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Sun Y, Zhao N, Sun H, Xu S, Lu Y, Xi H, Guo Z, Shi H. Transcriptome Profiling Reveals Molecular Responses to Salt Stress in Common Vetch ( Vicia sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:714. [PMID: 38475559 DOI: 10.3390/plants13050714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Common vetch (Vicia sativa L.) is an important annual diploid leguminous forage. In the present study, transcriptomic profiling in common vetch in response to salt stress was conducted using a salt-tolerant line (460) and a salt-sensitive line (429). The common responses in common vetch and the specific responses associated with salt tolerance in 460 were analyzed. Several KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, including plant hormone and MAPK (mitogen-activated protein kinase) signaling, galactose metabolism, and phenylpropanoid phenylpropane biosynthesis, were enriched in both lines, though some differentially expressed genes (DEGs) showed distinct expression patterns. The roots in 460 showed higher levels of lignin than in 429. α-linolenic acid metabolism, carotenoid biosynthesis, the photosynthesis-antenna pathway, and starch and sucrose metabolism pathways were specifically enriched in salt-tolerant line 460, with higher levels of accumulated soluble sugars in the leaves. In addition, higher transcript levels of genes involved in ion homeostasis and reactive oxygen species (ROS) scavenging were observed in 460 than in 429 in response to salt stress. The transcriptomic analysis in common vetch in response to salt stress provides useful clues for further investigations on salt tolerance mechanism in the future.
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Affiliation(s)
- Yanmei Sun
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Na Zhao
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongjian Sun
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan Xu
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiwen Lu
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haojie Xi
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Guo
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifan Shi
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
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Yang J, Yi J, Ma S, Wang Y, Song J, Li S, Feng Y, Sun H, Gao C, Yang R, Li Z, Cao Y, Yang P. Integrated physiological, metabolomic, and transcriptomic analyses elucidate the regulation mechanisms of lignin synthesis under osmotic stress in alfalfa leaf (Medicago sativa L.). BMC Genomics 2024; 25:174. [PMID: 38350871 PMCID: PMC10865589 DOI: 10.1186/s12864-024-10039-1] [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: 09/22/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Alfalfa, an essential forage crop known for its high yield, nutritional value, and strong adaptability, has been widely cultivated worldwide. The yield and quality of alfalfa are frequently jeopardized due to environmental degradation. Lignin, a constituent of the cell wall, enhances plant resistance to abiotic stress, which often causes osmotic stress in plant cells. However, how lignin responds to osmotic stress in leaves remains unclear. This study explored the effects of osmotic stress on lignin accumulation and the contents of intermediate metabolites involved in lignin synthesis in alfalfa leaves. Osmotic stress caused an increase in lignin accumulation and the alteration of core enzyme activities and gene expression in the phenylpropanoid pathway. We identified five hub genes (CSE, CCR, CADa, CADb, and POD) and thirty edge genes (including WRKYs, MYBs, and UBPs) by integrating transcriptome and metabolome analyses. In addition, ABA and ethylene signaling induced by osmotic stress regulated lignin biosynthesis in a contradictory way. These findings contribute to a new theoretical foundation for the breeding of high-quality and resistant alfalfa varieties.
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Affiliation(s)
- Jing Yang
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Jiangnan Yi
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Shihai Ma
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Yafang Wang
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Jiaxing Song
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Yueyan Feng
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Cai Gao
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Zhongxing Li
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China
| | - Yuman Cao
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China.
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, 712100, Yangling, China.
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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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Li C, Zhang H, Qi Y, Zhao Y, Duan C, Wang Y, Meng Z, Zhang Q. Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses. Int J Biol Macromol 2023; 253:126701. [PMID: 37673165 DOI: 10.1016/j.ijbiomac.2023.126701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/08/2023]
Abstract
ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.
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Affiliation(s)
- Chuanshun Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hengyang Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China; Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China
| | - Yuting Qi
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yaoyao Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China; Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China
| | - Chonghao Duan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China; Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China
| | - Yujiao Wang
- Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China
| | - Zhe Meng
- Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China.
| | - Quan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China; Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China.
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Li R, Fu R, Li M, Song Y, Li J, Chen C, Gu Y, Liang X, Nie W, Ma L, Wang X, Zhang H, Zhang H. Transcriptome profiling reveals multiple regulatory pathways of Tamarix chinensis in response to salt stress. PLANT CELL REPORTS 2023; 42:1809-1824. [PMID: 37733273 DOI: 10.1007/s00299-023-03067-w] [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: 08/08/2023] [Accepted: 09/03/2023] [Indexed: 09/22/2023]
Abstract
KEY MESSAGE Multiple regulatory pathways of T. chinensis to salt stress were identified through transcriptome data analysis. Tamarix chinensis (Tamarix chinensis Lour.) is a typical halophyte capable of completing its life cycle in soils with medium to high salinity. However, the mechanisms underlying its resistance to high salt stress are still largely unclear. In this study, transcriptome profiling analyses in different organs of T. chinensis plants in response to salt stress were carried out. A total number of 2280, 689, and 489 differentially expressed genes (DEGs) were, respectively, identified in roots, stems, and leaves, with more DEGs detected in roots than in stems and leaves. Gene Ontology (GO) term analysis revealed that they were significantly enriched in "biological processes" and "molecular functions". Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that "Beta-alanine metabolism" was the most differentially enriched pathway in roots, stems, and leaves. In pair-to-pair comparison of the most differentially enriched pathways, a total of 14 pathways, including 5 pathways in roots and leaves, 6 pathways in roots and stems, and 3 pathways in leaves and stems, were identified. Furthermore, genes encoding transcription factor, such as bHLH, bZIP, HD-Zip, MYB, NAC, WRKY, and genes associated with oxidative stress, starch and sucrose metabolism, and ion homeostasis, were differentially expressed with distinct organ specificity in roots, stems, and leaves. Our findings in this research provide a novel approach for exploring the salt tolerance mechanism of halophytes and identifying new gene targets for the genetic breeding of new plant cultivars with improved resistance to salt stress.
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Affiliation(s)
- Ruxia Li
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Rao Fu
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Meng Li
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Yanjing Song
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Junlin Li
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Chuanjie Chen
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Yinyu Gu
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Xiaoyan Liang
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Wenjing Nie
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Lan Ma
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Xiangyu Wang
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Haiyang Zhang
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China.
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China.
| | - Hongxia Zhang
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China.
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China.
- 3The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China.
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Dabravolski SA, Isayenkov SV. The regulation of plant cell wall organisation under salt stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1118313. [PMID: 36968390 PMCID: PMC10036381 DOI: 10.3389/fpls.2023.1118313] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Plant cell wall biosynthesis is a complex and tightly regulated process. The composition and the structure of the cell wall should have a certain level of plasticity to ensure dynamic changes upon encountering environmental stresses or to fulfil the demand of the rapidly growing cells. The status of the cell wall is constantly monitored to facilitate optimal growth through the activation of appropriate stress response mechanisms. Salt stress can severely damage plant cell walls and disrupt the normal growth and development of plants, greatly reducing productivity and yield. Plants respond to salt stress and cope with the resulting damage by altering the synthesis and deposition of the main cell wall components to prevent water loss and decrease the transport of surplus ions into the plant. Such cell wall modifications affect biosynthesis and deposition of the main cell wall components: cellulose, pectins, hemicelluloses, lignin, and suberin. In this review, we highlight the roles of cell wall components in salt stress tolerance and the regulatory mechanisms underlying their maintenance under salt stress conditions.
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Affiliation(s)
- Siarhei A. Dabravolski
- Department of Biotechnology Engineering, Braude Academic College of Engineering, Karmiel, Israel
| | - Stanislav V. Isayenkov
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics, National Academy of Science (NAS) of Ukraine, Kyiv, Ukraine
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7
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Li C, Duan C, Zhang H, Zhao Y, Meng Z, Zhao Y, Zhang Q. Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment. FRONTIERS IN PLANT SCIENCE 2022; 13:909527. [PMID: 35837468 PMCID: PMC9274170 DOI: 10.3389/fpls.2022.909527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Salt cress (Eutrema salsugineum), an Arabidopsis-related halophyte, can naturally adapt to various harsh climates and soil conditions; thus, it is considered a desirable model plant for deciphering mechanisms of salt and other abiotic stresses. Accumulating evidence has revealed that compared with Arabidopsis, salt cress possesses stomata that close more tightly and more succulent leaves during extreme salt stress, a noticeably higher level of proline, inositols, sugars, and organic acids, as well as stress-associated transcripts in unstressed plants, and they are induced rapidly under stress. In this review, we systematically summarize the research on the morphology, physiology, genome, gene expression and regulation, and protein and metabolite profile of salt cress under salt stress. We emphasize the latest advances in research on the genome adaptive evolution encountering saline environments, and epigenetic regulation, and discuss the mechanisms underlying salt tolerance in salt cress. Finally, we discuss the existing questions and opportunities for future research in halophytic Eutrema. Together, the review fosters a better understanding of the mechanism of plant salt tolerance and provides a reference for the research and utilization of Eutrema as a model extremophile in the future. Furthermore, the prospects for salt cress applied to explore the mechanism of salt tolerance provide a theoretical basis to develop new strategies for agricultural biotechnology.
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Affiliation(s)
- Chuanshun Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Chonghao Duan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Hengyang Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Yaoyao Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Zhe Meng
- Research Team of Plant Pathogen Microbiology and Immunology, College of Life Science, Shandong Normal University, Jinan, China
| | - Yanxiu Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Quan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
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Sun Y, Oh DH, Duan L, Ramachandran P, Ramirez A, Bartlett A, Tran KN, Wang G, Dassanayake M, Dinneny JR. Divergence in the ABA gene regulatory network underlies differential growth control. NATURE PLANTS 2022; 8:549-560. [PMID: 35501452 DOI: 10.1038/s41477-022-01139-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The phytohormone abscisic acid (ABA) is a central regulator of acclimation to environmental stress; however, its contribution to differences in stress tolerance between species is unclear. To establish a comparative framework for understanding how stress hormone signalling pathways diverge across species, we studied the growth response of four Brassicaceae species to ABA treatment and generated transcriptomic and DNA affinity purification and sequencing datasets to construct a cross-species gene regulatory network (GRN) for ABA. Comparison of genes bound directly by ABA-responsive element binding factors suggests that cis-factors are most important for determining the target loci represented in the ABA GRN of a particular species. Using this GRN, we reveal how rewiring of growth hormone subnetworks contributes to stark differences in the response to ABA in the extremophyte Schrenkiella parvula. Our study provides a model for understanding how divergence in gene regulation can lead to species-specific physiological outcomes in response to hormonal cues.
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Affiliation(s)
- Ying Sun
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lina Duan
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Andrea Ramirez
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kieu-Nga Tran
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Guannan Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA.
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9
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The Halophyte Dehydrin Sequence Landscape. Biomolecules 2022; 12:biom12020330. [PMID: 35204830 PMCID: PMC8869203 DOI: 10.3390/biom12020330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/04/2022] Open
Abstract
Dehydrins (DHNs) belong to the LEA (late embryogenesis abundant) family group II, that comprise four conserved motifs (the Y-, S-, F-, and K-segments) and are known to play a multifunctional role in plant stress tolerance. Based on the presence and order of these segments, dehydrins are divided into six subclasses: YnSKn, FnSKn, YnKn, SKn, Kn, and KnS. DHNs are rarely studied in halophytes, and their contribution to the mechanisms developed by these plants to survive in extreme conditions remains unknown. In this work, we carried out multiple genomic analyses of the conservation of halophytic DHN sequences to discover new segments, and examine their architectures, while comparing them with their orthologs in glycophytic plants. We performed an in silico analysis on 86 DHN sequences from 10 halophytic genomes. The phylogenetic tree showed that there are different distributions of the architectures among the different species, and that FSKn is the only architecture present in every plant studied. It was found that K-, F-, Y-, and S-segments are highly conserved in halophytes and glycophytes with a few modifications, mainly involving charged amino acids. Finally, expression data collected for three halophytic species (Puccinillia tenuiflora, Eutrema salsugenium, and Hordeum marinum) revealed that many DHNs are upregulated by salt stress, and the intensity of this upregulation depends on the DHN architecture.
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Ma H, Cai L, Lin J, Zhou K, Li QQ. Divergence in the Regulation of the Salt Tolerant Response Between Arabidopsis thaliana and Its Halophytic Relative Eutrema salsugineum by mRNA Alternative Polyadenylation. FRONTIERS IN PLANT SCIENCE 2022; 13:866054. [PMID: 35401636 PMCID: PMC8993227 DOI: 10.3389/fpls.2022.866054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 05/15/2023]
Abstract
Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in Arabidopsis thaliana and its halophytic relative Eutrema salsugineum with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both Arabidopsis and Eutrema, Eutrema possesses fewer APA genes than Arabidopsis (47% vs. 54%). However, the proportion of APA genes was significantly increased in Arabidopsis under salt stress but not in Eutrema. This indicated that Arabidopsis is more sensitive to salt stress and that Eutrema exhibits an innate response to such conditions. Both species utilized distal poly(A) sites under salt stress; however, only eight genes were found to overlap when their 3' untranslated region (UTR) lengthen genes were compared, thus revealing their distinct responses to salt stress. In Arabidopsis, genes that use distal poly(A) sites were enriched in response to salt stress. However, in Eutrema, the use of poly(A) sites was less affected and fewer genes were enriched. The transcripts with upregulated poly(A) sites in Arabidopsis showed enriched pathways in plant hormone signal transduction, starch and sucrose metabolism, and fatty acid elongation; in Eutrema, biosynthetic pathways (stilbenoid, diarylheptanoid, and gingerol) and metabolic pathways (arginine and proline) showed enrichment. APA was associated with 42% and 29% of the differentially expressed genes (DE genes) in Arabidopsis and Eutrema experiencing salt stress, respectively. Salt specific poly(A) sites and salt-inducible APA events were identified in both species; notably, some salt tolerance-related genes and transcription factor genes exhibited differential APA patterns, such as CIPK21 and LEA4-5. Our results suggest that adapted species exhibit more orderly response at the RNA maturation step under salt stress, while more salt-specific poly(A) sites were activated in Arabidopsis to cope with salinity conditions. Collectively, our findings not only highlight the importance of APA in the regulation of gene expression in response to salt stress, but also provide a new perspective on how salt-sensitive and salt-tolerant species perform differently under stress conditions through transcriptome diversity.
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Affiliation(s)
- Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
| | - Lingling Cai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Kaiyue Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
- *Correspondence: Qingshun Q. Li,
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