Increased lysine N-methylation of a 23-kDa protein during hepatic regeneration

The methylation of a 23-kDa nuclear protein increased after partial hepatectomy and methylation returned to basal levels after the initial stage of regeneration. The methylating enzyme was partially purified from rat liver by ammonium sulfate precipitation, DEAE-anion exchange chromatography and Butyl-Sepharose chromatography. The 23-kDa protein was purified from a nuclear fraction of liver tissue with SP-Sepharose. When the 23-kDa protein was methylated with the partially purified methyltransferase and analyzed on C(18) high performance liquid chromatography (HPLC), the methylated acceptor amino acid was monomethyl lysine (MML). Previously, only arginine N-methylation of specific substrate proteins has been reported during liver regeneration. However, in this report, we found that lysine N-methylation increased during early hepatic regeneration, suggesting that lysine N-methylation of the 23-kDa nuclear protein may play a functional role in hepatic regeneration. The methyltransferase did not methylate other proteins such as histones, hnRNPA1, or cytochrome C, suggesting the enzyme is a 23-kDa nuclear protein- specific lysine N-methyltransferase.     

Detection of the changes in cellular proteins in regenerating rat liver by high-resolution two-dimensional electrophoresis

The changes in cellular proteins in regenerating rat liver after partial hepatectomy were examined by high-resolution two-dimensional electrophoresis. The cellular proteins in regenerating rat livers were separated into two fractions (soluble and insoluble protein fractions) and the proteins in each fraction were analysed by means of two-dimensional electrophoresis. A rapid increase in three proteins and a rapid decrease in two proteins were detected after partial hepatectomy. The changes in these proteins were in parallel with the regeneration rate of liver, suggesting a close relationship with the proliferation of liver after partial hepatectomy.     

Chronological protein synthesis in regenerating rat liver

Liver regeneration has been studied for decades; however, its regulation remains unclear. In this study, we report a dynamic tracing of protein synthesis in rat regenerating liver with a new proteomic technique, ³⁵S in vivo labeling analysis for dynamic proteomics (SiLAD). Conventional proteomic techniques typically measure protein alteration in accumulated amounts. The SiLAD technique specifically detects protein synthesis velocity instead of accumulated amounts of protein through ³⁵S pulse labeling of newly synthesized proteins, providing a direct way for analyzing protein synthesis variations. Consequently, protein synthesis within short as 30 min was visualized and protein regulations in the first 8 h of regenerating liver were dynamically traced. Further, the 3.5–5 h post partial hepatectomy (PHx) was shown to be an important regulatory turning point by acute regulation of many proteins in the initiation of liver regeneration.     

Specificity analysis-based identification of new methylation targets of the SET7/9 protein lysine methyltransferase

We applied peptide array methylation to determine an optimized target sequence for the SET7/9 (KMT7) protein lysine methyltransferase. Based on this, we identified 91 new peptide substrates from human proteins, many of them better than known substrates. We confirmed methylation of corresponding protein domains in?vitro and in?vivo with a high success rate for strongly methylated peptides and showed methylation of nine nonhistone proteins (AKA6, CENPC1, MeCP2, MINT, PPARBP, ZDH8, Cullin1, IRF1, and [weakly] TTK) and of H2A and H2B, which more than doubles the number of known SET7/9 targets. SET7/9 is inhibited by phosphorylation of histone and nonhistone substrate proteins. One lysine in the MINT protein is dimethylated in?vitro and in?vivo demonstrating that the product pattern created by SET7/9 depends on the amino acid sequence context of the target site.     

Astragaloside IV Suppresses Hepatic Proliferation in Regenerating Rat Liver after 70% Partial Hepatectomy via Down-Regulation of Cell Cycle Pathway and DNA Replication

Astragaloside IV (AS-IV) is one of the major bio-active ingredients of huang qi which is the dried root of Astragalus membranaceus (a traditional Chinese medicinal plant). The pharmacological effects of AS-IV, including anti-oxidative, anti-cancer, and anti-diabetic effects have been actively studied, however, the effects of AS-IV on liver regeneration have not yet been fully described. Thus, the aim of this study was to explore the effects of AS-IV on regenerating liver after 70% partial hepatectomy (PHx) in rats. Differentially expressed mRNAs, proliferative marker and growth factors were analyzed. AS-IV (10 mg/kg) was administrated orally 2 h before surgery. We found 20 core genes showed effects of AS-IV, many of which were involved with functions related to DNA replication during cell division. AS-IV down-regulates MAPK signaling, PI3/Akt signaling, and cell cycle pathway. Hepatocyte growth factor (HGF) and cyclin D1 expression were also decreased by AS-IV administration. Transforming growth factor β1 (TGFβ1, growth regulation signal) was slightly increased. In short, AS-IV down-regulated proliferative signals and genes related to DNA replication. In conclusion, AS-IV showed anti-proliferative activity in regenerating liver tissue after 70% PHx.     

Ethanol elimination in regenerating rat liver: the roles of alcohol dehydrogenase and acetaldehyde.

The rate of ethanol elimination in vivo was studied with rats in which the energy consumption of the liver was increased by partial hepatectomy. Immediately after partial hepatectomy the activity of alcohol dehydrogenase in the liver remnant was not changed from that of the livers of sham-operated controls, but the rate of ethanol removal was significantly faster. Twenty-four h after the partial hepatectomy the activity of alcohol dehydrogenase was only 48 % of the activity measured in unoperated control rats. Therefore it is concluded that in normal liver the activity of ADH is in excess. In partially hepatectomized rats the rate of ethanol elimination was linearly correlated with the activity of alcohol dehydrogenase, which suggests that when the rate of NADH reoxidation is markedly increased, as in regenerating rat liver, the rate of ethanol elimination may be limited by the activity of alcohol dehydrogenase. The activity of aldehyde dehydrogenase and the concentration of acetaldehyde in the tail blood were not significantly changed from the level of unoperated rats during oxidation of ethanol.     

New method for synthesis of EZH2 methyltransferase inhibitor GSK126

GSK126 is a potent small-molecule inhibitor of S-adenosyl-methionine-competitive EZH2 methyltransferase and has the potential to be used clinically for preventing unwanted histone methylation of tumor suppressor genes. In this article, we describe a new synthetic route that has been developed for synthesizing the title compound through nine steps, starting from 2,5-dibromobenzoic acid. This synthetic method is economical and suitable for multigram-scale preparation of GSK126 and related N-alkylated indole derivatives.     

Radiorespirometric analysis of glucose metabolism in the rat during feeding with 3'-methyl-4-(dimethylamino)azobenzene--radiorespirometry after partial hepatectomy.

In previous papers we reported that the earlier peak time (PT) in radiorespiratory during feeding with 3'-methyl-4-(dimethylamino)azobenzene(3'-Me-DAB) is due to activation of the hexose monophosphate (HMP) pathway together with hepatic cell proliferation reflecting the toxic effects of this carcinogen. In this study, we investigated the correlation between the results of radiorespiratory and the levels of enzyme activities of HMP pathway in regenerating rat liver in connection with hepatic cell proliferation. [3H]Thymidine incorporation into rat liver DNA and the activities of hexokinase (HK) and glucose-6-phosphate dehydrogenase(G-6-PD) reached a maximum at the 3rd day after partial hepatectomy. On radiorespirometry using [U-14C] glucose, the peak time (PT) was much earlier at the 2nd to 3rd day after partial hepatectomy. The peak height (PH) decreased to less than 1/2 of the initial level at the 2nd, but began to recover from the 3rd day. The yield value (YV) remained below the initial level for 4 days after the operation.     

Genetically encoded fluorescent reporters of histone methylation in living cells

We report the design and characterization of two genetically encoded fluorescent reporters of histone protein methylation. The reporters are four-part chimeric proteins consisting of a substrate peptide from the N-terminus of histone H3 fused to a chromodomain (a natural methyllysine-specific recognition domain), sandwiched between a fluorescence resonance energy transfer (FRET)-capable pair of fluorophores, cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). Enzymatic methylation by a methyltransferase induces complexation of the methylated substrate peptide to the chromodomain, changing the FRET level between the flanking CFP and YFP domains. Reporters developed using the chromodomains from HP1 and Polycomb respond to enzymatic methylation at the lysine 9 and lysine 27 positions of histone H3, respectively, giving 60% and 28% YFP/CFP emission ratio increases in vitro or in single living cells. These reporters should be useful for studying gene silencing and X-chromosome inactivation with high spatial and temporal resolution in intact cells and may also aid in the search for conjectured histone demethylase activity.     

Characterization of the Phosphoryl-Nitrogen Linkages in Histone H4

In earlier work we nave described and partially characterized two histone kinases from regenerating rat liver and other tissues which catalyze the transfer of the γ-phosphoryl group from ATP to histones. The histone phosphates thus formed were observed to be acid-labile and base-stable. In the present study we report on the specificity of one of these enzymes, namely, the kinase which is optimally active at pH 9. This enzyme appears to be relatively specific for the two histidine residues of histone H4. These histidines occur at positions 18 and 75, and both are phosphorylated. However, when regenerating rat liver was the source of enzyme, the product was 1-phosphohistidine, whereas the enzyme from Walker-256 carcinosarcoma catalyzed the formation of 3-phosphohistidine.     

Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays

Histone methylation is an epigenetic mark essential for gene regulation and development. We introduce peptide SPOT synthesis to study sequence specificity of the Dim-5 histone-3 lysine-9 methyltransferase. Dim-5 recognizes R8-G12 of the H3 tail with T11 and G12 being the most important specificity determinants. Exchange of H3 tail residue S10 and T11 by E strongly reduced methylation by Dim-5, suggesting that phosphorylation of S10 or T11 may regulate the activity of Dim-5. In the Dim-5/peptide structure, E227 interacts with H3R8 and D209 with H3-S10. Mutations of E227 or D209 caused predictable changes in the substrate preference, illustrating that peptide recognition of histone methyltransferases can be altered by protein design. Comparative analyses of peptide arrays with wild-type and mutant enzymes, therefore, are well suited to investigate the target specificity of protein methyltransferases and study epigenetic crosstalk.     

Human hepatocyte morphology and functions in a multibore fiber bioreactor

The viability and liver specific functions of human hepatocytes in a multibore fiber bioreactor are reported. Human hepatocytes were cultured in the intraluminal compartment of the bioreactor. Human hepatocytes on the membranes maintained their round shape and showed focal adhesions as sites of interaction with the membrane surface. Cells in the bioreactor expressed liver specific functions, including synthetic and detoxification activity up to 14 d of culture. The results demonstrate that human hepatocytes cultured in the multibore fiber bioreactor are able to sustain the same in vivo liver functions in vitro.     

In vitro methylation of bacterial chemotaxis proteins: characterization of protein methyltransferase activity in crude extracts of Salmonella typhimurium

A specific in vitro assay was developed for the protein carboxyl methyltransferase that is involved in the chemotactic behavior of Salmonella typhimurium. This cytosolic enzyme catalyzes an S-adenosyl-L-methionine-dependent methyl esterification of glutamyl residues on a class of 60,000-dalton inner-membrane proteins. The activity was found to display a pH optimum of 6.5 and be sensitive to the concentration of salts in the assay medium. No detectable activity was found towards a variety of other proteins which serve as substrates for mammalian and other bacterial carboxyl methyltransferases. This assay was used to quantitate the methylation of the 60,000-dalton methyl-accepting proteins in response to chemoeffectors. Small but reproducible concentration-dependent changes in the initial rates of in vitro methylation were observed with chemotactic attractants and repellents. The specific methyltransferase activity was found to be absent in several mutants in flagellar synthesis (fla-), suggesting that the synthesis of this enzyme is coordinately regulated with that of flagellin and basal bodies. The hydrodynamic properties of the enzyme in crude extracts were determined by gel filtration and sucrose velocity gradient centrifugation, and a native molecular weight of 41,000 was calculated from these data.     

Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity

The present work demonstrates a novel signal-off electrochemical method for the determination of DNA methylation and the assay of methyltransferase activity using the electroactive complex [Ru(NH₃)₆]³⁺ (RuHex) as a signal transducer. The assay exploits the electrostatic interactions between RuHex and DNA strands. Thiolated single strand DNA1 was firstly self-assembled on a gold electrode via Au–S bonding, followed by hybridization with single strand DNA2 to form double strand DNA containing specific recognition sequence of DNA adenine methylation MTase and methylation-responsive restriction endonuclease Dpn I. The double strand DNA may adsorb lots of electrochemical species ([Ru(NH₃)₆]³⁺) via the electrostatic interaction, thus resulting in a high electrochemical signal. In the presence of DNA adenine methylation methyltransferase and S-adenosyl-l-methionine, the formed double strand DNA was methylated by DNA adenine methylation methyltransferase, then the double strand DNA can be cleaved by methylation-responsive restriction endonuclease Dpn I, leading to the dissociation of a large amount of signaling probes from the electrode. As a result, the adsorption amount of RuHex reduced, resulting in a decrease in electrochemical signal. Thus, a sensitive electrochemical method for detection of DNA methylation is proposed. The proposed method yielded a linear response to concentration of Dam MTase ranging from 0.25 to 10 U mL⁻¹ with a detection limit of 0.18 U mL⁻¹ (S/N = 3), which might promise this method as a good candidate for monitoring DNA methylation in the future.     

Targeted Histone Peptides: Insights into the Spatial Regulation of the Methyltransferase PRC2 by using a Surrogate of Heterotypic Chromatin

Eukaryotic genomes are dynamically regulated through a host of epigenetic stimuli. The substrate for these epigenetic transactions, chromatin, is a polymer of nucleosome building blocks. In native chromatin, each nucleosome can differ from its neighbors as a result of covalent modifications to both the DNA and the histone packaging proteins. The heterotypic nature of chromatin presents a formidable obstacle to biochemical studies seeking to understand the role of context on epigenetic regulation. A chemical approach to the production of heterotypic chromatin that can be used in such studies is introduced. This method involves the attachment of a user‐defined modified histone peptide to a designated nucleosome within the polymer by using a peptide nucleic acid (PNA) targeting compound. This strategy was applied to dissect the effect of chromatin context on the activity of the histone methyltransferase PRC2. The results show that PRC2 can be stimulated to produce histone H3 methylation from a defined nucleation site.     

Epigenetic Modifications Induced by Olive Oil and Its Phenolic Compounds: A Systematic Review

Many studies demonstrated that olive oil (especially extra virgin olive oil: EVOO) phenolic compounds are bioactive molecules with anti-cancer, anti-inflammatory, anti-aging and neuroprotective activities. These effects have been recently attributed to the ability of these compounds to induce epigenetics modifications such as miRNAs expression, DNA methylation and histone modifications. In this study, we systematically review and discuss, following the PRISMA statements, the epigenetic modifications induced by EVOO and its phenols in different experimental systems. At the end of literature search through “PubMed”, “Web of Science” and “Scopus”, 43 studies were selected.Among them, 22 studies reported data on miRNAs, 15 on DNA methylation and 13 on histone modification. Most of the “epigenomic” changes observed in response to olive oil phenols’ exposure were mechanistically associated with the cancer preventive and anti-inflammatory effects. In many cases, the epigenetics effects regarding the DNA methylation were demonstrated for olive oil but without any indication regarding the presence or not of phenols. Overall, the findings of the present systematic review may have important implications for understanding the epigenetic mechanisms behind the health effects of olive oil. However, generally no direct evidence was provided for the causal relationships between epigenetics modification and EVOO health related effects. Further studies are necessary to demonstrate the real physiological consequences of the epigenetics modification induced by EVOO and its phenolic compounds.