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Food Science & Nutrition Jun 2024The aims of this research were to investigate the usability of black grape pomace in the production of shalgam juice, which is a traditional fermented Turkish beverage,...
Evaluation of black grape pomace, a fruit juice by-product, in shalgam juice production: Effect on phenolic compounds, anthocyanins, resveratrol, tannin, and in vitro antioxidant activity.
The aims of this research were to investigate the usability of black grape pomace in the production of shalgam juice, which is a traditional fermented Turkish beverage, to transform the pomace into the high value-added product and to enrich the shalgam juice with phenolic compounds. Black grape pomace and black carrot were used as the sources of polyphenols and five different formulations were obtained according to the amounts of black carrot and black grape pomace. During the fermentation, the samples were taken at different periods and analyzed for anthocyanins, phenolic compounds, antioxidant activity, and tannin content. Gentisic, caffeic, ferulic, coumaric, and chlorogenic acids, catechin, glucosides of kaemferol and isorhamnetin, resveratrol, rutin, cyanidin-3-xylosylglucosylgalactoside, cyanidin-3-xylosylgalactoside, cyanidin-3-xylosylglucosylgalactoside acylated with sinapic acid, ferulic acid, or coumaric acid, and glucosides of cyanidin, petunidin, and malvidin were identified in the shalgam juices that contained both black grape pomace and black carrot in their formulation. Some of these polyphenols were not detected detect in the shalgam juices that were produced from only the black carrot or black grape pomace. During the fermentation, a decrease in the amount of anthocyanins originated from black carrots and an increase in the amount of anthocyanins orginated from black grape pomace were determined. Black grape pomace addition to the formulation before the fermentation caused an increase in the amount of tannin in the shalgam juice samples. Consequently, it is thought that black grape pomace can be fruitfully evaluated in shalgam juice production and can be enhanced by polyphenolic profile of shalgam juice.
PubMed: 38873455
DOI: 10.1002/fsn3.4104 -
Biomedicine & Pharmacotherapy =... Jul 2024The intricate crosstalk between long noncoding RNAs (lncRNAs) and epigenetic modifications such as chromatin/histone methylation and acetylation offer new perspectives... (Review)
Review
The intricate crosstalk between long noncoding RNAs (lncRNAs) and epigenetic modifications such as chromatin/histone methylation and acetylation offer new perspectives on the pathogenesis and treatment of kidney diseases. lncRNAs, a class of transcripts longer than 200 nucleotides with no protein-coding potential, are now recognized as key regulatory molecules influencing gene expression through diverse mechanisms. They modulate the epigenetic modifications by recruiting or blocking enzymes responsible for adding or removing methyl or acetyl groups, such as DNA, N6-methyladenosine (m6A) and histone methylation and acetylation, subsequently altering chromatin structure and accessibility. In kidney diseases such as acute kidney injury (AKI), chronic kidney disease (CKD), diabetic nephropathy (DN), glomerulonephritis (GN), and renal cell carcinoma (RCC), aberrant patterns of DNA/RNA/histone methylation and acetylation have been associated with disease onset and progression, revealing a complex interplay with lncRNA dynamics. Recent studies have highlighted how lncRNAs can impact renal pathology by affecting the expression and function of key genes involved in cell cycle control, fibrosis, and inflammatory responses. This review will separately address the roles of lncRNAs and epigenetic modifications in renal diseases, with a particular emphasis on elucidating the bidirectional regulatory effects and underlying mechanisms of lncRNAs in conjunction with DNA/RNA/histone methylation and acetylation, in addition to the potential exacerbating or renoprotective effects in renal pathologies. Understanding the reciprocal relationships between lncRNAs and epigenetic modifications will not only shed light on the molecular underpinnings of renal pathologies but also present new avenues for therapeutic interventions and biomarker development, advancing precision medicine in nephrology.
Topics: RNA, Long Noncoding; Humans; Epigenesis, Genetic; Histones; Acetylation; DNA Methylation; Kidney Diseases; Chromatin; Animals
PubMed: 38870627
DOI: 10.1016/j.biopha.2024.116922 -
Nanoscale Advances Jun 2024In this research, a heterogeneous acid catalyst was synthesized by room temperature encapsulation of phosphomolybdic acid (PMA) in the pores of the MIL-53 (Fe) metal...
In this research, a heterogeneous acid catalyst was synthesized by room temperature encapsulation of phosphomolybdic acid (PMA) in the pores of the MIL-53 (Fe) metal organic framework (MOF) under ultrasonic conditions. Then the catalytic activity of PMA@MIL-53 (Fe) was investigated in Friedel-Crafts -acylation of -fluorophenol, and this procedure was optimized using response surface methodology based on central composite design (RSM-CCD). The impact of critical reaction parameters including reaction duration, catalyst dosage, and PMA amount in the catalyst was optimized, leading to the formation of the target product in excellent yield at a short reaction time.
PubMed: 38868818
DOI: 10.1039/d3na01126g -
Molecular & Cellular Proteomics : MCP Jun 2024Histone post-translational modifications (PTMs) have crucial roles in a multitude of cellular processes, and their aberrant levels have been linked with numerous...
Histone post-translational modifications (PTMs) have crucial roles in a multitude of cellular processes, and their aberrant levels have been linked with numerous diseases, including cancer. Although histone PTM investigations have focused so far on methylations and acetylations, alternative long-chain acylations emerged as new dimension, as they are linked to cellular metabolic states and affect gene expression through mechanisms distinct from those regulated by acetylation. Mass spectrometry (MS) is the most powerful, comprehensive and unbiased method to study histone PTMs. However, typical MS-based protocols for histone PTM analysis do not allow identification of naturally occurring propionylation and butyrylation. Here, we present improved state-of-the-art sample preparation and analysis protocols to quantitate these classes of modifications. After testing different derivatization methods coupled to protease digestion, we profiled common histone PTMs and histone acylations in seven mouse tissues and human normal and tumor breast clinical samples, obtaining a map of propionylations and butyrylations found in different tissue contexts. A quantitative histone PTM analysis also revealed a contribution of histone acylations in discriminating different tissues, also upon perturbation with antibiotics, and breast cancer samples from the normal counterpart. Our results show that profiling only classical modifications is limiting and highlight the importance of using sample preparation methods that allows the analysis of the widest possible spectrum of histone modifications, paving the way for deeper insights into their functional significance in cellular processes and disease states.
PubMed: 38866077
DOI: 10.1016/j.mcpro.2024.100799 -
Journal of Chemical Information and... Jun 2024Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA...
Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA repair. One of the key post-translational modifications (PTMs) is the acetylation of lysine residues on histone tails. Epigenetic modifications are ubiquitous in the development of diseases, such as cancer and neurological disorders. Histone H2B tails are critical regulators of nucleosome dynamics, biological processes, and certain diseases. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome to demonstrate that acetylation of the histone tails changes their conformational space and interaction with DNA. We perform simulations of H2B tails, critical regulators of gene regulation, in both the lysine-acetylated (ACK) and unacetylated wild type (WT) states. To explore the effects of salt concentration, we use two different NaCl concentrations to perform simulations at microsecond time scales. Salt can modulate the effects of electrostatic interactions between the DNA phosphate backbone and histone tails. Upon acetylation, H2B tails shift their secondary structure helical propensity. The number of contacts between the DNA and the H2B tail decreases. We characterize the conformational dynamics of the H2B tails by principal component analysis (PCA). The ACK tails become more compact at increased salt concentrations, but conformations from the WT tails display the most contacts with DNA at both salt concentrations. Mainly, H2B acetylation may increase the DNA accessibility for regulatory proteins to bind, which can aid in gene regulation and NCP stability.
Topics: Molecular Dynamics Simulation; Histones; Nucleosomes; DNA; Acetylation; Protein Conformation; Principal Component Analysis
PubMed: 38865599
DOI: 10.1021/acs.jcim.4c00059 -
Acetylation of histones and non-histone proteins is not a mere consequence of ongoing transcription.Nature Communications Jun 2024In all eukaryotes, acetylation of histone lysine residues correlates with transcription activation. Whether histone acetylation is a cause or consequence of...
In all eukaryotes, acetylation of histone lysine residues correlates with transcription activation. Whether histone acetylation is a cause or consequence of transcription is debated. One model suggests that transcription promotes the recruitment and/or activation of acetyltransferases, and histone acetylation occurs as a consequence of ongoing transcription. However, the extent to which transcription shapes the global protein acetylation landscapes is not known. Here, we show that global protein acetylation remains virtually unaltered after acute transcription inhibition. Transcription inhibition ablates the co-transcriptionally occurring ubiquitylation of H2BK120 but does not reduce histone acetylation. The combined inhibition of transcription and CBP/p300 further demonstrates that acetyltransferases remain active and continue to acetylate histones independently of transcription. Together, these results show that histone acetylation is not a mere consequence of transcription; acetyltransferase recruitment and activation are uncoupled from the act of transcription, and histone and non-histone protein acetylation are sustained in the absence of ongoing transcription.
Topics: Acetylation; Histones; Transcription, Genetic; Humans; Ubiquitination; p300-CBP Transcription Factors; Protein Processing, Post-Translational; Histone Acetyltransferases; Lysine
PubMed: 38862536
DOI: 10.1038/s41467-024-49370-2 -
Genomics Jun 2024The investigation of dwarfing rootstocks for the establishment of high-generation seed orchards is a prospective avenue of research. In this investigation, Pinus...
The investigation of dwarfing rootstocks for the establishment of high-generation seed orchards is a prospective avenue of research. In this investigation, Pinus massoniana, Pinus yunnanensis var. pygmaea (P. pygmaea), and P. elliottii seedlings were used as rootstocks for grafting with P. massoniana scions. Grafting P. massoniana onto P. pygmaea rootstock resulted in observable phenotypic alterations in lateral branches, apical buds, and needle length. Certain characteristic metabolites of rootstocks, such as fatty acyls, pregnenolones, steroids, and steroid derivatives, were found to be highly expressed in scions after grafting. RNA-seq analysis revealed MYB-related, SBP, and bHLH demonstrating a significant positive correlation, while C2H2 and Orphans exhibited negative correlations with the differential intensity of metabolites related to lipids and lipid-like molecules. This study offers valuable insights for the establishment of rootstock breeding programs.
PubMed: 38857814
DOI: 10.1016/j.ygeno.2024.110882 -
Communications Biology Jun 2024Aspergillus fumigatus represents a public health problem due to the high mortality rate in immunosuppressed patients and the emergence of antifungal-resistant isolates....
Aspergillus fumigatus represents a public health problem due to the high mortality rate in immunosuppressed patients and the emergence of antifungal-resistant isolates. Protein acetylation is a crucial post-translational modification that controls gene expression and biological processes. The strategic manipulation of enzymes involved in protein acetylation has emerged as a promising therapeutic approach for addressing fungal infections. Sirtuins, NAD-dependent lysine deacetylases, regulate protein acetylation and gene expression in eukaryotes. However, their role in the human pathogenic fungus A. fumigatus remains unclear. This study constructs six single knockout strains of A. fumigatus and a strain lacking all predicted sirtuins (SIRTKO). The mutant strains are viable under laboratory conditions, indicating that sirtuins are not essential genes. Phenotypic assays suggest sirtuins' involvement in cell wall integrity, secondary metabolite production, thermotolerance, and virulence. Deletion of sirE attenuates virulence in murine and Galleria mellonella infection models. The absence of SirE alters the acetylation status of proteins, including histones and non-histones, and triggers significant changes in the expression of genes associated with secondary metabolism, cell wall biosynthesis, and virulence factors. These findings encourage testing sirtuin inhibitors as potential therapeutic strategies to combat A. fumigatus infections or in combination therapy with available antifungals.
Topics: Aspergillus fumigatus; Sirtuins; Virulence; Animals; Mice; Aspergillosis; Acetylation; Fungal Proteins; Gene Expression Regulation, Fungal; Virulence Factors; Moths
PubMed: 38851817
DOI: 10.1038/s42003-024-06383-3 -
Synthetic and Systems Biotechnology Dec 2024Four new -acylated aminoalkanoic acids, namely clonoroseins E-H (-), together with three previously identified analogs, clonoroseins A, B, and D (-), were identified...
Four new -acylated aminoalkanoic acids, namely clonoroseins E-H (-), together with three previously identified analogs, clonoroseins A, B, and D (-), were identified from the endophytic fungus strain 15020 (CR15020), using Feature-based Molecular Networking (FBMN). The elucidation of their chemical structures, including their absolute configurations, was achieved through spectroscopic analysis combined with quantum chemical calculations. Bioinformatics analyses suggested that an iterative type I HR-PKS (CrsE) generates the polyketide side chain of these clonoroseins. Furthermore, a downstream adenylate-forming enzyme of the PKS (CrsD) was suspected to function as an amide synthetase. CrsD potentially facilitates the transformation of the polyketide moiety into an acyl-AMP intermediate, followed by nucleophilic substitution with either β-alanine or γ-aminobutyric acid to produce amide derivatives. These findings significantly expand our understanding of PKS-related products originating from and also underscore the powerful application of FBMN analytical methods in characterization of new compounds.
PubMed: 38846337
DOI: 10.1016/j.synbio.2024.05.006 -
Nature Jun 2024Histone acetylation regulates gene expression, cell function and cell fate. Here we study the pattern of histone acetylation in the epithelial tissue of the Drosophila...
Histone acetylation regulates gene expression, cell function and cell fate. Here we study the pattern of histone acetylation in the epithelial tissue of the Drosophila wing disc. H3K18ac, H4K8ac and total lysine acetylation are increased in the outer rim of the disc. This acetylation pattern is controlled by nuclear position, whereby nuclei continuously move from apical to basal locations within the epithelium and exhibit high levels of H3K18ac when they are in proximity to the tissue surface. These surface nuclei have increased levels of acetyl-CoA synthase, which generates the acetyl-CoA for histone acetylation. The carbon source for histone acetylation in the rim is fatty acid β-oxidation, which is also increased in the rim. Inhibition of fatty acid β-oxidation causes H3K18ac levels to decrease in the genomic proximity of genes involved in disc development. In summary, there is a physical mark of the outer rim of the wing and other imaginal epithelia in Drosophila that affects gene expression.
Topics: Animals; Acetate-CoA Ligase; Acetyl Coenzyme A; Acetylation; Biological Transport; Cell Nucleus; Chromatin; Drosophila melanogaster; Drosophila Proteins; Fatty Acids; Gene Expression Regulation; Histones; Imaginal Discs; Lysine; Oxidation-Reduction; Wings, Animal
PubMed: 38839952
DOI: 10.1038/s41586-024-07471-4