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.

Keywords: abiotic stress; carrot; comparative modeling; expression pattern; molecular docking; phylogeny; reactive oxygen species; superoxide dismutase.

Figure 1

Symbolic domain structure of Daucus carota superoxide dismutases.

Figure 2

Phylogenetic tree analysis of SOD family genes of D. carota and other species. In this tree, different symbols are representing different plants: green square for D. carota, powder-blue star for Oryza sativa, red circle for Arabidopsis thaliana, blue triangle for Camellia sinensis, and pink triangle for Salvia miltiorrhiza. Three different strips represent the different groups. The phylogenetic tree was constructed using the MEGA7 maximum likelihood method.

Figure 3

(A) Conserved motif and (B) gene structure analysis of SOD family genes in D. carota.

Figure 4

Syntenic analysis of SOD family genes in A. thaliana, D. carota, G. max, S. lycopersicum, and S. bicolor. Blocks are representing the chromosomes and the duplicated genes are connected by lines.

Figure 5

Splice site analysis of 9 members of D. carota SOD gene family. Exons colored the same in each group conserved in length in that particular group.

Figure 6

The 3D structure modeling of DcSOD proteins. These are the final models predicted with different colors indicating different helices, sheets, and domains.

Figure 7

H₂O₂ docked against 9 DcSODs. The different color background of the diagram represents protein residues, conserved residues of the protein are also labeled, and the prominent red color represents the ligand (H₂O₂).

Figure 8

(A) Cis-regulatory elements in upstream 1 kb region of D. carota SOD coding sequences. Each element is given a specific color and depicts the presence of that element in genes. (B) Expression analysis of DcSOD gene family. Heatmap expression profiles of the genes in xylem and phloem tissues. (C) Expression analysis of DcSODs in roots under light/dark stress.

Figure 9

Relative qRT-PCR expression verification of DcSODs genes under cold, heat, salt, and drought stress. In nontreated plants, one (01) was the default expression value for each gene. Significant change in expression is indicated by an asterisk (p < 0.05 = > *, p < 0.01 = >**).