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Berthelier TH, Cabanac SC, Callot C, Bellec A, Mathé C, Jamet E, Dunand C. Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three Brassicaceae Species. Int J Mol Sci 2024; 25:1938. [PMID: 38339216 PMCID: PMC10856686 DOI: 10.3390/ijms25031938] [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: 12/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Climate change is expected to intensify the occurrence of abiotic stress in plants, such as hypoxia and salt stresses, leading to the production of reactive oxygen species (ROS), which need to be effectively managed by various oxido-reductases encoded by the so-called ROS gene network. Here, we studied six oxido-reductases families in three Brassicaceae species, Arabidopsis thaliana as well as Nasturtium officinale and Eutrema salsugineum, which are adapted to hypoxia and salt stress, respectively. Using available and new genomic data, we performed a phylogenomic analysis and compared RNA-seq data to study genomic and transcriptomic adaptations. This comprehensive approach allowed for the gaining of insights into the impact of the adaptation to saline or hypoxia conditions on genome organization (gene gains and losses) and transcriptional regulation. Notably, the comparison of the N. officinale and E. salsugineum genomes to that of A. thaliana highlighted changes in the distribution of ohnologs and homologs, particularly affecting class III peroxidase genes (CIII Prxs). These changes were specific to each gene, to gene families subjected to duplication events and to each species, suggesting distinct evolutionary responses. The analysis of transcriptomic data has allowed for the identification of genes related to stress responses in A. thaliana, and, conversely, to adaptation in N. officinale and E. salsugineum.
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Affiliation(s)
- Thomas Horst Berthelier
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Sébastien Christophe Cabanac
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRAE, 31320 Auzeville-Tolosane, France; (C.C.); (A.B.)
| | - Arnaud Bellec
- Centre National de Ressources Génomiques Végétales, INRAE, 31320 Auzeville-Tolosane, France; (C.C.); (A.B.)
| | - Catherine Mathé
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
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Scandola S, Mehta D, Li Q, Rodriguez Gallo MC, Castillo B, Uhrig RG. Multi-omic analysis shows REVEILLE clock genes are involved in carbohydrate metabolism and proteasome function. PLANT PHYSIOLOGY 2022; 190:1005-1023. [PMID: 35670757 PMCID: PMC9516735 DOI: 10.1093/plphys/kiac269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/12/2022] [Indexed: 06/01/2023]
Abstract
Plants are able to sense changes in their light environments, such as the onset of day and night, as well as anticipate these changes in order to adapt and survive. Central to this ability is the plant circadian clock, a molecular circuit that precisely orchestrates plant cell processes over the course of a day. REVEILLE (RVE) proteins are recently discovered members of the plant circadian circuitry that activate the evening complex and PSEUDO-RESPONSE REGULATOR genes to maintain regular circadian oscillation. The RVE8 protein and its two homologs, RVE 4 and 6 in Arabidopsis (Arabidopsis thaliana), have been shown to limit the length of the circadian period, with rve 4 6 8 triple-knockout plants possessing an elongated period along with increased leaf surface area, biomass, cell size, and delayed flowering relative to wild-type Col-0 plants. Here, using a multi-omics approach consisting of phenomics, transcriptomics, proteomics, and metabolomics we draw new connections between RVE8-like proteins and a number of core plant cell processes. In particular, we reveal that loss of RVE8-like proteins results in altered carbohydrate, organic acid, and lipid metabolism, including a starch excess phenotype at dawn. We further demonstrate that rve 4 6 8 plants have lower levels of 20S proteasome subunits and possess significantly reduced proteasome activity, potentially explaining the increase in cell-size observed in RVE8-like mutants. Overall, this robust, multi-omic dataset provides substantial insight into the far-reaching impact RVE8-like proteins have on the diel plant cell environment.
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Affiliation(s)
| | | | - Qiaomu Li
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | | | - Brigo Castillo
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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Wang N, Lin Y, Qi F, Xiaoyang C, Peng Z, Yu Y, Liu Y, Zhang J, Qi X, Deyholos M, Zhang J. Comprehensive Analysis of Differentially Expressed Genes and Epigenetic Modification-Related Expression Variation Induced by Saline Stress at Seedling Stage in Fiber and Oil Flax, Linum usitatissimum L. PLANTS (BASEL, SWITZERLAND) 2022; 11:2053. [PMID: 35956530 PMCID: PMC9370232 DOI: 10.3390/plants11152053] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/23/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The ability of different germplasm to adapt to a saline-alkali environment is critical to learning about the tolerance mechanism of saline-alkali stress in plants. Flax is an important oil and fiber crop in many countries. However, its molecular tolerance mechanism under saline stress is still not clear. In this study, we studied morphological, physiological characteristics, and gene expression variation in the root and leaf in oil and fiber flax types under saline stress, respectively. Abundant differentially expressed genes (DEGs) induced by saline stress, tissue/organ specificity, and different genotypes involved in plant hormones synthesis and metabolism and transcription factors and epigenetic modifications were detected. The present report provides useful information about the mechanism of flax response to saline stress and could lead to the future elucidation of the specific functions of these genes and help to breed suitable flax varieties for saline/alkaline soil conditions.
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Affiliation(s)
- Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Yujie Lin
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Chunxiao Xiaoyang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun 130000, China
| | - Ying Yu
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Yingnan Liu
- Institute of Natural Resource and Ecology, Heilongjiang Academy of Science, Harbin 150040, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Xin Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Michael Deyholos
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
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Li J, Evon P, Ballas S, Trinh HK, Xu L, Van Poucke C, Van Droogenbroeck B, Motti P, Mangelinckx S, Ramirez A, Van Gerrewey T, Geelen D. Sunflower Bark Extract as a Biostimulant Suppresses Reactive Oxygen Species in Salt-Stressed Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:837441. [PMID: 35845677 PMCID: PMC9285015 DOI: 10.3389/fpls.2022.837441] [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: 12/16/2021] [Accepted: 05/30/2022] [Indexed: 05/27/2023]
Abstract
A survey of plant-based wastes identified sunflower (Helianthus annuus) bark extract (SBE), produced via twin-screw extrusion, as a potential biostimulant. The addition of SBE to Arabidopsis (Arabidopsis thaliana) seedlings cultured in vitro showed a dose-dependent response, with high concentrations causing severe growth inhibition. However, when priming seeds with SBE, a small but significant increase in leaf area was observed at a dose of 0.5 g of lyophilized powder per liter. This optimal concentration of SBE in the culturing medium alleviated the growth inhibition caused by 100 mM NaCl. The recovery in shoot growth was accompanied by a pronounced increase in photosynthetic pigment levels and a stabilization of osmotic homeostasis. SBE-primed leaf discs also showed a similar protective effect. SBE mitigated salt stress by reducing the production of reactive oxygen species (ROS) (e.g., hydrogen peroxide) by about 30% and developing more expanded true leaves. This reduction in ROS levels was due to the presence of antioxidative agents in SBE and by activating ROS-eliminating enzymes. Polyphenols, carbohydrates, proteins, and other bioactive compounds detected in SBE may have contributed to the cellular redox homeostasis in salt-stressed plants, thus promoting early leaf development by relieving shoot apical meristem arrest. Sunflower stalks from which SBE is prepared can therefore potentially be valorized as a source to produce biostimulants for improving salt stress tolerance in crops.
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Affiliation(s)
- Jing Li
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Philippe Evon
- Laboratoire de Chimie Agro-Industrielle, Université de Toulouse, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École Nationale Supérieure des Ingénieurs en Arts Chimiques et Technologiques (ENSIACET), Toulouse, France
| | | | - Hoang Khai Trinh
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Biotechnology Research and Development Institute (BiRDI), Can Tho University, Can Tho, Vietnam
| | - Lin Xu
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Christof Van Poucke
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Pierfrancesco Motti
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sven Mangelinckx
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Aldana Ramirez
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thijs Van Gerrewey
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Cheng C, Wang J, Hou W, Malik K, Zhao C, Niu X, Liu Y, Huang R, Li C, Nan Z. Elucidating the Molecular Mechanisms by which Seed-Borne Endophytic Fungi, Epichloë gansuensis, Increases the Tolerance of Achnatherum inebrians to NaCl Stress. Int J Mol Sci 2021; 22:ijms222413191. [PMID: 34947985 PMCID: PMC8706252 DOI: 10.3390/ijms222413191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 12/29/2022] Open
Abstract
Seed-borne endophyte Epichloë gansuensis enhance NaCl tolerance in Achnatherum inebrians and increase its biomass. However, the molecular mechanism by which E. gansuensis increases the tolerance of host grasses to NaCl stress is unclear. Hence, we firstly explored the full-length transcriptome information of A. inebrians by PacBio RS II. In this work, we obtained 738,588 full-length non-chimeric reads, 36,105 transcript sequences and 27,202 complete CDSs from A. inebrians. We identified 3558 transcription factors (TFs), 15,945 simple sequence repeats and 963 long non-coding RNAs of A. inebrians. The present results show that 2464 and 1817 genes were differentially expressed by E. gansuensis in the leaves of E+ and E− plants at 0 mM and 200 mM NaCl concentrations, respectively. In addition, NaCl stress significantly regulated 4919 DEGs and 502 DEGs in the leaves of E+ and E− plants, respectively. Transcripts associated with photosynthesis, plant hormone signal transduction, amino acids metabolism, flavonoid biosynthetic process and WRKY TFs were differentially expressed by E. gansuensis; importantly, E. gansuensis up-regulated biology processes (brassinosteroid biosynthesis, oxidation–reduction, cellular calcium ion homeostasis, carotene biosynthesis, positive regulation of proteasomal ubiquitin-dependent protein catabolism and proanthocyanidin biosynthesis) of host grass under NaCl stress, which indicated an increase in the ability of host grasses’ adaptation to NaCl stress. In conclusion, our study demonstrates the molecular mechanism for E. gansuensis to increase the tolerance to salt stress in the host, which provides a theoretical basis for the molecular breed to create salt-tolerant forage with endophytes.
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Affiliation(s)
- Chen Cheng
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Jianfeng Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
- Correspondence:
| | - Wenpeng Hou
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
| | - Kamran Malik
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Chengzhou Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- Tibetan Medicine Research Center, College of Tibetan Medicine, Qinghai University, Xining 810016, China
| | - Xueli Niu
- School of Life Science and Technology, Lingnan Normal University, Zhanjiang 524048, China;
| | - Yinglong Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Rong Huang
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Chunjie Li
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
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