Influence of protocatechuic acid on gene expression in Blastobotrys raffinosifermentans LS3
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ABSTRACT:
ORGANISM(S): Blastobotrys raffinosifermentans
PROVIDER: GSE195808 | GEO | 2022/02/03
REPOSITORIES: GEO
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Project description:Gene expression profiling of Blastobotrys raffinosifermentans LS3 cells based on 6.025 annotated chromosomal Blastobotrys raffinosifermentans LS3 sequences and 36 putative mitochondrial gene oligos was performed following exposure to gallic acid. Microarray data were successfully used to identify expression changes of main candidate genes involved in tannic acid degradation, protocatechuic acid degradation, β-oxidation, the glyoxylate cycle, the methyl citrate cycle and the catabolism of the branched-chain amino acids valine, leucine and isoleucine.
2022-02-03 | GSE195801 | GEO
Project description:Lysine β-hydroxybutyrylation (Kbhb) is an evolutionarily conserved and widespread post-translational modification (PTM) in active gene transcription and cellular proliferation. However, its function remains unknown in phytopathogenic fungi. Here, we report a comprehensive identification of Kbhb in the rice false smut fungus Ustilaginoidea virens. Total 2,204 Kbhb sites were identified in 852 proteins. We found that β-hydroxybutyrylated proteins were enriched in mannose type O-glycan biosynthesis, citrate cycle (TCA cycle), ribosome, glycolysis/gluconeogenesis, proteasome, glyoxylate and dicarboxylate metabolism, alanine, aspartate and glutamate metabolism, pyruvate metabolism, biosynthesis of nucleotide sugars, butanoate metabolism, arginine biosynthesis, fructose and mannose metabolism, propanoate metabolism, methane metabolism, fatty acid degradation, β-alanine metabolism, valine, leucine and isoleucine degradation, phagosome, oxidative phosphorylation pathway. This suggests Kbhb might be involved in basic life functions of Ustilaginoidea virens.
2023-10-24 | PXD039304 | Pride
Project description:We investigated the physiological changes induced by indoleacetic acid (IAA) treatment in the totally sequenced Escherichia coli K-12 MG1655. We used DNA macroarrays to measure the mRNA levels for all the 4,290 E. coli protein-coding genes and observed that 50 genes (1.1 %) exhibited significantly different expression profiles. In particular, genes involved in the tricarboxylic acid cycle (TCA), glyoxylate shunt, and amino acid biosynthesis (leucine, isoleucine, valine and proline) were up-regulated, whereas the fermentative adhE gene was down-regulated. To confirm the indications obtained from the macroarray analysis we measured the activity of 33 enzymes involved in the central metabolism and found an activation of the TCA cycle and the glyoxylate shunt. Keywords: treatment
2006-06-01 | GSE4941 | GEO
Project description:For the first time in Lactococcus lactis, amino acid starvation response was characterized. The natural imposition of isoleucine starvation, by its consumption during growth, associated to transcript profiling, allowed defining exhaustively this stress stimulon. It consisted of a general induction of nitrogen metabolism (amino acid biosynthesis and transport, proteolytic system and proteases), a strong repression of genes encoding major physiological activities (translation, transcription, carbon metabolism, purine and pyrimidine biosynthesis and fatty acid metabolism) and the induction of unexpected cross responses to acid, osmotic and oxidative stresses. Keywords: stress response, time course Isoleucine starvation was imposed by the consumption of this amino acid during the growth of Lactococcus lactis IL1403 on ILV0.1 medium (CDM with ten-fold reduced concentrations of isoleucine, leucine and valine) and under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested in exponential phase and after 30 min, 1.7 h and 3.5 h of isoleucine starvation. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 2053 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. The 4 time-points were analyzed simultaneously and 3 independent repetitions were performed.
2010-06-25 | E-GEOD-4872 | biostudies-arrayexpress
Project description:Purpose:To gain insight into the spectrum of Brucella gene affected by the ClpP protease, as well as the genetic basis for the distinctive phenotypic properties exhibited by the clpP mutant strain. Methods: Three B. abortus 2308 and the three clpP mutant were grown in TSB at 37℃ until the log phase was reached, total RNA was isolated using the TRIzol according to the manufacturer’s instructions.The sequencing library of each RNA sample was prepared by using NEB Next Ultra Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer.The HiSeq 4000 platform was used to perform the transcriptome sequencing. Results: In total, 772 genes that exhibited different expression (Fold change>4, and FDR<0.05) were identified in the clpP mutant. In the clpP mutant strain, 376 genes were up-regulated and 396 genes were down-regulated. Conclusions: According to the result of COG analysis, the different expressed genes were mainly involved in Energy production and conversion, Cell wall/membrane/envelope biogenesis, and Carbohydrate transport and metabolism. KEGG pathway analysis demonstrated that the genes exhibited significant difference were primarily enriched in ABC transporters, beta-Lactam resistance, Oxidative phosphorylation, Cationic antimicrobial peptide (CAMP) resistance, Limonene and pinene degradation, Lysine degradation, Valine, leucine and isoleucine degradation, Chloroalkane and chloroalkene degradation, Ascorbate and aldarate metabolism, Tryptophan metabolism, Citrate cycle (TCA cycle), and Histidine metabolism.
2022-02-22 | GSE126915 | GEO
Project description:RNA was isolated from early stationary phase S. gordonii V288(OD620 nm ~ 1.8).Bacteria were grown in chemically defined synthetic media (FMC) ( K2HPO4, 300 µg ml-1; KH2PO4 440 µg ml-1; Na2HPO4, 3.15 mg ml-1; NaH2PO4, 2.05 mg ml-1; (NH4)2SO4 0.6 mg ml-1; sodium citrate, 225 µg ml-1; riboflavin, 0.4 µg ml-1; biotin, 0.01 µg ml-1; folic acid, 0.1 µg ml-1; pantothenate, 0.8 µg ml-1; p-aminobenzoic acid 0.1 µg ml-1; thiamine 0.4 µg ml-1; nicotinamide 2.0 µg ml-1; pyridoxamine 0.8 µg ml-1; D-glucose 20 mg ml-1; sodium acetate 6 mg ml-1; adenine 35 µg ml-1; guanine µg ml-1; uracil µg ml-1; MgSO4, 200 µg ml-1; NaCl, 10 µg ml-1; FeSO4, 10 µg ml-1; MnSO4 10 µg ml-1; glutamine 5 µg ml-1; L-glutamic acid, 300 µg ml-1; L-valine, 100 µg ml-1; 110 µg ml-1 of L-lysine, L-asparate, L-isoleucine, L-methionine, L-serine, L-phenylalanine and 200 µg ml-1 of L-alanine, L-cystine, L-histidine, glycine, L-hydroxyproline, L-proline, L-tryptophan and L-tyrosine, pH 6.5) (Terleckyj & Shockman, 1975; Terleckyj et al., 1975) at 37°C in 5% CO2.
2008-08-01 | E-MEXP-1712 | biostudies-arrayexpress
Project description:Abstract: Non-alcoholic steatohepatitis (NASH) is associated with a disturbed metabolism in liver and excessive accumulation of ectopic fat. Branched-chain amino acids (BCAAs) may beneficially modulate hepatic lipids, however it remains unclear whether individual BCAAs can attenuate already established NASH and oxidative-inflammatory stress associated with it. Therefore, mice were first put on a run-in fast food diet (FFD) for 26 weeks, these obese mice were then treated with individual BCAAs valine or isoleucine (3% of FFD) for another 12 weeks and compared to FFD controls. Valine and isoleucine treatment did not affect obesity, dyslipidemia, gut permeability or fecal fatty acid excretion, although significantly reduced hyperinsulinemia compared with FFD. Valine and isoleucine significantly reduced ALT, CK-18M30, and liver steatosis with a particularly pronounced effect on the microvesicular component (-61% by valine and -71% by isoleucine). Hepatic 4-hydroxynonenal (4-HNE) immunoreactivity, a marker for oxidative stress-induced lipid peroxidation, was also significantly decreased. Functional genomics analysis demonstrated that valine and isoleucine upregulated BCAA metabolism, deactivated master regulators of anabolic pathways related to steatosis (e.g. SREBPF1) and activated master regulators of mitochondrial biogenesis (e.g. PPARGC1a) and lipid catabolism (e.g. ACOX1, AMPK). The correction of critical metabolic pathways by valine and isoleucine was accompanied by a significant decrease of liver inflammation, and suppression of many FFD-stimulated cytokine and chemokine pathways including IL-1β, TNFα and CCR2 signaling. In conclusion, the dietary intervention with either valine or isoleucine corrected multiple metabolic processes in liver and reduced steatosis and inflammation with profound effects on oxidative stress and inflammatory pathways. Methods: Putative antifibrotic effects of butyrate were studied in Ldlr-/-.Leiden mice fed an obesogenic NASH-inducing diet (HFD) containing 2.5% (w/w) butyrate for 38 weeks and compared to an HFD control group. Antifibrotic mechanisms of butyrate were further investigated in TGF-β-stimulated primary human hepatic stellate cells (HSC). Results: HFD-fed mice developed obesity, insulin resistance, increased levels of plasma leptin, adipose tissue inflammation, gut permeability, dysbiosis and NASH-associated fibrosis. Butyrate corrected hyperinsulinemia, lowered plasma leptin levels and attenuated adipose tissue inflammation, without affecting gut permeability or microbiota composition. Butyrate lowered plasma ALT and CK-18M30 and attenuated hepatic steatosis and inflammation. Butyrate inhibited fibrosis development as demonstrated by decreased hepatic collagen content and Sirius-red-positive area. In TGF-β-stimulated HSC, butyrate dose-dependently reduced collagen deposition and decreased procollagen1α1 and PAI-1 protein expression. Transcriptomic analysis and subsequent pathway and upstream regulator analysis revealed deactivation of specific non-canonical TGF-β signaling pathways RhoA/Rock and PI3K/AKT and other important pro-fibrotic regulators (e.g. YAP/TAZ and MYC) by butyrate, providing a potential rationale for its antifibrotic effects. Conclusions: Butyrate protects against the development of obesity and insulin resistance-associated NASH and liver fibrosis. These antifibrotic effects are at least in part attributable to a direct effect on collagen production in hepatic stellate cells, as a result of inhibiting non-canonical TGF-β signaling.
2022-06-30 | GSE195798 | GEO
Project description:Purpose:In this study, we observed the effect of exogenous melatonin on the proliferation and pathogenicity of Alternaria alternata, judged the biological function of melatonin on Alternaria alternata, and found the key genes of melatonin regulating Alternaria alternata traits at the transcription level by RNA SEQ, and preliminarily revealed its mechanism of action. Methods:SNA medium with melatonin concentration of 50, 100, 500, 1000 and 1500 μ m was prepared and 30 ml plate was made. Take sterilized circular filter paper with a diameter of 1 cm, add 100 UL 50 CFU / cm3 spore suspension, transfer to SNA medium center, and culture upside down for 7 days Results:In this study, 20 metabolic pathways with the most significant KEGG enrichment were selected from the four control groups by P value analysis (Fig. 9). In 500 μ m vs control group, DEGs were mainly enriched in ribosome, glyoxylic acid and dicarboxylic acid metabolism pathways. In 1500 μ m vs control group, the metabolic pathways such as glyoxylic acid and dicarboxylic acid metabolism, valine, leucine and isoleucine degradation, ketone body synthesis and degradation, terpenoid main chain biosynthesis were the most significant; in 500 μ m vs 1500 μ m, DEGs were mainly enriched in eukaryotic ribosome biosynthesis and RNA polymerase pathway; 500 μ m vs 1500 μ M Compared with the control treatment, DEGs were significantly enriched among the three groups, and the pathways were rich, such as amino acid metabolism, glyoxylic acid and dicarboxylic acid metabolism, valine, leucine and isoleucine degradation, glyceride metabolism, glycolysis / gluconeogenesis, ABC transporter and so on. Conclusions:Nine DEGs related to the development and pathogenesis of streptozospora were obtained by transcriptional sequencing. The results showed that melatonin involved aflatoxin biosynthesis (sld1 and sld2, s-adenosine-l-methionine dependent methyltransferase synthesis), MAPK signal pathway (GLP), linoleic acid metabolism (HP1), heme peroxidase synthesis ）The results showed that the metabolism of selenium (THR), protein processing in endoplasmic reticulum (KHP, 30kda heat shock protein synthesis), glycolysis / glycometagenesis (PPL), and synthesis of non reductive poly ketoacetase (NPS) and heme peroxidase (HP2) were also studied. Among them, THR is related to proliferation regulation [49], sld1, sld2, NPs and ppl are related to pathogenicity , GLP is related to colony growth and pathogenicity, KHP is related to stress , HP1 and HP2 are related to antioxidant activity .
2021-03-28 | GSE170796 | GEO
Project description:Here we report on an RNAseq method in combination with spike-in cells to measure global changes in the transcription pattern after valine-induced isoleucine starvation of a standard E. coli K12 strain. Due to the spike-in method we were able to show that ribosomal RNA is degraded during isoleucine starvation and we showed how this change in cellular RNA content affect the estimated regulation of mRNA levels compared to if spike-in were not utilized. Our analysis also showed that induction of starvation by sudden addition of high valine concentrations provoked prominent regulatory responses outside of the expected ppGpp, RpoS and Lrp regulons
2019-11-19 | GSE136753 | GEO
Project description:The effect of environmental salinity on the gill proteome was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by LCMSMS data-independent acquisition (DIA) and Skyline. For this purpose, relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with data-independent acquisition (DIA) quantitative proteomics (Li et al. 2018). Osmoregulatory responses were distinguished from general stress responses based on the direction of protein abundance changes. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress in all six mesocosm experiments then it was considered an osmoregulatory protein. If protein abundance was always increased in all six mesocosm experiments independent of whether salinity was increased or decreased then it was considered a stress response protein. KEGG pathway analysis revealed that the inositol phosphate metabolism, salivary secretion, several endocrine and extracellular signaling, valine, leucine and isoleucine degradation, citrate cycle, and oxidative phosphorylation pathways contain most osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to pathways that represent proteostasis, immunity and intracellular signaling processes. General stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and several intracellular signaling pathways. Some proteins in these general stress response pathways are consistently down-regulated instead of being up-regulated during any type of salinity stress indicating that these KEGG pathways are not uniformly induced or repressed but that their function is being altered more intricately.
2020-09-24 | PXD017662 | panorama