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Xu Z, Xiao Y, Guo J, Lv Z, Chen W. Relevance and regulation of alternative splicing in plant secondary metabolism: current understanding and future directions. HORTICULTURE RESEARCH 2024; 11:uhae173. [PMID: 39135731 PMCID: PMC11317897 DOI: 10.1093/hr/uhae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/14/2024] [Indexed: 08/15/2024]
Abstract
The secondary metabolism of plants is an essential life process enabling organisms to navigate various stages of plant development and cope with ever-changing environmental stresses. Secondary metabolites, abundantly found in nature, possess significant medicinal value. Among the regulatory mechanisms governing these metabolic processes, alternative splicing stands out as a widely observed post-transcriptional mechanism present in multicellular organisms. It facilitates the generation of multiple mRNA transcripts from a single gene by selecting different splicing sites. Selective splicing events in plants are widely induced by various signals, including external environmental stress and hormone signals. These events ultimately regulate the secondary metabolic processes and the accumulation of essential secondary metabolites in plants by influencing the synthesis of primary metabolites, hormone metabolism, biomass accumulation, and capillary density. Simultaneously, alternative splicing plays a crucial role in enhancing protein diversity and the abundance of the transcriptome. This paper provides a summary of the factors inducing alternative splicing events in plants and systematically describes the progress in regulating alternative splicing with respect to different secondary metabolites, including terpenoid, phenolic compounds, and nitrogen-containing compounds. Such elucidation offers critical foundational insights for understanding the role of alternative splicing in regulating plant metabolism and presents novel avenues and perspectives for bioengineering.
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Affiliation(s)
- Zihan Xu
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ying Xiao
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jinlin Guo
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611103, China
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611130, China
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611103, China
| | - Zongyou Lv
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wansheng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
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Meng R, Li Z, Kang X, Zhang Y, Wang Y, Ma Y, Wu Y, Dong S, Li X, Gao L, Chu X, Yang G, Yuan X, Wang J. High Overexpression of SiAAP9 Leads to Growth Inhibition and Protein Ectopic Localization in Transgenic Arabidopsis. Int J Mol Sci 2024; 25:5840. [PMID: 38892028 PMCID: PMC11172308 DOI: 10.3390/ijms25115840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Amino acid permeases (AAPs) transporters are crucial for the long-distance transport of amino acids in plants, from source to sink. While Arabidopsis and rice have been extensively studied, research on foxtail millet is limited. This study identified two transcripts of SiAAP9, both of which were induced by NO3- and showed similar expression patterns. The overexpression of SiAAP9L and SiAAP9S in Arabidopsis inhibited plant growth and seed size, although SiAAP9 was found to transport more amino acids into seeds. Furthermore, SiAAP9-OX transgenic Arabidopsis showed increased tolerance to high concentrations of glutamate (Glu) and histidine (His). The high overexpression level of SiAAP9 suggested its protein was not only located on the plasma membrane but potentially on other organelles, as well. Interestingly, sequence deletion reduced SiAAP9's sensitivity to Brefeldin A (BFA), and SiAAP9 had ectopic localization on the endoplasmic reticulum (ER). Protoplast amino acid uptake experiments indicated that SiAAP9 enhanced Glu transport into foxtail millet cells. Overall, the two transcripts of SiAAP9 have similar functions, but SiAAP9L shows a higher colocalization with BFA compartments compared to SiAAP9S. Our research identifies a potential candidate gene for enhancing the nutritional quality of foxtail millet through breeding.
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Affiliation(s)
- Ru Meng
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Zhipeng Li
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Xueting Kang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Yujia Zhang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Yiru Wang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Yuchao Ma
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Yanfeng Wu
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Shuqi Dong
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong 030801, China
| | - Xiaorui Li
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong 030801, China
| | - Lulu Gao
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Xiaoqian Chu
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Guanghui Yang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
| | - Xiangyang Yuan
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong 030801, China
| | - Jiagang Wang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (R.M.); (Z.L.); (X.K.); (Y.Z.); (Y.W.); (Y.M.); (Y.W.); (S.D.); (X.L.); (L.G.); (X.C.); (G.Y.)
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Jinzhong 030801, China
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Wang H, Guo Y, Hao X, Zhang W, Xu Y, He W, Li Y, Cai S, Zhao X, Song X. Alternative Splicing for Leucanthemella linearis NST1 Contributes to Variable Abiotic Stress Resistance in Transgenic Tobacco. Genes (Basel) 2023; 14:1549. [PMID: 37628601 PMCID: PMC10454811 DOI: 10.3390/genes14081549] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Leucanthemella linearis is a marsh plant in the family Compositae. It has good water and moisture resistance and ornamental properties, which makes it one of the important materials for chrysanthemum breeding and genetic improvement. The NST1 (NAC secondary wall enhancement factor 1) gene is associated with the thickening of the secondary walls of fiber cells in the plant ducts and the secondary xylem and plays an important role in plant stress resistance. In this study, two variable spliceosomes of the NST1 gene were identified from a chrysanthemum plant by using bioinformatics, qRT-PCR, transgene, and paraffin section methods to explore the molecular mechanism of the variable splicing of NST1 under abiotic stress. The results show that only three amino acids were found to be different between the two LlNST1 variants. After being treated with salt, drought, and low temperatures, analysis of the expression levels of the LlNST1 and LlNST1.1 genes in Ll showed that LlNST1.1 could respond to low temperatures and salt stress and had a weak response to drought stress. However, the expression level of LlNST1 under the three treatments was lower than that of LlNST1.1. LlNST1 transgenic tobacco showed increased saline-alkali resistance and low-temperature resistance at the seedling stage. LlNST1.1 transgenic tobacco also showed enhanced saline-alkali resistance and drought resistance at the seedling stage. In conclusion, the functions of the two variable spliceosomes of the NST1 gene are very different under abiotic stress. Therefore, this study verified the function of the variable spliceosome of NST1 and improved the stress resistance of the chrysanthemum plant under examination by regulating the expression of the NST protein, which lays a material foundation for the improvement of plant stress resistance materials and has important significance for the study of the resistance of chrysanthemum plants to abiotic stress.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xuebin Song
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.W.); (Y.G.); (X.H.); (W.Z.); (Y.X.); (W.H.); (Y.L.); (S.C.); (X.Z.)
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Hajibarat Z, Saidi A. Senescence-associated proteins and nitrogen remobilization in grain filling under drought stress condition. J Genet Eng Biotechnol 2022; 20:101. [PMID: 35819732 PMCID: PMC9276853 DOI: 10.1186/s43141-022-00378-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022]
Abstract
Background Plants use escape strategies including premature senescence and leaf reduction to cope in response to drought stress, which in turn reduces plant leaves and photosynthesis. This strategy allows the new generation (seeds) to survive under drought but, plants experience more yield loss during stress condition. The amount of damage caused by drought stress is compensated by the expression of genes involved in regulating leaf aging. Leaf senescence alters the expression of thousands of genes and ultimately affecting grain protein content, grain yield, and nitrogen utilization efficiency. Also, under drought stress, nitrogen in the soil will not become as much available and causes the beginning and acceleration of the senescence process of leaves. The main body of the abstract This review identified proteins signaling and functional proteins involved in senescence. Further, transcription factors and cell wall degradation enzymes (proteases) related to senescence during drought stress were surveyed. We discuss the regulatory pathways of genes as a result of the degradation of proteins during senescence process. Senescence is strongly influenced by plant hormones and environmental factors including the availability of nitrogen. During maturity or drought stress, reduced nitrogen uptake can cause nitrogen to be remobilized from leaves and stems to seeds, eventually leading to leaf senescence. Under these conditions, genes involved in chloroplast degradation and proteases show increased expression. The functional (proteases) and regulatory proteins such as protein kinases and phosphatases as well as transcription factors (AP2/ERF, NAC, WRKY, MYB, and bZIP) are involved in leaf senescence and drought stress. Short conclusion In this review, senescence-associated proteins involved in leaf senescence and regulatory and functional proteins in response to drought stress during grain filling were surveyed. The present study predicts on the role of nitrogen transporters, transcription factors and regulatory genes involved in the late stages of plant growth with the aim of understanding their mechanisms of action during grain filling stage. For a better understanding, the relevant evidence for the balance between grain filling and protein breakdown during grain filling in cereals is presented.
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Affiliation(s)
- Zohreh Hajibarat
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
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Platel R, Lucau-Danila A, Baltenweck R, Maia-Grondard A, Chaveriat L, Magnin-Robert M, Randoux B, Trapet P, Halama P, Martin P, Hilbert JL, Höfte M, Hugueney P, Reignault P, Siah A. Bioinspired Rhamnolipid Protects Wheat Against Zymoseptoria tritici Through Mainly Direct Antifungal Activity and Without Major Impact on Leaf Physiology. FRONTIERS IN PLANT SCIENCE 2022; 13:878272. [PMID: 35720601 PMCID: PMC9204090 DOI: 10.3389/fpls.2022.878272] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Rhamnolipids (RLs), glycolipids biosynthesized by the Pseudomonas and Burkholderia genera, are known to display various activities against a wide range of pathogens. Most previous studies on RLs focused on their direct antimicrobial activity, while only a few reports described the mechanisms by which RLs induce resistance against phytopathogens and the related fitness cost on plant physiology. Here, we combined transcriptomic and metabolomic approaches to unravel the mechanisms underlying RL-induced resistance in wheat against the hemibiotrophic fungus Zymoseptoria tritici, a major pathogen of this crop. Investigations were carried out by treating wheat plants with a bioinspired synthetic mono-RL with a 12-carbon fatty acid tail, dodecanoyl α/β-L-rhamnopyranoside (Rh-Est-C12), under both infectious and non-infectious conditions to examine its potential wheat defense-eliciting and priming bioactivities. Whereas, Rh-Est-C12 conferred to wheat a significant protection against Z. tritici (41% disease severity reduction), only a slight effect of this RL on wheat leaf gene expression and metabolite accumulation was observed. A subset of 24 differentially expressed genes (DEGs) and 11 differentially accumulated metabolites (DAMs) was scored in elicitation modalities 2, 5, and 15 days post-treatment (dpt), and 25 DEGs and 17 DAMs were recorded in priming modalities 5 and 15 dpt. Most changes were down-regulations, and only a few DEGs and DAMs associated with resistance to pathogens were identified. Nevertheless, a transient early regulation in gene expression was highlighted at 2 dpt (e.g., genes involved in signaling, transcription, translation, cell-wall structure, and function), suggesting a perception of the RL by the plant upon treatment. Further in vitro and in planta bioassays showed that Rh-Est-C12 displays a significant direct antimicrobial activity toward Z. tritici. Taken together, our results suggest that Rh-Est-C12 confers protection to wheat against Z. tritici through direct antifungal activity and, to a lesser extent, by induction of plant defenses without causing major alterations in plant metabolism. This study provides new insights into the modes of action of RLs on the wheat-Z. tritici pathosystem and highlights the potential interest in Rh-Est-C12, a low-fitness cost molecule, to control this pathogen.
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Affiliation(s)
- Rémi Platel
- Joint Research Unit 1158 BioEcoAgro, Junia, Univ. Lille, Univ. Liège, UPJV, Univ. Artois, ULCO, INRAE, Lille, France
| | - Anca Lucau-Danila
- Joint Research Unit 1158 BioEcoAgro, Junia, Univ. Lille, Univ. Liège, UPJV, Univ. Artois, ULCO, INRAE, Lille, France
| | | | | | - Ludovic Chaveriat
- Univ. Artois, UniLasalle, ULR 7519–Unité Transformations and Agroressources, Béthune, France
| | - Maryline Magnin-Robert
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université du Littoral Côte d'Opale, Calais, France
| | - Béatrice Randoux
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université du Littoral Côte d'Opale, Calais, France
| | - Pauline Trapet
- Joint Research Unit 1158 BioEcoAgro, Junia, Univ. Lille, Univ. Liège, UPJV, Univ. Artois, ULCO, INRAE, Lille, France
| | - Patrice Halama
- Joint Research Unit 1158 BioEcoAgro, Junia, Univ. Lille, Univ. Liège, UPJV, Univ. Artois, ULCO, INRAE, Lille, France
| | - Patrick Martin
- Univ. Artois, UniLasalle, ULR 7519–Unité Transformations and Agroressources, Béthune, France
| | - Jean-Louis Hilbert
- Joint Research Unit 1158 BioEcoAgro, Junia, Univ. Lille, Univ. Liège, UPJV, Univ. Artois, ULCO, INRAE, Lille, France
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | | | - Philippe Reignault
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université du Littoral Côte d'Opale, Calais, France
| | - Ali Siah
- Joint Research Unit 1158 BioEcoAgro, Junia, Univ. Lille, Univ. Liège, UPJV, Univ. Artois, ULCO, INRAE, Lille, France
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Mondal R, Madhurya K, Saha P, Chattopadhyay SK, Antony S, Kumar A, Roy S, Roy D. Expression profile, transcriptional and post-transcriptional regulation of genes involved in hydrogen sulphide metabolism connecting the balance between development and stress adaptation in plants: a data-mining bioinformatics approach. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:602-617. [PMID: 34939301 DOI: 10.1111/plb.13378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Recent research focused on novel aspects of sulphur and sulphur-containing molecules in fundamental plant processes has highlighted the importance of these compounds. Currently, the focus has shifted to the efficacy of hydrogen sulphide (H2 S) as signalling compounds that regulate different development and stress mitigation in plants. Accordingly, we used an in silico approach to study the differential expression patterns of H2 S metabolic genes at different growth/development stages and their tissue-specific expression patterns under a range of abiotic stresses. Moreover, to understand the multilevel regulation of genes involved in H2 S metabolism, we performed computation-based promoter analysis, alternative splice variant analysis, prediction of putative miRNA targets and co-expression network analysis. Gene expression analysis suggests that H2 S biosynthesis is highly influenced by developmental and stress stimuli. The functional annotation of promoter structures reveales a wide range of plant hormone and stress responsive cis-regulatory elements (CREs) that regulate H2 S metabolism. Co-expression analysis suggested that genes involved in H2 S metabolism are also associated with different metabolic processes. In this data-mining study, the primary focus was to understand the genetic architecture governing pathways of H2 S metabolism in different cell compartments under various developmental and stress signalling cascades. The present study will help to understand the genetic architecture of H2 S metabolism via cysteine metabolism and the functional roles of these genes in development and stress tolerance mechanisms.
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Affiliation(s)
- R Mondal
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, India
| | - K Madhurya
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, India
| | - P Saha
- Department of Botany, Durgapur Government College, Durgapur, India
| | - S K Chattopadhyay
- Directorate of Distance Education, Vidyasagar University Midnapore (West), Midnapore, India
| | - S Antony
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, India
| | - A Kumar
- Host Plant Division, Central Muga Eri Research & Training Institute, Central Silk Board, Ministry of Textile, Govt. of India, Jorhat, India
| | - S Roy
- Department of Botany, Santipur College, Nadia, India
| | - D Roy
- Department of Botany, Seth Anandram Jaipuria College, Kolkata, India
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Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions. Sci Rep 2022; 12:9153. [PMID: 35650424 PMCID: PMC9160059 DOI: 10.1038/s41598-022-13158-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022] Open
Abstract
Drought is the most detrimental abiotic stress to sugarcane production. Nevertheless, transcriptomic analyses remain scarce for field-grown plants. Here we performed comparative transcriptional profiling of two contrasting sugarcane genotypes, ‘IACSP97-7065’ (drought-sensitive) and ‘IACSP94-2094’ (drought-tolerant) grown in a drought-prone environment. Physiological parameters and expression profiles were analyzed at 42 (May) and 117 (August) days after the last rainfall. The first sampling was done under mild drought (soil water potential of −60 kPa), while the second one was under severe drought (soil water potential of −75 kPa). Microarray analysis revealed a total of 622 differentially expressed genes in both sugarcane genotypes under mild and severe drought stress, uncovering about 250 exclusive transcripts to ‘IACSP94-2094’ involved in oxidoreductase activity, transcriptional regulation, metabolism of amino acids, and translation. Interestingly, the enhanced antioxidant system of ‘IACSP94-2094’ may protect photosystem II from oxidative damage, which partially ensures stable photochemical activity even after 117 days of water shortage. Moreover, the tolerant genotype shows a more extensive set of responsive transcription factors, promoting the fine-tuning of drought-related molecular pathways. These results help elucidate the intrinsic molecular mechanisms of a drought-tolerant sugarcane genotype to cope with ever-changing environments, including prolonged water deficit, and may be useful for plant breeding programs.
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Distinctive Physio-Biochemical Properties and Transcriptional Changes Unfold the Mungbean Cultivars Differing by Their Response to Drought Stress at Flowering Stage. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Mungbean is a nutritionally and economically important pulse crop cultivated around Asia, mainly in India. The crop is sensitive to drought at various developmental stages of its growing period. However, there is limited or almost no research on a comparative evaluation of mung-bean plants at the flowering stage under drought conditions. Hence, the aim of this research was to impose the drought stress on two mungbean cultivars VRM (Gg) 1 and CO6 at the flowering stage and assess the physio-biochemical and transcriptional changes. After imposing the drought stress, we found that VRM (Gg) 1 exhibited a low reduction in physiological traits (Chlorophyll, relative water content, and plant dry mass) and high proline content than CO6. Additionally, VRM (Gg) 1 has a low level of H2O2 and MDA contents and higher antioxidant enzymes (SOD, POD, and CAT) activity than CO6 during drought stress. The transcriptional analysis of photosynthesis (PS II-PsbP, PS II-LHC, PS I-PsaG/PsaK, and PEPC 3), antioxidant (SOD 2, POD, CAT 2), and drought-responsive genes (HSP-90, DREB2C, NAC 3 and AREB 2) show that VRM (Gg) 1 had increased transcripts more than CO6 under drought stress. Taken together, VRM (Gg) 1 had a better photosynthetic performance which resulted in fewer reductions in chlorophyll, relative water content, and plant dry mass during drought stress. In addition, higher antioxidative enzyme activities led to lower H2O2 and MDA levels, limiting oxidative damage in VRM (Gg) 1. This was positively correlated with increased transcripts of photosynthesis and antioxidant-related genes in VRM (Gg) 1. Further, the increased transcripts of drought-responsive genes indicate that VRM (Gg) 1 has a better genetic basis against drought stress than CO6. These findings help to understand the mungbean response to drought stress and will aid in the development of genotypes with greater drought tolerance by utilizing natural genetic variants.
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Yuan Y, Yang X, Feng M, Ding H, Khan MT, Zhang J, Zhang M. Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response. BMC Genomics 2021; 22:622. [PMID: 34404342 PMCID: PMC8371785 DOI: 10.1186/s12864-021-07689-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. RESULTS A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genomic sequence and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. CONCLUSIONS This is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane.
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Affiliation(s)
- Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Mengfan Feng
- State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Hongyan Ding
- State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | | | - Jisen Zhang
- Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
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10
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Aleem M, Raza MM, Haider MS, Atif RM, Ali Z, Bhat JA, Zhao T. Comprehensive RNA-seq analysis revealed molecular pathways and genes associated with drought tolerance in wild soybean (Glycine soja Sieb. and Zucc.). PHYSIOLOGIA PLANTARUM 2021; 172:707-732. [PMID: 32984966 DOI: 10.1111/ppl.13219] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Drought stress at the germination stage is an important environmental stress limiting crop yield. Hence, our study investigated comparative root transcriptome profiles of four contrasting soybean genotypes viz., drought-tolerant (PI342618B/DTP and A214/DTL) and drought-sensitive (NN86-4/DSP and A195/DSL) under drought stress using RNA-Seq approach. A total of 4850 and 6272 differentially expressed genes (DEGs) were identified in tolerant (DTP and DTL) and sensitive (DSP and DSL) genotypes, respectively. Principle component analysis (PCA) and correlation analysis revealed higher correlation between DTP and DTL. Both gene ontology (GO) and MapMan analyses showed that the drought response was enriched in DEGs associated with water and auxin transport, cell wall/membrane, antioxidant activity, catalytic activity, secondary metabolism, signaling and transcription factor (TF) activities. Out of 981 DEGs screened from above terms, only 547 showed consistent opposite expression between contrasting genotypes. Twenty-eight DEGs of 547 were located on Chr.08 rich in QTLs and "Hotspot regions" associated with drought stress, and eight of them showed non-synonymous single nucleotide polymorphism. Hence, 10 genes (including above eight genes plus two hub genes) were predicated as possible candidates regulating drought tolerance, which needs further functional validation. Overall, the transcriptome profiling provided in-depth understanding about the genetic mechanism and candidate genes underlying drought tolerance in soybean.
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Affiliation(s)
- Muqadas Aleem
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad M Raza
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Muhammad S Haider
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Rana M Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Javaid A Bhat
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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11
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Nawae W, Shearman JR, Tangphatsornruang S, Punpee P, Yoocha T, Sangsrakru D, Naktang C, Sonthirod C, Wirojsirasak W, Ukoskit K, Sriroth K, Klomsa-Ard P, Pootakham W. Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome. PeerJ 2020; 8:e9608. [PMID: 33240580 PMCID: PMC7676377 DOI: 10.7717/peerj.9608] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/05/2020] [Indexed: 01/17/2023] Open
Abstract
Sugarcane contributes 80% of global sugar production and to bioethanol generation for the bioenergy industry. Its productivity is threatened by drought that can cause up to 60% yield loss. This study used RNA-Seq to gain a better understanding of the underlying mechanism by which drought-tolerant sugarcane copes with water stress. We compared gene expression in KPS01-12 (drought-tolerant genotype) and UT12 (drought-sensitive genotype) that have significantly different yield loss rates under drought conditions. We treated KPS01-12 and UT12 with mild and moderate water stress and found differentially expressed genes in various biological processes. KPS01-12 had higher expression of genes that were involved in water retention, antioxidant secondary metabolite biosynthesis, and oxidative and osmotic stress response than UT12. In contrast, the sensitive genotype had more down-regulated genes that were involved in photosynthesis, carbon fixation and Calvin cycle than the tolerant genotype. Our obtained expression profiles suggest that the tolerant sugarcane has a more effective genetic response than the sensitive genotype at the initiation of drought stress. The knowledge gained from this study may be applied in breeding programs to improve sugarcane production in drought conditions.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Jeremy R Shearman
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Prapat Punpee
- Mitr Phol Sugarcane Research Center Co., Ltd., Phu Khiao, Chaiyaphum, Thailand
| | - Thippawan Yoocha
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Warodom Wirojsirasak
- Mitr Phol Sugarcane Research Center Co., Ltd., Phu Khiao, Chaiyaphum, Thailand.,Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Campus), Pathum Thani, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Campus), Pathum Thani, Thailand
| | - Klanarong Sriroth
- Mitr Phol Sugarcane Research Center Co., Ltd., Phu Khiao, Chaiyaphum, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Sugarcane Research Center Co., Ltd., Phu Khiao, Chaiyaphum, Thailand
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
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12
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Javed T, Shabbir R, Ali A, Afzal I, Zaheer U, Gao SJ. Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement. PLANTS (BASEL, SWITZERLAND) 2020; 9:E491. [PMID: 32290272 PMCID: PMC7238037 DOI: 10.3390/plants9040491] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023]
Abstract
Increasing vulnerability of crops to a wide range of abiotic and biotic stresses can have a marked influence on the growth and yield of major crops, especially sugarcane (Saccharum spp.). In response to various stresses, plants have evolved a variety of complex defense systems of signal perception and transduction networks. Transcription factors (TFs) that are activated by different pathways of signal transduction and can directly or indirectly combine with cis-acting elements to modulate the transcription efficiency of target genes, which play key regulators for crop genetic improvement. Over the past decade, significant progresses have been made in deciphering the role of plant TFs as key regulators of environmental responses in particular important cereal crops; however, a limited amount of studies have focused on sugarcane. This review summarizes the potential functions of major TF families, such as WRKY, NAC, MYB and AP2/ERF, in regulating gene expression in the response of plants to abiotic and biotic stresses, which provides important clues for the engineering of stress-tolerant cultivars in sugarcane.
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Affiliation(s)
- Talha Javed
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
- Seed Physiology Lab., Department of Agronomy, University of Agriculture, Faisalabad-38040, Pakistan;
| | - Rubab Shabbir
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
- Seed Physiology Lab., Department of Agronomy, University of Agriculture, Faisalabad-38040, Pakistan;
| | - Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
| | - Irfan Afzal
- Seed Physiology Lab., Department of Agronomy, University of Agriculture, Faisalabad-38040, Pakistan;
| | - Uroosa Zaheer
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
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