Genome-Wide Characterization of Superoxide Dismutase (SOD) Genes in Daucus carota: Novel Insights Into Structure, Expression, and Binding Interaction With Hydrogen Peroxide (H2O2) Under Abiotic Stress Condition

Abstract

Superoxide dismutase (SOD) proteins are important antioxidant enzymes that help plants to grow, develop, and respond to a variety of abiotic stressors. SOD gene family has been identified in a number of plant species but not yet in Daucus carota. A total of 9 DcSOD genes, comprising 2 FeSODs, 2 MnSODs, and 5 Cu/ZnSODs, are identified in the complete genome of D. carota, which are dispersed in five out of nine chromosomes. Based on phylogenetic analysis, SOD proteins from D. carota were categorized into two main classes (Cu/ZnSODs and MnFeSODs). It was predicted that members of the same subgroups have the same subcellular location. The phylogenetic analysis was further validated by sequence motifs, exon–intron structure, and 3D protein structures, with each subgroup having a similar gene and protein structure. Cis-regulatory elements responsive to abiotic stresses were identified in the promoter region, which may contribute to their differential expression. Based on RNA-seq data, tissue-specific expression revealed that DcCSD2 had higher expression in both xylem and phloem. Moreover, DcCSD2 was differentially expressed in dark stress. All SOD genes were subjected to qPCR analysis after cold, heat, salt, or drought stress imposition. SODs are antioxidants and play a critical role in removing reactive oxygen species (ROS), including hydrogen peroxide (H2O2). DcSODs were docked with H2O2 to evaluate their binding. The findings of this study will serve as a basis for further functional insights into the DcSOD gene family.

Genetic Diversity in Natural Populations of Rhodiola Species of Different Adaptation Strategies

“…The mechanism of action of proteins encoding superoxide dismutase genes comprises the successive reduction and oxidation of the metal of the active center of the enzyme by superoxide anion radicals, avoiding the conversion of the superoxide anion radical into a harmful hydroxyl radical and therefore having a favorable effect on plant growth and development and their response to abiotic stress [ 42 , 48 , 49 ]. At the same time, the regulatory regions, intron sequences, and coding portions of the SOD genes had the most variability.…”

Comparative genomics analysis of pheophorbide a oxygenase (PAO) genes in eight pyrus genomes and their regulatory role in multiple stress responses in Chinese pear (Pyrus bretschneideri)

“…The 3D structures of eight Dangshansuli PAOs (DaPAO1-DaPAO8) were predicted using AlphaFold2 ( https://alphafold.ebi.ac.uk/ ) ( Jumper et al, 2021 ). The accuracy of these predicted structures was assessed through the SAVES server ( https://saves.mbi.ucla.edu/ ) ( Zameer et al, 2022 ) and MolProbity ( http://molprobity.biochem.duke.edu/ ) ( Davis et al, 2007 ). Finally, the UCSF ChimeraX software ( Goddard et al, 2018 ) was utilized to visualize these structures ( Neupane et al, 2018 ; Zia et al, 2024 ).…”

Genome-wide identification and expression profiling of two-component system (TCS) genes in Brassica oleracea in response to shade stress

“…The expression level of genes was estimated using the cufflinks tool, which provided FPKM values. FPKM values were used to generate a heatmap ( Azeem et al, 2022 ; Zameer et al, 2022 ). Heatmap was generated using TBtools ( Chen et al, 2018 ).…”