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MLife Sep 2023Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems. , which are among the most abundant microorganisms in...
Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems. , which are among the most abundant microorganisms in marine sediment, have been proposed to mediate anaerobic lignin degradation. However, the mechanism of bathyarchaeial lignin degradation remains unclear. Here, we report an enrichment culture of , named Baizosediminiarchaeum ligniniphilus DL1YTT001 (. B. ligniniphilus), from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions. . B. ligniniphilus possesses and highly expresses novel methyltransferase 1 (MT1, ) for transferring methoxyl groups from lignin monomers to cob(I)alamin. MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages. Heterologous expression of the gene confirmed -demethylation activity. The genes were identified in metagenomic data sets from a wide range of coastal sediments, and they were highly expressed in coastal sediments from the East China Sea. These findings suggest that , capable of -demethylation via their novel and specific methyltransferases, are ubiquitous in coastal sediments.
PubMed: 38817817
DOI: 10.1002/mlf2.12082 -
Chemical Science May 2024P450-catalyzed -demethylation reactions have recently attracted particular attention because of their potential applications in lignin bioconversion. We recently enabled...
P450-catalyzed -demethylation reactions have recently attracted particular attention because of their potential applications in lignin bioconversion. We recently enabled the peroxygenase activity of CYP199A4, a NADH-dependent cytochrome P450 monooxygenase from , by engineering a hydrogen peroxide (HO) tunnel. In this report, we reveal by crystallography and molecule dynamics simulations that key residues located at one of the water tunnels in CYP199A4 play a crucial gating role, which enhances the peroxygenase activity by regulating the inflow of HO. These results provide a more complete understanding of the mechanism by which monooxygenase is converted into peroxygenase activity through the HO tunnel engineering (HTE) strategy. Furthermore, a library of engineered CYP199A4 peroxygenases was constructed to explore their application potentials for -demethylation of various methoxy-substituted benzoic acid derivatives. The engineered CYP199A4 peroxygenases showed good functional group tolerance and preferential -demethylation at the - or -position, indicating potential -demethylation of H- and G-type lignin monomers. This work reveals the feasibility of the HTE strategy in creating P450 peroxygenase from a mechanistic perspective, laying the foundation for developing an effective P450 -demethylase applicable in lignin bioconversion.
PubMed: 38817576
DOI: 10.1039/d4sc02418d -
Epigenomes May 2024In living cells, some reactions can be conducted by more than one enzyme and sometimes it is difficult to establish which enzyme is responsible. Such is the case with...
In living cells, some reactions can be conducted by more than one enzyme and sometimes it is difficult to establish which enzyme is responsible. Such is the case with proteins from the TET family, capable of converting 5-methyl-2'-deoxycytidine (5-mdC) in DNA to 5-(hydroxymethyl)-2'-deoxycytidine (5-hmdC) and further to 5-formyl-2'-deoxycytidine (5-fdC) and 5-carboxy-2'-deoxycytidine (5-cadC). The estimation of the efficiency of particular TETs in particular oxidative reactions and different cell types is important but experimentally difficult. Here, we propose an approach with mathematical modeling in which methylation and known deoxycytidine modification pathways are presented by 343 possible model versions with assumed different combinations of TET1, 2, and 3 activities in different pathways. Model parameters were calculated on the basis of 5-mdC, 5-hmdC, 5-fdC, 5-cadC, and 5-hmdU levels experimentally assessed in five human cultured cell lines and previously published. Selection of the model versions that give in simulations the best average fit to experimental data suggested that not all TET proteins participate in all modification reactions and that TET3 activity may be especially important in the reaction of 5-fdC removal.
PubMed: 38804367
DOI: 10.3390/epigenomes8020018 -
Biochemistry and Biophysics Reports Jul 2024RUNX2 is a transcription factor crucial for bone formation. Mutant mice with varying levels of expression display dosage-dependent skeletal abnormalities, underscoring...
RUNX2 is a transcription factor crucial for bone formation. Mutant mice with varying levels of expression display dosage-dependent skeletal abnormalities, underscoring the importance of dosage control in skeletal formation. RUNX2 activity is regulated by several molecular mechanisms, including epigenetic modification such as DNA methylation. In this study, we investigated whether targeted repressive epigenome editing including hypermethylation to the Runx2-DMR/CpG island shore could influence expression using Cas9-based epigenome-editing tools. Through the transient introduction of CRISPRoff-v2.1 and gRNAs targeting Runx2-DMR into MC3T3-E1 cells, we successfully induced hypermethylation of the region and concurrently reduced expression during osteoblast differentiation. Although the epigenome editing of Runx2-DMR did not impact the expression of RUNX2 downstream target genes, these results indicate a causal relationship between the epigenetic status of the Runx2-DMR and transcription. Additionally, we observed that hypermethylation of the Runx2-DMR persisted for at least 24 days under growth conditions but decreased during osteogenic differentiation, highlighting an endogenous DNA demethylation activity targeting the Runx2-DMR during the differentiation process. In summary, our study underscore the usefulness of the epigenome editing technology to evaluate the function of endogenous genetic elements and revealed that the Runx2-DMR methylation is actively regulated during osteoblast differentiation, subsequently could influence expression.
PubMed: 38799114
DOI: 10.1016/j.bbrep.2024.101733 -
Journal of Hazardous Materials Jul 2024Identifying metabolism and detoxification mechanisms of Hg in biota has important implications for biomonitoring, ecotoxicology, and food safety. Compared to marine...
Identifying metabolism and detoxification mechanisms of Hg in biota has important implications for biomonitoring, ecotoxicology, and food safety. Compared to marine mammals and waterbirds, detoxification of MeHg in fish is understudied. Here, we investigated Hg detoxification in Atlantic bluefin tuna Thunnus thynnus using organ-specific Hg and Se speciation data, stable Hg isotope signatures, and Hg and Se particle measurements in multiple tissues. Our results provide evidence for in vivo demethylation and biomineralization of HgSe particles, particularly in spleen and kidney. We observed a maximum range of 1.83‰ for δHg between spleen and lean muscle, whereas ΔHg values were similar across all tissues. Mean percent methylmercury ranged from 8% in spleen to 90% in lean muscle. The particulate masses of Hg and Se were higher in spleen and kidney (Hg: 61% and 59%, Se: 12% and 6%, respectively) compared to muscle (Hg: 2%, Se: 0.05%). Our data supports the hypothesis of an organ-specific, two-step detoxification of methylmercury in wild marine fish, consisting of demethylation and biomineralization, like reported for waterbirds. While mass dependent fractionation signatures were highly organ specific, stable mass independent fractionation signatures across all tissues make them potential candidates for source apportionment studies of Hg using ABFT.
Topics: Animals; Methylmercury Compounds; Tuna; Mercury Isotopes; Water Pollutants, Chemical; Kidney; Spleen; Inactivation, Metabolic; Mercury; Environmental Monitoring; Muscles; Selenium
PubMed: 38795488
DOI: 10.1016/j.jhazmat.2024.134699 -
Molecular Pain May 2024Irritable bowel syndrome (IBS) is a prevalent functional gastrointestinal disease characterized by chronic visceral pain with a complex etiology and challenging...
Irritable bowel syndrome (IBS) is a prevalent functional gastrointestinal disease characterized by chronic visceral pain with a complex etiology and challenging treatment. Although accumulating evidence supports the involvement of central nervous system sensitization in the development of visceral pain, the precise molecular mechanisms remain incompletely understood. In this study, we highlight the critical regulatory role of lysine-specific demethylase 6B (KDM6B) in the anterior cingulate cortex (ACC) in chronic visceral pain. To simulate clinical IBS conditions, we utilized the neonatal maternal deprivation (NMD) mouse model. Our results demonstrated that NMD induced chronic visceral pain and anxiety-like behaviors in mice. Notably, the protein expression level of KDM6B significantly increased in the ACC of NMD mice, leading to a reduction in the expression level of H32K7me3. Immunofluorescence staining revealed that KDM6B primarily co-localizes with neurons in the ACC, with minimal presence in microglia and astrocytes. Injecting GSK-J4 (a KDM6B-specific inhibitor) into ACC of NMD mice, resulted in a significant alleviation in chronic visceral pain and anxiety-like behaviors, as well as a remarkable reduction in NR2B expression level. ChIP assay further indicated that KDM6B regulates NR2B expression by influencing the demethylation of H3K27me3. In summary, our findings underscore the critical role of KDM6B in regulating chronic visceral pain and anxiety-like behaviors in NMD mice. These insights provide a basis for further understanding the molecular pathways involved in IBS and may pave the way for targeted therapeutic interventions.
PubMed: 38795338
DOI: 10.1177/17448069241260349 -
Plants (Basel, Switzerland) May 2024As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally,... (Review)
Review
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
PubMed: 38794470
DOI: 10.3390/plants13101400 -
Plants (Basel, Switzerland) May 2024Pectin is a structural polysaccharide and a major component of plant cell walls. Pectate lyases are a class of enzymes that degrade demethylated pectin by cleaving the...
Pectin is a structural polysaccharide and a major component of plant cell walls. Pectate lyases are a class of enzymes that degrade demethylated pectin by cleaving the α-1,4-glycosidic bond, and they play an important role in plant growth and development. Currently, little is known about the gene family members and their involvement in salt stress in potato. In this study, we utilized bioinformatics to identify members of the potato pectate lyase gene family and analyzed their gene and amino acid sequence characteristics. The results showed that a total of 27 members of the pectate lyase gene family were identified in potato. Phylogenetic tree analysis revealed that these genes were divided into eight groups. Analysis of their promoters indicated that several members' promoter regions contained a significant number of hormone and stress response elements. Further, we found that several members responded positively to salt treatment under single salt and mixed salt stress. Since exhibited a consistent expression pattern under both single and mixed salt stress conditions, its subcellular localization was determined. The results indicated that StPL18 is localized in the endoplasmic reticulum membrane. The results will establish a foundation for analyzing the functions of potato pectate lyase family members and their expression under salt stress.
PubMed: 38794393
DOI: 10.3390/plants13101322 -
Microorganisms Apr 2024Demethylation inhibitors (DMIs), including prochloraz, are popular fungicides to control citrus postharvest pathogens such as (green mold). However, many strains have...
Demethylation inhibitors (DMIs), including prochloraz, are popular fungicides to control citrus postharvest pathogens such as (green mold). However, many strains have developed prochloraz resistance, which decreases drug efficacy. Specific major facilitator superfamily (MFS) transporter gene , encoding drug-efflux pump protein MFS2, has been identified in strain F6 (PdF6) to confer fungal strain prochloraz resistance. However, except for the drug-efflux pump function of MFS2, other mechanisms relating to the Pd are not fully clear. The present study reported a transcriptome investigation on the -defective strain. Comparing to the wild-type strain, the -defective strain showed 717 differentially expressed genes (DEGs) without prochloraz induction, and 1221 DEGs with prochloraz induction. The obtained DEGs included multiple isoforms of MFS transporter-encoding genes, ATP-binding cassette (ABC) transporter-encoding genes, and multidrug and toxic compound extrusion (MATE) family protein-encoding genes. Many of these putative drug-efflux pump protein-encoding genes had significantly lower transcript abundances in the -defective strain at prochloraz induction, as compared to the wild-type strain, including twenty-two MFS transporter-encoding genes ( to ), two ABC transporter-encoding genes ( and ), and three MATE protein-encoding genes ( to ). The prochloraz induction on special drug-efflux pump protein genes in the wild-type strain was not observed in the -defective strain, including , , , , , and . On the other hand, the up-regulation of other drug-efflux pump protein genes in the -defective strain cannot recover the fungal prochloraz resistance, including , , , , , and to . The functional enrichment of DEGs based on Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and euKaryotic Orthologous Groups (KOG) database resources suggested some essential contributors to the -relating prochloraz resistance, including ribosome biosynthesis-related genes, oxidative phosphorylation genes, steroid biosynthesis-related genes, fatty acid and lipid metabolism-related genes, and carbon- and nitrogen-metabolism-related genes. The results indicated that the MFS2 transporter might be involved in the regulation of multiple drug-efflux pump protein gene expressions and multiple metabolism-related gene expressions, thus playing an important role in developing prochloraz resistance.
PubMed: 38792718
DOI: 10.3390/microorganisms12050888 -
Molecules (Basel, Switzerland) May 2024Compound 7-16 was designed and synthesized in our previous study and was identified as a more potential selective 5-HT receptor antagonist and inverse agonist for...
Compound 7-16 was designed and synthesized in our previous study and was identified as a more potential selective 5-HT receptor antagonist and inverse agonist for treating Parkinson's disease psychosis (PDP). Then, the metabolism, disposition, and excretion properties of 7-16 and its potential inhibition on transporters were investigated in this study to highlight advancements in the understanding of its therapeutic mechanisms. The results indicate that a total of 10 metabolites of 7-16/[C]7-16 were identified and determined in five species of liver microsomes and in rats using UPLC-Q Exactive high-resolution mass spectrometry combined with radioanalysis. Metabolites formed in human liver microsomes could be covered by animal species. 7-16 is mainly metabolized through mono-oxidation (M470-2) and N-demethylation (M440), and the CYP3A4 isozyme was responsible for both metabolic reactions. Based on the excretion data in bile and urine, the absorption rate of 7-16 was at least 74.7%. 7-16 had weak inhibition on P-glycoprotein and no effect on the transport activity of OATP1B1, OATP1B3, OAT1, OAT3, and OCT2 transporters. The comprehensive pharmacokinetic properties indicate that 7-16 deserves further development as a new treatment drug for PDP.
Topics: Humans; Animals; Rats; Parkinson Disease; Microsomes, Liver; Serotonin 5-HT2 Receptor Antagonists; Male; Serotonin 5-HT2 Receptor Agonists
PubMed: 38792047
DOI: 10.3390/molecules29102184