Functional characterization and expression profiling of glyoxalase III genes in date palm grown under abiotic stresses

Tracing the intraspecies expansion of glyoxalase genes and their expanding roles across the genus Oryza

The genus Oryza is of utmost importance to human civilization as two of its species became agronomically productive and widely cultivated, and also because wild rice is a treasure trove of beneficial alleles that can be used for crop improvement. Most of the wild rice genotypes are known for their stress tolerance several times more than the domesticated rice varieties. In this study, we aimed to carry out an exhaustive genomic survey to identify glyoxalase I (GLYI) and glyoxalase II (GLYII) genes across the 11 rice genomes sequenced so far. Notably, we found the putatively functional metal-dependent GLYI and GLYII enzymes to be conserved throughout domestication and a few homologous pairs to have undergone beneficial mutations to drive positive selection, and thus, acquire newer functions. Interestingly, we also report four newly identified GLYII members in O. sativa subsp. japonica in addition to the three previously reported GLYII genes. The presence of different types of cis-elements in the promoter region of the glyoxalase genes gives insights into their role and regulation under various developmental processes besides stress adaptation. Publicly available data suggests the role of glyoxalase genes particularly in salinity stress in both wild and cultivated rice as is also confirmed through qRT-PCR. Interestingly, we found less accumulation of MG and concurrently higher enzymatic activity of GLYI and GLYII proteins in stressed seedlings of selected wild rice genotypes indicating that glyoxalases indeed contribute to the intrinsic stress tolerance of wild rice.

The dual role of methylglyoxal in plant stress response and regulation of DJ-1 protein

Methylglyoxal (MG) is a highly reactive metabolic intermediate that plays important roles in plant salt stress response. This review explores the sources of MG in plants, how salt stress promotes MG production, and the dual role of MG under salt stress conditions. Both the positive role of low concentrations of MG as a signalling molecule and the toxic effects of high concentrations of MG in plant response to salt stress are discussed. The MG detoxification pathways, especially the glyoxalase system, are described in detail. Special attention is given to the novel role of the DJ-1 protein in the glyoxalase system as glyoxalase III to remove MG, and as a deglycase to decrease glycation damage caused by MG on DNA, proteins, and other biomolecules. This review aims to provide readers with comprehensive perspectives on the functions of MG in plant salt stress response, the roles of the DJ-1 protein in MG detoxification and repair of glycation-damaged molecules, as well as the broader functional implications of MG in plant salt stress tolerance. New perspectives on maintaining plant genome stability, breeding for salt-tolerant crop varieties, and improving crop quality are discussed.

Genomic identification, characterization, and stress-induced expression profiling of glyoxalase and D-lactate dehydrogenase gene families in Capsicum annuum

BACKGROUND

Capsicum annuum, a significant agricultural and nutritional crop, faces production challenges due to its sensitivity to various abiotic stresses. Glyoxalase (GLY) and D-lactate dehydrogenase (D-LDH) enzymes play vital roles in mitigating these stresses by detoxifying the stress-induced cytotoxin, methylglyoxal (MG).

METHODS

A genome-wide study was conducted to identify and characterize glyoxalase I (GLYI), glyoxalase II (GLYII), unique glyoxalase III or DJ-1 (GLYIII), and D-LDH gene candidates in Capsicum annuum. The identified members were evaluated based on their evolutionary relationships with known orthologues, as well as their gene and protein features. Their expression patterns were examined in various tissues, developmental stages, and in response to abiotic stress conditions using RNA-seq data and qRT-PCR.

RESULTS

A total of 19 GLYI, 9 GLYII, 3 DJ-1, and 11 D-LDH members were identified, each featuring characteristic domains: glyoxalase, metallo-β-lactamase, DJ-1_PfpI, and FAD_binding_4, respectively. Phylogenetic analysis revealed distinct clades depending on functional diversification. Expression profiling demonstrated significant variability under stress conditions, underscoring their potential roles in stress modulation. Notably, gene-specific responses were observed with CaGLYI-2, CaGLYI-7, CaGLYII-6, CaDJ-1 A, and CaDLDH-1 showed upregulation under salinity, drought, oxidative, heat, and cold stresses, while downregulation were shown for CaGLYI-3, CaGLYII-1, CaDJ-1B, and CaDJ-1 C. Remarkably, CaGLYI-1 presented a unique expression pattern, upregulated against drought and salinity but downregulated under oxidative, heat, and cold stress.

CONCLUSION

The identified GLY and D-LDH gene families in Capsicum annuum exhibited differential expression patterns under different abiotic stresses. Specifically, CaGLYI-2, CaGLYI-7, CaGLYII-6, CaDJ-1 A, and CaDLDH-1 were upregulated in response to all five analyzed abiotic stressors, highlighting their critical role in stress modulation amidst climate change. This study enhances our understanding of plant stress physiology and opens new avenues for developing stress-resilient crop varieties, crucial for sustainable agriculture.

Genome-Wide Analysis and Expression Profiling of Glyoxalase Gene Families Under Abiotic Stresses in Cucumber (Cucumis sativus L.)

The glyoxalase pathway, consisting of glyoxalase I (GLYI) and glyoxalase II (GLYII), is an enzymatic system that converts cytotoxic methylglyoxal to non-toxic S-D-lactoylglutathione. Although the GLY gene family has been analyzed in Arabidopsis, rice, grape, cabbage, and soybean, cucumber studies are lacking. Here, we analyzed the cucumber GLY gene family, identifying 13 CsGLYI and 2 CsGLYII genes. Furthermore, we investigated the physicochemical properties, phylogenetic relationships, chromosomal localization and colinearity, gene structure, conserved motifs, cis-regulatory elements, and protein-protein interaction networks of the CsGLY family. They were primarily localized in the cytoplasm, chloroplasts, and mitochondria, with a minor presence in the nucleus. The classification of CsGLYI and CsGLYII genes into five classes closely resembled the homologous genes in Arabidopsis and soybean. Additionally, hormone-responsive elements dominated the promoter region of GLY genes, alongside light- and stress-responsive elements. The predicted interaction proteins of CsGLYIs and CsGLYIIs exerted a significant role in cellular respiration, amino acid synthesis, and metabolism, as well as methylglyoxal catabolism. In addition, the expression profiles of GLY genes were distinct in different tissues of cucumber as well as under diverse abiotic stresses. This study is conducive to the further exploration of the functional diversity among glyoxalase genes and the mechanisms of stress responses in cucumber.

Methylglyoxal detoxifying gene families in tomato: Genome-wide identification, evolution, functional prediction, and transcript profiling

Methylglyoxal (MG) is a highly cytotoxic molecule produced in all biological systems, which could be converted into non-toxic D-lactate by an evolutionarily conserved glyoxalase pathway. Glutathione-dependent glyoxalase I (GLYI) and glyoxalase II (GLYII) are responsible for the detoxification of MG into D-lactate in sequential reactions, while DJ-1 domain containing glyoxalase III (GLYIII) catalyzes the same reaction in a single step without glutathione dependency. Afterwards, D-lactate dehydrogenase (D-LDH) converts D-lactate into pyruvate, a metabolically usable intermediate. In the study, a comprehensive genome-wide investigation has been performed in one of the important vegetable plants, tomato to identify 13 putative GLYI, 4 GLYII, 3 GLYIII (DJ-1), and 4 D-LDH genes. Expression pattern analysis using microarray data confirmed their ubiquitous presence in different tissues and developmental stages. Moreover, stress treatment of tomato seedlings and subsequent qRT-PCR demonstrated upregulation of SlGLYI-2, SlGLYI-3, SlGLYI-6A, SlGLYII-1A, SlGLYII-3B, SlDJ-1A, SlDLDH-1 and SlDLDH-4 in response to different abiotic stresses, whereas SlGLYI-6B, SlGLYII-1B, SlGLYII-3A, SlDJ-1D and SlDLDH-2 were downregulated. Expression data also revealed SlGLYII-1B, SlGLYI-1A, SlGLYI-2, SlDJ-1D, and SlDLDH-4 were upregulated in response to various pathogenic infections, indicating the role of MG detoxifying enzymes in both plant defence and stress modulation. The functional characterization of each of these members could lay the foundation for the development of stress and disease-resistant plants promoting sustainable agriculture and production.

A glutathione-independent DJ-1/Pfp1 domain containing glyoxalase III, OsDJ-1C, functions in abiotic stress adaptation in rice

MAIN CONCLUSION

Overexpression of OsDJ-1C in rice improves root architecture, photosynthesis, yield and abiotic stress tolerance through modulating methylglyoxal levels, antioxidant defense, and redox homeostasis. Exposure to abiotic stresses leads to elevated methylglyoxal (MG) levels in plants, impacting seed germination and root growth. In response, the activation of NADPH-dependent aldo-keto reductase and glutathione (GSH)-dependent glyoxalase enzymes helps to regulate MG levels and reduce its toxic effects. However, detoxification may not be carried out effectively due to the limitation of GSH and NADPH in plants under stress. Recently, a novel enzyme called glyoxalase III (GLY III) has been discovered which can detoxify MG in a single step without needing GSH. To understand the physiological importance of this pathway in rice, we overexpressed the gene encoding GLYIII enzyme (OsDJ-1C) in rice. It was observed that OsDJ-1C overexpression in rice regulated MG levels under stress conditions thus, linked well with plants' abiotic stress tolerance potential. The OsDJ-1C overexpression lines displayed better root architecture, improved photosynthesis, and reduced yield penalty compared to the WT plants under salinity, and drought stress conditions. These plants demonstrated an improved GSH/GSSG ratio, reduced level of reactive oxygen species, increased antioxidant capacity, and higher anti-glycation activity thereby indicating that the GLYIII mediated MG detoxification plays a significant role in plants' ability to reduce the impact of abiotic stress. Furthermore, these findings imply the potential of OsDJ-1C in crop improvement programs.

A TaSnRK1α Modulates TaPAP6L-Mediated Wheat Cold Tolerance through Regulating Endogenous Jasmonic Acid

Here, a sucrose non-fermenting-1-related protein kinase alpha subunit (TaSnRK1α-1A) is identified as associated with cold stress through integration of genome-wide association study, bulked segregant RNA sequencing, and virus-induced gene silencing. It is confirmed that TaSnRK1α positively regulates cold tolerance by transgenes and ethyl methanesulfonate (EMS) mutants. A plastid-lipid-associated protein 6, chloroplastic-like (TaPAP6L-2B) strongly interacting with TaSnRK1α-1A is screened. Molecular chaperone DJ-1 family protein (TaDJ-1-7B) possibly bridged the interaction of TaSnRK1α-1A and TaPAP6L-2B. It is further revealed that TaSnRK1α-1A phosphorylated TaPAP6L-2B. Subsequently, a superior haplotype TaPAP6L-2B30S /38S is identified and confirmed that both R30S and G38S are important phosphorylation sites that influence TaPAP6L-2B in cold tolerance. Overexpression (OE) and EMS-mutant lines verified TaPAP6L positively modulating cold tolerance. Furthermore, transcriptome sequencing revealed that TaPAP6L-2B-OE lines significantly increased jasmonic acid (JA) content, possibly by improving precursor α-linolenic acid contributing to JA synthesis and by repressing JAR1 degrading JA. Exogenous JA significantly improved the cold tolerance of wheat plants. In summary, TaSnRK1α profoundly regulated cold stress, possibly through phosphorylating TaPAP6L to increase endogenous JA content of wheat plants.

Identification and molecular evolution of the GLX genes in 21 plant species: a focus on the Gossypium hirsutum

BACKGROUND

The glyoxalase system includes glyoxalase I (GLXI), glyoxalase II (GLXII) and glyoxalase III (GLXIII), which are responsible for methylglyoxal (MG) detoxification and involved in abiotic stress responses such as drought, salinity and heavy metal.

RESULTS

In this study, a total of 620 GLX family genes were identified from 21 different plant species. The results of evolutionary analysis showed that GLX genes exist in all species from lower plants to higher plants, inferring that GLX genes might be important for plants, and GLXI and GLXII account for the majority. In addition, motif showed an expanding trend in the process of evolution. The analysis of cis-acting elements in 21 different plant species showed that the promoter region of the GLX genes were rich in phytohormones and biotic and abiotic stress-related elements, indicating that GLX genes can participate in a variety of life processes. In cotton, GLXs could be divided into two groups and most GLXIs distributed in group I, GLXIIs and GLXIIIs mainly belonged to group II, indicating that there are more similarities between GLXII and GLXIII in cotton evolution. The transcriptome data analysis and quantitative real-time PCR analysis (qRT-PCR) show that some members of GLX family would respond to high temperature treatment in G.hirsutum. The protein interaction network of GLXs in G.hirsutum implied that most members can participate in various life processes through protein interactions.

CONCLUSIONS

The results elucidated the evolutionary history of GLX family genes in plants and lay the foundation for their functions analysis in cotton.

Genome-wide analysis and expression profiling of glyoxalase gene families in oat (Avena sativa) indicate their responses to abiotic stress during seed germination

Abiotic stresses have deleterious effects on seed germination and seedling establishment, leading to significant crop yield losses. Adverse environmental conditions can cause the accumulation of methylglyoxal (MG) within plant cells, which can negatively impact plant growth and development. The glyoxalase system, which consists of the glutathione (GSH)-dependent enzymes glyoxalase I (GLX1) and glyoxalase II (GLX2), as well as the GSH-independent glyoxalase III (GLX3 or DJ-1), plays a crucial role in detoxifying MG. However, genome-wide analysis of glyoxalase genes has not been performed for one of the agricultural important species, oat (Avena sativa). This study identified a total of 26 AsGLX1 genes, including 8 genes encoding Ni²⁺-dependent GLX1s and 2 genes encoding Zn²⁺-dependent GLX1s. Additionally, 14 AsGLX2 genes were identified, of which 3 genes encoded proteins with both lactamase B and hydroxyacylglutathione hydrolase C-terminal domains and potential catalytic activity, and 15 AsGLX3 genes encoding proteins containing double DJ-1 domains. The domain architecture of the three gene families strongly correlates with the clades observed in the phylogenetic trees. The AsGLX1, AsGLX2, and AsGLX3 genes were evenly distributed in the A, C, and D subgenomes, and gene duplication of AsGLX1 and AsGLX3 genes resulted from tandem duplications. Besides the core cis-elements, hormone responsive elements dominated the promoter regions of the glyoxalase genes, and stress responsive elements were also frequently observed. The subcellular localization of glyoxalases was predicted to be primarily in the cytoplasm, chloroplasts, and mitochondria, with a few presents in the nucleus, which is consistent with their tissue-specific expression. The highest expression levels were observed in leaves and seeds, indicating that these genes may play important roles in maintaining leaf function and ensuring seed vigor. Moreover, based on in silico predication and expression pattern analysis, AsGLX1-7A, AsGLX2-5D, AsDJ-1-5D, AsGLX1-3D2, and AsGLX1-2A were suggested as promising candidate genes for improving stress resistance or seed vigor in oat. Overall, the identification and analysis of the glyoxalase gene families in this study can provide new strategies for improving oat stress resistance and seed vigor.

Involvement of osmoregulation, glyoxalase, and non-glyoxalase systems in signaling molecule glutamic acid-boosted thermotolerance in maize seedlings

Glutamic acid (Glu) is not only an important protein building block, but also a signaling molecule in plants. However, the Glu-boosted thermotolerance and its underlying mechanisms in plants still remain unclear. In this study, the maize seedlings were irrigated with Glu solution prior to exposure to heat stress (HS), the seedlings' thermotolerance as well as osmoregulation, glyoxalase, and non-glyoxalase systems were evaluated. The results manifested that the seedling survival and tissue vitality after HS were boosted by Glu, while membrane damage was reduced in comparison with the control seedlings without Glu treatment, indicating Glu boosted the thermotolerance of maize seedlings. Additionally, root-irrigation with Glu increased its endogenous level, reinforced osmoregulation system (i.e., an increase in the levels of proline, glycine betaine, trehalose, and total soluble sugar, as well as the activities of pyrroline-5-carboxylate synthase, betaine dehydrogenase, and trehalose-5-phosphate phosphatase) in maize seedlings under non-HS and HS conditions compared with the control. Also, Glu treatment heightened endogenous methylglyoxal level and the activities of glyoxalase system (glyoxalase I, glyoxalase II, and glyoxalase III) and non-glyoxalase system (methylglyoxal reductase, lactate dehydrogenase, aldo-ketoreductase, and alkenal/alkenone reductase) in maize seedlings under non-HS and HS conditions as compared to the control. These data hint that osmoregulation, glyoxalase, and non-glyoxalase systems are involved in signaling molecule Glu-boosted thermotolerance of maize seedlings.

Recent advances in date palm genomics: A comprehensive review

As one of the oldest fruit trees of the Arabian peninsula, other Middle-Eastern countries, and also North Africa, the date palm (Phoenix dactylifera L.), is highly significant for the economy of the region. Listed as part of UNESCO’s Intangible Cultural Heritage of Humanity, the date palm is believed to be the first tree cultivated by human beings, and was probably first harvested for its fruit nearly 7,000 years ago. Initial research efforts in date palm genetics focused on understanding the genetic diversity of date palm germplasm collections and its phylogenetic history, both important prerequisites for plant improvement. Despite various efforts, the center of origin of the date palm is still unclear, although genomic studies suggest two probable domestication events: one in the Middle East and the other in North Africa, with two separate gene pools. The current review covers studies related to omics analyses that have sought to decipher the present genetic diversity of the date palm. With advances and cost reductions in sequencing technologies, rapid progress has been made in the past few years in date palm genomics research. Along with organellar genomes, several reference genomes of the date palm are now available. In addition, several genotypes have been re-sequenced, either to detect single nucleotide polymorphisms (SNPs), or to study domestication and identification of key genes/loci associated with important agronomic traits, such as sex, fruit color, and sugar composition. These genomics research progress has paved the way to perform fast-track and precise germplasm improvement processes in date palm. In this study, we review the advances made in the genetics and genomics of the date palm so as to strategize targeted crop improvement plans for marginal areas of the Middle Eastern peninsula, North Africa, and other parts of the world.

Glyoxalase III enhances salinity tolerance through reactive oxygen species scavenging and reduced glycation

Methylglyoxal (MG) is a metabolically generated highly cytotoxic compound that accumulates in all living organisms, from Escherichia coli to humans, under stress conditions. To detoxify MG, nature has evolved reduced glutathione (GSH)-dependent glyoxalase and NADPH-dependent aldo-keto reductase systems. But both GSH and NADPH have been reported to be limiting in plants under stress conditions, and thus detoxification might not be performed efficiently. Recently, glyoxalase III (GLY III)-like enzyme activity has been reported from various species, which can detoxify MG without any cofactor. In the present study, we have tested whether an E. coli gene, hchA, encoding a functional GLY III, could provide abiotic stress tolerance to living systems. Overexpression of this gene showed improved tolerance in E. coli and Saccharomyces cerevisiae cells against salinity, dicarbonyl, and oxidative stresses. Ectopic expression of the E. coli GLY III gene (EcGLY-III) in transgenic tobacco plants confers tolerance against salinity at both seedling and reproductive stages as indicated by their height, weight, membrane stability index, and total yield potential. Transgenic plants showed significantly increased glyoxalase and antioxidant enzyme activity that resisted the accumulation of excess MG and reactive oxygen species (ROS) during stress. Moreover, transgenic plants showed more anti-glycation activity to inhibit the formation of advanced glycation end product (AGE) that might prevent transgenic plants from stress-induced senescence. Taken together, all these observations indicate that overexpression of EcGLYIII confers salinity stress tolerance in plants and should be explored further for the generation of stress-tolerant plants.