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Zhang X, Luo Z, Marand AP, Yan H, Jang H, Bang S, Mendieta JP, Minow MAA, Schmitz RJ. A spatially resolved multi-omic single-cell atlas of soybean development. Cell 2024:S0092-8674(24)01273-X. [PMID: 39742806 DOI: 10.1016/j.cell.2024.10.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/26/2024] [Accepted: 10/31/2024] [Indexed: 01/04/2025]
Abstract
Cis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored the conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DNA binding with one finger 11 (DOF11) motif that were co-upregulated in late peripheral endosperm, and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.
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Affiliation(s)
- Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Ziliang Luo
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Alexandre P Marand
- Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Sohyun Bang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - John P Mendieta
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Mark A A Minow
- Department of Genetics, University of Georgia, Athens, GA, USA
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2
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Jing T, Xing Q, Shi Y, Liu X, Müller-Xing R. Depletion of Gibberellin Signaling Up-Regulates LBD16 Transcription and Promotes Adventitious Root Formation in Arabidopsis Leaf Explants. Int J Mol Sci 2024; 25:13340. [PMID: 39769105 PMCID: PMC11678481 DOI: 10.3390/ijms252413340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 11/24/2024] [Accepted: 12/03/2024] [Indexed: 01/11/2025] Open
Abstract
Adventitious root (AR) formation in plants originates from non-root organs such as leaves and hypocotyls. Auxin signaling is essential for AR formation, but the roles of other phytohormones are less clear. In Arabidopsis, at least two distinct mechanisms can produce ARs, either from hypocotyls as part of the general root architecture or from wounded organs during de novo root regeneration (DNRR). In previous reports, gibberellin acid (GA) appeared to play reverse roles in both types of ARs, since GA treatment blocks etiolation-induced AR formation from hypocotyls, whereas GA synthesis and signaling mutants apparently displayed reduced DNRR from detached leaves. In order to clarify this contradiction, we employed the GA biosynthesis inhibitor paclobutrazol (PBZ) and found that PBZ had positive effects on both types of AR formation in Arabidopsis. Consistently, GA treatment had negative effects on both AR formation mechanisms, while loss of GA synthesis and signaling promoted DNRR under our conditions. Our results show that PBZ treatment can rescue declined AR formation in difficult-to-root leaf explants such as erecta receptor mutants. Furthermore, transcriptional profiling revealed that PBZ treatment altered GA, brassinosteroids, and auxin responses, which included the up-regulation of LBD16 that is well known for its pivotal role in AR initiation.
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Affiliation(s)
- Tingting Jing
- College of Life Science, Northeast Forestry University, Harbin 150040, China (X.L.)
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China;
- Plant Epigenetics and Development, Lushan Botanical Garden, Chinese Academy of Sciences, Nanchang 330114, China
| | - Qian Xing
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China;
- Plant Epigenetics and Development, Lushan Botanical Garden, Chinese Academy of Sciences, Nanchang 330114, China
- College of Life Science, Nanchang University, Nanchang 330047, China
| | - Yunfeng Shi
- College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xuemei Liu
- College of Life Science, Northeast Forestry University, Harbin 150040, China (X.L.)
| | - Ralf Müller-Xing
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China;
- Plant Epigenetics and Development, Lushan Botanical Garden, Chinese Academy of Sciences, Nanchang 330114, China
- College of Life Science, Nanchang University, Nanchang 330047, China
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3
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Chen Y, Zhang H, Chen W, Gao Y, Xu K, Sun X, Huo L. The role of ethylene in the regulation of plant response mechanisms to waterlogging stress. PLANT CELL REPORTS 2024; 43:278. [PMID: 39531178 DOI: 10.1007/s00299-024-03367-9] [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: 05/06/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024]
Abstract
Waterlogging stands as a common environmental challenge, significantly affecting plant growth, yield, and, in severe cases, survival. In response to waterlogging stress, plants exhibit a series of intricate physiologic, metabolic, and morphologic adaptations. Notably, the gaseous phytohormone ethylene is rapidly accumulated in the plant submerged tissues, assuming an important regulatory factor in plant-waterlogging tolerance. In this review, we summarize recent advances in research on the mechanisms of ethylene in the regulation of plant responses to waterlogging stress. Recent advances found that both ethylene biosynthesis and signal transduction make indispensable contributions to modulating plant adaptation mechanisms to waterlogged condition. Ethylene was also discovered to play an important role in plant physiologic metabolic responses to waterlogging stress, including the energy mechanism, morphologic adaptation, ROS regulation and interactions with other phytohormones. The comprehensive exploration of ethylene and its associated genes provides valuable insights into the precise strategies to leverage ethylene metabolism for enhancing plant resistance to waterlogging stress.
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Affiliation(s)
- Yunyun Chen
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Hao Zhang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Wenxin Chen
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Yongbin Gao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Kai Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Liuqing Huo
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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Yu X, An J, Liang J, Yang W, Zeng Z, Zhang M, Wu H, Liu S, Cao X. Comparative Analysis of Two Soybean Cultivars Revealed Tolerance Mechanisms Underlying Soybean Adaptation to Flooding. Curr Issues Mol Biol 2024; 46:12442-12456. [PMID: 39590333 PMCID: PMC11592816 DOI: 10.3390/cimb46110739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 10/25/2024] [Accepted: 10/28/2024] [Indexed: 11/28/2024] Open
Abstract
Flooding stress poses a significant challenge to soybean cultivation, impacting plant growth, development, and ultimately yield. In this study, we investigated the responses of two distinct soybean cultivars: flooding-tolerant Nanxiadou 38 (ND38) and flooding-sensitive Nanxiadou 45 (ND45). To achieve this, healthy seedlings were cultivated with the water surface consistently maintained at 5 cm above the soil surface. Our objective was to elucidate the physiological and molecular adaptations of the two cultivars. Under flooding stress, seedlings of both cultivars exhibited significant dwarfing and a notable decrease in root length. While there were no significant differences in the dry weight of aboveground shoots, the dry weight of underground shoots in ND38 was strikingly decreased following flooding. Additionally, total chlorophyll content decreased significantly following flooding stress, indicating impaired photosynthetic performance of the cultivars. Moreover, malondialdehyde (MDA) levels increased significantly after flooding, particularly in the ND45 cultivar, suggesting heightened oxidative stress. Expression analysis of methylation and demethylation genes indicated that MET1 and DME play crucial roles in response to flooding stress in soybeans. Meanwhile, analysis of the hemoglobin family (GLBs), aquaporin family (AQPs), glycolytic pathway-related genes, and NAC transcription factor-related genes identified GLB1-1 and GLB1-2, GLB2-2, PIP2-6, PIP2-7, TIP2-2, TIP4-1, TIP5-1, Gm02G222400 (fructose-bisphosphate aldolase), Gm19G017200 (glucose-6-phosphate isomerase), and Gm04G213900 (alcohol dehydrogenase 1) as key contributors to flooding tolerance in both soybean cultivars. These findings provide crucial insights into the physiological and molecular mechanisms underlying flooding tolerance in soybeans, which could guide future molecular breeding strategies for the development of flooding-tolerant soybean cultivars.
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Affiliation(s)
- Xiaobo Yu
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China; (X.Y.); (J.A.); (J.L.); (W.Y.); (Z.Z.); (M.Z.); (H.W.)
- Sweetpotato and Leguminosae Germplasm Innovation and Utilization Key Laboratory of Sichuan Province, Nanchong 637000, China
| | - Jiangang An
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China; (X.Y.); (J.A.); (J.L.); (W.Y.); (Z.Z.); (M.Z.); (H.W.)
- Sweetpotato and Leguminosae Germplasm Innovation and Utilization Key Laboratory of Sichuan Province, Nanchong 637000, China
| | - Jianqiu Liang
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China; (X.Y.); (J.A.); (J.L.); (W.Y.); (Z.Z.); (M.Z.); (H.W.)
- Sweetpotato and Leguminosae Germplasm Innovation and Utilization Key Laboratory of Sichuan Province, Nanchong 637000, China
| | - Wenying Yang
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China; (X.Y.); (J.A.); (J.L.); (W.Y.); (Z.Z.); (M.Z.); (H.W.)
- Sweetpotato and Leguminosae Germplasm Innovation and Utilization Key Laboratory of Sichuan Province, Nanchong 637000, China
| | - Zhaoqiong Zeng
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China; (X.Y.); (J.A.); (J.L.); (W.Y.); (Z.Z.); (M.Z.); (H.W.)
- Sweetpotato and Leguminosae Germplasm Innovation and Utilization Key Laboratory of Sichuan Province, Nanchong 637000, China
| | - Mingrong Zhang
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China; (X.Y.); (J.A.); (J.L.); (W.Y.); (Z.Z.); (M.Z.); (H.W.)
- Sweetpotato and Leguminosae Germplasm Innovation and Utilization Key Laboratory of Sichuan Province, Nanchong 637000, China
| | - Haiying Wu
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China; (X.Y.); (J.A.); (J.L.); (W.Y.); (Z.Z.); (M.Z.); (H.W.)
- Sweetpotato and Leguminosae Germplasm Innovation and Utilization Key Laboratory of Sichuan Province, Nanchong 637000, China
| | - Sichen Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China
| | - Xiaoning Cao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China
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Zhang Y, Zhang Y, Yu Z, Wang H, Ping B, Liu Y, Liang J, Ma F, Zou Y, Zhao T. Insights into ACO genes across Rosaceae: evolution, expression, and regulatory networks in fruit development. Genes Genomics 2024; 46:1209-1223. [PMID: 39141243 DOI: 10.1007/s13258-024-01551-5] [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: 02/01/2024] [Accepted: 07/05/2024] [Indexed: 08/15/2024]
Abstract
BACKGROUND ACO (1-aminocyclopropane-1-carboxylic acid) serves as a pivotal enzyme within the plant ethylene synthesis pathway, exerting influence over critical facets of plant biology such as flowering, fruit ripening, and seed development. OBJECTIVE This study aims to identify ACO genes from representative Rosaceae genomes, reconstruct their phylogenetic relationships by integrating synteny information, and investigate their expression patterns and networks during fruit development. METHODS we utilize a specialized Hidden Markov Model (HMM), crafted on the sequence attributes of ACO gene-encoded proteins, to systematically identify and analyze ACO gene family members across 12 representative species within the Rosaceae botanical family. Through transcriptome analysis, we delineate the expression patterns of ACO genes in six distinct Rosaceae fruits. RESULTS Our investigation reveals the presence of 62 ACO genes distributed among the surveyed Rosaceae species, characterized by hydrophilic proteins predominantly expressed within the cytoplasm. Phylogenetic analysis categorizes these ACO genes into three discernible classes, namely Class I, Class II, and Class III. Further scrutiny via collinearity assessment indicates a lack of collinearity relationships among these classes, highlighting variations in conserved motifs and promoter types within each class. Transcriptome analysis unveils significant disparities in both expression levels and trends of ACO genes in fruits exhibiting respiratory bursts compared to those that do not. Employing Weighted Gene Co-Expression Network Analysis (WGCNA), we discern that the co-expression correlation of ACO genes within loquat fruit notably differs from that observed in apples. Our findings, derived from Gene Ontology (GO) enrichment results, signify the involvement of ACO genes and their co-expressed counterparts in biological processes linked to terpenoid metabolism and carbohydrate synthesis in loquat. Moreover, our exploration of gene regulatory networks (GRN) highlights the potential pivotal role of the GNAT transcription factor (Ejapchr1G00010380) in governing the overexpression of the ACO gene (Ejapchr10G00001110) within loquat fruits. CONCLUSION The constructed HMM of ACO proteins offers a precise and systematic method for identifying plant ACO proteins, facilitating phylogenetic reconstruction. ACO genes from representative Rosaceae fruits exhibit diverse expression and regulative patterns, warranting further function characterizations.
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Affiliation(s)
- Yuxin Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yirong Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Ze Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Hanyu Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Boya Ping
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yunxiao Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jiakai Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Yangjun Zou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Tao Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
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Li L, Su Y, Xiang W, Huang G, Liang Q, Dun B, Zhang H, Xiao Z, Qiu L, Zhang J, Wu D. Transcriptomic network underlying physiological alterations in the stem of Myricaria laxiflora in response to waterlogging stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116991. [PMID: 39236657 DOI: 10.1016/j.ecoenv.2024.116991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/29/2024] [Accepted: 08/31/2024] [Indexed: 09/07/2024]
Abstract
Myricaria laxiflora is an endangered shrub plant with remarkable tolerance to waterlogging stress, however, little attention has been paid to understanding the underlying mechanisms. Here, physiological and transcriptomic approaches were applied to uncover the physiological and molecular reconfigurations in the stem of M. laxiflora in response to waterlogging stress. The accumulation of the contents of H2O2 and malonaldehyde (MDA) alongside increased activities of enzymes for scavenging the reactive oxygen species (ROS) in the stem of M. laxiflora were observed under waterlogging stress. The principal component analysis (PCA) of transcriptomes from five different timepoints uncovered PC1 counted for 17.3 % of total variations and separated the treated and non-treated samples. A total of 8714 genes in the stem of M. laxiflora were identified as differentially expressed genes (DEGs) under waterlogging stress, which could be assigned into two different subgroups with distinct gene expression patterns and biological functions. The DEGs involved in glycolysis were generally upregulated, whereas opposite results were observed for nitrogen uptake and the assimilation pathway. The contents of abscisic acid (ABA) and jasmonic acid (JA) were sharply decreased alongside the decreased mRNA levels of the genes involved in corresponding synthesis pathways upon waterlogging stress. A network centered by eight key transcription factors has been constructed, which uncovered the inhibited cell division processes in the stem of M. laxiflora upon waterlogging stress. Taken together, the obtained results showed that glycolysis, nitrogen metabolism and meristem activities played an important role in the stem of M. laxiflora in response to waterlogging stress.
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Affiliation(s)
- Linbao Li
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Yang Su
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Weibo Xiang
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Guiyun Huang
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Qianyan Liang
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Bicheng Dun
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Haibo Zhang
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Zhiqiang Xiao
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Liwen Qiu
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Jun Zhang
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China
| | - Di Wu
- Yangtze River Biodiversity Research Centre, China Three Gorges Corporation, Wuhan 443133, China; Hubei Key Laboratory of Rare Resource Plants in Three Gorges Reservoir Area, Yichang 443100, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Wuhan 100083, China.
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Yoo YH, Cho SY, Lee I, Kim N, Lee SK, Cho KS, Kim EY, Jung KH, Hong WJ. Characterization of the Regulatory Network under Waterlogging Stress in Soybean Roots via Transcriptome Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:2538. [PMID: 39339513 PMCID: PMC11435190 DOI: 10.3390/plants13182538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 09/30/2024]
Abstract
Flooding stress caused by climate change is a serious threat to crop productivity. To enhance our understanding of flooding stress in soybean, we analyzed the transcriptome of the roots of soybean plants after waterlogging treatment for 10 days at the V2 growth stage. Through RNA sequencing analysis, 870 upregulated and 1129 downregulated differentially expressed genes (DEGs) were identified and characterized using Gene Ontology (GO) and MapMan software (version 3.6.0RC1). In the functional classification analysis, "alcohol biosynthetic process" was the most significantly enriched GO term in downregulated DEGs, and phytohormone-related genes such as ABA, cytokinin, and gibberellin were upregulated. Among the transcription factors (TFs) in DEGs, AP2/ERFs were the most abundant. Furthermore, our DEGs encompassed eight soybean orthologs from Arabidopsis and rice, such as 1-aminocyclopropane-1-carboxylate oxidase. Along with a co-functional network consisting of the TF and orthologs, the expression changes of those genes were tested in a waterlogging-resistant cultivar, PI567343. These findings contribute to the identification of candidate genes for waterlogging tolerance in soybean, which can enhance our understanding of waterlogging tolerance.
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Affiliation(s)
- Yo-Han Yoo
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Seung-Yeon Cho
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea; (S.-Y.C.); (E.Y.K.)
| | - Inhye Lee
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Namgeol Kim
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Seuk-Ki Lee
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Kwang-Soo Cho
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Eun Young Kim
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea; (S.-Y.C.); (E.Y.K.)
| | - Ki-Hong Jung
- Graduate School of Green Bio-Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea;
| | - Woo-Jong Hong
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea; (S.-Y.C.); (E.Y.K.)
- Graduate School of Green Bio-Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea;
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8
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Hua D, Rao RY, Chen WS, Yang H, Shen Q, Lai NW, Yang LT, Guo J, Huang ZR, Chen LS. Adaptive Responses of Hormones to Nitrogen Deficiency in Citrus sinensis Leaves and Roots. PLANTS (BASEL, SWITZERLAND) 2024; 13:1925. [PMID: 39065452 PMCID: PMC11280038 DOI: 10.3390/plants13141925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Some citrus orchards in China often experience nitrogen (N) deficiency. For the first time, targeted metabolomics was used to examine N-deficient effects on hormones in sweet orange (Citrus sinensis (L.) Osbeck cv. Xuegan) leaves and roots. The purpose was to validate the hypothesis that hormones play a role in N deficiency tolerance by regulating root/shoot dry weight ratio (R/S), root system architecture (RSA), and leaf and root senescence. N deficiency-induced decreases in gibberellins and indole-3-acetic acid (IAA) levels and increases in cis(+)-12-oxophytodienoic acid (OPDA) levels, ethylene production, and salicylic acid (SA) biosynthesis might contribute to reduced growth and accelerated senescence in leaves. The increased ethylene formation in N-deficient leaves might be caused by increased 1-aminocyclopropanecarboxylic acid and OPDA and decreased abscisic acid (ABA). N deficiency increased R/S, altered RSA, and delayed root senescence by lowering cytokinins, jasmonic acid, OPDA, and ABA levels and ethylene and SA biosynthesis, increasing 5-deoxystrigol levels, and maintaining IAA and gibberellin homeostasis. The unchanged IAA concentration in N-deficient roots involved increased leaf-to-root IAA transport. The different responses of leaf and root hormones to N deficiency might be involved in the regulation of R/S, RSA, and leaf and root senescence, thus improving N use efficiency, N remobilization efficiency, and the ability to acquire N, and hence conferring N deficiency tolerance.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Li-Song Chen
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.H.); (R.-Y.R.); (W.-S.C.); (H.Y.); (Q.S.); (N.-W.L.); (L.-T.Y.); (J.G.); (Z.-R.H.)
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9
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Omelyanchuk NA, Lavrekha VV, Bogomolov AG, Dolgikh VA, Sidorenko AD, Zemlyanskaya EV. Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1905. [PMID: 39065433 PMCID: PMC11280061 DOI: 10.3390/plants13141905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.
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Affiliation(s)
- Nadya A. Omelyanchuk
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Viktoriya V. Lavrekha
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton G. Bogomolov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Vladislav A. Dolgikh
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksandra D. Sidorenko
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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10
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Zhang X, Luo Z, Marand AP, Yan H, Jang H, Bang S, Mendieta JP, Minow MA, Schmitz RJ. A spatially resolved multiomic single-cell atlas of soybean development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601616. [PMID: 39005400 PMCID: PMC11244997 DOI: 10.1101/2024.07.03.601616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Cis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.
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Affiliation(s)
- Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
- These authors contributed equally: Xuan Zhang, Ziliang Luo, Alexandre P. Marand
| | - Ziliang Luo
- Department of Genetics, University of Georgia, Athens, GA, USA
- These authors contributed equally: Xuan Zhang, Ziliang Luo, Alexandre P. Marand
| | - Alexandre P. Marand
- Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally: Xuan Zhang, Ziliang Luo, Alexandre P. Marand
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
- Current address: College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Sohyun Bang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | - Mark A.A. Minow
- Department of Genetics, University of Georgia, Athens, GA, USA
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11
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Rankenberg T, van Veen H, Sedaghatmehr M, Liao CY, Devaiah MB, Stouten EA, Balazadeh S, Sasidharan R. Differential leaf flooding resilience in Arabidopsis thaliana is controlled by ethylene signaling-activated and age-dependent phosphorylation of ORESARA1. PLANT COMMUNICATIONS 2024; 5:100848. [PMID: 38379284 PMCID: PMC11211547 DOI: 10.1016/j.xplc.2024.100848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/19/2024] [Accepted: 02/18/2024] [Indexed: 02/22/2024]
Abstract
The phytohormone ethylene is a major regulator of plant adaptive responses to flooding. In flooded plant tissues, ethylene quickly increases to high concentrations owing to its low solubility and diffusion rates in water. Ethylene accumulation in submerged plant tissues makes it a reliable cue for triggering flood acclimation responses, including metabolic adjustments to cope with flood-induced hypoxia. However, persistent ethylene accumulation also accelerates leaf senescence. Stress-induced senescence hampers photosynthetic capacity and stress recovery. In submerged Arabidopsis, senescence follows a strict age-dependent pattern starting with the older leaves. Although mechanisms underlying ethylene-mediated senescence have been uncovered, it is unclear how submerged plants avoid indiscriminate breakdown of leaves despite high systemic ethylene accumulation. We demonstrate that although submergence triggers leaf-age-independent activation of ethylene signaling via EIN3 in Arabidopsis, senescence is initiated only in old leaves. EIN3 stabilization also leads to overall transcript and protein accumulation of the senescence-promoting transcription factor ORESARA1 (ORE1) in both old and young leaves during submergence. However, leaf-age-dependent senescence can be explained by ORE1 protein activation via phosphorylation specifically in old leaves, independent of the previously identified age-dependent control of ORE1 via miR164. A systematic analysis of the roles of the major flooding stress cues and signaling pathways shows that only the combination of ethylene and darkness is sufficient to mimic submergence-induced senescence involving ORE1 accumulation and phosphorylation. Hypoxia, most often associated with flooding stress in plants, appears to have no role in these processes. Our results reveal a mechanism by which plants regulate the speed and pattern of senescence during environmental stresses such as flooding. Age-dependent ORE1 activity ensures that older, expendable leaves are dismantled first, thus prolonging the life of younger leaves and meristematic tissues that are vital to whole-plant survival.
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Affiliation(s)
- Tom Rankenberg
- Plant Stress Resilience, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hans van Veen
- Plant Stress Resilience, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Evolutionary Plant-Ecophysiology, Groningen Institute for Evolutionary LIfe Sciences, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Mastoureh Sedaghatmehr
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Che-Yang Liao
- Experimental and Computational Plant Development, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Muthanna Biddanda Devaiah
- Experimental and Computational Plant Development, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Evelien A Stouten
- Plant Stress Resilience, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | | | - Rashmi Sasidharan
- Plant Stress Resilience, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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12
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Cosgrove DJ. Structure and growth of plant cell walls. Nat Rev Mol Cell Biol 2024; 25:340-358. [PMID: 38102449 DOI: 10.1038/s41580-023-00691-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Plant cells build nanofibrillar walls that are central to plant growth, morphogenesis and mechanics. Starting from simple sugars, three groups of polysaccharides, namely, cellulose, hemicelluloses and pectins, with very different physical properties are assembled by the cell to make a strong yet extensible wall. This Review describes the physics of wall growth and its regulation by cellular processes such as cellulose production by cellulose synthase, modulation of wall pH by plasma membrane H+-ATPase, wall loosening by expansin and signalling by plant hormones such as auxin and brassinosteroid. In addition, this Review discusses the nuanced roles, properties and interactions of cellulose, matrix polysaccharides and cell wall proteins and describes how wall stress and wall loosening cooperatively result in cell wall growth.
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Affiliation(s)
- Daniel J Cosgrove
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA.
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13
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Zeng F, Ma Z, Feng Y, Shao M, Li Y, Wang H, Yang S, Mao J, Chen B. Mechanism of the Pulvinus-Driven Leaf Movement: An Overview. Int J Mol Sci 2024; 25:4582. [PMID: 38731801 PMCID: PMC11083266 DOI: 10.3390/ijms25094582] [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: 03/22/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Leaf movement is a manifestation of plant response to the changing internal and external environment, aiming to optimize plant growth and development. Leaf movement is usually driven by a specialized motor organ, the pulvinus, and this movement is associated with different changes in volume and expansion on the two sides of the pulvinus. Blue light, auxin, GA, H+-ATPase, K+, Cl-, Ca2+, actin, and aquaporin collectively influence the changes in water flux in the tissue of the extensor and flexor of the pulvinus to establish a turgor pressure difference, thereby controlling leaf movement. However, how these factors regulate the multicellular motility of the pulvinus tissues in a species remains obscure. In addition, model plants such as Medicago truncatula, Mimosa pudica, and Samanea saman have been used to study pulvinus-driven leaf movement, showing a similarity in their pulvinus movement mechanisms. In this review, we summarize past research findings from the three model plants, and using Medicago truncatula as an example, suggest that genes regulating pulvinus movement are also involved in regulating plant growth and development. We also propose a model in which the variation of ion flux and water flux are critical steps to pulvinus movement and highlight questions for future research.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (F.Z.); (Z.M.); (Y.F.); (M.S.); (Y.L.); (H.W.); (S.Y.); (J.M.)
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14
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Khan S, Alvi AF, Saify S, Iqbal N, Khan NA. The Ethylene Biosynthetic Enzymes, 1-Aminocyclopropane-1-Carboxylate (ACC) Synthase (ACS) and ACC Oxidase (ACO): The Less Explored Players in Abiotic Stress Tolerance. Biomolecules 2024; 14:90. [PMID: 38254690 PMCID: PMC10813531 DOI: 10.3390/biom14010090] [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: 11/14/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Ethylene is an essential plant hormone, critical in various physiological processes. These processes include seed germination, leaf senescence, fruit ripening, and the plant's response to environmental stressors. Ethylene biosynthesis is tightly regulated by two key enzymes, namely 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylate oxidase (ACO). Initially, the prevailing hypothesis suggested that ACS is the limiting factor in the ethylene biosynthesis pathway. Nevertheless, accumulating evidence from various studies has demonstrated that ACO, under specific circumstances, acts as the rate-limiting enzyme in ethylene production. Under normal developmental processes, ACS and ACO collaborate to maintain balanced ethylene production, ensuring proper plant growth and physiology. However, under abiotic stress conditions, such as drought, salinity, extreme temperatures, or pathogen attack, the regulation of ethylene biosynthesis becomes critical for plants' survival. This review highlights the structural characteristics and examines the transcriptional, post-transcriptional, and post-translational regulation of ACS and ACO and their role under abiotic stress conditions. Reviews on the role of ethylene signaling in abiotic stress adaptation are available. However, a review delineating the role of ACS and ACO in abiotic stress acclimation is unavailable. Exploring how particular ACS and ACO isoforms contribute to a specific plant's response to various abiotic stresses and understanding how they are regulated can guide the development of focused strategies. These strategies aim to enhance a plant's ability to cope with environmental challenges more effectively.
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Affiliation(s)
- Sheen Khan
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (S.K.); (S.S.)
| | - Ameena Fatima Alvi
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (S.K.); (S.S.)
| | - Sadaf Saify
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (S.K.); (S.S.)
| | - Noushina Iqbal
- Department of Botany, Jamia Hamdard, New Delhi 110062, India;
| | - Nafees A. Khan
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (S.K.); (S.S.)
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15
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Han K, Zhao Y, Sun Y, Li Y. NACs, generalist in plant life. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2433-2457. [PMID: 37623750 PMCID: PMC10651149 DOI: 10.1111/pbi.14161] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Plant-specific NAC proteins constitute a major transcription factor family that is well-known for its roles in plant growth, development, and responses to abiotic and biotic stresses. In recent years, there has been significant progress in understanding the functions of NAC proteins. NAC proteins have a highly conserved DNA-binding domain; however, their functions are diverse. Previous understanding of the structure of NAC transcription factors can be used as the basis for their functional diversity. NAC transcription factors consist of a target-binding domain at the N-terminus and a highly versatile C-terminal domain that interacts with other proteins. A growing body of research on NAC transcription factors helps us comprehend the intricate signalling network and transcriptional reprogramming facilitated by NAC-mediated complexes. However, most studies of NAC proteins have been limited to a single function. Here, we discuss the upstream regulators, regulatory components and targets of NAC in the context of their prospective roles in plant improvement strategies via biotechnology intervention, highlighting the importance of the NAC transcription factor family in plants and the need for further research.
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Affiliation(s)
- Kunjin Han
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Ye Zhao
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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16
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Zhu Z, Dai Y, Yu G, Zhang X, Chen Q, Kou X, Mehareb EM, Raza G, Zhang B, Wang B, Wang K, Han J. Dynamic physiological and transcriptomic changes reveal memory effects of salt stress in maize. BMC Genomics 2023; 24:726. [PMID: 38041011 PMCID: PMC10690987 DOI: 10.1186/s12864-023-09845-w] [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: 09/11/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Pre-exposing plants to abiotic stresses can induce stress memory, which is crucial for adapting to subsequent stress exposure. Although numerous genes involved in salt stress response have been identified, the understanding of memory responses to salt stress remains limited. RESULTS In this study, we conducted physiological and transcriptional assays on maize plants subjected to recurrent salt stress to characterize salt stress memory. During the second exposure to salt stress, the plants exhibited enhanced salt resistance, as evidenced by increased proline content and higher POD and SOD activity, along with decreased MDA content, indicative of physiological memory behavior. Transcriptional analysis revealed fewer differentially expressed genes and variations in response processes during the second exposure compared to the first, indicative of transcriptional memory behavior. A total of 2,213 salt stress memory genes (SMGs) were identified and categorized into four response patterns. The most prominent group of SMGs consisted of genes with elevated expression during the first exposure to salt stress but reduced expression after recurrent exposure to salt stress, or vice versa ([+ / -] or [- / +]), indicating that a revised response is a crucial process in plant stress memory. Furthermore, nine transcription factors (TFs) (WRKY40, WRKY46, WRKY53, WRKY18, WRKY33, WRKY70, MYB15, KNAT7, and WRKY54) were identified as crucial factors related to salt stress memory. These TFs regulate over 53% of SMGs, underscoring their potential significance in salt stress memory. CONCLUSIONS Our study demonstrates that maize can develop salt stress memory, and the genes identified here will aid in the genetic improvement of maize and other crops.
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Affiliation(s)
- Zhiying Zhu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yan Dai
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Guangrun Yu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Qi Chen
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Xiaobing Kou
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Eid M Mehareb
- Sugar Crops Research Institute, Agricultural Research Center, Giza, 12619, Egypt
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China.
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China.
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, China.
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17
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Xing M, Huang K, Zhang C, Xi D, Luo H, Pei J, Ruan R, Liu H. Transcriptome Analysis Reveals the Molecular Mechanism and Responsive Genes of Waterlogging Stress in Actinidia deliciosa Planch Kiwifruit Plants. Int J Mol Sci 2023; 24:15887. [PMID: 37958870 PMCID: PMC10649176 DOI: 10.3390/ijms242115887] [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: 09/20/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Waterlogging stress is one of the major natural issues resulting in stunted growth and loss of agricultural productivity. Cultivated kiwifruits are popular for their rich vitamin C content and unique flavor among consumers, while commonly sensitive to waterlogging stress. The wild kiwifruit plants are usually obliged to survive in harsh environments. Here, we carried out a transcriptome analysis by high-throughput RNA sequencing using the root tissues of Actinidia deliciosa (a wild resource with stress-tolerant phenotype) after waterlogging for 0 d, 3 d, and 7 d. Based on the RNA sequencing data, a high number of differentially expressed genes (DEGs) were identified in roots under waterlogging treatment, which were significantly enriched into four biological processes, including stress response, metabolic processes, molecular transport, and mitotic organization, by gene ontology (GO) simplify enrichment analysis. Among these DEGs, the hypoxia-related genes AdADH1 and AdADH2 were correlated well with the contents of acetaldehyde and ethanol, and three transcription factors Acc26216, Acc08443, and Acc16908 were highly correlated with both AdADH1/2 genes and contents of acetaldehyde and ethanol. In addition, we found that there might be an evident difference among the promoter sequences of ADH genes from A. deliciosa and A. chinensis. Taken together, our results provide additional information on the waterlogging response in wild kiwifruit plants.
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Affiliation(s)
| | | | | | | | | | | | | | - Hui Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China; (M.X.); (K.H.); (C.Z.); (D.X.); (H.L.); (J.P.); (R.R.)
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18
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Rahman KU, Ali K, Rauf M, Arif M. Aspergillus nomiae and fumigatus Ameliorating the Hypoxic Stress Induced by Waterlogging through Ethylene Metabolism in Zea mays L. Microorganisms 2023; 11:2025. [PMID: 37630585 PMCID: PMC10459883 DOI: 10.3390/microorganisms11082025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Transient and prolonged waterlogging stress (WS) stimulates ethylene (ET) generation in plants, but their reprogramming is critical in determining the plants' fate under WS, which can be combated by the application of symbiotically associated beneficial microbes that induce resistance to WS. The present research was rationalized to explore the potential of the newly isolated 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing fungal endophytic consortium of Aspergillus nomiae (MA1) and Aspergillus fumigatus (MA4) on maize growth promotion under WS. MA1 and MA4 were isolated from the seeds of Moringa oleifera L., which ably produced a sufficient amount of IAA, proline, phenols, and flavonoids. MA1 and MA4 proficiently colonized the root zone of maize (Zea mays L.). The symbiotic association of MA1 and MA4 promoted the growth response of maize compared with the non-inoculated plants under WS stress. Moreover, MA1- and MA4-inoculated maize plants enhanced the production of total soluble protein, sugar, lipids, phenolics, and flavonoids, with a reduction in proline content and H2O2 production. MA1- and MA4-inoculated maize plants showed an increase in the DPPH activity and antioxidant enzyme activities of CAT and POD, along with an increased level of hormonal content (GA3 and IAA) and decreased ABA and ACC contents. Optimal stomatal activity in leaf tissue and adventitious root formation at the root/stem junction was increased in MA1- and MA4-inoculated maize plants, with reduced lysigenous aerenchyma formation, ratio of cortex-to-stele, water-filled cells, and cell gaps within roots; increased tight and round cells; and intact cortical cells without damage. MA1 and MA4 induced a reduction in deformed mesophyll cells, and deteriorated epidermal and vascular bundle cells, as well as swollen metaxylem, phloem, pith, and cortical area, in maize plants under WS compared with control. Moreover, the transcript abundance of ethylene-responsive gene ZmEREB180, responsible for the induction of the WS tolerance in maize, showed optimally reduced expression sufficient for induction in WS tolerance, in MA1- and MA4-inoculated maize plants under WS compared with the non-inoculated control. The existing research supported the use of MA1 and MA4 isolates for establishing the bipartite mutualistic symbiosis in maize to assuage the adverse effects of WS by optimizing ethylene production.
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Affiliation(s)
- Khalil Ur Rahman
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
| | - Kashmala Ali
- Department of Botany, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
| | - Mamoona Rauf
- Department of Botany, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
| | - Muhammad Arif
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
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19
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Geldhof B, Pattyn J, Van de Poel B. From a different angle: genetic diversity underlies differentiation of waterlogging-induced epinasty in tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1178778. [PMID: 37324684 PMCID: PMC10264670 DOI: 10.3389/fpls.2023.1178778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
In tomato, downward leaf bending is a morphological adaptation towards waterlogging, which has been shown to induce a range of metabolic and hormonal changes. This kind of functional trait is often the result of a complex interplay of regulatory processes starting at the gene level, gated through a plethora of signaling cascades and modulated by environmental cues. Through phenotypical screening of a population of 54 tomato accessions in a Genome Wide Association Study (GWAS), we have identified target genes potentially involved in plant growth and survival during waterlogging and subsequent recovery. Changes in both plant growth rate and epinastic descriptors revealed several associations to genes possibly supporting metabolic activity in low oxygen conditions in the root zone. In addition to this general reprogramming, some of the targets were specifically associated to leaf angle dynamics, indicating these genes might play a role in the induction, maintenance or recovery of differential petiole elongation in tomato during waterlogging.
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Affiliation(s)
- Batist Geldhof
- Molecular Plant Hormone Physiology Lab, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jolien Pattyn
- Molecular Plant Hormone Physiology Lab, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Bram Van de Poel
- Molecular Plant Hormone Physiology Lab, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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20
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Singh P, Jaiswal S, Kushwaha A, Gahlowt P, Mishra V, Tripathi DK, Singh SP, Gupta R, Singh VP. Peroxynitrite is essential for aerenchyma formation in rice roots under waterlogging conditions. PLANTA 2023; 258:2. [PMID: 37208534 DOI: 10.1007/s00425-023-04148-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/27/2023] [Indexed: 05/21/2023]
Abstract
MAIN CONCLUSION In this study, we report that peroxynitrite is necessary for ethylene-mediated aerenchyma formation in rice roots under waterlogging conditions. Plants under waterlogging stress face anoxygenic conditions which reduce their metabolism and induce several adaptations. The formation of aerenchyma is of paramount importance for the survival of plants under waterlogging conditions. Though some studies have shown the involvement of ethylene in aerenchyma formation under waterlogging conditions, the implication of peroxynitrite (ONOO-) in such a developmental process remains elusive. Here, we report an increase in aerenchyma formation in rice roots exposed to waterlogging conditions under which the number of aerenchyma cells and their size was further enhanced in response to exogenous ethephon (a donor of ethylene) or SNP (a donor of nitric oxide) treatment. Application of epicatechin (a peroxynitrite scavenger) to waterlogged plants inhibited the aerenchyma formation, signifying that ONOO- might have a role in aerenchyma formation. Interestingly, epicatechin and ethephon co-treated waterlogged plants were unable to form aerenchyma, indicating the necessity of ONOO- in ethylene-mediated aerenchyma formation under waterlogging conditions. Taken together, our results highlight the role of ONOO- in ethylene-mediated aerenchyma formation in rice and could be used in the future to develop waterlogging stress-tolerant varieties of rice.
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Affiliation(s)
- Pooja Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Saumya Jaiswal
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Ajayraj Kushwaha
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Priya Gahlowt
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Vipul Mishra
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Durgesh Kumar Tripathi
- Crop Nanobiology and Molecular Stress Physiology Lab Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida, 201313, India
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208001, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul, 02707, South Korea
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India.
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21
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Wang Y, Xu Y, Xu J, Sun W, Lv Z, Manzoor MA, Liu X, Shen Z, Wang J, Liu R, Whiting MD, Jiu S, Zhang C. Oxygenation alleviates waterlogging-caused damages to cherry rootstocks. MOLECULAR HORTICULTURE 2023; 3:8. [PMID: 37789432 PMCID: PMC10515082 DOI: 10.1186/s43897-023-00056-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/21/2023] [Indexed: 10/05/2023]
Abstract
Waterlogging has occurred more frequently in recent years due to climate change, so it is a huge threat to crop yield and quality. Sweet cherry, a fruit tree with a high economic value, is sensitive to waterlogging stress. One of the most effective methods for enhancing the waterlogging tolerance of sweet cherries is to select waterlogging-tolerant rootstocks. However, the waterlogging tolerance of different cherry rootstocks, and the underlying mechanism remains uncharacterized. Thus, we first evaluated the waterlogging resistance of five sweet cherry rootstocks planted in China. The data showed that 'Gisela 12' and 'Colt' were the most waterlogging-sensitive and -tolerant among the five tested varieties, respectively. Oxygenation effectively alleviated the adverse impacts of waterlogging stress on cherry rootstocks. Moreover, we found that the waterlogging group had lower relative water content, Fv/Fm value, net photosynthetic rate, and higher antioxidant enzyme activities, whereas the oxygenated group performed better in all these parameters. RNA-Seq analysis revealed that numerous DEGs were involved in energy production, antioxidant metabolism, hormone metabolism pathways, and stress-related transcription factors. These findings will help provide management strategies to enhance the waterlogging tolerance of cherry rootstocks and thereby achieve higher yield and better quality of cherries.
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Affiliation(s)
- Yuxuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jieming Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanxia Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhiyu Shen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Matthew D Whiting
- Department of Horticulture, Washington State University, Prosser, WA, 99350, USA
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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22
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Tyagi A, Ali S, Park S, Bae H. Exploring the Potential of Multiomics and Other Integrative Approaches for Improving Waterlogging Tolerance in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:1544. [PMID: 37050170 PMCID: PMC10096958 DOI: 10.3390/plants12071544] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Soil flooding has emerged as a serious threat to modern agriculture due to the rapid global warming and climate change, resulting in catastrophic crop damage and yield losses. The most detrimental effects of waterlogging in plants are hypoxia, decreased nutrient uptake, photosynthesis inhibition, energy crisis, and microbiome alterations, all of which result in plant death. Although significant advancement has been made in mitigating waterlogging stress, it remains largely enigmatic how plants perceive flood signals and translate them for their adaptive responses at a molecular level. With the advent of multiomics, there has been significant progress in understanding and decoding the intricacy of how plants respond to different stressors which have paved the way towards the development of climate-resistant smart crops. In this review, we have provided the overview of the effect of waterlogging in plants, signaling (calcium, reactive oxygen species, nitric oxide, hormones), and adaptive responses. Secondly, we discussed an insight into past, present, and future prospects of waterlogging tolerance focusing on conventional breeding, transgenic, multiomics, and gene-editing approaches. In addition, we have also highlighted the importance of panomics for developing waterlogging-tolerant cultivars. Furthermore, we have discussed the role of high-throughput phenotyping in the screening of complex waterlogging-tolerant traits. Finally, we addressed the current challenges and future perspectives of waterlogging signal perception and transduction in plants, which warrants future investigation.
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Affiliation(s)
| | | | | | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
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23
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D'Incà E, Foresti C, Orduña L, Amato A, Vandelle E, Santiago A, Botton A, Cazzaniga S, Bertini E, Pezzotti M, Giovannoni J, Vrebalov J, Matus JT, Tornielli GB, Zenoni S. The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine. PLANT PHYSIOLOGY 2023:kiad050. [PMID: 36718552 DOI: 10.1093/plphys/kiad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/03/2022] [Accepted: 12/11/2022] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the most widely cultivated fruit crops because the winemaking industry has huge economic relevance worldwide. Uncovering the molecular mechanisms controlling the developmental progression of plant organs will prove essential for maintaining high-quality grapes, expressly in the context of climate change, which impairs the ripening process. Through a deep inspection of transcriptomic data, we identified VviNAC60, a member of the NAC transcription factor family, as a putative regulator of grapevine organ maturation. We explored VviNAC60 binding landscapes through DNA affinity purification followed by sequencing and compared bound genes with transcriptomics datasets from grapevine plants stably and transiently overexpressing VviNAC60 to define a set of high-confidence targets. Among these, we identified key molecular markers associated with organ senescence and fruit ripening. Physiological, metabolic, and promoter activation analyses showed that VviNAC60 induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of STAY-GREEN PROTEIN 1 (VviSGR1) and VviMYBA1, respectively, with the latter being up-regulated through a VviNAC60-VviNAC03 regulatory complex. Despite sharing a closer phylogenetic relationship with senescence-related homologues to the NAC transcription factor AtNAP, VviNAC60 complemented the non-ripening(nor) mutant phenotype in tomato (Solanum lycopersicum), suggesting a dual role as an orchestrator of both ripening- and senescence-related processes. Our data support VviNAC60 as a regulator of processes initiated in the grapevine vegetative- to mature-phase organ transition and therefore as a potential target for enhancing the environmental resilience of grapevine by fine-tuning the duration of the vegetative phase.
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Affiliation(s)
- Erica D'Incà
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Chiara Foresti
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Elodie Vandelle
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Alessandro Botton
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Italy
| | - Stefano Cazzaniga
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Edoardo Bertini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - James Giovannoni
- USDA-ARS Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Tower Road, Cornell Campus, Ithaca, NY 14853, USA
| | - Julia Vrebalov
- USDA-ARS Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Tower Road, Cornell Campus, Ithaca, NY 14853, USA
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | | | - Sara Zenoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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24
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Michaud O, Krahmer J, Galbier F, Lagier M, Galvão VC, Ince YÇ, Trevisan M, Knerova J, Dickinson P, Hibberd JM, Zeeman SC, Fankhauser C. Abscisic acid modulates neighbor proximity-induced leaf hyponasty in Arabidopsis. PLANT PHYSIOLOGY 2023; 191:542-557. [PMID: 36135791 PMCID: PMC9806605 DOI: 10.1093/plphys/kiac447] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/08/2022] [Indexed: 05/27/2023]
Abstract
Leaves of shade-avoiding plants such as Arabidopsis (Arabidopsis thaliana) change their growth pattern and position in response to low red to far-red ratios (LRFRs) encountered in dense plant communities. Under LRFR, transcription factors of the phytochrome-interacting factor (PIF) family are derepressed. PIFs induce auxin production, which is required for promoting leaf hyponasty, thereby favoring access to unfiltered sunlight. Abscisic acid (ABA) has also been implicated in the control of leaf hyponasty, with gene expression patterns suggesting that LRFR regulates the ABA response. Here, we show that LRFR leads to a rapid increase in ABA levels in leaves. Changes in ABA levels depend on PIFs, which regulate the expression of genes encoding isoforms of the enzyme catalyzing a rate-limiting step in ABA biosynthesis. Interestingly, ABA biosynthesis and signaling mutants have more erect leaves than wild-type Arabidopsis under white light but respond less to LRFR. Consistent with this, ABA application decreases leaf angle under white light; however, this response is inhibited under LRFR. Tissue-specific interference with ABA signaling indicates that an ABA response is required in different cell types for LRFR-induced hyponasty. Collectively, our data indicate that LRFR triggers rapid PIF-mediated ABA production. ABA plays a different role in controlling hyponasty under white light than under LRFR. Moreover, ABA exerts its activity in multiple cell types to control leaf position.
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Affiliation(s)
| | - Johanna Krahmer
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Génopode Building, Lausanne CH-1015, Switzerland
| | - Florian Galbier
- Plant Biochemistry, Department of Biology, ETH Zürich, Universität-Str. 2, CH-8092 Zürich, Switzerland
| | | | | | | | - Martine Trevisan
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Génopode Building, Lausanne CH-1015, Switzerland
| | - Jana Knerova
- Department of Plant Sciences, Downing Street, Cambridge, University of Cambridge, CB2 3EA, UK
| | - Patrick Dickinson
- Department of Plant Sciences, Downing Street, Cambridge, University of Cambridge, CB2 3EA, UK
| | - Julian M Hibberd
- Department of Plant Sciences, Downing Street, Cambridge, University of Cambridge, CB2 3EA, UK
| | - Samuel C Zeeman
- Plant Biochemistry, Department of Biology, ETH Zürich, Universität-Str. 2, CH-8092 Zürich, Switzerland
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25
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Jonsson K, Ma Y, Routier-Kierzkowska AL, Bhalerao RP. Multiple mechanisms behind plant bending. NATURE PLANTS 2023; 9:13-21. [PMID: 36581759 DOI: 10.1038/s41477-022-01310-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
To survive, plants constantly adapt their body shape to their environment. This often involves remarkably rapid bending of their organs such as stems, leaves and roots. Since plant cells are enclosed by stiff cell walls, they use various strategies for bending their organs, which differ from bending mechanisms of soft animal tissues and involve larger physical forces. Here we attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. We argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.
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Affiliation(s)
- Kristoffer Jonsson
- IRBV, Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Yuan Ma
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Rishikesh P Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
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26
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Wang Z, Wei X, Wang Y, Sun M, Zhao P, Wang Q, Yang B, Li J, Jiang YQ. WRKY29 transcription factor regulates ethylene biosynthesis and response in arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:134-145. [PMID: 36403487 DOI: 10.1016/j.plaphy.2022.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
The gaseous phytohormone ethylene participates in a lot of physiological processes in plants. 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS, EC 4.4.1.14) and the ACC oxidase (ACO, EC 1.14.17.4) are key enzymes in ethylene biosynthesis. However, how ACSs and ACOs are regulated at the transcriptional level is largely unknown. In the present study, we showed that an Arabidopsis (Arabidopsis thaliana) WRKY-type transcription factor (TF), WRKY29 positively regulated the expression of ACS5, ACS6, ACS8, ACS11 and ACO5 genes and thus promoted basal ethylene production. WRKY29 protein was localized in nuclei and was a transcriptional activator. Overexpression of WRKY29 caused pleiotropic effect on plant growth, development and showed obvious response even without ACC treatment. Inducible overexpression of WRKY29 also reduced primary root elongation and lateral root growth. A triple response assay of overexpression and mutant seedlings of WRKY29 showed that overexpression seedlings had shorter hypocotyls than the transgenic GFP (Green Fluorescence Protein) control, while mutants had no difference from wild-type. A qRT-PCR assay demonstrated that expression of multiple ACSs and ACO5 was up-regulated in WRKY29 overexpression plants. A transactivation assay through dual luciferase reporter system confirmed the regulation of promoters of ACS5, ACS6, ACS8, ACS11 and ACO5 by WRKY29. Both in vivo chromatin immunoprecipitation (ChIP)- quantitative PCR and in vitro electrophoretic mobility shift assay (EMSA) revealed that WRKY29 directly bound to the promoter regions of its target genes. Taken together, these results suggest that WRKY29 is a novel TF positively regulating ethylene production by modulating the expression of ACS and ACO genes.
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Affiliation(s)
- Zhaoqiang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiangyan Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Yiqiao Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Mengting Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Peiyu Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Qiannan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Bo Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China.
| | - Jing Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Yuan-Qing Jiang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China.
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27
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Rehman B, Javed J, Rauf M, Khan SA, Arif M, Hamayun M, Gul H, Khilji SA, Sajid ZA, Kim WC, Lee IJ. ACC deaminase-producing endophytic fungal consortia promotes drought stress tolerance in M.oleifera by mitigating ethylene and H 2O 2. FRONTIERS IN PLANT SCIENCE 2022; 13:967672. [PMID: 36618664 PMCID: PMC9814162 DOI: 10.3389/fpls.2022.967672] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Introduction Drought has become more prevalent due to dramatic climate change worldwide. Consequently, the most compatible fungal communities collaborate to boost plant development and ecophysiological responses under environmental constraints. However, little is known about the specific interactions between non-host plants and endophytic fungal symbionts that produce growth-promoting and stress-alleviating hormones during water deficits. Methods The current research was rationalized and aimed at exploring the influence of the newly isolated, drought-resistant, ACC deaminase enzyme-producing endophytic fungi Trichoderma gamsii (TP), Fusarium proliferatum (TR), and its consortium (TP+TR) from a xerophytic plant Carthamus oxycantha L. on Moringa oleifera L. grown under water deficit induced by PEG-8000 (8% osmoticum solution). Results The current findings revealed that the co-inoculation promoted a significant enhancement in growth traits such as dry weight (217%), fresh weight (123%), root length (65%), shoot length (53%), carotenoids (87%), and chlorophyll content (76%) in comparison to control plants under water deficit. Total soluble sugars (0.56%), proteins (132%), lipids (43%), flavonoids (52%), phenols (34%), proline (55%), GA3 (86%), IAA (35%), AsA (170%), SA (87%), were also induced, while H2O2 (-45%), ABA (-60%) and ACC level (-77%) was decreased by co-inoculation of TP and TR in M. oleifera plants, compared with the non-inoculated plants under water deficit. The co-inoculum (TP+TR) also induced the antioxidant potential and enzyme activities POX (325%), CAT activity (166%), and AsA (21%), along with a lesser decrease (-2%) in water potential in M. oleifera plants with co-inoculation under water deficit compared with non-inoculated control. The molecular analysis for gene expression unraveled the reduced expression of ethylene biosynthesis and signaling-related genes up to an optimal level, with an induction of antioxidant enzymatic genes by endophytic co-inoculation in M. oleifera plants under water deficit, suggesting their role in drought stress tolerance as an essential regulatory function. Conclusion The finding may alert scientists to consider the impacts of optimal reduction of ethylene and induction of antioxidant potential on drought stress tolerance in M. oleifera. Hence, the present study supports the use of compatible endophytic fungi to build a bipartite mutualistic symbiosis in M. oleifera non-host plants to mitigate the negative impacts of water scarcity in arid regions throughout the world.
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Affiliation(s)
- Bushra Rehman
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Javeria Javed
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mamoona Rauf
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sumera Afzal Khan
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Muhammad Arif
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Humaira Gul
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sheza Ayaz Khilji
- Department of Botany, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | | | - Won-Chan Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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28
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Kanapin A, Rozhmina T, Bankin M, Surkova S, Duk M, Osyagina E, Samsonova M. Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration. Int J Mol Sci 2022; 23:14536. [PMID: 36498863 PMCID: PMC9738745 DOI: 10.3390/ijms232314536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection.
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Affiliation(s)
- Alexander Kanapin
- Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Tatyana Rozhmina
- Laboratory of Breeding Technologies, Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Mikhail Bankin
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Svetlana Surkova
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Duk
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia
| | - Ekaterina Osyagina
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
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Welch T, Bayon C, Rudd JJ, Kanyuka K, Kettles GJ. Induction of distinct plant cell death programs by secreted proteins from the wheat pathogen Zymoseptoria tritici. Sci Rep 2022; 12:17880. [PMID: 36284131 PMCID: PMC9596407 DOI: 10.1038/s41598-022-22660-9] [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: 07/18/2022] [Accepted: 10/18/2022] [Indexed: 01/20/2023] Open
Abstract
Cell death processes in eukaryotes shape normal development and responses to the environment. For plant-microbe interactions, initiation of host cell death plays an important role in determining disease outcomes. Cell death pathways are frequently initiated following detection of pathogen-derived molecules which can lead to resistance or susceptibility to disease depending on pathogen lifestyle. We previously identified several small secreted proteins (SSPs) from the wheat-infecting fungus Zymoseptoria tritici that induce rapid cell death in Nicotiana benthamiana following Agrobacterium-mediated delivery and expression (agroinfiltration). Here we investigated whether the execution of host cells was mechanistically similar in response to different Z. tritici SSPs. Using RNA sequencing, we found that transient expression of four Z. tritici SSPs led to massive transcriptional reprogramming within 48 h of agroinfiltration. We observed that distinct host gene expression profiles were induced dependent on whether cell death occurs in a cell surface immune receptor-dependent or -independent manner. These gene expression profiles involved differential transcriptional networks mediated by WRKY, NAC and MYB transcription factors. In addition, differential expression of genes belonging to different classes of receptor-like proteins and receptor-like kinases was observed. These data suggest that different Z. tritici SSPs trigger differential transcriptional reprogramming in plant cells.
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Affiliation(s)
- Thomas Welch
- grid.6572.60000 0004 1936 7486Birmingham Institute of Forest Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK ,grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Carlos Bayon
- grid.418374.d0000 0001 2227 9389Wheat Pathogenomics Team, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Jason J. Rudd
- grid.418374.d0000 0001 2227 9389Wheat Pathogenomics Team, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Kostya Kanyuka
- grid.17595.3f0000 0004 0383 6532Cambridge Crop Research, National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Graeme J. Kettles
- grid.6572.60000 0004 1936 7486Birmingham Institute of Forest Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK ,grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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Yang C, Huang Y, Lv P, Antwi-Boasiako A, Begum N, Zhao T, Zhao J. NAC Transcription Factor GmNAC12 Improved Drought Stress Tolerance in Soybean. Int J Mol Sci 2022; 23:ijms231912029. [PMID: 36233329 PMCID: PMC9570484 DOI: 10.3390/ijms231912029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/28/2022] [Accepted: 10/08/2022] [Indexed: 11/24/2022] Open
Abstract
NAC transcription factors (TFs) could regulate drought stresses in plants; however, the function of NAC TFs in soybeans remains unclear. To unravel NAC TF function, we established that GmNAC12, a NAC TF from soybean (Glycine max), was involved in the manipulation of stress tolerance. The expression of GmNAC12 was significantly upregulated more than 10-fold under drought stress and more than threefold under abscisic acid (ABA) and ethylene (ETH) treatment. In order to determine the function of GmNAC12 under drought stress conditions, we generated GmNAC12 overexpression and knockout lines. The present findings showed that under drought stress, the survival rate of GmNAC12 overexpression lines increased by more than 57% compared with wild-type plants, while the survival rate of GmNAC12 knockout lines decreased by at least 46%. Furthermore, a subcellular localisation analysis showed that the GmNAC12 protein is concentrated in the nucleus of the tobacco cell. In addition, we used a yeast two-hybrid assay to identify 185 proteins that interact with GmNAC12. Gene ontology (GO) and KEGG analysis showed that GmNAC12 interaction proteins are related to chitin, chlorophyll, ubiquitin–protein transferase, and peroxidase activity. Hence, we have inferred that GmNAC12, as a key gene, could positively regulate soybean tolerance to drought stress.
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Affiliation(s)
- Chengfeng Yang
- 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 210095, China
| | - Yanzhong Huang
- 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 210095, China
- National Forage Breeding Innovation Base (JAAS), Key Laboratory for Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Peiyun Lv
- 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 210095, China
| | - Augustine Antwi-Boasiako
- 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 210095, China
- Crops Research Institute, Council for Scientific and Industrial Research, Kumasi AK420, Ghana
| | - Naheeda Begum
- 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 210095, 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 210095, China
- Correspondence: (T.Z.); (J.Z.)
| | - Jinming 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 210095, China
- Correspondence: (T.Z.); (J.Z.)
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The wild allotetraploid sesame genome provides novel insights into evolution and lignan biosynthesis. J Adv Res 2022:S2090-1232(22)00233-8. [PMID: 36265763 PMCID: PMC10403651 DOI: 10.1016/j.jare.2022.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION The wild tetraploid sesame (Sesamum schinzianum), an ancestral relative of diploid cultivated sesame, grows in the tropical desert of the African Plateau. As a valuable seed resource, wild sesame has several advantageous traits, such as strong environmental adaptability and an extremely high content of sesamolin in its seeds. High-quality genome assembly is essential for a detailed understanding of genome structure, genome evolution and crop improvement. OBJECTIVES Here, we generated two high-quality chromosome-scale genomes from S. schinzianum and a cultivated diploid elite sesame (Sesamum indicum L.) to investigate the potential genetic basis underlying these traits of wild sesame. METHODS The long-read data from PacBio Sequel II platform and high-throughput chromosome conformation capture (Hi-C) data were used to construct high-quality sesame genome. Then dissecting the molecular mechanisms of sesame evolution and lignan biosynthesis through comparative genomics and transcriptomics. RESULTS We found evidence of divergent evolution that involved differences in the number, sequence and expression level of homologous genes between the two sets of subgenomes from allotetraploids in S. schinzianum, all of which might be driven by subfunctionalization after polyploidization. Furthermore, it was found that a great number of genes involved in the stress response have undergone positive selection and resulted from gene family expansion in the wild sesame genome compared with the cultivated sesame genome, which, overall, is associated with adaptative evolution to the environment. We hypothesized that the sole functional member CYP92B14 (SscC22g35272) could be associated with high content of sesamolin in wild sesame seeds. CONCLUSION This study provides high-quality wild allotetraploid sesame and cultivated sesame genomes, reveals evolutionary features of the allotetraploid genome and provides novel insights into lignan synthesis pathways. Meanwhile, the wild sesame genome will be an important resource to conduct comparative genomic and evolutionary studies and plant improvement programmes.
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Endophytic Fungal Consortia Enhance Basal Drought-Tolerance in Moringa oleifera by Upregulating the Antioxidant Enzyme (APX) through Heat Shock Factors. Antioxidants (Basel) 2022; 11:antiox11091669. [PMID: 36139743 PMCID: PMC9495891 DOI: 10.3390/antiox11091669] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Global climate change has imposed harsh environmental conditions such as drought. Naturally, the most compatible fungal consortia operate synergistically to enhance plant growth and ecophysiological responses against abiotic strains. Yet, little is known about the interactions between phytohormone-producing endophytic fungal symbionts and plant growth under drought stress. The existing research was rationalized to recognize the role of newly isolated drought-resistant, antioxidant-rich endophytic fungal consortia hosting a xerophytic plant, Carthamus oxycantha L., inoculated to Moringa oleifera L. grown under drought stress of 8% PEG (polyethylene glycol-8000). Under drought stress, the combined inoculation of endophytic strain Microdochium majus (WA), Meyerozyma guilliermondi (TG), and Aspergillus aculeatus (TL3) exhibited a significant improvement in growth attributes such as shoot fresh weight (1.71-fold), shoot length (0.86-fold), root length (0.65-fold), dry weight (2.18-fold), total chlorophyll (0.46-fold), and carotenoids (0.87-fold) in comparison to control (8% PEG). Primary and secondary metabolites were also increased in M. oleifera inoculated with endophytic consortia, under drought stress, such as proteins (1.3-fold), sugars (0.58-fold), lipids (0.41-fold), phenols (0.36-fold), flavonoids (0.52-fold), proline (0.6-fold), indole acetic acid (IAA) (4.5-fold), gibberellic acid (GA) (0.7-fold), salicylic acid (SA) (0.8-fold), ascorbic acid (ASA) (1.85-fold), while abscisic acid (ABA) level was decreased (−0.61-fold) in comparison to the control (8% PEG). Under drought stress, combined inoculation (WA, TG, TL3) also promoted the antioxidant activities of enzymes such as ascorbate peroxidase (APX) (3.5-fold), catalase (CAT) activity (1.7-fold), and increased the total antioxidant capacity (TAC) (0.78-fold) with reduced reactive oxygen species (ROS) such as H2O2 production (-0.4-fold), compared to control (8% PEG), and stomatal aperture was larger (3.5-fold) with a lesser decrease (-0.02-fold) in water potential. Moreover, combined inoculation (WA, TG, TL3) up regulated the expression of MolHSF3, MolHSF19, and MolAPX genes in M. oleifera under drought stress, compared to the control (8% PEG), is suggestive of an important regulatory role for drought stress tolerance governed by fungal endophytes. The current research supports the exploitation of the compatible endophytic fungi for establishing the tripartite mutualistic symbiosis in M. oleifera to alleviate the adverse effects of drought stress through strong antioxidant activities.
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NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis. Sci Rep 2022; 12:11264. [PMID: 35787631 PMCID: PMC9253118 DOI: 10.1038/s41598-022-14429-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. ‘Thermomemory’ is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Arabidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like ataf1, anac055 mutants show improved thermomemory, revealing a potential co-control of both NAC TFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.
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Rauf M, Ur-Rahman A, Arif M, Gul H, Ud-Din A, Hamayun M, Lee IJ. Immunomodulatory Molecular Mechanisms of Luffa cylindrica for Downy Mildews Resistance Induced by Growth-Promoting Endophytic Fungi. J Fungi (Basel) 2022; 8:689. [PMID: 35887445 PMCID: PMC9324744 DOI: 10.3390/jof8070689] [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: 06/16/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/27/2023] Open
Abstract
Downy mildew (DM), caused by P. cubensis, is harmful to cucurbits including luffa, with increased shortcomings associated with its control through cultural practices, chemical fungicides, and resistant cultivars; there is a prompt need for an effective, eco-friendly, economical, and safe biocontrol approach. Current research is therefore dealt with the biocontrol of luffa DM1 through the endophytic fungi (EF) consortium. Results revealed that T. harzianum (ThM9) and T. virens (TvA1) showed pathogen-dependent inducible metabolic production of squalene and gliotoxins by higher gene expression induction of SQS1/ERG9 (squalene synthase) and GliP (non-ribosomal peptide synthetase). Gene expression of lytic enzymes of EF was also induced with subsequently higher enzyme activities upon confrontation with P. cubensis. EF-inoculated luffa seeds showed efficient germination with enhanced growth potential and vigor of seedlings. EF-inoculated plants showed an increased level of growth-promoting hormone GA with higher gene expression of GA2OX8. EF-pre-inoculated seedlings were resistant to DM and showed an increased GSH content and antioxidant enzyme activities (SOD, CAT, POD). The level of MDA, H2O2, REL, and disease severity was reduced by EF. ACC, JA, ABA, and SA were overproduced along with higher gene expression of LOX, ERF, NCED2, and PAL. Expression of defense-marker genes (PPO, CAT2, SOD, APX, PER5, LOX, NBS-LRR, PSY, CAS, Ubi, MLP43) was also modulated in EF-inoculated infected plants. Current research supported the use of EF inoculation to effectively escalate the systemic immunity against DM corresponding to the significant promotion of induced systemic resistance (ISR) and systemic acquired resistance (SAR) responses through initiating the defense mechanism by SA, ABA, ET, and JA biosynthesis and signaling pathways in luffa.
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Affiliation(s)
- Mamoona Rauf
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Mardan 23200, Pakistan; (M.R.); (A.U.-R.); (H.G.)
| | - Asim Ur-Rahman
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Mardan 23200, Pakistan; (M.R.); (A.U.-R.); (H.G.)
| | - Muhammad Arif
- Department of Biotechnology, Garden Campus, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Mardan 23200, Pakistan
| | - Humaira Gul
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Mardan 23200, Pakistan; (M.R.); (A.U.-R.); (H.G.)
| | - Aziz Ud-Din
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 21120, Pakistan;
| | - Muhammad Hamayun
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Mardan 23200, Pakistan; (M.R.); (A.U.-R.); (H.G.)
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
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Li L, Huang G, Xiang W, Zhu H, Zhang H, Zhang J, Ding Z, Liu J, Wu D. Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:924490. [PMID: 35755690 PMCID: PMC9226631 DOI: 10.3389/fpls.2022.924490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/23/2022] [Indexed: 06/01/2023]
Abstract
Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.
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Affiliation(s)
- Linbao Li
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Guiyun Huang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Weibo Xiang
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Haofei Zhu
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Haibo Zhang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Jun Zhang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Zehong Ding
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Jihong Liu
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Di Wu
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
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Wang X, Komatsu S. The Role of Phytohormones in Plant Response to Flooding. Int J Mol Sci 2022; 23:6383. [PMID: 35742828 PMCID: PMC9223812 DOI: 10.3390/ijms23126383] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Climatic variations influence the morphological, physiological, biological, and biochemical states of plants. Plant responses to abiotic stress include biochemical adjustments, regulation of proteins, molecular mechanisms, and alteration of post-translational modifications, as well as signal transduction. Among the various abiotic stresses, flooding stress adversely affects the growth of plants, including various economically important crops. Biochemical and biological techniques, including proteomic techniques, provide a thorough understanding of the molecular mechanisms during flooding conditions. In particular, plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by an elaborate hormonal signaling network. With the help of these findings, the main objective is to identify plant responses to flooding and utilize that information for the development of flood-tolerant plants. This review provides an insight into the role of phytohormones in plant response mechanisms to flooding stress, as well as different mitigation strategies that can be successfully administered to improve plant growth during stress exposure. Ultimately, this review will expedite marker-assisted genetic enhancement studies in crops for developing high-yield lines or varieties with flood tolerance.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Fiorucci AS, Michaud O, Schmid-Siegert E, Trevisan M, Allenbach Petrolati L, Çaka Ince Y, Fankhauser C. Shade suppresses wound-induced leaf repositioning through a mechanism involving PHYTOCHROME KINASE SUBSTRATE (PKS) genes. PLoS Genet 2022; 18:e1010213. [PMID: 35622862 PMCID: PMC9197076 DOI: 10.1371/journal.pgen.1010213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 06/14/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022] Open
Abstract
Shaded plants challenged with herbivores or pathogens prioritize growth over defense. However, most experiments have focused on the effect of shading light cues on defense responses. To investigate the potential interaction between shade-avoidance and wounding-induced Jasmonate (JA)-mediated signaling on leaf growth and movement, we used repetitive mechanical wounding of leaf blades to mimic herbivore attacks. Phenotyping experiments with combined treatments on Arabidopsis thaliana rosettes revealed that shade strongly inhibits the wound effect on leaf elevation. By contrast, petiole length is reduced by wounding both in the sun and in the shade. Thus, the relationship between the shade and wounding/JA pathways varies depending on the physiological response, implying that leaf growth and movement can be uncoupled. Using RNA-sequencing, we identified genes with expression patterns matching the hyponastic response (opposite regulation by both stimuli, interaction between treatments with shade dominating the wound signal). Among them were genes from the PKS (Phytochrome Kinase Substrate) family, which was previously studied for its role in phototropism and leaf positioning. Interestingly, we observed reduced shade suppression of the wounding effect in pks2pks4 double mutants while a PKS4 overexpressing line showed constitutively elevated leaves and was less sensitive to wounding. Our results indicate a trait-specific interrelationship between shade and wounding cues on Arabidopsis leaf growth and positioning. Moreover, we identify PKS genes as integrators of external cues in the control of leaf hyponasty further emphasizing the role of these genes in aerial organ positioning. Plants face different types of stressful situations without the ability to relocate to favorable environments. For example, increasing plant density reduces access to sunlight as plants start to shade each other. Foliar shading represents a stress that many plants cope with by changing their morphology. This includes elongation of stem-like structures and repositioning of leaves to favor access to unfiltered sunlight. Plants also defend themselves against various pathogens including herbivores. Defense mechanisms include the production of deterrent chemical and morphological adaptations such as stunted growth and downwards leaf repositioning. Here we studied the morphological response of plants when simultaneously facing shade and herbivore stress. When facing both stresses petiole growth was intermediate between the shade-enhanced and wound-repressed response. In contrast, the shade cue overrides the wounding cue leading to a similar upwards leaf repositioning in the combined treatments or in the response to shade alone. Using gene expression analyses and genetics we identified two members of the Phytochrome Kinase Substrate family as playing a signal integration role when plants simultaneously faced both stresses. This contributes to our understanding of the mechanisms underlying plant morphological adaptations when facing multiple stresses.
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Affiliation(s)
- Anne-Sophie Fiorucci
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Olivier Michaud
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Martine Trevisan
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Laure Allenbach Petrolati
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Yetkin Çaka Ince
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Christian Fankhauser
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Wang J, Liu XF, Zhang HQ, Allan AC, Wang WQ, Yin XR. Transcriptional and post-transcriptional regulation of ethylene biosynthesis by exogenous acetylsalicylic acid in kiwifruit. HORTICULTURE RESEARCH 2022; 9:uhac116. [PMID: 35937863 PMCID: PMC9347011 DOI: 10.1093/hr/uhac116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Levels of ethylene, implicated in the induction of fruit ripening in a diverse array of plants, are influenced by genetic and environmental factors, such as other plant hormones. Among these, salicylic acid (SA) and its derivative, acetylsalicylic acid (ASA), have been demonstrated to inhibit ethylene biosynthesis in fruit, yet the underlying regulatory mechanisms remain elusive. Here, we showed that treatment with exogenous ASA dramatically reduced ethylene production, as well as activities of ACC synthase (ACS) and ACC oxidase (ACO), in kiwifruit tissues. Comparative transcriptome analysis indicated the differential expression of ethylene biosynthetic genes (AdACS1/2 and AdACO5). A screen of transcription factors indicated that AdERF105L and AdWRKY29 were ASA-responsive regulators of AdACS1/2 and AdACO5, respectively. In addition to these genes, AdACS3 and AdACO3 were abundantly expressed in both ASA-treated and control tissues. AdACS3 protein was phosphorylated and stabilized by AdMPK16, a mitogen-activated protein kinase, while AdACO3 activity was enhanced by AdAP, an aspartic peptidase. Exogenous ASA downregulated AdMPK16 and AdAP, thereby influencing ethylene biosynthesis at a post-transcriptional level. These findings led us to propose a multidimensional system for inhibition of ethylene biosynthesis by ASA, inducing differential expression of some ethylene biosynthesis genes, as well as differential effects on protein activity on other targets.
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Affiliation(s)
- Jian Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou Zhejiang, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou Zhejiang, 310058, China
| | - Xiao-fen Liu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou Zhejiang, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou Zhejiang, 310058, China
| | - Hui-qin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou Zhejiang, 310021, China
| | - Andrew C Allan
- New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | | | - Xue-ren Yin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou Zhejiang, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou Zhejiang, 310058, China
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Mahmood K, Torres-Jerez I, Krom N, Liu W, Udvardi MK. Transcriptional Programs and Regulators Underlying Age-Dependent and Dark-Induced Senescence in Medicago truncatula. Cells 2022; 11:cells11091570. [PMID: 35563875 PMCID: PMC9103780 DOI: 10.3390/cells11091570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 12/10/2022] Open
Abstract
In forage crops, age-dependent and stress-induced senescence reduces forage yield and quality. Therefore, delaying leaf senescence may be a way to improve forage yield and quality as well as plant resilience to stresses. Here, we used RNA-sequencing to determine the molecular bases of age-dependent and dark-induced leaf senescence in Medicago truncatula. We identified 6845 differentially expressed genes (DEGs) in M3 leaves associated with age-dependent leaf senescence. An even larger number (14219) of DEGs were associated with dark-induced senescence. Upregulated genes identified during age-dependent and dark-induced senescence were over-represented in oxidation–reduction processes and amino acid, carboxylic acid and chlorophyll catabolic processes. Dark-specific upregulated genes also over-represented autophagy, senescence and cell death. Mitochondrial functions were strongly inhibited by dark-treatment while these remained active during age-dependent senescence. Additionally, 391 DE transcription factors (TFs) belonging to various TF families were identified, including a core set of 74 TFs during age-dependent senescence while 759 DE TFs including a core set of 338 TFs were identified during dark-induced senescence. The heterologous expression of several senescence-induced TFs belonging to NAC, WKRY, bZIP, MYB and HD-zip TF families promoted senescence in tobacco leaves. This study revealed the dynamics of transcriptomic responses to age- and dark-induced senescence in M. truncatula and identified senescence-associated TFs that are attractive targets for future work to control senescence in forage legumes.
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Affiliation(s)
- Kashif Mahmood
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA; (K.M.); (I.T.-J.); (N.K.); (W.L.)
- Noble Research Institute, L.L.C., Ardmore, OK 73401, USA
| | - Ivone Torres-Jerez
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA; (K.M.); (I.T.-J.); (N.K.); (W.L.)
- Noble Research Institute, L.L.C., Ardmore, OK 73401, USA
| | - Nick Krom
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA; (K.M.); (I.T.-J.); (N.K.); (W.L.)
| | - Wei Liu
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA; (K.M.); (I.T.-J.); (N.K.); (W.L.)
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX 76201, USA
| | - Michael K. Udvardi
- Noble Research Institute, L.L.C., Ardmore, OK 73401, USA
- Centre for Crop Science, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Correspondence:
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Ayatollahi Z, Kazanaviciute V, Shubchynskyy V, Kvederaviciute K, Schwanninger M, Rozhon W, Stumpe M, Mauch F, Bartels S, Ulm R, Balazadeh S, Mueller-Roeber B, Meskiene I, Schweighofer A. Dual control of MAPK activities by AP2C1 and MKP1 MAPK phosphatases regulates defence responses in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2369-2384. [PMID: 35088853 PMCID: PMC9015810 DOI: 10.1093/jxb/erac018] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades transmit environmental signals and induce stress and defence responses in plants. These signalling cascades are negatively controlled by specific Ser/Thr protein phosphatases of the type 2C (PP2C) and dual-specificity phosphatase (DSP) families that inactivate stress-induced MAPKs; however, the interplay between phosphatases of these different types has remained unknown. This work reveals that different Arabidopsis MAPK phosphatases, the PP2C-type AP2C1 and the DSP-type MKP1, exhibit both specific and overlapping functions in plant stress responses. Each single mutant, ap2c1 and mkp1, and the ap2c1 mkp1 double mutant displayed enhanced stress-induced activation of the MAPKs MPK3, MPK4, and MPK6, as well as induction of a set of transcription factors. Moreover, ap2c1 mkp1 double mutants showed an autoimmune-like response, associated with increased levels of the stress hormones salicylic acid and ethylene, and of the phytoalexin camalexin. This phenotype was reduced in the ap2c1 mkp1 mpk3 and ap2c1 mkp1 mpk6 triple mutants, suggesting that the autoimmune-like response is due to MAPK misregulation. We conclude that the evolutionarily distant MAPK phosphatases AP2C1 and MKP1 contribute crucially to the tight control of MAPK activities, ensuring appropriately balanced stress signalling and suppression of autoimmune-like responses during plant growth and development.
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Affiliation(s)
- Zahra Ayatollahi
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Vaiva Kazanaviciute
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Volodymyr Shubchynskyy
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Kotryna Kvederaviciute
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Manfred Schwanninger
- Department of Chemistry, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Wilfried Rozhon
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, Strenzfelder Allee 28, D-06406 Bernburg, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Felix Mauch
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Sebastian Bartels
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestraße 1, D-79104 Freiburg, Germany
| | - Roman Ulm
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, 30 Quai E. Ansermet, CH-1211 Geneva, Switzerland
| | - Salma Balazadeh
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, D-14476 Potsdam, Germany
- University of Potsdam, Karl-Liebknecht-Straße 24, D-14476 Potsdam, Germany
- Institute of Biology Leiden (IBL), Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Bernd Mueller-Roeber
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, D-14476 Potsdam, Germany
- University of Potsdam, Karl-Liebknecht-Straße 24, D-14476 Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Ruski 139 Blvd., Plovdiv 4000, Bulgaria
| | - Irute Meskiene
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Alois Schweighofer
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
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Liu J, Chen Y, Wang WQ, Liu JH, Zhu CQ, Zhong YP, Zhang HQ, Liu XF, Yin XR. Transcription factors AcERF74/75 respond to waterlogging stress and trigger alcoholic fermentation-related genes in kiwifruit. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111115. [PMID: 34895544 DOI: 10.1016/j.plantsci.2021.111115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Kiwifruit plants have a fleshy, shallow root system which is sensitive to waterlogging stress, which results in a decrease in crop yield or even plants death. Although the waterlogging stress responses in kiwifruit have attracted much attention, the underlying molecular mechanism remains unclear. In this study, waterlogging led to drastic inhibition of root growth of 'Donghong' kiwifruit (Actinidia chinensis) plants grown in vitro, which was accompanied by significant elevation of endogenous acetaldehyde and ethanol contents. RNA-seq of roots of plants waterlogged for 0, 1 and 2 days revealed that a total of 149 genes were up- or down-regulated, including seven biosynthetic genes related to the glycolysis/gluconeogenesis pathway and 10 transcription factors. Analyses with real-time PCR, dual-luciferase assays and EMSA demonstrated that AcERF74 and AcERF75, two members of the ERF-VII subfamily, directly upregulated AcADH1 (alcohol dehydrogenase). Moreover, the overexpression of AcERF74/75 in transgenic calli resulted in dramatic increase of endogenous ethanol contents through the triggering of AcADH1 and AcADH2 expression. Although the AcPDC2 (pyruvate decarboxylase) expression was also enhanced in transgenic lines, the endogenous acetaldehyde contents showed no significant changes. These results illustrated that AcERF74/75 are two transcriptional activators on alcoholic fermentation related genes and are responsive to waterlogging stress in kiwifruit.
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Affiliation(s)
- Jiao Liu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Yue Chen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Wen-Qiu Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Chang-Qing Zhu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Yun-Peng Zhong
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Hui-Qin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China.
| | - Xiao-Fen Liu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China.
| | - Xue-Ren Yin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
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Geldhof B, Pattyn J, Eyland D, Carpentier S, Van de Poel B. A digital sensor to measure real-time leaf movements and detect abiotic stress in plants. PLANT PHYSIOLOGY 2021; 187:1131-1148. [PMID: 34618089 PMCID: PMC8566216 DOI: 10.1093/plphys/kiab407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/02/2021] [Indexed: 05/31/2023]
Abstract
Plant and plant organ movements are the result of a complex integration of endogenous growth and developmental responses, partially controlled by the circadian clock, and external environmental cues. Monitoring of plant motion is typically done by image-based phenotyping techniques with the aid of computer vision algorithms. Here we present a method to measure leaf movements using a digital inertial measurement unit (IMU) sensor. The lightweight sensor is easily attachable to a leaf or plant organ and records angular traits in real-time for two dimensions (pitch and roll) with high resolution (measured sensor oscillations of 0.36 ± 0.53° for pitch and 0.50 ± 0.65° for roll). We were able to record simple movements such as petiole bending, as well as complex lamina motions, in several crops, ranging from tomato to banana. We also assessed growth responses in terms of lettuce rosette expansion and maize seedling stem movements. The IMU sensors are capable of detecting small changes of nutations (i.e. bending movements) in leaves of different ages and in different plant species. In addition, the sensor system can also monitor stress-induced leaf movements. We observed that unfavorable environmental conditions evoke certain leaf movements, such as drastic epinastic responses, as well as subtle fading of the amplitude of nutations. In summary, the presented digital sensor system enables continuous detection of a variety of leaf motions with high precision, and is a low-cost tool in the field of plant phenotyping, with potential applications in early stress detection.
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Affiliation(s)
- Batist Geldhof
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
| | - Jolien Pattyn
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
| | - David Eyland
- Department of Biosystems, Division of Crop Biotechnics, Tropical Crop Improvement Laboratory, University of Leuven, Leuven 3001, Belgium
| | - Sebastien Carpentier
- Department of Biosystems, Division of Crop Biotechnics, Tropical Crop Improvement Laboratory, University of Leuven, Leuven 3001, Belgium
- Bioversity International, Leuven, 3001, Belgium
| | - Bram Van de Poel
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
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Understanding a Mechanistic Basis of ABA Involvement in Plant Adaptation to Soil Flooding: The Current Standing. PLANTS 2021; 10:plants10101982. [PMID: 34685790 PMCID: PMC8537370 DOI: 10.3390/plants10101982] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022]
Abstract
Soil flooding severely impairs agricultural crop production. Plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by the elaborated hormonal signaling network. The most prominent of these hormones is ethylene, which has been firmly established as a critical signal in flooding tolerance. ABA (abscisic acid) is also known as a “stress hormone” that modulates various responses to abiotic stresses; however, its role in flooding tolerance remains much less established. Here, we discuss the progress made in the elucidation of morphological adaptations regulated by ABA and its crosstalk with other phytohormones under flooding conditions in model plants and agriculturally important crops.
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A Gain-of-Function Mutant of IAA7 Inhibits Stem Elongation by Transcriptional Repression of EXPA5 Genes in Brassica napus. Int J Mol Sci 2021; 22:ijms22169018. [PMID: 34445724 PMCID: PMC8396470 DOI: 10.3390/ijms22169018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/09/2023] Open
Abstract
Plant height is one of the most important agronomic traits of rapeseeds. In this study, we characterized a dwarf Brassica napus mutant, named ndf-2, obtained from fast neutrons and DES mutagenesis. Based on BSA-Seq and genetic properties, we identified causal mutations with a time-saving approach. The ndf-2 mutation was identified on chromosome A03 and can result in an amino acid substitution in the conserved degron motif (GWPPV to EWPPV) of the Auxin/indole-3-acetic acid protein 7 (BnaA03.IAA7) encoded by the causative gene. Aux/IAA protein is one of the core components of the auxin signaling pathway, which regulates many growth and development processes. However, the molecular mechanism of auxin signal regulating plant height is still not well understood. In the following work, we identified that BnaARF6 and BnaARF8 as interactors of BnaA03.IAA7 and BnaEXPA5 as a target of BnaARF6 and BnaARF8. The three genes BnaA03.IAA7, BnaARF6/8 and BnaEXPA5 were highly expressed in stem, suggesting that these genes were involved in stem development. The overexpression of BnaEXPA5 results in larger rosettes leaves and longer inflorescence stems in Arabidopsis thaliana. Our results indicate that BnaA03.IAA7- and BnaARF6/8-dependent auxin signal control stem elongation and plant height by regulating the transcription of BnaEXPA5 gene, which is one of the targets of this signal.
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Melo BP, Lourenço-Tessutti IT, Fraga OT, Pinheiro LB, de Jesus Lins CB, Morgante CV, Engler JA, Reis PAB, Grossi-de-Sá MF, Fontes EPB. Contrasting roles of GmNAC065 and GmNAC085 in natural senescence, plant development, multiple stresses and cell death responses. Sci Rep 2021; 11:11178. [PMID: 34045652 PMCID: PMC8160357 DOI: 10.1038/s41598-021-90767-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/10/2021] [Indexed: 01/16/2023] Open
Abstract
NACs are plant-specific transcription factors involved in controlling plant development, stress responses, and senescence. As senescence-associated genes (SAGs), NACs integrate age- and stress-dependent pathways that converge to programmed cell death (PCD). In Arabidopsis, NAC-SAGs belong to well-characterized regulatory networks, poorly understood in soybean. Here, we interrogated the soybean genome and provided a comprehensive analysis of senescence-associated Glycine max (Gm) NACs. To functionally examine GmNAC-SAGs, we selected GmNAC065, a putative ortholog of Arabidopsis ANAC083/VNI2 SAG, and the cell death-promoting GmNAC085, an ANAC072 SAG putative ortholog, for analyses. Expression analysis of GmNAC065 and GmNAC085 in soybean demonstrated (i) these cell death-promoting GmNACs display contrasting expression changes during age- and stress-induced senescence; (ii) they are co-expressed with functionally different gene sets involved in stress and PCD, and (iii) are differentially induced by PCD inducers. Furthermore, we demonstrated GmNAC065 expression delays senescence in Arabidopsis, a phenotype associated with enhanced oxidative performance under multiple stresses, higher chlorophyll, carotenoid and sugar contents, and lower stress-induced PCD compared to wild-type. In contrast, GmNAC085 accelerated stress-induced senescence, causing enhanced chlorophyll loss, ROS accumulation and cell death, decreased antioxidative system expression and activity. Accordingly, GmNAC065 and GmNAC085 targeted functionally contrasting sets of downstream AtSAGs, further indicating that GmNAC85 and GmNAC065 regulators function inversely in developmental and environmental PCD.
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Affiliation(s)
- Bruno Paes Melo
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Brazil.
- Embrapa Genetic Resources and Biotechnology, CENARGEN, Brasília, Brazil.
- Pole Sophia Agrobiotech, Institute Nacional de la Recherche Agronomique, INRAE, Sophia Antipolis, France.
- National Institute in Science and Technology in Plant-Pest Interactions, NCTIPP, Bioagro, Viçosa, Brazil.
| | - Isabela Tristan Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, CENARGEN, Brasília, Brazil
- Pole Sophia Agrobiotech, Institute Nacional de la Recherche Agronomique, INRAE, Sophia Antipolis, France
- National Institute in Science and Technology, INCT Plant Stress-Biotech, CENARGEN, Brasília, Brazil
| | - Otto Teixeira Fraga
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Brazil
- National Institute in Science and Technology in Plant-Pest Interactions, NCTIPP, Bioagro, Viçosa, Brazil
| | - Luanna Bezerra Pinheiro
- Embrapa Genetic Resources and Biotechnology, CENARGEN, Brasília, Brazil
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, Brazil
- National Institute in Science and Technology, INCT Plant Stress-Biotech, CENARGEN, Brasília, Brazil
| | - Camila Barrozo de Jesus Lins
- Embrapa Genetic Resources and Biotechnology, CENARGEN, Brasília, Brazil
- National Institute in Science and Technology, INCT Plant Stress-Biotech, CENARGEN, Brasília, Brazil
| | - Carolina Vianna Morgante
- Embrapa Genetic Resources and Biotechnology, CENARGEN, Brasília, Brazil
- National Institute in Science and Technology, INCT Plant Stress-Biotech, CENARGEN, Brasília, Brazil
| | - Janice Almeida Engler
- Pole Sophia Agrobiotech, Institute Nacional de la Recherche Agronomique, INRAE, Sophia Antipolis, France
| | - Pedro Augusto Braga Reis
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Brazil
- National Institute in Science and Technology in Plant-Pest Interactions, NCTIPP, Bioagro, Viçosa, Brazil
| | - Maria Fátima Grossi-de-Sá
- Embrapa Genetic Resources and Biotechnology, CENARGEN, Brasília, Brazil
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, Brazil
- National Institute in Science and Technology, INCT Plant Stress-Biotech, CENARGEN, Brasília, Brazil
| | - Elizabeth Pacheco Batista Fontes
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Brazil.
- National Institute in Science and Technology in Plant-Pest Interactions, NCTIPP, Bioagro, Viçosa, Brazil.
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Transcriptome Analysis Reveals Genes of Flooding-Tolerant and Flooding-Sensitive Rapeseeds Differentially Respond to Flooding at the Germination Stage. PLANTS 2021; 10:plants10040693. [PMID: 33916802 PMCID: PMC8065761 DOI: 10.3390/plants10040693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 12/31/2022]
Abstract
Flooding results in significant crop yield losses due to exposure of plants to hypoxic stress. Various studies have reported the effect of flooding stress at seedling establishment or later stages. However, the molecular mechanism prevailing at the germination stage under flooding stress remains enigmatic. The present study highlights the comparative transcriptome analysis in two rapeseed lines, i.e., flooding-tolerant (Santana) and -sensitive (23651) lines under control and 6-h flooding treatments at the germination stage. A total of 1840 up-regulated and 1301 down-regulated genes were shared by both lines in response to flooding. There were 4410 differentially expressed genes (DEGs) with increased expression and 4271 DEGs with reduced expression shared in both control and flooding conditions. Gene ontology (GO) enrichment analysis revealed that “transcription regulation”, “structural constituent of cell wall”, “reactive oxygen species metabolic”, “peroxidase”, oxidoreductase”, and “antioxidant activity” were the common processes in rapeseed flooding response. In addition, the processes such as “hormone-mediated signaling pathway”, “response to organic substance response”, “motor activity”, and “microtubule-based process” are likely to confer rapeseed flooding resistance. Mclust analysis clustered DEGs into nine modules; genes in each module shared similar expression patterns and many of these genes overlapped with the top 20 DEGs in some groups. This work provides a comprehensive insight into gene responses and the regulatory network in rapeseed flooding stress and provides guidelines for probing the underlying molecular mechanisms in flooding resistance.
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Li Q, Zhou S, Liu W, Zhai Z, Pan Y, Liu C, Chern M, Wang H, Huang M, Zhang Z, Tang J, Du H. A chlorophyll a oxygenase 1 gene ZmCAO1 contributes to grain yield and waterlogging tolerance in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3155-3167. [PMID: 33571996 DOI: 10.1093/jxb/erab059] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 02/07/2021] [Indexed: 05/16/2023]
Abstract
Chlorophylls function in photosynthesis, and are critical to plant developmental processes and responses to environmental stimuli. Chlorophyll b is synthesized from chlorophyll a by chlorophyll a oxygenase (CAO). Here, we characterize a yellow-green leaf (ygl) mutant and identify the causal gene which encodes a chlorophyll a oxygenase in maize (ZmCAO1). A 51 bp Popin transposon insertion in ZmCAO1 strongly disrupts its transcription. Low enzyme activity of ZmCAO1 leads to reduced concentrations of chlorophyll a and chlorophyll b, resulting in the yellow-green leaf phenotype of the ygl mutant. The net photosynthetic rate, stomatal conductance, and transpiration rate are decreased in the ygl mutant, while concentrations of δ-aminolevulinic acid (ALA), porphobilinogen (PBG) and protochlorophyllide (Pchlide) are increased. In addition, a ZmCAO1 mutation results in down-regulation of key photosynthetic genes, limits photosynthetic assimilation, and reduces plant height, ear size, kernel weight, and grain yield. Furthermore, the zmcao1 mutant shows enhanced reactive oxygen species production leading to sensitivity to waterlogging. These results demonstrate the pleiotropy of ZmCAO1 function in photosynthesis, grain yield, and waterlogging tolerance in maize.
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Affiliation(s)
- Qin Li
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R.China
| | - Shuangzhen Zhou
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R.China
| | - Wenyu Liu
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R.China
| | - Zhensheng Zhai
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R.China
| | - Yitian Pan
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R.China
| | - Changchang Liu
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R.China
| | - Mawsheng Chern
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616,USA
| | - Hongwei Wang
- Hubei Collaborative Innovation Center for Grain Crops, Yangzte University, Jingzhou 434025, P.R. China
| | - Min Huang
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R.China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070,P.R.China
| | - Jihua Tang
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046,P.R.China
| | - Hewei Du
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R.China
- Hubei Collaborative Innovation Center for Grain Crops, Yangzte University, Jingzhou 434025, P.R. China
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Fooyontphanich K, Morcillo F, Joët T, Dussert S, Serret J, Collin M, Amblard P, Tangphatsornruang S, Roongsattham P, Jantasuriyarat C, Verdeil JL, Tranbarger TJ. Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission. BMC PLANT BIOLOGY 2021; 21:92. [PMID: 33573592 PMCID: PMC7879690 DOI: 10.1186/s12870-021-02874-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Fruit abscission depends on cell separation that occurs within specialized cell layers that constitute an abscission zone (AZ). To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. RESULTS Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. CONCLUSIONS The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.
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Affiliation(s)
- Kim Fooyontphanich
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- Grow A Green Co, Ltd. 556 Maha Chakraphat Rd. Namaung, Chachoengsao, Chachoengsao Province, 24000, Thailand
| | - Fabienne Morcillo
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- CIRAD, DIADE, F-34398, Montpellier, France
| | - Thierry Joët
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Stéphane Dussert
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Julien Serret
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Myriam Collin
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | | | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency, 111 Thailand Science Park, Phahonyothin Road, Pathum Thani, Thailand
| | - Peerapat Roongsattham
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- Department of Genetics, Faculty of Science, Kasetsart University Bangkhen Campus, 50 Phahonyothin Road Jatujak, Bangkok, Thailand
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University Bangkhen Campus, 50 Phahonyothin Road Jatujak, Bangkok, Thailand
| | - Jean-Luc Verdeil
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Timothy J Tranbarger
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France.
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Pattyn J, Vaughan‐Hirsch J, Van de Poel B. The regulation of ethylene biosynthesis: a complex multilevel control circuitry. THE NEW PHYTOLOGIST 2021; 229:770-782. [PMID: 32790878 PMCID: PMC7820975 DOI: 10.1111/nph.16873] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/04/2020] [Indexed: 05/06/2023]
Abstract
The gaseous plant hormone ethylene is produced by a fairly simple two-step biosynthesis route. Despite this pathway's simplicity, recent molecular and genetic studies have revealed that the regulation of ethylene biosynthesis is far more complex and occurs at different layers. Ethylene production is intimately linked with the homeostasis of its general precursor S-adenosyl-l-methionine (SAM), which experiences transcriptional and posttranslational control of its synthesising enzymes (SAM synthetase), as well as the metabolic flux through the adjacent Yang cycle. Ethylene biosynthesis continues from SAM by two dedicated enzymes: 1-aminocyclopropane-1-carboxylic (ACC) synthase (ACS) and ACC oxidase (ACO). Although the transcriptional dynamics of ACS and ACO have been well documented, the first transcription factors that control ACS and ACO expression have only recently been discovered. Both ACS and ACO display a type-specific posttranslational regulation that controls protein stability and activity. The nonproteinogenic amino acid ACC also shows a tight level of control through conjugation and translocation. Different players in ACC conjugation and transport have been identified over the years, however their molecular regulation and biological significance is unclear, yet relevant, as ACC can also signal independently of ethylene. In this review, we bring together historical reports and the latest findings on the complex regulation of the ethylene biosynthesis pathway in plants.
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Affiliation(s)
- Jolien Pattyn
- Molecular Plant Hormone Physiology LaboratoryDivision of Crop BiotechnicsDepartment of BiosystemsUniversity of LeuvenWillem de Croylaan 42Leuven3001Belgium
| | - John Vaughan‐Hirsch
- Molecular Plant Hormone Physiology LaboratoryDivision of Crop BiotechnicsDepartment of BiosystemsUniversity of LeuvenWillem de Croylaan 42Leuven3001Belgium
| | - Bram Van de Poel
- Molecular Plant Hormone Physiology LaboratoryDivision of Crop BiotechnicsDepartment of BiosystemsUniversity of LeuvenWillem de Croylaan 42Leuven3001Belgium
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50
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Shan W, Kuang JF, Wei W, Fan ZQ, Deng W, Li ZG, Bouzayen M, Pirrello J, Lu WJ, Chen JY. MaXB3 Modulates MaNAC2, MaACS1, and MaACO1 Stability to Repress Ethylene Biosynthesis during Banana Fruit Ripening. PLANT PHYSIOLOGY 2020; 184:1153-1171. [PMID: 32694134 PMCID: PMC7536691 DOI: 10.1104/pp.20.00313] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/09/2020] [Indexed: 05/19/2023]
Abstract
Ethylene plays a critical regulatory role in climacteric fruit ripening, and its biosynthesis is fine-tuned at the transcriptional and posttranslational levels. Nevertheless, the mechanistic link between transcriptional and posttranslational regulation of ethylene biosynthesis during fruit ripening is largely unknown. This study uncovers a coordinated transcriptional and posttranslational mechanism of controlling ethylene biosynthesis during banana (Musa acuminata) fruit ripening. NAC (NAM, ATAF, and CUC) proteins MaNAC1 and MaNAC2 repress the expression of MaERF11, a protein previously known to negatively regulate ethylene biosynthesis genes MaACS1 and MaACO1 A RING E3 ligase MaXB3 interacts with MaNAC2 to promote its ubiquitination and degradation, leading to the inhibition of MaNAC2-mediated transcriptional repression. In addition, MaXB3 also targets MaACS1 and MaACO1 for proteasome degradation. Further evidence supporting the role of MaXB3 is provided by its transient and ectopic overexpression in banana fruit and tomato (Solanum lycopersicum), respectively, which delays fruit ripening via repressing ethylene biosynthesis and thus ethylene response. Strikingly, MaNAC1 and MaNAC2 directly repress MaXB3 expression, suggesting a feedback regulatory mechanism that maintains a balance of MaNAC2, MaACS1, and MaACO1 levels. Collectively, our findings establish a multilayered regulatory cascade involving MaXB3, MaNACs, MaERF11, and MaACS1/MaACO1 that controls ethylene biosynthesis during climacteric ripening.
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Affiliation(s)
- Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhong-Qi Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Deng
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Zheng-Guo Li
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Mondher Bouzayen
- Génomique et Biotechnologie des Fruits, Université de Toulouse, INRA, Castanet-Tolosan 31320, France
| | - Julien Pirrello
- Génomique et Biotechnologie des Fruits, Université de Toulouse, INRA, Castanet-Tolosan 31320, France
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
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