase, gelatinase, and pectinase. Importantly, enzyme production was observed across a broad pH range (6.5 to 10) and temperature spectrum, indicating the versatility and adaptability of SR-7 to different environmental conditions. The findings suggest that SR-7 holds promise as a valuable resource for the pharmaceutical and industrial sectors. Its capacity to produce thermostable enzymes suitable for a range of applications underscores its potential contribution to biotechnological processes. By harnessing the enzymatic capabilities of thermophilic bacteria like SR-7, industries can pursue more sustainable and efficient production methods, reducing reliance on traditional chemical processes and enhancing overall productivity. Further research into the enzymatic properties and genetic mechanisms of SR-7 may unveil additional avenues for its utilization in various industrial processes.

NUAKs promote mTOR/c-Myc-induced glucose and glutamine reprogramming for cell growth and metastasis in breast cancer cells

Breast cancer progression and metastasis are closely connected to changes in glucose and glutamine metabolism. While Novel (nua) kinase family 1 (NUAK1) and Novel (nua) kinase family 2 (NUAK2), which are two members of the AMPK-related kinases, have been associated with breast tumorigenesis, their role in the metabolic reprogramming that occurs during breast cancer progression remains unclear. Our research uncovers that NUAKs expression is significantly higher in breast cancer tissues and cell lines, and it is positively related to glycolysis, the pentose phosphate pathway (PPP), glutamine metabolism, and a poor prognosis for breast cancer patients. We show that NUAKs significantly increase metabolic reprogramming, including aerobic glycolysis, PPP, and glutamine metabolism in triple negative breast cancer subtypes but only induce aerobic glycolysis and PPP in luminal breast cancer subtypes to meet the anabolic demands of rapidly dividing breast cancer cells. In contrast, the depletion of NUAKs has the opposite effect. Mechanistic insights reveal that NUAKs activate mammalian target of rapamycin (mTOR) signaling, which in turn upregulates the c-Myc transcription factor, a crucial regulator of glucose and glutamine metabolic gene expression. Moreover, we demonstrate that NUAKs enhance mTOR/c-Myc signaling pathways, leading to increased glucose and glutamine reprogramming, which supports rapid cell proliferation and metastatic potential in breast cancer cells. Importantly, pretreating breast cancer cells with mTOR inhibitors blocked the metabolic reprogramming and tumor-promoting effect of NUAK1/2. Therefore, targeting NUAKs may represent a novel therapeutic strategy for the treatment of breast cancer.

Microalgal and Cyanobacterial Biomasses Modified the Activity of Extracellular Products from Bacillus pumilus: An In Vitro and In Vivo Assessment.

This study investigates the postbiotic potential of extracellular products (ECPs) from Bacillus pumilus strains cultivated on microalgae-supplemented media. We assessed enzymatic and antimicrobial activities to select ECPs that enhance the digestive processes in gilthead seabream. Additionally, we explored the in vitro enzymatic capacity of the chosen postbiotics to hydrolyze macromolecules in microalgae. Finally, a feeding trial was conducted to determine the in vivo effects of the ECPs on Sparus aurata. In vitro enzymatic assays demonstrated diverse hydrolytic capacities among ECPs. All conditions exhibited antimicrobial activity against Photobacterium damselae subsp. piscicida, with variation in inhibitory effects against Vibrio harveyi and Tenacibaculum maritimum. Furthermore, in vitro assays revealed differences in protein hydrolysis and soluble protein concentration, influencing amino acid and reducing sugar release from microalgal biomass. These analyses facilitated a selection to test ECPs in vivo. Lastly, the in vivo experiment revealed no differences in the growth performance, nutrient utilization, and general metabolism of S. aurata fed the experimental diets. Dietary inclusion of postbiotics increased the activity of key digestive enzymes in fish compared to the control group, and particularly, values increased significantly when the fish were fed with the ECP-nanoparticulate-supplemented diet. In conclusion, the inclusion of microalgae in the culture media significantly influences the activity of extracellular products from B. pumilus strains, as evidenced in both in vitro and in vivo assays.