Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa

Verma, Deepika; Lakhanpal, Neha; Singh, Kashmir

doi:10.1186/s12864-019-5593-5

Cited by 96 publications

(59 citation statements)

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“…Evolutionary tree results showed that the SOD proteins from different plants can be divided into two major clades (Fig. 1), which is consistent with the previous classification of SODs in many plants (Verma, Lakhanpal & Singh, 2019;Wang et al, 2017). The ZmSODs showed a close clustering relationship with proximal species, indicating that this gene family was relatively conserved in evolution.…”

Section: Discussionsupporting

confidence: 88%

“…Previous studies showed that the expression patterns of SOD family gene members in plants are related to various stress conditions. Elements in the promoter regions of plants can respond to stress conditions and improve gene transcription level, thereby improving SOD enzyme activity and enhancing plant resistance to stress (Verma, Lakhanpal & Singh, 2019;Wang et al, 2017;Zhou et al, 2017). Here, we identified many promoter cis-elements that may respond to biotic and abiotic stresses (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Superoxide dismutase (SOD) is the first line of defense in the antioxidant enzyme system and can reduce toxic effects of ROS by catalyzing the dismutation of superoxide radicals to H 2 O 2 and O 2 (Pan et al, 2020;Xu et al, 2013). Many SOD genes have been studied in plants (Verma, Lakhanpal & Singh, 2019;Wang et al, 2017Wang et al, , 2018a. Depending on the metal cofactor, plant SOD enzymes can be divided into three groups: copper-zinc superoxide dismutase (Cu/ZnSOD), iron-superoxide dismutase (FeSOD), and manganese superoxide dismutase (MnSOD) (Fink & Scandalios, 2002;Li et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

Zang

Shang

et al. 2020

PeerJ

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Superoxide dismutases (SODs) serve as the first line of defense in the plant antioxidant enzyme system, and play a primary role in the removal of reactive oxygen species (ROS). However, our understanding of the functions of the SOD family in Zostera marina is limited. In this study, a systematic analysis was conducted on the characteristics of the SOD genes in Z. marina at the whole-genome level. Five SOD genes were identified, consisting of two Cu/ZnSODs, two FeSODs, and one MnSOD. Phylogenetic analysis showed that ZmSOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs). Sequence motifs, gene structure, and the 3D-modeled protein structures further supported the phylogenetic analysis, with each subgroup having similar motifs, exon-intron structures, and protein structures. Additionally, several cis-elements were identified that may respond to biotic and abiotic stresses. Transcriptome analysis revealed expression diversity of ZmSODs in various tissues. Moreover, qRT-PCR analysis showed that the expression level of most ZmSOD genes trended to decreased expression with the increase of temperature, indicating that heat stress inhibits expression of ZmSODs and may result in reduced ability of ZmSODs to scavenge ROS. Our results provide a basis for further functional research on the SOD gene family in Z. marina, which will help to determine the molecular mechanism of ZmSOD genes in response to environmental stress.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

Zang

Shang

et al. 2020

PeerJ

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“…Antioxidant enzymes SOD play significantly roles in plant response to abiotic stresses by reducing the molecular oxygen and hydrogen peroxide in plant cells. The plant SOD family genes have been identified and characterized in some species at the genome-wide level (Feng et al, 2016;Verma, Lakhanpal & Singh, 2019). However, the roles of soybean SOD family genes in regulating various abiotic stresses, especially alkaline stress, are rarely reported.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Duanmu

Qiao

et al. 2020

PeerJ

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Background Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported. Methods We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR. Results In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1–2), FeSODs (GmFSD1–5) and Cu/ZnSODs (GmCSD1–6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.

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“…For example, there are 7 SODS in Arabidopsis [33], 10 SODs in Cakile maritima [34], and 4 SODs in pepper [35]. A total of 29 and 18 SOD genes have been identified in Brassica juncea and Brassica rapa, respectively [36]. The evolutionary relationship study among plants need more works.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis Reveals Cu/Zn SODs Acting as Hub Genes of SODs in Hylocereus undatus Induced by Trypsin during Storage

Pang

Liu

et al. 2020

Antioxidants

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It has been revealed by us that superoxide scavenging is a new activity of trypsin. In this study, the synergistic mechanisms of trypsin and superoxide dismutases (SODs) were evaluated in Hylocereus undatus (pitaya). Trypsin significantly improved the storage quality of H. undatus, including weight loss impediment and decrease of cellular injury. The regulatory mechanisms of 16 SOD genes by trypsin were revealed using transcriptomic analysis on H. undatus. Results revealed that important physiological metabolisms, such as antioxidant activities or metal ion transport were induced, and defense responses were inhibited by trypsin. Furthermore, the results of protein-protein interaction (PPI) networks showed that besides the entire ROS network, the tiny SODs sub-network was also a scale-free network. Cu/Zn SODs acted as the hub that SODs synergized with trypsin during the storage of H. undatus.Trypsin is a widely used protease. It has been confirmed that trypsin significantly impacts on the free radical scavenging activities of flavonoids [8]. Our previous results also showed that trypsin scavenges superoxide anions (O 2 • − ) and protects cells [9].In the area of phytopathology, transcriptomic analysis has been successful used on lots of plants [10][11][12][13]. However, few of transcriptomic works have been focused on the preservation of fruits. The mechanisms of betalain biosynthesis have been investigated in H. undatus [2], and the concision analysis of antioxidant system induced by trypsin has also been investigated in our previous paper [14]. Considering the superoxide scavenging activity of trypsin, the function and synergistic mechanisms of trypsin with SODs impact on the quality of H. undatus during storage is an interesting work. The mechanisms of postharvest quality of fruits still need more works.Protein-protein interaction (PPI) networks analyses help us to figure out the regulatory mechanisms of proteins [15]. Plugins of Cytoscape, including NetworkAnalyzer, Molecular Complex Detection (MCODE), and cytoHubba, could score and rank the nodes or obtain clusters in the PPI network [16].In the current work, the regulatory mechanisms of trypsin on the H. undatus by cooperating with SODs were investigated. The changes in expression of SODs of H. undatus peels were analyzed. Analyses of gene ontology (GO) and KEGG enrichment of ROS or SOD related genes were performed, and the PPI network of ROS related genes and sub-network of SODs and their first neighbors were constructed. The hub genes of SODs regulated by trypsin during storage were further screened by cytoHubba and MCODE of cytoscape.

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Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa

Cited by 96 publications

References 61 publications

Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Transcriptomic Analysis Reveals Cu/Zn SODs Acting as Hub Genes of SODs in Hylocereus undatus Induced by Trypsin during Storage

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