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Biomolecules Jan 2024Holm oak () is considered to be one of the major structural elements of Mediterranean forests and the agrosilvopastoral Spanish "dehesa", making it an outstanding...
Holm oak () is considered to be one of the major structural elements of Mediterranean forests and the agrosilvopastoral Spanish "dehesa", making it an outstanding example of ecological and socioeconomic sustainability in forest ecosystems. The exotic is one of the most aggressive pathogens of woody species and, together with drought, is considered to be one of the main drivers of holm oak decline. The effect of and response to inoculation were studied in the offspring of mother trees from two Andalusian populations, Cordoba and Huelva. At the two locations, acorns collected from both symptomatic (damaged) and asymptomatic (apparently healthy) trees were sampled. Damage symptoms, mortality, and chlorophyll fluorescence were evaluated in seedlings inoculated under humid and drought conditions. The effect and response depended on the population and were more apparent in Huelva than in Cordoba. An integrated proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, including amino acid metabolism pathways in Huelva, and terpenoid and flavonoid biosynthesis in Cordoba. However, no differential response was observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus was activated in response to defective photosynthetic activity in inoculated plants, which seemed to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may have conferred higher resistance in the Cordoba population. Some enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates.
Topics: Ecosystem; Quercus; Droughts; Phytophthora; Proteomics; Trees; Seedlings; Flavonoids
PubMed: 38397397
DOI: 10.3390/biom14020160 -
International Journal of Molecular... Feb 2024Hepatocellular carcinoma (HCC), the main pathological type of liver cancer, is related to risk factors such as viral hepatitis, alcohol intake, and non-alcoholic fatty...
Hepatocellular carcinoma (HCC), the main pathological type of liver cancer, is related to risk factors such as viral hepatitis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD). The constitutive activation of the PI3K/AKT signaling pathway is common in HCC and has essential involvement in tumor progression. The serine/threonine kinase AKT has several downstream substrates, which have been implicated in the regulation of cellular metabolism. However, the contribution of each of the three AKT isoforms, i.e., AKT1, AKT2 and AKT3, to HCC metabolism has not been comprehensively investigated. In this study, we analyzed the functional role of AKT1, AKT2 and AKT3 in HCC metabolism. The overexpression of activated AKT1, AKT2 and AKT3 isoforms in the human HCC cell lines Hep3B and Huh7 resulted in higher oxygen consumption rate (OCR), ATP production, maximal respiration and spare respiratory capacity in comparison to vector-transduced cells. Vice versa, lentiviral vector-mediated knockdowns of each AKT isoform reduced OCR in both cell lines. Reduced OCR rates observed in the three AKT isoform knockdowns were associated with reduced extracellular acidification rates (ECAR) and reduced lactate production in both analyzed cell lines. Mechanistically, the downregulation of OCR by AKT isoform knockdowns correlated with an increased phosphorylation of the pyruvate dehydrogenase on Ser232, which negatively regulates the activity of this crucial gatekeeper of mitochondrial respiration. In summary, our data indicate that each of the three AKT isoforms is able to upregulate OCR, ECAR and lactate production independently of each other in human HCC cells through the regulation of the pyruvate dehydrogenase.
Topics: Humans; Carcinoma, Hepatocellular; Cell Line, Tumor; Lactic Acid; Liver Neoplasms; Oxidoreductases; Oxygen; Phosphatidylinositol 3-Kinases; Protein Isoforms; Proto-Oncogene Proteins c-akt; Pyruvates
PubMed: 38396845
DOI: 10.3390/ijms25042168 -
Journal of Fungi (Basel, Switzerland) Feb 2024The medium-chain dehydrogenase/reductase (MDR) superfamily contains many members that are widely present in organisms and play important roles in growth, metabolism, and...
Genome-Wide Identification and Characterization of the Medium-Chain Dehydrogenase/Reductase Superfamily of and Its Involvement in the Regulation of Fluconazole Resistance.
The medium-chain dehydrogenase/reductase (MDR) superfamily contains many members that are widely present in organisms and play important roles in growth, metabolism, and stress resistance but have not been studied in . In this study, bioinformatics and RNA sequencing methods were used to analyze the MDR superfamily of and its regulatory effect on fluconazole resistance. A phylogenetic tree was constructed using , , and and 73 were identified, all of which contained NADPH-binding motifs. contained 20 that were unevenly distributed across six chromosomes. () had similar 3D structures but varied greatly in their genetic evolution at different phylum levels. RNA-seq and gene expression analyses revealed that the fluconazole-resistant strain upregulates xylitol dehydrogenase, and downregulated alcohol dehydrogenase and sorbitol dehydrogenase concluded that the fluconazole-resistant strain was less selective toward carbon sources and had higher adaptability to the environment. Overall, our study contributes to our understanding of , providing a basis for further analysis of the genes associated with drug resistance in .
PubMed: 38392795
DOI: 10.3390/jof10020123 -
Biology Feb 2024Ammonium (NH) toxicity is ubiquitous in plants. To investigate the underlying mechanisms of this toxicity and bicarbonate (HCO)-dependent alleviation, wheat plants were...
Ammonium (NH) toxicity is ubiquitous in plants. To investigate the underlying mechanisms of this toxicity and bicarbonate (HCO)-dependent alleviation, wheat plants were hydroponically cultivated in half-strength Hoagland nutrient solution containing 7.5 mM NO (CK), 7.5 mM NH (SA), or 7.5 mM NH + 3 mM HCO (AC). Transcriptomic analysis revealed that compared to CK, SA treatment at 48 h significantly upregulated the expression of genes encoding fermentation enzymes (pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH), and lactate dehydrogenase (LDH)) and oxygen consumption enzymes (respiratory burst oxidase homologs, dioxygenases, and alternative oxidases), downregulated the expression of genes encoding oxygen transporters (PIP-type aquaporins, non-symbiotic hemoglobins), and those involved in energy metabolism, including tricarboxylic acid (TCA) cycle enzymes and ATP synthases, but upregulated the glycolytic enzymes in the roots and downregulated the expression of genes involved in the cell cycle and elongation. The physiological assay showed that SA treatment significantly increased PDC, ADH, and LDH activity by 36.69%, 43.66%, and 61.60%, respectively; root ethanol concentration by 62.95%; and lactate efflux by 23.20%, and significantly decreased the concentrations of pyruvate and most TCA cycle intermediates, the complex V activity, ATP content, and ATP/ADP ratio. As a consequence, SA significantly inhibited root growth. AC treatment reversed the changes caused by SA and alleviated the inhibition of root growth. In conclusion, NH treatment alone may cause hypoxic stress in the roots, inhibit energy generation, suppress cell division and elongation, and ultimately inhibit root growth, and adding HCO remarkably alleviates the NH-induced inhibitory effects on root growth largely by attenuating the hypoxic stress.
PubMed: 38392319
DOI: 10.3390/biology13020101 -
Frontiers in Plant Science 2023With current trends in global climate change, both flooding episodes and higher levels of CO have been key factors to impact plant growth and stress tolerance. Very...
INTRODUCTION
With current trends in global climate change, both flooding episodes and higher levels of CO have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO (eCO).
METHODS
We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO and flooding.
RESULTS
Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO. We found that sole treatment of eCO and flooding had significant abundances of , and . Whereas the combination of flooding and eCO2 conditions showed a significant abundance of and . Rhizospheric extra-cellular enzyme activities were significantly higher in eCO than flooding or its combination with eCO. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of and in floodings and eCO treatments in soybean plant root or shoot parts.
CONCLUSION
This work suggests that climatic-induced changes in eCO and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO.
PubMed: 38389716
DOI: 10.3389/fpls.2023.1295674 -
The ISME Journal Jan 2024The synthetic buffer compound TRIS (2-amino-2-(hydroxymethyl)propane-1,3-diol) is used in countless applications, and no detailed information on its degradation has been...
The synthetic buffer compound TRIS (2-amino-2-(hydroxymethyl)propane-1,3-diol) is used in countless applications, and no detailed information on its degradation has been published so far. Herein, we describe the discovery of a complete bacterial degradation pathway for TRIS. By serendipity, a Pseudomonas strain was isolated from sewage sludge that was able to grow with TRIS as only carbon and nitrogen source. Genome and transcriptome analyses revealed two adjacent gene clusters embedded in a mobile genetic element on a conjugative plasmid to be involved in TRIS degradation. Heterologous gene expression revealed cluster I to encode a TRIS uptake protein, a TRIS alcohol dehydrogenase, and a TRIS aldehyde dehydrogenase, catalyzing the oxidation of TRIS into 2-hydroxymethylserine. Gene cluster II encodes a methylserine hydroxymethyltransferase (mSHMT) and a d-serine dehydratase that plausibly catalyze the conversion of 2-hydroxymethylserine into pyruvate. Conjugational plasmid transfer into Pseudomonas putida KT2440 enabled this strain to grow with TRIS and with 2-hydromethylserine, demonstrating that the complete TRIS degradation pathway can be transmitted by horizontal gene transfer. Subsequent enrichments from wastewater purification systems led to the isolation of further TRIS-degrading bacteria from the Pseudomonas and Shinella genera carrying highly similar TRIS degradation gene clusters. Our data indicate that TRIS degradation evolved recently via gene recruitment and enzyme adaptation from multiple independent metabolic pathways, and database searches suggest that the TRIS degradation pathway is now globally distributed. Overall, our study illustrates how engineered environments can enhance the emergence of new microbial metabolic pathways in short evolutionary time scales.
Topics: Pseudomonas putida; Pseudomonas; Multigene Family; Oxidation-Reduction; Metabolic Networks and Pathways
PubMed: 38365256
DOI: 10.1093/ismejo/wrad023 -
BMC Plant Biology Feb 2024The color of endopleura is a vital factor in determining the economic value and aesthetics appeal of nut. Walnuts (Juglans) are a key source of edible nuts, high in...
BACKGROUND
The color of endopleura is a vital factor in determining the economic value and aesthetics appeal of nut. Walnuts (Juglans) are a key source of edible nuts, high in proteins, amino acids, lipids, carbohydrates. Walnut had a variety endopleura color as yellow, red, and purple. However, the regulation of walnut endopleura color remains little known.
RESULTS
To understand the process of coloration in endopleura, we performed the integrative analysis of transcriptomes and metabolomes at two developmental stages of walnut endopleura. We obtained total of 4,950 differentially expressed genes (DEGs) and 794 metabolites from walnut endopleura, which are involved in flavonoid and phenolic biosynthesis pathways. The enrichment analysis revealed that the cinnamic acid, coniferyl alcohol, naringenin, and naringenin-7-O-glucoside were important metabolites in the development process of walnut endopleura. Transcriptome and metabolome analyses revealed that the DEGs and differentially regulated metabolites (DRMs) were significantly enriched in flavonoid biosynthesis and phenolic metabolic pathways. Through co-expression analysis, CHS (chalcone synthase), CHI (chalcone isomerase), CCR (cinnamoyl CoA reductase), CAD (cinnamyl alcohol dehydrogenase), COMT (catechol-Omethyl transferase), and 4CL (4-coumaroyl: CoA-ligase) may be the key genes that potentially regulate walnut endopleura color in flavonoid biosynthesis and phenolic metabolic pathways.
CONCLUSIONS
This study illuminates the metabolic pathways and candidate genes that underlie the endopleura coloration in walnuts, lay the foundation for further study and provides insights into controlling nut's colour.
Topics: Nuts; Transcriptome; Juglans; Fruit; Flavonoids; Gene Expression Profiling; Gene Expression Regulation, Plant
PubMed: 38350847
DOI: 10.1186/s12870-024-04790-6 -
Microbial Cell Factories Feb 2024Corn cob is a major waste mass-produced in corn agriculture. Corn cob hydrolysate containing xylose, arabinose, and glucose is the hydrolysis product of corn cob....
Corn cob is a major waste mass-produced in corn agriculture. Corn cob hydrolysate containing xylose, arabinose, and glucose is the hydrolysis product of corn cob. Herein, a recombinant Escherichia coli strain BT-10 was constructed to transform corn cob hydrolysate into 1,2,4-butanetriol, a platform substance with diversified applications. To eliminate catabolite repression and enhance NADPH supply for alcohol dehydrogenase YqhD catalyzed 1,2,4-butanetriol generation, ptsG encoding glucose transporter EIICB and pgi encoding phosphoglucose isomerase were deleted. With four heterologous enzymes including xylose dehydrogenase, xylonolactonase, xylonate dehydratase, α-ketoacid decarboxylase and endogenous YqhD, E. coli BT-10 can produce 36.63 g/L 1,2,4-butanetriol with a productivity of 1.14 g/[L·h] using xylose as substrate. When corn cob hydrolysate was used as the substrate, 43.4 g/L 1,2,4-butanetriol was generated with a productivity of 1.09 g/[L·h] and a yield of 0.9 mol/mol. With its desirable characteristics, E. coli BT-10 is a promising strain for commercial 1,2,4-butanetriol production.
Topics: Escherichia coli; Zea mays; Metabolic Engineering; Xylose; Glucose; Fermentation; Butanols
PubMed: 38347493
DOI: 10.1186/s12934-024-02317-0 -
Foods (Basel, Switzerland) Jan 2024Pursh (Penthoraceae) is a traditional herb used in Miao medical systems that is also processed into foods (e.g., tea products) in China. Different processing methods...
Pursh (Penthoraceae) is a traditional herb used in Miao medical systems that is also processed into foods (e.g., tea products) in China. Different processing methods significantly affect the volatile compounds, phenolic constituents, and biological activities. This study aimed to produce green tea leaves (GTL), black tea leaves (BTL), and untreated leaves (UL) to investigate differences in their flavor substances, functional components, antioxidant activity, alcohol dehydrogenase (ADH) activity, and acetaldehyde dehydrogenase (ALDH) activity. The results showed that 63, 56, and 56 volatile compounds were detected in UL, GTL, and BTL, respectively, of which 43 volatile compounds were identified as differential metabolites among them. The total phenolic content (97.13-179.34 mg GAE/g DW), flavonoid content (40.07-71.93 mg RE/g DW), and proanthocyanidin content (54.13-65.91 mg CE/g DW) exhibited similar trends, decreasing in the order of UL > BTL > GTL. Fourteen phenolic compounds were determined, of which gallic acid, (-)-epicatechin, and pinocembrin 7--glucoside showed a sharp decrease in content from UL to BTL, while the content of pinocembrin 7--(3″--galloy-4″, 6″-hexahydroxydiphenoyl)-glucoside and pinocembrin significantly increased. GTL showed better DPPH/ABTS scavenging ability and ferric-reducing ability than UL. The ADH and ALDH activities decreased in the order of GTL > UL > BTL. Therefore, tea products made with leaves contained an abundance of functional compounds and showed satisfactory antioxidant and hepatoprotective activities, which are recommended for daily consumption.
PubMed: 38338534
DOI: 10.3390/foods13030399 -
Plants (Basel, Switzerland) Jan 2024While morphological and functional traits enable hydrophytes to survive under waterlogging and partial or complete submergence, the data on responses of...
While morphological and functional traits enable hydrophytes to survive under waterlogging and partial or complete submergence, the data on responses of psammophytes-sand plants-to flooding are very limited. We analyzed the effect of 5- and 10-day soil flooding on the photosynthetic apparatus and the synthesis of alcohol dehydrogenase (ADH), heat shock proteins 70 (HSP70), and ethylene in seedlings of psammophytes and using electron microscopy, chlorophyll fluorescence induction, and biochemical methods. It was found that seedlings growing under soil flooding differed from those growing in stationary conditions with such traits as chloroplast ultrastructure, pigment content, chlorophyll fluorescence induction, and the dynamics of ADH, HSP, and ethylene synthesis. Although flooding caused no apparent damage to the photosynthetic apparatus in all the variants, a significant decrease in total photosynthesis efficiency was observed in both studied plants, as indicated by decreased values of φR0 and PI. More noticeable upregulation of ADH in , as well as increasing HSP70 level and more intensive ethylene emission in , indicate species-specific differences in these traits in response to short-term soil flooding. Meanwhile, the absence of systemic anaerobic metabolic adaptation to prolonged hypoxia causes plant death.
PubMed: 38337946
DOI: 10.3390/plants13030413