Role of Epigenetic Mechanisms in Regulating the Activity of 2-OGDH and MDH in Maize Leaves (Zea mays L.) during Hypoxia

Molecular and epigenetic ways of regulating the activity of key TCA enzymes, 2-oxoglutarate dehydrogenase (2-OGDH) and malate dehydrogenase (MDH), in maize (Zea mays L.) leaves under hypoxic conditions were studied. It has been shown that regulation of the rate of enzyme functioning under stress conditions is caused not by conformational transformations of protein molecules but by changes in the transcriptional activity of their genes. Analysis into the level of transcripts of genes encoding 2-OGDH and MDH revealed a correlation with changes in the total enzymatic activity. When plants were incubated under hypoxic conditions, a decrease in the expression of the 2-OGDH and MDH genes was observed. It was found that fluctuations in the content of gene transcripts ogdh-1 and ogdh-3 is associated with a change in the methyl status of CG-dinucleotides in their promoters. An increase in the expression of these genes is associated with a decrease in the degree of methylation of their promoters. Conversely, a decrease in the relative level of transcripts is caused by an increase in the amount of methylated CG-dinucleotides. It is concluded that regulating the functioning of 2-oxoglutarate dehydrogenase and malate dehydrogenase under conditions of low oxygen concentrations takes place by means of an epigenetic mechanism, that is, by changing the methyl status of their gene promoters.

Keywords: Zea mays; 2-oxoglutarate dehydrogenase; malate dehydrogenase; hypoxia; transcription; methylation; DNA

Abbreviations : 2-OGDH—2-oxoglutarate dehydrogenase; MDH—malate dehydrogenase; MS-PCR—methyl-specific polymerase chain reaction.

The natural habitat of many plants is often subject to flooding, which leads to a lack of oxygen in the soil cover, hypoxia, which causes significant changes in the functioning of both the whole organism and its individual enzyme systems [[1]–[3]]. The transformation of the airways is possible in different ways. With anoxia, there is an increase in the proportion of glycolysis and pentose phosphate pathway [[4]] as well as the use of alternative pathways for the oxidation of reduced coenzymes [[5]]. According to some literature data, with a decrease in the concentration of intracellular ATP by 15–20%, inhibition of the leading energy-dependent functional metabolic processes is observed [[7]]. Under conditions of hypoxia, the mitochondrial respiratory chain participates in the formation of the body's response system to oxygen deficiency, thus providing an adaptive response [[8]–[10]].

The 2-oxoglutarate dehydrogenase complex (2‑OGDC, EC 1.2.4.2) is a complex multienzyme system that includes three independent enzymes that provide oxidative decarboxylation of 2-oxoglutarate (2OH) with the formation of succinyl-CoA: 2-oxoglutarate dehydrogenase (2-OGDH, E1, EC 1.2.4.2.), dihydrolipoamide succinyltransferase (DLST, E2, EC 2.3.1.61), and dehydrolipoamide dehydrogenase (DLD, E3, EC 1.8.1.4.). It is known that a change in the activity of 2-OGDC is observed under hypoxic conditions in heterotrophic organisms [[11]]. For plants with a C3-type of metabolism, the inhibitory effect of low oxygen concentrations on the functioning of 2‑OGDC has been shown [[4], [12]]. The first component of 2-OGDC is maize 2-oxoglutarate dehydrogenase (Zea mays L.), which is encoded by three genes located on different chromosomes. The first gene ogdh-1 is localized on chromosome two (LOC100383579, Gene ID: 100383579) and consists of ten exons. The second gene ogdh-2, previously annotated as encoding 2-OGDH, is now recognized as a pseudo-genome located on chromosome nine (LOC103639200, Gene ID: 103639200), and it is represented by 15 exons. The third gene ogdh-3 encodes a 2-OGDH-like protein and is located on chromosome ten (TIDP3354, Gene ID: 100383847), and it consists of nine exons. There is evidence that 2-OGDC, in addition to mitochondrial, also has nuclear localization, providing the process of succinylation due to binding to lysine acetyltransferase 2A (KAT2A) from the promoter regions of genes, which indicates the role of this multienzyme complex in the epigenetic regulation of the genome [[13]].

The malate dehydrogenase system is ubiquitous in the plant cell. Malate dehydrogenase (MDH, EC 1.1.1.37) is an enzyme that catalyzes the reversible oxidation of malate to oxaloacetate. Analysis of the international GenBank database and literature revealed ten NAD+-dependent malate dehydrogenase genes localized in different chromosomes [[14]]. At the same time, the mitochondrial forms of the enzyme are encoded by two genes located on different chromosomes: the gene mMdh (Gene ID: 100274264) on chromosome six and gene mMdh-2 (Gene ID: 100273428) on chromosome eight from seven exons.

Mitochondrial MDH participates in the Krebs cycle while using NAD+. There are MDH (malic enzyme, EC 1.1.1.39), which catalyzes the decarboxylation reaction, participating both in the production of NADH and in the regulation of the level of carbon dioxide inside cells. It is known that hypoxia has a significant effect on the activity of malate dehydrogenases. Prolonged exposure of plants to hypoxic conditions leads to an increase in the activity of NADH-MDH in the roots and leaves of wheat, which indicates a shift in the equilibrium of the reaction towards the formation of malate [[16]].

There is a lot of evidence that, under conditions of hypoxia, there is an increase in the level of intracellular succinate in a plant organism due to the activation of additional metabolic pathways: activation of the GABA shunt, switching on the mechanism of the conversion of 2-oxoglutarate bypassing 2-OGDC through the activation of 2-oxoglutarate oxygenase (2OHO, EC 1.14.11), and as a result of the work of alanine aminotransferase (ALT, EC 2.6.1.2) [[4], [12], [17]].

Thus, the important points in the mechanism of the stress-induced response of the plant organism to hypoxia are such enzyme systems as the 2-oxoglutarate dehydrogenase complex and the malate dehydrogenase system. We have previously shown that the functioning of succinate dehydrogenase in maize under hypoxic conditions is regulated by changes in the methylation status of individual CG dinucleotides of gene promoters [[18]].

The aim of this work is to study the methylation status of CpG islands of gene promoters in regulating the functioning of the 2-OGDH and MDH enzymes in maize leaves under conditions of low oxygen concentrations.

We used 10−12-day-old maize (Zea mays L.) leaves of the Voronezhkaya-76 variety grown hydroponically with a 10-h daylight hours and light intensity of 25 W/m2 in a climatic chamber (LabTech, South Korea). The action of low oxygen concentrations in the environment was carried out by placing plants with a previously removed root system for 24 h in a vacuum desiccator, which was supplied with nitrogen. Plants with a previously removed root system, placed in a vacuum desiccator under normal aeration, were used as a control group. To exclude the effect of the photosynthetic system, both groups of plants were preliminarily exposed in the dark for 24 h before the experiment. Throughout the experiment, the plants were also kept in the absence of light sources.

To isolate the mitochondrial fraction, a weighed portion (5 g) of maize leaves was ground in a porcelain mortar with an isolation medium: 0.15 M potassium phosphate buffer (pH 7.4), 0.4 M sucrose, 2.5 mM EDTA, 1 mM potassium chloride, 4 mM magnesium chloride, 0.05% Triton X-100 at a ratio of 1 : 10. The homogenate was filtered and centrifuged for 3 min at 3000 g in an Eppendorf 5804R centrifuge (Eppendorf, Germany). The supernatant was centrifuged for 10 min at 18 000 g. The isolated mitochondrial fraction was destroyed by osmotic shock in a medium containing 0.15 M potassium phosphate buffer (pH 7.4). The degree of mitochondrial destruction was more than 90%, which was controlled by microscopy on an Olympus CX41RF (Olympus, Japan). The resulting mitochondrial fraction was used to determine the activity of 2-OGDH and MDH. All manipulations were performed at 4°C.

The activity of 2-OGDH was determined spectrometrically on an SF-2000 (ZAO OKB Spectr, Russia) by the rate of formation of NADH in the reaction mixture of the following composition: 0.1 M potassium as phosphate buffer (pH 7.5), 0.05% Triton X-100, 0.5 mM MgCl2, 2 mM NAD+, 0.12 mM lithium-CoA, 0.2 mM thiamine diphosphate, 2.5 mM Cys-HCl, 1 mM AMP, 1 mM potassium 2-oxoglutarate, 5E lipoamide dehydrogenase (Sigma, United States) [[19]]. The control used a medium without potassium 2-oxoglutarate.

The MDH activity was determined spectrophotometrically at a wavelength of 340 nm (absorption of reduced NADH) in a spectrophotometric medium of the following composition: 100 mM Tris-HCl, pH 8.0, 1 mM oxaloacetate, 0.2 mM NADH, 10 mM MgCl2 [[20]].

RNA was isolated from plants by phenol-chloroform extraction [[21]].

Reverse transcription of mRNA was performed using M-MuLV reverse transcriptase (Evrogen, Russia). The selection of primers was carried out on the basis of nucleotide sequences from GenBank using the Primer-BLAST program (Supplementary Tables 1, 2). Real-time polymerase chain reaction was performed using the LightCycler96 (Roche, Sweden) with SybrGreen I dye (Evrogen). The amount of template was controlled by parallel amplification of the elongation factor ef-1α [[22]]. Total RNA without the reverse transcription step was used as a negative control. The relative level of expression of the studied genes was determined using the 2-ΔΔCt-method [[23]].

DNA was isolated using the PROBA-GS kit (DNA-Technology, Russia) according to the manufacturer's recommendations. To study changes in the methylation status of CpG-dinucleotides of gene promoters ogdh-1, ogdh-2, ogdh-3, 2-oxoglutarate dehydrogenase and gene promoter mMdh malate dehydrogenase DNA samples were modified [[24]]. The analysis of the promoters of the studied genes for the presence of CpG islands and the selection of primers for MS-PCR were performed using the MethPrimer program. The sequences of primers for MS-PCR are presented in the Supplementary (Tables 3, 4).

The experiments were carried out in 3–4 replicates, and analytical determinations for each sample were performed in triplicate. A preliminary assessment of the nature of the distribution was carried out by asymmetry and excess (Excel, Microsoft Office) as well as using the Kolmogorov–Smirnov test. The obtained values made it possible to evaluate the nature of the distribution as normal. Student's t-test was used with multiple comparison correction (Bonferroni correction) [[25]]. Additionally, we used one-way ANOVA, which showed that the factor studied in the work really had an effect (the effect of the factor is significant when P < 0.05).

The study showed that, in the first hours of incubation of plants in an environment with a low oxygen content, a strong decrease in the activity of 2-OGDH was observed starting from the first hour of the experiment (Fig. 1). The group of control plants did not show significant changes in the total enzymatic activity (changes within the range of fluctuations). Analysis of the dynamics of the activity of the mitochondrial form of MDH also showed a decrease in enzymatic activity in the first hours of the experiment: the number of enzymatic units decreased by almost 3.5 times in comparison with the control group of plants (Fig. 2).

Graph: Fig. 1. Dynamics of the enzymatic activity of 2-oxoglutarate dehydrogenase in maize leaves under hypoxic conditions. (1) Control group of plants; (2) experimental group of plants.

Graph: Fig. 2. Dynamics of the enzymatic activity of mitochondrial malate dehydrogenase in maize leaves under hypoxic conditions. (1) Control group of plants; (2) experimental group of plants.

Regulation of the rate of enzyme functioning under stressful conditions can be associated both with conformational transformations of protein molecules and with a change in the transcriptional activity of the genes of the studied enzymes. In this regard, we conducted a study of the level of transcripts of genes 2-OGDH and MDH under conditions of different gas composition.

Analysis of the level of transcripts of genes encoding 2-OGDH enzymes revealed a correlation with changes in overall enzymatic activity. In the group of plants incubated in an environment with a low oxygen content, a decrease in gene expression was observed in 2-OGDH (ogdh-1, ogdh-2, ogdh-3) by 7.4, 3.3, and 1.7 times, respectively (Figs. 3–5). Gradual decrease in the relative level of transcripts under hypoxic conditions was also characteristic of the gene for the mitochondrial form of MDH (mMdh). By the 24th hour of the experiment, the level of transcripts of the studied gene began to decrease (Fig. 6). The data obtained indicate the regulation of the 2-OGDH and MDH genes at the genome level in maize leaves during hypoxia.

Graph: Fig. 3. Dynamics of change relative level gene transcripts ogdh-1 and the degree of methylation of the promoter CG-dinucleotides in maize leaves under hypoxic conditions.

Graph: Fig. 4. Dynamics of changes in the relative level of gene transcripts ogdh-2 and the degree of methylation of the promoter CG-dinucleotides in maize leaves under hypoxic conditions.

Graph: Fig. 5. Dynamics of changes in the relative level of gene transcripts ogdh-3 and the degree of methylation of the promoter CG-dinucleotides in maize leaves under hypoxic conditions.

Graph: Fig. 6. Dynamics of change in the relative level of gene transcripts mMdh and the degree of methylation of the promoter CG-dinucleotides in maize leaves under hypoxic conditions.

It has already been mentioned that the work of some mitochondrial enzymes (succinate dehydrogenase, fumarate hydratase, ATP citrate lyase) is regulated epigenetically by changing the methyl status of individual CG-dinucleotides of their gene promoters [[18], [26]]. In this regard, we analyzed the promoter regions of genes encoding 2-OGDH and MDH. Gene Promoter Analysis ogdh-1, encoding 2-oxoglutarate dehydrogenase for the presence of CpG islands, showed that this gene does not contain a single CpG island in the promoter region (Fig. 7a). Gene analysis of ogdh-2 revealed the presence of three CpG islands in the promoter region with sizes of 118, 120, and 180 bp. (Fig. 7b). Gene promoter ogdh-3 contained two CpG islands with sizes of 116 and 591 bp, respectively (Fig. 7c).

Graph: Fig. 7. Analysis of the promoters of the studied genes Z. mays for the presence of CpG islands: (a) gene ogdh-1 2-oxoglutarate dehydrogenase, (b) gene ogdh-2 2-oxoglutarate dehydrogenase; (c) gene ogdh-3 2-oxoglutarate dehydrogenases; (d) gene mMdh mitochondrial malate dehydrogenase. Vertical lines indicate the positions of the CG-dinucleotides.

Gene research mMdh, which encodes the mitochondrial form of malate dehydrogenase, showed that its promoter contains two islands with a high content of CG-dinucleotides, the sizes of which are 110 and 157 bp. (Fig. 7d). The presence of CpG islands in the promoter region may indicate a possible mechanism of regulation of the work of the studied genes by changing the degree of methylation [[28]].

As a result of the study on the effect of the gas composition on the degree of methylation of CG-dinucleotides included in the gene promoter ogdh-1 in the maize genome, it was found that hypoxia causes significant changes in the methyl status of the studied CG-dinucleotides. It was found that a decrease in the level of transcripts of the studied gene was accompanied by a gradual increase in the degree of methylation of individual CG-dinucleotides from 25 to 75% (Fig. 3).

For gene ogdh-2, it was found that hypoxia does not cause changes in the methyl status of the studied CG-dinucleotides. Throughout the entire experiment, the degree of methylated dinucleotides was 25% in the group of plants, which were incubated in a gas environment with a low oxygen content. The control group of plants, during the entire experiment under conditions of a normal gas environment, showed similar results (25% of the studied CpG-dinucleotides were methylated).

As a result of the study of the degree of gene methylation in ogdh-3, it was shown that low oxygen concentrations cause a change in the methyl status of CG-dinucleotides. At the beginning of the experiment, the degree of methylated dinucleotides was 50%. A decrease in the values of the relative level of transcripts of this gene was accompanied by an increase in the amount of methylated cytosines. After 24 h from the beginning of the experiment, the degree of promoter methylation was 75%. Throughout the experiment, no change in the degree of methylation of CG dinucleotides was observed in the control group of plants under normal conditions (50% of all studied cytosines were methylated). The gene encoding the mitochondrial form of MDH also showed a correlation between the content of the transcript of the studied gene and the change in its methyl status. The amount of methylated cytosines in the gene promoter increased from 25 to 75% during the entire experiment.

Thus, changes in the activity of mitochondrial enzymes 2-OGDH and MDH in maize leaves under hypoxic conditions are due to the state of the genetic apparatus of the cell. It was found that fluctuations in the content of gene transcripts ogdh-1 and ogdh-3 are associated with a change in the methyl status of CG-dinucleotides in their promoters. An increase in gene expression is associated with a decrease in the degree of methylation of their promoters, while a decrease in the values of the relative level of transcripts was caused by an increase in the amount of methylated CG-dinucleotides. Therefore, the regulation of the functioning of 2-oxoglutarate dehydrogenase and malate dehydrogenase under conditions of low oxygen concentrations is carried out at the epigenetic level by changing the methyl status of the promoters of their genes.

This study was financially supported by the Russian Foundation for Basic Research (project no. 20-04-00296).

Conflict of interests. The authors declare that they have no conflicts of interest.

Statement on the welfare of humans or animals. This article does not contain any studies involving animals performed by any of the authors.

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