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<p>MDH (Malate dehydrogenase) is an enzyme in citric acid cycle that catalyzes the conversion between malate and oxaloacetate. This ubiquitous plant enzyme plays a critical role in a plant’s adaptation to abiotic stress through its involvement in regulating metabolic pathways, maintaining redox balance, supporting energy production, and contribution to osmotic adjustment. In this study, comprehensive bioinformatics analysis tools were used to genome-wide identify and characterize the <i>MDH</i> gene family in soybean (<i>Glycine max</i> L.). In this study, twelve <i>MDH</i> genes (renamed as <i>GmMDH1</i> to <i>GmMDH12</i>) in soybeans were analyzed corresponding to the <i>MDH</i> genes of Arabidopsis thaliana. The genes were spread out unevenly across eight chromosomes of the entire genome most of which were localized on the chloroplast which were categorized into five distinct groups and one outgroup based on their phylogenetic tree analysis. Based on the evolutionary analysis, the MDH protein from tomato, apple, and soybean shared a close relationship. The conserved domain and motif analysis provided identical sequences among the members of GmMDH proteins. The exon-intron structure showed only three <i>MDH</i> genes possessed no intron. Six segmental duplications involving twelve genes have been identified. Notably, all the genes revealed their evolution through purifying selection. The development of the <i>GmMDH</i> family is most likely due to the significant role that these events played in the development process. The <i>cis</i>-regulatory element analysis demonstrated that the <i>GmMDH</i> genes exhibited ubiquitous expression in distinct tissue-specific areas, responded to various abiotic stressors, and were influenced by phytohormone responses. ERF, LBD, and MYB were major transcription factors for <i>GmMDH</i> genes, predicted by transcription factor analysis. The analysis of putative micro-RNAs in <i>GmMDH</i> genes showed crucial regulatory mechanisms to control abiotic stress. Regarding, the protein-protein interactions, GmMDH proteins demonstrated homology with Arabidopsis proteins and showed the various metabolic activities. Expression profiling of <i>GmMDH</i> in response to various abiotic treatments such as dehydration, salt, and drought showed up and down-regulation activity. Two <i>GmMDH</i> genes, <i>GmMDH5</i> and <i>GmMDH10</i> showed higher expression in dehydration, salt, and drought in managing and confronting these conditions. Moreover, the findings from this study provide useful information on the <i>GmMDH</i> gene family which could pave the way to advanced wet lab experiments to unravel the details of functional mechanism in the putative <i>GmMDH</i> genes as well as to develop new soybean cultivars tolerant to various abiotic stresses in breeding programs.</p>

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Soybean Malate Dehydrogenase: Evolutionary Relationship, Characterization of Their Functional Regulatory Elements, and Expression Profiles in Response to Abiotic Stresses

  • 期刊论文

  • 发表日期：

    2025年1月29日

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  • Shohel Ul Islam,
  • Sumaiya Khatun,
  • Mazharul Islam,
  • Fatema Tuz Zohra,
  • Amina Rownaq,
  • Shaikh Mizanur Rahman,
  • Abdur Rauf Sarkar

摘要

MDH (Malate dehydrogenase) is an enzyme in citric acid cycle that catalyzes the conversion between malate and oxaloacetate. This ubiquitous plant enzyme plays a critical role in a plant’s adaptation to abiotic stress through its involvement in regulating metabolic pathways, maintaining redox balance, supporting energy production, and contribution to osmotic adjustment. In this study, comprehensive bioinformatics analysis tools were used to genome-wide identify and characterize the MDH gene family in soybean (Glycine max L.). In this study, twelve MDH genes (renamed as GmMDH1 to GmMDH12) in soybeans were analyzed corresponding to the MDH genes of Arabidopsis thaliana. The genes were spread out unevenly across eight chromosomes of the entire genome most of which were localized on the chloroplast which were categorized into five distinct groups and one outgroup based on their phylogenetic tree analysis. Based on the evolutionary analysis, the MDH protein from tomato, apple, and soybean shared a close relationship. The conserved domain and motif analysis provided identical sequences among the members of GmMDH proteins. The exon-intron structure showed only three MDH genes possessed no intron. Six segmental duplications involving twelve genes have been identified. Notably, all the genes revealed their evolution through purifying selection. The development of the GmMDH family is most likely due to the significant role that these events played in the development process. The cis-regulatory element analysis demonstrated that the GmMDH genes exhibited ubiquitous expression in distinct tissue-specific areas, responded to various abiotic stressors, and were influenced by phytohormone responses. ERF, LBD, and MYB were major transcription factors for GmMDH genes, predicted by transcription factor analysis. The analysis of putative micro-RNAs in GmMDH genes showed crucial regulatory mechanisms to control abiotic stress. Regarding, the protein-protein interactions, GmMDH proteins demonstrated homology with Arabidopsis proteins and showed the various metabolic activities. Expression profiling of GmMDH in response to various abiotic treatments such as dehydration, salt, and drought showed up and down-regulation activity. Two GmMDH genes, GmMDH5 and GmMDH10 showed higher expression in dehydration, salt, and drought in managing and confronting these conditions. Moreover, the findings from this study provide useful information on the GmMDH gene family which could pave the way to advanced wet lab experiments to unravel the details of functional mechanism in the putative GmMDH genes as well as to develop new soybean cultivars tolerant to various abiotic stresses in breeding programs.