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Shao L, Li L, Huang X, Fu Y, Yang D, Li C, Yang J. Identification of C2H2 zinc finger genes through genome-wide association study and functional analyses of LkZFPs in response to stresses in Larix kaempferi. BMC PLANT BIOLOGY 2023; 23:298. [PMID: 37268918 DOI: 10.1186/s12870-023-04298-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/19/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND C2H2 zinc finger proteins (C2H2-ZFPs), one of the largest transcription factors, play a variety of roles in plant development and growth as well as stress response. While, the evolutionary history and expression profile of the C2H2-ZFP genes in Larix kaempferi (LkZFPs) have not been reported so far. RESULTS In this study, the whole genome of the LkZFPs was identified and characterized, including physicochemical properties, phylogenetic relationships, conservative motifs, the promoter cis-elements and Gene Ontology (GO) annotation. We identified 47 LkZFPs and divided them into four subfamilies based on phylogenetic analysis and conserved motifs. Subcellular localization prediction showed that most of the LkZFPs were located in the nucleus. Promoter cis-element analysis suggested that the LkZFPs may be involved in the regulation of stress responses. Moreover, Real-time quantitative PCR (RT-qPCR) results showed that Q-type LkZFP genes were involved in the response to abiotic stress, such as salt, drought and hormone stresses. Subcellular localization results showed that LkZFP7 and LkZFP37 were located in the nucleus, LkZFP32 was located in both cytoplasm and nucleus. CONCLUSION The identification and functional analysis of LkZFPs suggested that some LkZFP genes might play important roles in coping with both biological and abiotic stresses. These results could further increase understanding of the function of the LkZFPs, and provide some research direction and theoretical support.
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Affiliation(s)
- Liying Shao
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Lu Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Xun Huang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yanrui Fu
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Da Yang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Jingli Yang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Yu W, Kong G, Chao J, Yin T, Tian H, Ya H, He L, Zhang H. Genome-wide identification of the rubber tree superoxide dismutase ( SOD) gene family and analysis of its expression under abiotic stress. PeerJ 2022; 10:e14251. [PMID: 36312747 PMCID: PMC9610661 DOI: 10.7717/peerj.14251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
Background The rubber tree (Hevea brasiliensis) is the only species capable of producing high-quality natural rubber for commercial use, and is often subjected to various abiotic stresses in non-traditional rubber plantation areas. Superoxide dismutase (SOD) is a vital metalloenzyme translated by a SOD gene family member and acts as a first-line of protection in plant cells by catalysing the disproportionation of reactive oxygen species (ROS) to produce H2O2 and O2. However, the SOD gene family is not reported in rubber trees. Methods Here, we used hidden markov model (HMM) and BLASTP methods to identify SOD genes in the H. brasiliensis genome. Phylogenetic tree, conserved motifs, gene structures, cis elements, and gene ontology annotation (GO) analyses were performed using MEGA 6.0, MEME, TBtools, PlantCARE, and eggNOG database, respectively. HbSOD gene expression profiles were analysed using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results We identified nine HbSOD genes in the rubber tree genome, including five HbCSDs, two HbFSDs, and two HbMSDs. Phylogenetic relationship analysis classified the SOD proteins from the rubber tree and other related species into three subfamilies. The results of gene structure and conserved motif analysis illustrated that most HbSOD genes have similar exon-intron numbers and conserved motifs in the same evolutionary branch. Five hormone-related, four stress-related, and light-responsive elements were detected in the HbSODs' promoters. HbSODs were expressed in different tissues, gradually increased with leaf development, and were abundantly expressed in mature leaves. HbCSD2 and HbCSD4 was significantly upregulated under low and high temperatures, and salt stress, except for HbCSD2, by heat. Furthermore, most HbSOD genes were significantly upregulated by drought, except HbMSD2. These findings imply that these genes may play vital roles in rubber tree stress resistance. Our results provide a basis for further studies on the functions of HbSOD genes in rubber trees and stress response mechanisms.
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Affiliation(s)
- Wencai Yu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China,Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Guanghong Kong
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Jinquan Chao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan Province, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China
| | - Hai Tian
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Huajin Ya
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Ligang He
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China
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Zameer R, Fatima K, Azeem F, ALgwaiz HIM, Sadaqat M, Rasheed A, Batool R, Shah AN, Zaynab M, Shah AA, Attia KA, AlKahtani MDF, Fiaz S. Genome-Wide Characterization of Superoxide Dismutase (SOD) Genes in Daucus carota: Novel Insights Into Structure, Expression, and Binding Interaction With Hydrogen Peroxide (H 2O 2) Under Abiotic Stress Condition. FRONTIERS IN PLANT SCIENCE 2022; 13:870241. [PMID: 35783965 PMCID: PMC9246500 DOI: 10.3389/fpls.2022.870241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/08/2022] [Indexed: 05/27/2023]
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.
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Affiliation(s)
- Roshan Zameer
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hussah I. M. ALgwaiz
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Asima Rasheed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Riffat Batool
- Department of Botany, GC Women University, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Anis Ali Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Muneera D. F. AlKahtani
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
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Foliar application of nano-zinc oxide crystals improved zinc biofortification in cauliflower (Brassica oleracea L. var. botrytis). APPLIED NANOSCIENCE 2022. [DOI: 10.1007/s13204-022-02455-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Zhang Y, Li G, Si L, Liu N, Gao T, Yang Y. Effects of tea polyphenols on the activities of antioxidant enzymes and the expression of related gene in the leaves of wheat seedlings under salt stress. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:65447-65461. [PMID: 34319523 DOI: 10.1007/s11356-021-15492-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Longchun 30, a new wheat variety, was used to investigate seedling growth, element absorption, and antioxidant response under 150 mM NaCl and tea polyphenols (TP) (25 and 100 mg L-1) treatments alone or in combination, thus revealing TP-alleviating mechanism on the salt damage to plants. 150 mM NaCl stress alone inhibited the seedling growth, increased sodium content and reactive oxygen species (ROS) accumulation, but reduced potassium (K) and calcium (Ca) levels at different culture times, thus resulting in the oxidative damage to the leaves. Even though 25 or 100 mg L-1 TP treatment alone led to the significant increases of O2·- and H2O2 generation, TP-treated leaves exhibited the reduction of relative electrical conductivity and no change of malondialdehyde content. Moreover, high TP concentration alone stimulated the seedling growth. In addition, the activities and gene expression of superoxide dismutase, catalase, and peroxidase (POD) as well as diamine oxidase and polyamine oxidase were changed to different degrees due to NaCl or TP treatment alone. Further study showed that the presence of 25 or 100 mg L-1 TP promoted the growth, increased K+ and Ca2+ contents, and reduced O2·- and H2O2 accumulation in salt-stressed wheat seedlings. Taken together, salinity-inhibitory effect on the growth of wheat seedlings might be associated with salt-induced imbalance of element content and the increase of oxidative damage resulting from ROS accumulation, while the application of TP effectively alleviated salinity-inhibitory effect on the seedling growth and improved the tolerance of wheat seedlings to salt environment, which might be associated with the increases of K+ and Ca2+ contents as well as the reduction of oxidative damage in the leaves of wheat seedlings under NaCl and TP treatment in combination.
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Affiliation(s)
- Ya Zhang
- School of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Guiying Li
- School of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Lianbang Si
- School of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Na Liu
- School of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Tianpeng Gao
- The Engineering Research Center of Mining Pollution Treatment and Ecological Restoration of Gansu Province, Lanzhou, 730070, People's Republic of China
- College of Biological and Environmental Engineering, Xi`an University, Xi`an, 710065, People's Republic of China
| | - Yingli Yang
- School of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China.
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Iqbal Qureshi AM, Sofi MU, Dar NA, Khan MH, Mahdi SS, Dar ZA, Bangroo S, El-Serehy HA, Hefft DI, Popescu SM. Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa. Saudi J Biol Sci 2021; 28:5526-5537. [PMID: 34588862 PMCID: PMC8459115 DOI: 10.1016/j.sjbs.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/18/2021] [Accepted: 08/01/2021] [Indexed: 01/17/2023] Open
Abstract
Superoxide Dismutase SODs are defense associated proteins that detoxify ROS and primarily serve as scavengers. They have been described in numerous plant species, but their in-depth characterization in Brassica rapa has not been reported. Therefore, the present investigation on genome wide study of SOD gene family was conducted to identify BrSOD genes, their domain-based organization, gene structure analysis, phylogenetic analysis, intron-exon structure of genes and expression analysis. The sequence characterization of Super oxide dismutase gene family in Brassica rapa, their syntenic associateship of conserved motifs and phylogenetic correlationship, prediction of cis-elements and determing the expression analysis in distinct tissues namely plant callus, root, stem, leaf, flower, and silique under abiotic conditions have been analysed using different software’s. The study on SOD gene family identified 17 BrSOD genes which were grouped into eight BrCu-ZnSODs and nine BrFe-MnSODs domain-based organization. Furthermore, the conserved character of BrSODs were confirmed by intron-exon organisation, motif arrangements and domain architectural investigations. Expression analysis using RNA Sequence data of different developmental stages proclaimed that genes were manifested in all six tissues with an exception of BrCu-ZnSOD3, which was not manifested in roots; however, whose transcript was detected in all other tested tissues. The study has genome wide insight into the occurrence and functional specifications of BrSOD gene family in Brassica rapa that can be potentially utilized in breeding program for resilience to climate change and abiotic stresses tolerance Brassica variety.
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Affiliation(s)
- Asif M Iqbal Qureshi
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Mehraj Uddin Sofi
- HMAARI, Leh, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - N A Dar
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - M H Khan
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - S S Mahdi
- Division of Agronomy, FoA Wadura, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Zahoor A Dar
- DARS, Rangreth, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Shabir Bangroo
- Division of Soil Sciences, FoH, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Hamed A El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyad, 11451, Saudi Arabia
| | - Daniel Ingo Hefft
- University Centre Reaseheath, Reaseheath College, Nantwich CW5 6DF, UK
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, 200585, Romania
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7
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Zhang G, Ding Q, Wei B. Genome-wide identification of superoxide dismutase gene families and their expression patterns under low-temperature, salt and osmotic stresses in watermelon and melon. 3 Biotech 2021; 11:194. [PMID: 33927985 DOI: 10.1007/s13205-021-02726-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/10/2021] [Indexed: 12/01/2022] Open
Abstract
The growth and development of watermelon and melon are affected by abiotic stresses such as cold, salinity and drought. Plant superoxide dismutase (SOD) proteins exerted great effects on plant growth, development and response to abiotic stresses. However, little is known about the characteristics of watermelon and melon SOD gene families and their expression patterns under abiotic stresses. In this study, the genome-wide identification of SOD genes and their expression patterns under abiotic stresses has been done in watermelon and melon. Seven SODs were identified in watermelon and melon, respectively. Chromosome location indicated that the SODs were dispersedly distributed on 4-6 chromosomes. Almost all the SOD proteins contained 300 amino acids or less and the intron numbers of SODs ranged from 5 to 7. On the basis of phylogenetic analysis, the SODs were classified into six sub-groups which was also verified by similar motif composition, gene structure and sub-cellular location. Gene ontology analysis displayed that many SOD proteins participated in binding, catalytic, antioxidant activity and stimulus-response. Cis-regulatory elements related to stresses and hormones were found in the promoters of the SODs. Based on the quantitative real-time PCR, most of CmSOD and ClSOD genes showed obvious up-regulation under low-temperature, NaCl and PEG6000 treatments. The abiotic stress-responsive SOD genes were identified to improve watermelon and melon tolerance against abiotic stresses. This was a preliminary study to describe the genome-wide analysis of SOD gene family in watermelon and melon, and the results would facilitate further study of gene cloning and functional verification of SOD genes response to abiotic stresses in watermelon and melon. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02726-7.
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Affiliation(s)
- Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu China
| | - Qian Ding
- College of Floriculture, Weifang Engineering Vocational College, Qingzhou, 262500 Shandong China
| | - Bingqiang Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu China
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Qin L, Chen E, Li F, Yu X, Liu Z, Yang Y, Wang R, Zhang H, Wang H, Liu B, Guan Y, Ruan Y. Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet ( Setaria italica L.). Int J Mol Sci 2020; 21:ijms21228520. [PMID: 33198267 PMCID: PMC7696101 DOI: 10.3390/ijms21228520] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.
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Affiliation(s)
- Ling Qin
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China;
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Erying Chen
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Feifei Li
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Xiao Yu
- College of Life Science, Shandong Normal University, Jinan 250014, China;
| | - Zhenyu Liu
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Yanbing Yang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Runfeng Wang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Huawen Zhang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Hailian Wang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Bin Liu
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Yan’an Guan
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
- College of Life Science, Shandong Normal University, Jinan 250014, China;
- Correspondence: (Y.G.); (Y.R.); Tel.: +86-531-6665-8115 (Y.G.); +86-731-8467-3684 (Y.R.)
| | - Ying Ruan
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China;
- Correspondence: (Y.G.); (Y.R.); Tel.: +86-531-6665-8115 (Y.G.); +86-731-8467-3684 (Y.R.)
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Genome-wide identification and expression analysis of the superoxide dismutase (SOD) gene family in Salvia miltiorrhiza. Gene 2020; 742:144603. [PMID: 32198126 DOI: 10.1016/j.gene.2020.144603] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/19/2022]
Abstract
Adverse environmental conditions, such as salinity, cold, drought, heavy metals, and pathogens affect the yield and quality of Salvia miltiorrhiza, a well-known medicinal plant used for the treatment of cardiovascular and cerebrovascular diseases. Superoxide dismutase (SOD), a key enzyme of antioxidant system in plants, plays a vital role in protecting plants against various biotic and abiotic stresses via scavenging the reactive oxygen species produced by organisms. However, little is known about the SOD gene family in S. miltiorrhiza. In this study, eight SOD genes, including three Cu/Zn-SODs, two Fe-SODs and three Mn-SODs, were identified in the S. miltiorrhiza genome. Their gene structures, promoters, protein features, phylogenetic relationships, and expression profiles were comprehensively investigated. Gene structure analysis implied that most SmSODs have different introns/exons distrbution patterns. Many cis-elements related to different stress responses or plant hormones were found in the promoter of each SmSOD. Expression profile analysis indicated that SmSODs exhibited diverse responses to cold, salt, drought, heavy metal, and plant hormones. Additionally, 31 types of TFs regulating SmSODs were predicted and analyzed. These findings provided valuable information for further researches on the functions and applications of SmSODs in S. miltiorrhiza growth and adaptation to stress.
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Zhou C, Zhu C, Fu H, Li X, Chen L, Lin Y, Lai Z, Guo Y. Genome-wide investigation of superoxide dismutase (SOD) gene family and their regulatory miRNAs reveal the involvement in abiotic stress and hormone response in tea plant (Camellia sinensis). PLoS One 2019; 14:e0223609. [PMID: 31600284 PMCID: PMC6786557 DOI: 10.1371/journal.pone.0223609] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023] Open
Abstract
Superoxide dismutases (SODs), as a family of metalloenzymes related to the removal of reactive oxygen species (ROS), have not previously been investigated at genome-wide level in tea plant. In this study, 10 CsSOD genes were identified in tea plant genome, including 7 Cu/Zn-SODs (CSDs), 2 Fe-SODs (FSDs) and one Mn-SOD (MSD), and phylogenetically classified in three subgroups, respectively. Physico-chemical characteristic, conserved motifs and potential protein interaction analyses about CsSOD proteins were carried out. Exon-intron structures and codon usage bias about CsSOD genes were also examined. Exon-intron structures analysis revealed that different CsSOD genes contained various number of introns. On the basis of the prediction of regulatory miRNAs of CsSODs, a modification 5’ RNA ligase-mediated (RLM)-RACE was performed and validated that csn-miR398a-3p-1 directly cleaves CsCSD4. By prediction of cis-acting elements, the expression patterns of 10 CsSOD genes and their regulatory miRNAs were detected under cold, drought, exogenous methyl jasmonate (MeJA) and gibberellin (GA3) treatments. The results showed that most of CsSODs except for CsFSD2 were induced under cold stress and CsCSDs may play primary roles under drought stress; exogenous GA3 and MeJA could also stimulated/inhibited distinct CsSODs at different stages. In addition, we found that csn-miR398a-3p-1 negatively regulated the expression of CsCSD4 may be a crucial regulatory mechanism under cold stress. This study provides a certain basis for the studies about stress resistance in tea plants, even provide insight into comprehending the classification, evolution, diverse functions and influencing factors of expression patterns for CsSOD genes.
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Affiliation(s)
- Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Tea Science of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail:
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Wang W, Liu D, Chen D, Cheng Y, Zhang X, Song L, Hu M, Dong J, Shen F. MicroRNA414c affects salt tolerance of cotton by regulating reactive oxygen species metabolism under salinity stress. RNA Biol 2019; 16:362-375. [PMID: 30676211 PMCID: PMC6380294 DOI: 10.1080/15476286.2019.1574163] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 10/27/2022] Open
Abstract
Salinity stress is a major abiotic stress affecting the productivity and fiber quality of cotton. Although reactive oxygen species (ROS) play critical roles in plant stress responses, their complex molecular regulatory mechanism under salinity stress is largely unknown in cotton, especially microRNA (miRNA)-mediated regulation of superoxide dismutase gene expression. Here, we report that a cotton iron superoxide dismutase gene GhFSD1 and the cotton miRNA ghr-miR414c work together in response to salinity stress. The miRNA ghr-miR414c targets the coding sequence region of GhFSD1, inhibiting expression of transcripts of this antioxidase gene, which represents the first line of defense against stress-induced ROS. Expression of GhFSD1 was induced by salinity stress. Under salinity stress, ghr-miR414c showed expression patterns opposite to those of GhFSD1. Ectopic expression of GhFSD1 in Arabidopsis conferred salinity stress tolerance by improving primary root growth and biomass, whereas Arabidopsis constitutively expressing ghr-miR414c showed hypersensitivity to salinity stress. Silencing GhFSD1 in cotton caused an excessive hypersensitive phenotype to salinity stress, whereas overexpressing miR414c decreased the expression of GhFSD1 and increased sensitivity to salinity stress, yielding a phenotype similar to that of GhFSD1-silenced cotton. Taken together, our results demonstrated that ghr-miR414c was involved in regulation of plant response to salinity stress by targeting GhFSD1 transcripts. This study provides a new strategy and method for plant breeding in order to improve plant salinity tolerance.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Dan Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Dongdong Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Yingying Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Lirong Song
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Mengjiao Hu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Jie Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
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