Interconversion Of Metabolites Research Articles

Antimicrobial and antioxidant activities of peptide derived from turmeric plant (Curcuma longa L).

The overuse and inappropriate use of antibiotics have led to the emergence of several antibiotic resistant bacteria. As a result, there is growing interest in exploring alternative agents as antimicrobial peptides (AMPs), which operate through unique mechanisms to effectively counteract bacterial resistance. In this study, peptides smaller than 3 kDa were isolated by cation exchange chromatography, anion exchange chromatography and reverse-phase chromatography. Subsequently, 12 candidate peptides were selected and chemically synthesized for a comparative study of growth inhibition in pathogenic bacteria. They demonstrated potent antibacterial activity toward A. baumannii, S. epidermidis, S. aureus, and S. enterica. Exposure to the Cur-1 peptide induced changes in bacterial proteins associated with metabolite interconversion and translation. In addition, all peptides derived from turmeric peptic hydrolysate exhibited antioxidant activity as assessed by ABTS, DPPH and FRAP assays. Cur-1 peptide displayed both high antibacterial and antioxidant potential, positioning it as a promising natural option for antibacterial management and applications within food industry.

Molecular mechanisms of sulforaphane in Alzheimer’s disease: insights from an in-silico study

This study was to identify the molecular pathways that may explain sulforaphane’s Alzheimer’s disease (AD) benefits using multiple advanced in silico approaches. We found that sulforaphane regulates 45 targets, including TNF, INS, and BCL2. Therefore, it may help treat AD by reducing neuroinflammation, insulin resistance, and apoptosis. The important relationships were co-expression and pathways. 45 targets were linked to the midbrain, metabolite interconversion enzymes, 14q23.3 and 1q31.1 chromosomes, and modified residues. “Amyloid precursor protein catabolic process”, “regulation of apoptotic signaling pathway”, and “positive regulation of nitric oxide biosynthetic process” were the main pathways, while NFKB1, SP1, RELA, hsa-miR-17-5p, hsa-miR-16-5p, and hsa-miR-26b-5p were transcription factors and miRNAs implicated in sulforaphane In AD treatment, miRNA sponges, dexibuprofen, and sulforaphane may be effective. Furthermore, its unique physicochemical, pharmacokinetic, and biological qualities make sulforaphane an effective AD treatment, including efficient gastrointestinal absorption, drug-like properties, absence of CYP450 enzyme inhibition, not being a substrate for P-glycoprotein, ability to cross the blood–brain barrier, glutathione S-transferase substrate, immunostimulant effects, and antagonistic neurotransmitter effects. Sulforaphane is a promising compound for AD management. Further work is needed to elucidate its therapeutic effects based on our findings, including genes, miRNAs, molecular pathways, and transcription factors.

Alteration of the metabolite interconversion enzyme in sperm and Sertoli cell of non-obstructive azoospermia: a microarray data and in-silico analysis

Numerous variables that regulate the metabolism of Sertoli cells and sperm have been identified, one of which is sex steroid hormones. These hormones play a vital role in maintaining energy homeostasis, influencing the overall metabolic balance of the human body. The proper functioning of the reproductive system is closely linked to energy status, as the reproductive axis responds to metabolic signals. The aim of this study was to investigate the gene expression patterns of metabolite interconversion enzymes in testicular cells (Sertoli cells and spermatogonia) of non-obstructive azoospermia (NOA) patients, as compared to normal controls, to understand the molecular mechanisms contributing to NOA. We used microarray and bioinformatics techniques to analyze 2912 genes encoding metabolite interconversion enzymes, including methyltransferase, monooxygenase, transmembrane reductase, and phosphohydrolase, in both testicular cells and normal samples. In sperm, the upregulation of MOXD1, ACAD10, PCYT1A, ARG1, METTL6, GPLD1, MAOA, and CYP46A1 was observed, while ENTPD2, CPT1C, ADC, and CYB5B were downregulated. Similarly, in the Sertoli cells of three NOA patients, RPIA, PIK3C3, LYPLA2, CA11, MBOAT7, and HDHD2 were upregulated, while NAA25, MAN2A1, CYB561, PNPLA5, RRM2, and other genes were downregulated. Using STRING and Cytoscape, we predicted the functional and molecular interactions of these proteins and identified key hub genes. Pathway enrichment analysis highlighted significant roles for G1/S-specific transcription, pyruvate metabolism, and citric acid metabolism in sperm, and the p53 signaling pathway and folate metabolism in Sertoli cells. Additionally, Weighted Gene Co-expression Network Analysis (WGCNA) and single-cell RNA sequencing (scRNA-seq) were performed to validate these findings, revealing significant alterations in gene expression and cellular distribution in NOA patients. Together, these results provide new insights into the molecular mechanisms underlying NOA and identify potential therapeutic targets.

Exogenous interactome analysis of bovine viral diarrhea virus-host using network based-approach and identification of hub genes and important pathways involved in virus pathogenesis

Bovine viral diarrhea (BVD) is one of the most important diseases in livestock, caused by BVD virus (BVDV). During the pathogenesis of the virus, many interactions occur between host and viral proteins. Studying these interactions can help better understand the pathogenesis of the virus, identify putative functional proteins, and find new treatment and prevention strategies. To this aim, a BVDV-host protein-protein interaction (PPI) network map was constructed using Cytoscape and analyzed with cytoHubba, Kyoto Encyclopedia of Genes and Genomics (KEGG), Gene Ontology (GO), and Protein Analysis Through Evolutionary Relationships (PANTHER). Npro with 125 connections had the greatest number of interactions with host proteins. CD46, EEF-2, and TXN genes were detected as hub genes using different ranking algorithms in cytoHubba. BVDV interactions with its host mainly focus on targeting translation, protein synthesis, and cellular metabolism pathways. Different classes of proteins including translational proteins, nucleic acid metabolism proteins, metabolite interconversion enzymes, and protein-modifying enzymes are affected by BVDV. These findings improve our understanding of the effects of the virus on the cell. Hub genes and key pathways identified in the present study can serve as targets for novel BVDV prevention or treatment strategies.

A diverse proteome is present and enzymatically active in metabolite extracts

Metabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. This is a ubiquitous feature across several common extraction and sample types. By combining post-resuspension stable isotope addition and enzyme inhibitors, we demonstrate in-extract metabolite interconversions due to residual transaminase activity. We extend these findings with untargeted metabolomics where we observe extensive protein-mediated metabolite changes, including in-extract formation of glutamate dipeptide and depletion of total glutathione. Finally, we present a simple extraction workflow that integrates 3 kDa filtration for protein removal as a superior method for polar metabolomics. In this work, we uncover a previously unrecognized, protein-mediated source of observer effects in metabolomics experiments with broad-reaching implications across all research fields using metabolomics and molecular metabolism.

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

BackgroundSwitchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress.ResultsIn total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls.ConclusionOur study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.

Unraveling the Global Proteome and Phosphoproteome of Prostate Cancer Patient-Derived Xenografts.

Overall, our study highlights the importance of protein-based identification when compared with RNA and provides a rich resource of new and feasible targets for clinical assay development and in understanding the underlying biology of these tumors.

Plasma Proteomic Analysis Reveals the Potential Role of Lectin and Alternative Complement Pathways in IgA Vasculitis Pathogenesis.

IgA vasculitis (IgAV) is the most common form of childhood vasculitis. A better understanding of its pathophysiology is required to identify new potential biomarkers and treatment targets. to assess the underlying molecular mechanisms in the pathogenesis of IgAV using an untargeted proteomics approach. Thirty-seven IgAV patients and five healthy controls were enrolled. Plasma samples were collected on the day of diagnosis before any treatment was initiated. We used nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to investigate the alterations in plasma proteomic profiles. For the bioinformatics analyses, databases including Uniprot, PANTHER, KEGG, Reactome, Cytoscape, and IntAct were used. Among the 418 proteins identified in the nLC-MS/MS analysis, 20 had significantly different expressions in IgAV patients. Among them, 15 were upregulated and 5 were downregulated. According to the KEGG pathway and function classification analysis, complement and coagulation cascades were the most enriched pathways. GO analyses showed that the differentially expressed proteins were mainly involved in defense/immunity proteins and the metabolite interconversion enzyme family. We also investigated molecular interactions in the identified 20 proteins of IgAV patients. We extracted 493 interactions from the IntAct database for the 20 proteins and used Cytoscape for the network analyses. Our results clearly suggest the role of the lectin and alternate complement pathways in IgAV. The proteins defined in the pathways of cell adhesion may serve as biomarkers. Further functional studies may lead the way to better understanding of the disease and new therapeutic options for IgAV treatment.

Response to microplastic exposure: An exploration into the sea urchin immune cell proteome

It is now known that the Mediterranean Sea currently is one of the major hotspot for microplastics (MPs; < 5 mm) pollution and that the risks will be even more pronounced in the coming years. Thus, the in-depth study of the mechanisms underlying the MPs toxicity in key Mediterranean organisms, subjected to high anthropic pressures, has become a categorical imperative to pursue. Here, we explore for the first time the sea urchins immune cells profile combined to their proteome upon in vivo exposure (72 h) to different concentrations of polystyrene-microbeads (micro-PS) starting from relevant environmental concentrations (10, 50, 103, 104 MP/L). Every 24 h, immunological parameters were monitored. After 72 h, the abundance of MPs was examined in various organs and coelomocytes were collected for proteomic analysis based on a shotgun label free proteomic approach. While sea urchins treated with the lowest concentration tested (10 and 50 micro-PS/L) did not show the presence of micro-PS in any tissue, in the specimens exposed to the highest concentration (103 and 104 micro-PS) there was an internalisation of 9.75 ± 2.75 and 113.75 ± 34.5 MP/g, respectively. Proteomic analyses revealed that MPs exposure altered coelomocytes protein profile not only compared to the control group but also among the different micro-PS concentrations and these variations are micro-PS concentration dependent. The proteins exclusively expressed in the coelomocytes of specimens exposed to MPs are mainly metabolite interconversion enzymes, involved in cellular processes, indicating a severe alteration of the cellular metabolic pathways. Overall, these findings provide new insights on the mode of action of MPs in the sea urchin immune cells both at the molecular and cellular level.

Obesity- and sex-related metabolism of arginine and nitric oxide in adults

There is growing interest in the supplementation of arginine (Arg) and citrulline (Cit) in obesity due to their potential anti-obesogenic and anti-inflammatory properties. However, there is no consensus on the metabolic changes in Arg kinetics in obesity. This exploratory cross-sectional study aimed to investigate the association between obesity, sex, and sex-by-obesity interaction on whole-body Arg kinetics in a large group of human subjects. We studied 83 nonobese [BMI (kg/m2) <30] and 80 morbidly obese (BMI >30) middle-aged individuals (40% males) enrolled in the MEDIT (Metabolism of Disease with Isotope Tracers) trial. After body-composition measurement by DXA, we collected arterial(ized) blood samples for amino acid (AA) concentrations, markers of inflammation [high-sensitivity C-reactive protein (hs-CRP)], liver function, and glucose in a postabsorptive state. We administered a pulse of AA stable tracers and measured whole-body production (WBP) of Arg, Cit, ornithine (Orn), phenylalanine, and tyrosine, and calculated their clearance (disposal capacity) and metabolite interconversions [markers for NO and de novo Arg production, systemic Arg hydrolysis, and whole-body protein breakdown (wbPB)]. We measured plasma enrichments by LC-MS/MS and statistics by Fisher's exact test or analysis of (co)variance. Significance was set at P<0.05. Obese individuals were normoglycemic and characterized by low-grade inflammation (P<0.0001) and greater wbPB (P=0.0298). We found lower plasma Cit concentration (P<0.0001) in the obese group but no differences in the WBP of Arg, Cit, and Orn. Furthermore, we observed overproduction of NO (P<0.0001) in obesity but lower de novo Arg production (P=0.0007). The WBP of Arg was lower in females for almost all Arg-related AAs, except for plasma Cit and NO production. Alterations in Arg metabolism are present in morbid obesity. Further studies are needed to investigate if these changes could be related to factors such as increased Arg requirement in obesity or metabolic adaptation.

Proteomic analysis of Atg8-dependent recruitment of phagosomal proteins in the enteric protozoan parasite Entamoeba histolytica.

Autophagy is one of the bulk degradation systems and is conserved throughout eukaryotes. In the enteric protozoan parasite Entamoeba histolytica, the causative agent of human amebiasis, Atg8 is not exclusively involved in autophagy per se but also in other membrane traffic-related pathways such as phagosome biogenesis. We previously reported that repression of atg8 gene expression by antisense small RNA-mediated transcriptional gene silencing (gs) resulted in growth retardation, delayed endocytosis, and reduced acidification of endosomes and phagosomes. In this study, to better understand the role of Atg8 in phagocytosis and trogocytosis, we conducted a comparative proteomic analysis of phagosomes isolated from wild type and atg8-gs strains. We found that 127 and 107 proteins were detected >1.5-fold less or more abundantly, respectively, in phagosomes isolated from the atg8-gs strain, compared to the control strain. Among 127 proteins whose abundance was reduced in phagosomes from atg8-gs, a panel of proteins related to fatty acid metabolism, phagocytosis, and endoplasmic reticulum (ER) homeostasis was identified. Various lysosomal hydrolases and their receptors also tend to be excluded from phagosomes by atg8-gs, reinforcing the notion that Atg8 is involved in phagosomal acidification and digestion. On the contrary, among 107 proteins whose abundance increased in phagosomes from atg8-gs strain, ribosome-related proteins and metabolite interconversion enzymes are enriched. We further investigated the localization of several representative proteins, including adenylyl cyclase-associated protein and plasma membrane calcium pump, both of which were demonstrated to be recruited to phagosomes and trogosomes via an Atg8-dependent mechanism. Taken together, our study has provided the basis of the phagosome proteome to further elucidate molecular events in the Atg8-dependent regulatory network of phagosome/trogosome biogenesis in E. histolytica.

Abstract P2070: Insights Into RBM20 Cardiomyopathy Revealed By Global Proteomics

Patients with missense mutations in RNA binding motif protein 20 (RBM20), an RNA binding protein and splicing factor, develop a clinically aggressive form of dilated cardiomyopathy (DCM). Recent studies revealed that DCM-linked RBM20 missense mutations promote re-localization of the protein from the nucleus to the cytoplasm where it forms ribonucleoprotein (RNP) granules—non-membrane bound assemblies formed from RNAs and RNA regulatory proteins. The sequestration of RNAs and RNA regulatory proteins in these granules has the potential to dramatically alter the landscape of protein expression in the cardiomyocyte; yet, how RBM20 missense mutations impact global gene expression at the protein level has not been explored. Herein, we utilized mass spectrometry (MS)-based proteomics to identify global changes in protein expression in cardiac tissue harvested from mutation knock-in (KI) mice harboring the DCM-linked S637A and S639G RBM20 mutations. Our analysis revealed a total of 212 and 190 differentially expressed proteins (DEPs) in S637A and S639G KI mice, respectively, relative to wild-type. In general, identified DEPs were similar between KI mice with 81 and 38 proteins commonly up- and down-regulated, respectively. Consistent with mutant RBM20-mediated granule formation, 15 and 12 of the up-regulated proteins in S637A and S639G KI mice, respectively, have previously been implicated in granule assembly. Other up-regulated proteins in KI mice included chaperones and cytoskeletal proteins, as well as proteins involved in RNA metabolism and metabolite interconversion. Interestingly, proteins involved in the regulation of metabolite interconversion were also the most common protein class down-regulated in both KI mice, suggesting that broad changes in cellular metabolism may be a common feature associated with the RBM20 S637A and S639G missense mutations. Additionally, our proteomics analysis confirmed the differential expression of approximately 20-30% of previously identified differentially expressed genes based on RNAseq analyses from S637A and S639G KI mice. Our results provide the first glimpse of global changes in gene expression at the protein level associated with the RBM20 S637A and S639G missense mutations.

Mechanistic insight of the potential of geraniol against Alzheimer’s disease

BackgroundAlzheimer’s disease (AD) as a neurodegenerative disease occupies 3/5–4/5 cases among patients with dementia, yet its pathogenetic mechanism remains unclear. Geraniol, on the other hand, is a well-known extract from essential oils of aromatic plants and has been proven that it has outstanding neuroprotective effects as well as ameliorating influence in memory impairment. Therefore, the present study aims to elucidate the potential of geraniol against AD by network pharmacology-based approach combined with molecular modeling study.Materials and methodsFirstly, we evaluated the druggability of geraniol by ADME method. Then, we obtained the geraniol targets and AD-related targets from multiple open data sources. Afterward, we calculated the intersection through a Venn diagram to find common targets, and via Panther classification system to categorize them. In order to gain a macroscopic understanding of these common targets, we carried out GO terms and KEGG pathways enrichment analyses, according to which we constructed a compound–target–pathway–disease network. In addition, we built a preliminary PPI network which was further analyzed both functionally and topologically. Consequently, five hub targets were sorted out. Finally, we conducted molecular docking and molecular dynamic simulation to validate our findings.ResultsIn the present study, the pharmacological properties of geraniol were assessed according to ADME and Lipinski’s rule, which demonstrate promising druggability. Then, from 10,972 AD-related targets and 33 geraniol targets, 29 common targets were identified, among which 38.1% of them are metabolite interconversion enzymes, 23.8% are protein modifying enzymes, 33.3% are transmembrane receptors, and the rest are transporters. Enrichment analyses hint that geraniol is involved in cholinergic synapse, serotonergic synapse, and neuroactive ligand–receptor interaction. We also built a preliminary PPI network to investigate the interplay between these targets and their extensive interactions. Then, by functionally clustering the preliminary PPI network, we gained a cluster of proteins which formed a subnetwork with score of 8.476, and 22 nodes. Its results of GO terms and KEGG pathways enrichment analyses once again suggests that geraniol actively participates in cholinergic synapse, serotonergic synapse, and neuroactive ligand–receptor interaction, which are believed to be strongly associated with AD pathogenesis. Besides, topological analyses of the preliminary PPI network helped find 5 hub targets (i.e., CHRM3, PRKCA, PRKCD, JAK1, JAK2). To verify their interaction with geraniol molecule, we conducted molecular docking, and found that CHRM3 possesses the highest affinity in binding, indicating that geraniol molecules are closely bound to each hub target, and CHRM3 may serve as a key target of geraniol against AD. It was then further confirmed by molecular dynamic simulation, the result of which supports our hypothesis.ConclusionThe present study shares a mechanistic insight of the potential of geraniol against AD, giving a reference to future experimental studies.

Transcriptomic Characteristics Associated With Aging in the Thyroid Gland.

The aging thyroid is associated with a plethora of morphological and functional changes. Limited studies have addressed the gene expression signature in the aging thyroid, except for sporadic reports using data from postmortem samples in the Genotype-Tissue Expression (GTEx) project. In this investigation, we analyzed the RNA sequencing data of 58 samples of normal-appearing counterpart thyroid tissues from The Cancer Genome Atlas. Aging-correlated genes were identified by determining the Spearman rank-order correlation between patient age and gene expression level. Additionally, we performed gene set enrichment analysis and conducted a weighted correlation network analysis. The results were compared with those analyzed using the GTEx data. The over-represented protein class of aging-correlated genes is mainly metabolite interconversion enzymes. Our analyses identified alterations in immune and inflammatory responses, mitochondrial functions, cytoskeletal proteins, as well as amino acid and cytochrome P450 metabolism. There was no significant association between thyroid differentiation and age. Our findings may shed molecular light on thyroid disorders in the geriatric population.

Total phenolic, isothiocyanate and radicle elongation determination of mung bean sprout during germination affected by different variables of pulsed electric field treatment

Mung bean germination started with moisture uptake, biochemical modification, interconversion and biosynthesis of metabolites. Mung bean sprout was commonly used a fresh salad vegetable with available amino acids, dietary fiber, minerals, vitamins and phytonutrients. Pulsed electric field (PEF) was a prominent technology as a green approach for improvement of seed germination. This research evaluated some technical parameters of PEF such as pulse electric field strength (300-1500 kV/cm), pulse number (50-250) and pulse width (1.0-3.0 µs) at a stable frequency 1 Hz in ambient temperature on the total phenolic, isothiocyanate and radicle elongation of mung bean sprout. Results showed that pulse electric field strength and pulse number significantly increased isothiocyanate and total phenolic content while retardation of root length extension. Meanwhile pulse width showed a negative impact on total phenolic, isothiocyanate while extending root length extension. PEF should be conducted at pulse electric field strength (1200 kV/cm), pulse number (150), pulse width (1.5 µs) to retain the highest isothiocyanate (33.96±0.35 nmol/sprout) and total phenolic (221.30±1.46 mg GAE/100 g) while keeping a fair radicle elongation (8.39±0.17 mm). PEF treatment would be a promising non-lethal technology feasible for mung bean seed sprouting improvement.

Proteomic Analysis of the Colistin-resistant E. coli Clinical Isolate: Explorations of the Resistome.

Antimicrobial resistance is a worldwide problem after the emergence of colistin resistance since it was the last option left to treat carbapenemase-resistant bacterial infections. The mcr gene and its variants are one of the causes for colistin resistance. Besides mcr genes, some other intrinsic genes are also involved in colistin resistance but still need to be explored. The aim of this study was to investigate differential proteins expression of colistin-resistant E. coli clinical isolate and to understand their interactive partners as future drug targets. In this study, we have employed the whole proteome analysis through LC-MS/MS. The advance proteomics tools were used to find differentially expressed proteins in the colistin-resistant Escherichia coli clinical isolate compared to susceptible isolate. Gene ontology and STRING were used for functional annotation and protein-protein interaction networks, respectively. LC-MS/MS analysis showed overexpression of 47 proteins and underexpression of 74 proteins in colistin-resistant E. coli. These proteins belong to DNA replication, transcription and translational process; defense and stress related proteins; proteins of phosphoenol pyruvate phosphotransferase system (PTS) and sugar metabolism. Functional annotation and protein-protein interaction showed translational and cellular metabolic process, sugar metabolism and metabolite interconversion. We conclude that these protein targets and their pathways might be used to develop novel therapeutics against colistin-resistant infections. These proteins could unveil the mechanism of colistin resistance.

Identification of PDE10A related proteins via proteomic analysis

Objective: Phosphodiesterase 10A (PDE10A) regulates the expression of secondary messengers of cyclic adenosine monophosphate and cyclic guanosine monophosphate, which control several intracellular signaling pathways. Recently, deactivation of PDE10A has been a notable target for the treatment of neurodegenerative diseases. Herein, we identified the effects of PDE10A inhibition on protein profile using TAK-063 under physiological conditions in mice. Materials and Methods: In this study, 8-12 weeks old male C57BL6/J mice were divided into vehicle or 3 mg/kg TAK-063 groups. Thirty minutes after oral delivery of vehicle or TAK-063, animals were sacrificed and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) mediated proteomic analyses were performed from tissue samples taken from the striatum region of mice. After the LC-MS/MS analysis, identified proteins were classified based on biological activity, molecular function, and signal transduction pathways using PANTHER (protein annotation through evolutionary relationship, http://www.pantherdb.org/) program. Results: As a result of proteomic analyses, 1873 different proteins were identified. Sixty-one different proteins changed significantly depending on the administration of TAK-063. Accarding to PANTHER classification, a significant part of the identified proteins found to be in the metabolite interconversion enzyme, transporter, and protein modifying enzyme category. The molecular function classification includes the catalytic activity, transporter activity, and binding functions. The signal transduction pathway analysis demonstrated that PDE10A affects ATP synthesis, FGF signaling, EGF receptor signaling, Huntington's Disease, Parkinson's Disease, pyrimidine metabolism, and ubiquitin-proteasome signal transduction pathways. Discussion: In conclusion, TAK-063 mediated PDE10 deactivation is an essential target in the mechanism of energy metabolism and neurodegenerative diseases.

Interconversion between methoxylated, hydroxylated and sulfated metabolites of PCB 3 in whole poplar plants

Methoxylated polychlorinated biphenyls (MeO-PCBs) are overlooked metabolites of PCBs. In general, they are more toxic to plants than their parent congeners. However, information on the fate of MeO-PCBs and the relationship between methoxylated, hydroxylated and sulfated metabolites of PCBs in plants is scarce. In this work, poplar plants (Populus deltoides × nigra, DN34) were hydroponically and separately exposed to 4′-methoxy-4-monochlorobiphenyl (4′-MeO-PCB 3) and 4′-PCB 3 sulfate for 10 days to investigate the uptake, translocation and metabolism of MeO-PCBs and the relationship between methoxy-PCBs, hydroxyl-PCBs and PCB sulfates within plants. Results showed that 4′-MeO-PCB 3 and 4′-PCB 3 sulfate were taken up by the roots of poplar plants and translocated from roots to shoots and leaves. 4′-OH-PCB 3 and 4′-PCB 3 sulfate were identified as the hydroxylated metabolite and sulfate metabolite of 4′-MeO-PCB 3 in poplar, respectively. In the backward reaction, 4′-OH-PCB 3 and 4′-MeO-PCB 3 were found as metabolites of 4′-PCB 3 sulfate. For exposure groups, the yields of 4′-OH-PCB 3 produced from 4′-MeO-PCB 3 and 4′-PCB 3 sulfate were 1.29% and 0.13% respectively. The yield of 4′-PCB 3 sulfate which originated from 4′-MeO-PCB 3 in wood and root samples of exposure groups was only 0.02%. Only 0.04% of the initial mass of 4′-PCB 3 sulfate was transformed to 4′-MeO-PCB 3 in the exposure groups. The sulfation yield of 4′-OH-PCB 3 was higher than hydrolysis yield of 4′-PCB 3 sulfate, indicating that formation of PCB sulfates was predominant over the reverse reaction, the formation of hydroxy-PCBs. These results provide new perspective on the transport, metabolism, and fate of MeO-PCBs, and also help to better understand sources of OH-PCBs and PCB sulfates in the environment. This study provides the first evidence of interconversion of sulfate metabolites from methoxy-PCBs and methoxy-PCBs from PCB sulfates.

Not just shrivelling: time-series profiling of the biochemical changes in Corvina (&lt;i&gt;Vitis vinifera&lt;/i&gt; L.) berries subjected to post-harvest withering

The grape berry withering process is often seen as a means to concentrate the constituents of the berry via water removal, however, recent molecular studies have indicated that the reprogramming of biosynthetic pathways that impart the unique aroma and flavour of the final wine also occur. Metabolic analysis was performed using GC-MS and LC-MS on Corvina berry dehydrated for up to 108 days. The temporal pattern of metabolic changes and time-series relationship between various classes of metabolites were investigated on berries sampled at 23-time points. Principal component analysis of both GC-MS and LC-MS datasets revealed three distinct phases of post-harvest withering; early (day 0–28), mid (day 35–66) and late (day 69–108) stages. Stress-associated amino acids such as proline, serine, ethanolamine, and leucine accumulated significantly during the mid and late stages of the drying process while phosphorylated glucose and fructose, sucrose, kestose and resveratrol increased massively across time. Unlike most of the identified metabolites, low molecular weight flavanols exhibited a consistent pattern of decline during the withering period. Our network analysis revealed that increased metabolic network connectivity occurred during the middle stage of withering, thus reflecting more coordinated metabolite changes while reduced network connectivity at early and late stages indicates minimal metabolite perturbation during these stages. The current prolonged berry withering experiment revealed the timing of metabolite interconversions in the central metabolism and provided critical clues that link the concentration effect, protein degradation, and the onset of stress-like conditions in drying berries.

Erythromycin Treatment of Brassica campestris Seedlings Impacts the Photosynthetic and Protein Synthesis Pathways.

Erythromycin (Ery) is a commonly used veterinary drug that prevents infections and promotes the growth of farm animals. Ery is often detected in agricultural fields due to the effects of manure application in the ecosystem. However, there is a lack of information on Ery toxicity in crops. In this study, we performed a comparative proteomic analysis to identify the molecular mechanisms of Ery toxicity during seedling growth based on our observation of a decrease in chlorophyll (Chl) contents using Brassica campestris. A total of 452 differentially abundant proteins (DAPs) were identified including a ribulose-1,5-bisphosphate carboxylase (RuBisCO). The proteomic analysis according to gene ontology (GO) classification revealed that many of these DAPs responding to Ery treatment functioned in a cellular process and a metabolic process. The molecular function analysis showed that DAPs classified within catalytic activity were predominantly changed by Ery, including metabolite interconversion enzyme and protein modifying enzyme. An analysis of functional pathways using MapMan revealed that many photosynthesis components were downregulated, whereas many protein biosynthesis components were upregulated. A good relationship was observed between protein and transcript abundance in a photosynthetic pathway, as determined by qPCR analysis. These combined results suggest that Ery affects plant physiological activity by downregulating protein abundance in the photosynthetic pathway.