Evaluation of the Moonlighting Histone H3 Specific Protease (H3ase) Activity and the Dehydrogenase Activity of Glutamate Dehydrogenase (GDH)

The N-terminus of Histone H3 is proteolytically processed in aged chicken liver. A histone H3 N-terminus specific endopeptidase (named H3ase) has been purified from the nuclear extract of aged chicken liver. By sequencing and a series of biochemical methods including the demonstration of H3ase activity in bacterially expressed GDH, it was established that the H3ase activity was a moonlighting protease activity of glutamate dehydrogenase (GDH). However, the active site for the H3ase in the GDH remains elusive. Here, using cross-linking studies of the homogenously purified H3ase, we show that the GDH and the H3ase remain in the same native state. Further, the H3ase and GDH activities could be uncoupled by partial denaturation of GDH, suggesting strong evidence for the involvement of different active sites for GDH and H3ase activities. Through densitometry of the H3ase clipped H3 products, the H3ase activity was quantified and it was compared with the GDH activity of the chicken liver nuclear GDH. Furthermore, the H3ase mostly remained distributed in the perinuclear area as demonstrated by MNase digestion and immuno-localization of H3ase in chicken liver nuclei, as well as cultured mouse hepatocyte cells, suggesting that H3ase demonstrated regulated access to the chromatin. The present study thus broadly compares the H3ase and GDH activities of the chicken liver GDH.

TIM-3/Galectin-9 interaction and glutamine metabolism in AML cell lines, HL-60 and THP-1

BACKGROUND

T cell immunoglobulin and mucin-domain containing-3 (TIM-3) is a cell surface molecule that was first discovered on T cells. However, recent studies revealed that it is also highly expressed in acute myeloid leukemia (AML) cells and it is related to AML progression. As, Glutamine appears to play a prominent role in malignant tumor progression, especially in their myeloid group, therefore, in this study we aimed to evaluate the relation between TIM-3/Galectin-9 axis and glutamine metabolism in two types of AML cell lines, HL-60 and THP-1.

METHODS

Cell lines were cultured in RPMI 1640 which supplemented with 10% FBS and 1% antibiotics. 24, 48, and 72 h after addition of recombinant Galectin-9 (Gal-9), RT-qPCR analysis, RP-HPLC and gas chromatography techniques were performed to evaluate the expression of glutaminase (GLS), glutamate dehydrogenase (GDH) enzymes, concentration of metabolites; Glutamate (Glu) and alpha-ketoglutarate (α-KG) in glutaminolysis pathway, respectively. Western blotting and MTT assay were used to detect expression of mammalian target of rapamycin complex (mTORC) as signaling factor, GLS protein and cell proliferation rate, respectively.

RESULTS

The most mRNA expression of GLS and GDH in HL-60 cells was seen at 72 h after Gal-9 treatment (p = 0.001, p = 0.0001) and in THP-1 cell line was observed at 24 h after Gal-9 addition (p = 0.001, p = 0.0001). The most mTORC and GLS protein expression in HL-60 and THP-1 cells was observed at 72 and 24 h after Gal-9 treatment (p = 0.0001), respectively. MTT assay revealed that Gal-9 could promote cell proliferation rate in both cell lines (p = 0.001). Glu concentration in HL-60 and α-KG concentration in both HL-60 (p = 0.03) and THP-1 (p = 0.0001) cell lines had a decreasing trend. But, Glu concentration had an increasing trend in THP-1 cell line (p = 0.0001).

CONCLUSION

Taken together, this study suggests TIM-3/Gal-9 interaction could promote glutamine metabolism in HL-60 and THP-1 cells and resulting in AML development.

Evaluation of decursin and its isomer decursinol angelate as potential inhibitors of human glutamate dehydrogenase activity through in silico and enzymatic assay screening

Glutaminolysis is a typical hallmark of malignant tumors across different cancers. Glutamate dehydrogenase (GDH, GLUD1) is one such enzyme involved in the conversion of glutamate to α-ketoglutarate. High levels of GDH are associated with numerous diseases and is also a prognostic marker for predicting metastasis in colorectal cancer. Therefore, inhibiting GDH can be a crucial therapeutic target. Here in this study, we performed molecular docking analysis of 8 different plants derived single compounds collected from pubChem database for screening and selected decursin (DN) and decursinol angelate (DA). We performed molecular dynamics simulation (MD), monitored the stability, interaction for protein and docked ligand at 50 ns, and evaluated the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation on the twoselected compounds along with a standard inhibitor epigallocatechin gallate (EGCG) as reference. The final results showed the formation of stable hydrogen bond interactions by DN and DA in the residues of R400 and Y386 at the ADP activation site of GDH, which was important for the selective inhibition of GDH activity. Additionally, the total binding energy of DN and DA were -115.5 kJ/mol and -106.2 kJ/mol, which was higher than the standard reference GDH inhibitor EGCG (-92.8 kJ/mol). Furthermore, biochemical analysis for GDH inhibition substantiated our computational results and established DN and DA as novel GDH inhibitor. The percentage of IC₅₀ inhibition for DN and DA were 1.035 μM and 1.432 μM. Conclusively, DN and DA can be a novel therapeutic drug for inhibition of glutamate dehydrogenase.

Glutamate metabolism and recycling at the excitatory synapse in health and neurodegeneration

Glutamate is the primary excitatory neurotransmitter of the brain. Cellular homeostasis of glutamate is of paramount importance for normal brain function and relies on an intricate metabolic collaboration between neurons and astrocytes. Glutamate is extensively recycled between neurons and astrocytes in a process known as the glutamate-glutamine cycle. The recycling of glutamate is closely linked to brain energy metabolism and is essential to sustain glutamatergic neurotransmission. However, a considerable amount of glutamate is also metabolized and serves as a metabolic hub connecting glucose and amino acid metabolism in both neurons and astrocytes. Disruptions in glutamate clearance, leading to neuronal overstimulation and excitotoxicity, have been implicated in several neurodegenerative diseases. Furthermore, the link between brain energy homeostasis and glutamate metabolism is gaining attention in several neurological conditions. In this review, we provide an overview of the dynamics of synaptic glutamate homeostasis and the underlying metabolic processes with a cellular focus on neurons and astrocytes. In particular, we review the recently discovered role of neuronal glutamate uptake in synaptic glutamate homeostasis and discuss current advances in cellular glutamate metabolism in the context of Alzheimer's disease and Huntington's disease. Understanding the intricate regulation of glutamate-dependent metabolic processes at the synapse will not only increase our insight into the metabolic mechanisms of glutamate homeostasis, but may reveal new metabolic targets to ameliorate neurodegeneration.

Glutamate dehydrogenase is essential in the acclimation of Virgilia divaricata, a legume indigenous to the nutrient-poor Mediterranean-type ecosystems of the Cape Fynbos

Glutamate dehydrogenase (NAD(H)- GDH, EC 1.4.1.2) is an important enzyme in nitrogen (N) metabolism. It serves as a link between C and N metabolism, in its role of assimilating ammonia into glutamine or deaminating glutamate into 2-oxoglutarate and ammonia. GDH may also have a key in the N assimilation of legumes growing in P-poor soils. Virgilia divaricata is such a legume, growing in the nutrient limited soils of the mediterranean-type Cape fynbos ecosystem. In order to understand the role of GDH in the nitrogen nutrition of V. divaricata, the aim of this study was to identify the GDH gene transcripts, their relative expressions and enzyme activity in P-stressed roots and nodules during N metabolism. During P deficiency there was a reduction in total plant biomass as well as total plant P concentration. The analysis of the GDH cDNA sequences in V. divaricata revealed the presence of GHD1 and GHD2 subunits, these corresponding to the GDH1, GDH-B and GDH3 genes of legumes and non-legume plants. The relative expression of GDH1 and GDH2 genes in the roots and nodules, indicates that two the subunits were differently regulated depending on the organ type, rather than P supply. Although both transcripts appeared to be ubiquitously expressed in the roots and nodules, the GDH2 transcript evidently predominated over those of GDH1. Furthermore, the higher expression of both GDH transcripts in the roots than nodules, suggests that roots are more reliant on on GDH in P-poor soils, than nodules. With regards to GHD activity, both aminating and deaminating GDH activities were differently affected by P deficiency in roots and nodules. This may function to assimilate N and regulate internal C and N in the roots and nodules. The variation in GDH1 and GDH2 transcript expression and GDH enzyme activities, indicate that the enzyme may be regulated by post-translational modification, instead of by gene expression during P deficiency in V. divaricata.

Performance of laboratory tests for detection for Clostridioides difficile: A multicenter prospective study in Japan

BACKGROUND

The optimal and practical laboratory diagnostic approach for detection of Clostridioides difficile to aid in the diagnosis of C. difficile infection (CDI) is controversial. A two-step algorithm with initial detection of glutamate dehydrogenase (GDH) or nucleic acid amplification test (NAAT) alone are recommended as a predominant method for C. difficile detection in developed countries. The aim of this study was to compare the performance of enzyme immunoassays (EIA) detecting toxins A and B, NAAT detecting the toxin B gene, and GDH compared to toxigenic culture (TC) for C. difficile as the gold standard, in patients prospectively and actively assessed with clinically significant diarrhea in 12 medical facilities in Japan.

METHODS

A total of 650 stool specimens were collected from 566 patients with at least three diarrheal bowel movements (Bristol stool grade 6-7) in the preceding 24 h. EIA and GDH were performed at each hospital, and NAAT and toxigenic C. difficile culture with enriched media were performed at the National Institute of Infectious Diseases. All C. difficile isolates recovered were analyzed by PCR-ribotyping.

RESULTS

Compared to TC, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of EIA were 41%, 96%, 75% and 84%, respectively, and for NAAT were 74%, 98%, 91%, and 92%, respectively. In 439 specimens tested with GDH, the sensitivity, specificity, PPV, and NPV were 73%, 87%, 65%, and 91%, and for an algorithm (GDH plus toxin EIA, arbitrated by NAAT) were 71%, 96%, 85%, and 91%, respectively. Among 157 isolates recovered, 75% of isolates corresponded to one of PCR-ribotypes (RTs) 002, 014, 018/018", and 369; RT027 was not isolated. No clear differences in the sensitivities of any of EIA, NAAT and GDH for four predominant RTs were found.

CONCLUSION

The analytical sensitivities of NAAT and GDH-algorithm to detect toxigenic C. difficile in this study were lower than most previous reports. This study also found low PPV of EIAs. The optimal method to detect C. difficile or its toxins to assist in the diagnosis of CDI needs further investigation.

Energy saving and improvement of metabolism of cultured tobacco cells upon exposure to 2-D clinorotation

Studies have confirmed that on the ground, the plant cells must expend energy to maintain positional homeostasis against gravity. Under microgravity conditions, such energy may be saved for other process such as biosynthesis of beneficial metabolites for growth. This hypothesis was examined on a cell line of tobacco (Nicotiana tabacum cv. Burley 21). The cells were continuously treated with 2-D clinostat for 1 week. Exposure to clinorotation conditions increased biomass and total protein. Total content of soluble sugar also increased which may provide more precursors for Krebs cycle and adenosine triphosphate (ATP) production. In the case of 2-D clinorotation, the expression and activity of glutamate producing enzyme, glutamate dehydrogenase (GDH) increased, whereas the activity of glutamate decarboxylase (GAD) decreased. Regarding the role of GAD in initiation of gamma amino butyric acid (GABA) shunt, it is plausible that under clinorotation condition, the tobacco cells directed their metabolism toward saving energy for Krebs cycling and more production of ATP rather than shifting to side paths such as GABA shunt. Improvement of radical scavenging enzymes activity and increase of the contents of phenolic compounds and certain peroxide neutralizing amino acids, e.g., His, Pro, Ser, and Asp under clinorotation conditions decreased membrane lipid peroxidation and maintained the growth potential of tobacco cells.

Subtype analysis of Giardia duodenalis isolates from municipal and domestic raw wastewaters in Iran

A total of 54 raw wastewater samples collected from three urban treatment plants and two slaughterhouses in Tehran, Iran, were assessed for the presence of the Giardia cysts using immunofluorescence with monoclonal antibodies. To characterize the cysts at the molecular level, the three genetic loci were amplified and sequenced. The assemblages A (37.5 %) and E (58.3 %) were detected in livestock wastewater samples. Assemblage A, which is composed of only G. duodenalis genotype, was detected in 100 % of urban wastewater samples. The subassemblages A2, A3, A-I, A-II, and E3 were identified with β-giardin, triose phosphate isomerase, and glutamate dehydrogenase genes. This study is the first to report on G. duodenalis genotypes in aquatic environmental samples in Iran.

Evaluation of sub-cellular distribution of glutamate dehydrogenase (GDH) in Drosophila melanogaster larvae

Glutamate dehydrogenase (GDH) enzyme was conventionally known as a mitochondrial marker. However, subsequently it was reported to be present in the nuclei as well. So far, the nuclear distribution of GDH has been reported in a number of organisms including yeast, rat, cow, chicken. However, the sub-cellular distribution of GDH, illustrated by in situ methods still remains elusive. Here, by assaying the GDH activity and by immuno-blotting using anti-GDH antibody in the fractionated nuclear and cytoplasmic fractions of Drosophila larvae, we demonstrate the cytoplasmic distribution of GDH. This observation was further supported by in situ immunostaining of salivary gland, Malpighian tubules and eye imaginal discs of Drosophila larvae. Collectively, our results demonstrate that in Drosophila larvae, GDH is not found in the nucleus, but is localized exclusively in the cytoplasm.

Chicken liver glutamate dehydrogenase (GDH) demonstrates a histone H3 specific protease (H3ase) activity in vitro

Site-specific proteolysis of the N or C-terminus of histone tails has emerged as a novel form of irreversible post-translational modifications assigned to histones. Though there are many reports describing histone specific proteolysis, there are very few studies on purification of a histone specific protease. Here, we demonstrate a histone H3 specific protease (H3ase) activity in chicken liver nuclear extract. H3ase was purified to homogeneity and identified as glutamate dehydrogenase (GDH) by sequencing. A series of biochemical experiments further confirmed that the H3ase activity was due to GDH. The H3ase clipped histone H3 products were sequenced by N-terminal sequencing and the precise clipping sites of H3ase were mapped. H3ase activity was only specific to chicken liver as it was not demonstrated in other tissues like heart, muscle and brain of chicken. We assign a novel serine like protease activity to GDH which is specific to histone H3.