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Chen A, Li J, Wang H, Zhao P. Identification and Expression Profile of NCED Genes in Arachis hypogaea L. during Drought Stress. Int J Mol Sci 2024; 25:5564. [PMID: 38791604 PMCID: PMC11122452 DOI: 10.3390/ijms25105564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024] Open
Abstract
Peanut (Arachis hypogaea L.) is an important crop that provides essential proteins and oils for human and animal consumption. 9-cis-epoxycarotenoid dioxygenase (NCED) have been found can play a vital role in abscisic acid (ABA) biosynthesis and may be a response to drought stress. Until now, in Arachis hypogaea, no information about the NCED gene family has been reported and the importance of NCED-related drought tolerance is unclear. In this study, eight NCED genes in Arachis hypogaea, referred to as AhNCEDs, are distributed across eight chromosomes, with duplication events in AhNCED1 and AhNCED2, AhNCED3 and AhNCED4, and AhNCED6 and AhNCED7. Comparative analysis revealed that NCED genes are highly conserved among plant species, including Pisum sativum, Phaseolus vulgaris, Glycine max, Arabidopsis thaliana, Gossypium hirsutum, and Oryza sativa. Further promoter analysis showed AhNCEDs have ABA-related and drought-inducible elements. The phenotyping of Arachis hypogaea cultivars NH5 and FH18 demonstrated that NH5 is drought-tolerant and FH18 is drought-sensitive. Transcriptome expression analysis revealed the differential regulation of AhNCEDs expression in both NH5 and FH18 cultivars under drought stress. Furthermore, compared to the Arachis hypogaea cultivar FH18, the NH5 exhibited a significant upregulation of AhNCED1/2 expression under drought. To sum up, this study provides an insight into the drought-related AhNCED genes, screened out the potential candidates to regulate drought tolerance and ABA biosynthesis in Arachis hypogaea.
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Affiliation(s)
- Ao Chen
- Guangzhou Dublin International College of Life Sciences and Technology, South China Agricultural University, Guangzhou 510642, China;
| | - Jingyan Li
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (J.L.); (H.W.)
| | - Heping Wang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (J.L.); (H.W.)
| | - Puyan Zhao
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (J.L.); (H.W.)
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Sami A, Haider MZ, Shafiq M, Sadiq S, Ahmad F. Genome-wide identification and in-silico expression analysis of CCO gene family in sunflower (Helianthus annnus) against abiotic stress. PLANT MOLECULAR BIOLOGY 2024; 114:34. [PMID: 38568355 PMCID: PMC10991017 DOI: 10.1007/s11103-024-01433-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/21/2024] [Indexed: 04/05/2024]
Abstract
Carotenoid cleavage oxygenases (CCOs) enzymes play an important role in plant growth and development by producing a wide array of apocarotenoids and their derivatives. These compounds are vital for colouring flowers and fruits and synthesizing plant hormones such as abscisic acid and strigolactones. Despite their importance, the gene family responsible for CCO enzymes in sunflowers has not been identified. In this study, we identify the CCO genes of the sunflower plant to fill this knowledge gap. Phylogenetic and synteny analysis indicated that the Helianthus annnus CCO (HaCCO) genes were conserved in different plant species and they could be divided into three subgroups based on their conserved domains. Analysis using MEME tool and multiple sequence alignment identified conserved motifs in the HaCCO gene sequence. Cis-regulatory elements (CREs) analysis of the HaCCO genes indicated the presence of various responsive elements related to plant hormones, development, and responses to both biotic and abiotic stresses. This implies that these genes may respond to plant hormones, developmental cues, and drought stress, offering potential applications in the development of more resistant crops. Genes belonging to the 9-cis-epoxy carotenoid dioxygenases (NCED) subgroups predominantly exhibited chloroplast localization, whereas the genes found in other groups are primarily localized in the cytoplasm. These 21 identified HaCCOs were regulated by 60 miRNAs, indicating the crucial role of microRNAs in gene regulation in sunflowers. Gene expression analysis under drought stress revealed significant up-regulation of HaNCED16 and HaNCED19, genes that are pivotal in ABA hormone biosynthesis. During organ-specific gene expression analysis, HaCCD12 and HaCCD20 genes exhibit higher activity in leaves, indicating a potential role in leaf pigmentation. This study provides a foundation for future research on the regulation and functions of the CCO gene family in sunflower and beyond. There is potential for developing molecular markers that could be employed in breeding programs to create new sunflower lines resistant to biotic and abiotic stresses.
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Affiliation(s)
- Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, P.O BOX. 54590, Pakistan
| | - Muhammad Zeeshan Haider
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, P.O BOX. 54590, Pakistan
| | - Muhammad Shafiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, P.O BOX. 54590, Pakistan
| | - Saleh Sadiq
- Institute of Biochemistry, Biotechnology, and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Farooq Ahmad
- Sustainable Forest Management Research Institute (iuFOR), University of Valladolid and INIA, Avenida de Madrid, Palencia, 34004, Spain.
- Department of Vegetable Production and Forest Resources, University of Valladolid, Avda. de Madrid, Palencia, 34004, Spain.
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Pasandideh Arjmand M, Samizadeh Lahiji H, Mohsenzadeh Golfazani M, Biglouei MH. Evaluation of protein's interaction and the regulatory network of some drought-responsive genes in Canola under drought and re-watering conditions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1085-1102. [PMID: 37829706 PMCID: PMC10564702 DOI: 10.1007/s12298-023-01345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/14/2023]
Abstract
Drought stress is one of the most important environmental stresses that severely limits the growth and yield of Canola. The re-watering can compensate for the damage caused by drought stress. Investigation of protein's interaction of genes involved in important drought-responsive pathways and their regulatory network by microRNAs (miRNAs) under drought and re-watering conditions are helpful approaches to discovering drought-stress tolerance and recovery mechanisms. In this study, the protein's interaction and functional enrichment analyses of glycolysis, pentose phosphate, glyoxylate cycle, fatty acid biosynthesis, heat shock factor main genes, and the regulatory network of key genes by miRNAs were investigated by in silico analysis. Then, the relative expression of key genes and their related miRNAs were investigated in tolerant and susceptible genotypes of Canola under drought and re-watering conditions by Real-time PCR technique. The bna-miR156b/c/g, bna-miR395d/e/f, bna-miR396a, and all the studied key genes except HSFA1E and PK showed changes in expression levels in one or both genotypes after re-watering. The PPC1 and HSFB2B expression decreased, whereas the MLS and CAC3 expression increased in both genotypes under re-watering treatment after drought stress. It could cause the regulation of oxaloacetate production, the increase of the glyoxylate cycle, lipid biosynthesis, and the reduction of the negative regulation of HSFs under re-watering conditions. It seems that PPC1, G6PD2, MLS, CAC3, and HSFB2B were involved in the recovery mechanisms after drought stress of Canola. They were regulated by drought-responsive miRNAs to respond appropriately to drought stress. Therefore, regulating these genes could be important in plant recovery mechanisms. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01345-1.
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Affiliation(s)
- Maryam Pasandideh Arjmand
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | | | - Mohammad Hassan Biglouei
- Department of Water Engineering, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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Shoko R, Magogo B, Pullen J, Mudziwapasi R, Ndlovu J. Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress. Commun Integr Biol 2023; 16:2193000. [PMID: 36969388 PMCID: PMC10038031 DOI: 10.1080/19420889.2023.2193000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
In order to understand the mechanism of desiccation tolerance in Xerophyta schlechteri, we carried out an in silico study to identify hub proteins and functional modules in the nuclear proteome of the leaves. Protein-protein interaction networks were constructed and analyzed from proteome data obtained from Abdalla and Rafudeen. We constructed networks in Cytoscape using the GeneMania software and analyzed them using a Network Analyzer. Functional enrichment analysis of key proteins in the respective networks was done using GeneMania network enrichment analysis, and GO (Gene Ontology) terms were summarized using REViGO. Also, community analysis of differentially expressed proteins was conducted using the Cytoscape Apps, GeneMania and ClusterMaker. Functional modules associated with the communities were identified using an online tool, ShinyGO. We identified HSP 70-2 as the super-hub protein among the up-regulated proteins. On the other hand, 40S ribosomal protein S2-3 (a protein added by GeneMANIA) was identified as a super-hub protein associated with the down-regulated proteins. For up-regulated proteins, the enriched biological process terms were those associated with chromatin organization and negative regulation of transcription. In the down-regulated protein-set, terms associated with protein synthesis were significantly enriched. Community analysis identified three functional modules that can be categorized as chromatin organization, anti-oxidant activity and metabolic processes.
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Affiliation(s)
- Ryman Shoko
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- CONTACT Ryman Shoko Department of Biology, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
| | - Babra Magogo
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Jessica Pullen
- Department of Animal Science and Rangeland Management, Lupane State University, Lupane, Zimbabwe
| | - Reagan Mudziwapasi
- Department of Research and Innovation, Midlands State University, Gweru, Zimbabwe
| | - Joice Ndlovu
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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Raza A, Salehi H, Rahman MA, Zahid Z, Madadkar Haghjou M, Najafi-Kakavand S, Charagh S, Osman HS, Albaqami M, Zhuang Y, Siddique KHM, Zhuang W. Plant hormones and neurotransmitter interactions mediate antioxidant defenses under induced oxidative stress in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:961872. [PMID: 36176673 PMCID: PMC9514553 DOI: 10.3389/fpls.2022.961872] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/03/2022] [Indexed: 05/24/2023]
Abstract
Due to global climate change, abiotic stresses are affecting plant growth, productivity, and the quality of cultivated crops. Stressful conditions disrupt physiological activities and suppress defensive mechanisms, resulting in stress-sensitive plants. Consequently, plants implement various endogenous strategies, including plant hormone biosynthesis (e.g., abscisic acid, jasmonic acid, salicylic acid, brassinosteroids, indole-3-acetic acid, cytokinins, ethylene, gibberellic acid, and strigolactones) to withstand stress conditions. Combined or single abiotic stress disrupts the normal transportation of solutes, causes electron leakage, and triggers reactive oxygen species (ROS) production, creating oxidative stress in plants. Several enzymatic and non-enzymatic defense systems marshal a plant's antioxidant defenses. While stress responses and the protective role of the antioxidant defense system have been well-documented in recent investigations, the interrelationships among plant hormones, plant neurotransmitters (NTs, such as serotonin, melatonin, dopamine, acetylcholine, and γ-aminobutyric acid), and antioxidant defenses are not well explained. Thus, this review discusses recent advances in plant hormones, transgenic and metabolic developments, and the potential interaction of plant hormones with NTs in plant stress response and tolerance mechanisms. Furthermore, we discuss current challenges and future directions (transgenic breeding and genome editing) for metabolic improvement in plants using modern molecular tools. The interaction of plant hormones and NTs involved in regulating antioxidant defense systems, molecular hormone networks, and abiotic-induced oxidative stress tolerance in plants are also discussed.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hajar Salehi
- Laboratory of Plant Cell Biology, Department of Biology, Bu-Ali Sina University, Hamedan, Iran
| | - Md Atikur Rahman
- Grassland and Forage Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Zainab Zahid
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Maryam Madadkar Haghjou
- Department of Biology, Plant Physiology, Faculty of Science, Lorestan University, Khorramabad, Iran
| | - Shiva Najafi-Kakavand
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Hany S. Osman
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Mohammed Albaqami
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Yuhui Zhuang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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