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Xue Y, Zhou C, Feng N, Zheng D, Shen X, Rao G, Huang Y, Cai W, Liu Y, Zhang R. Transcriptomic and Lipidomic Analysis Reveals Complex Regulation Mechanisms Underlying Rice Roots' Response to Salt Stress. Metabolites 2024; 14:244. [PMID: 38668372 PMCID: PMC11052231 DOI: 10.3390/metabo14040244] [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: 03/30/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Rice (Oryza sativa L.), a crucial food crop that sustains over half the world's population, is often hindered by salt stress during various growth stages, ultimately causing a decrease in yield. However, the specific mechanism of rice roots' response to salt stress remains largely unknown. In this study, transcriptomics and lipidomics were used to analyze the changes in the lipid metabolism and gene expression profiles of rice roots in response to salt stress. The results showed that salt stress significantly inhibited rice roots' growth and increased the roots' MDA content. Furthermore, 1286 differentially expressed genes including 526 upregulated and 760 downregulated, were identified as responding to salt stress in rice roots. The lipidomic analysis revealed that the composition and unsaturation of membrane lipids were significantly altered. In total, 249 lipid molecules were differentially accumulated in rice roots as a response to salt stress. And most of the major phospholipids, such as phosphatidic acid (PA), phosphatidylcholine (PC), and phosphatidylserine (PS), as well as major sphingolipids including ceramide (Cer), phytoceramide (CerP), monohexose ceramide (Hex1Cer), and sphingosine (SPH), were significantly increased, while the triglyceride (TG) molecules decreased. These results suggested that rice roots mitigate salt stress by altering the fluidity and integrity of cell membranes. This study enhances our comprehension of salt stress, offering valuable insights into changes in the lipids and adaptive lipid remodeling in rice's response to salt stress.
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Affiliation(s)
- Yingbin Xue
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Chenyu Zhou
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
| | - Naijie Feng
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Xuefeng Shen
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Gangshun Rao
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Yongxiang Huang
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Wangxiao Cai
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China;
| | - Ying Liu
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
| | - Rui Zhang
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (Y.X.); (C.Z.); (N.F.); (D.Z.); (X.S.); (G.R.); (Y.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
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Kitavi M, Gemenet DC, Wood JC, Hamilton JP, Wu S, Fei Z, Khan A, Buell CR. Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis. PLANT DIRECT 2023; 7:e532. [PMID: 37794882 PMCID: PMC10546384 DOI: 10.1002/pld3.532] [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: 01/28/2023] [Revised: 04/22/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Sweetpotato, Ipomoea batatas (L.), a key food security crop, is negatively impacted by heat, drought, and salinity stress. The orange-fleshed sweetpotato cultivar "Beauregard" was exposed to heat, salt, and drought treatments for 24 and 48 h to identify genes responding to each stress condition in leaves. Analysis revealed both common (35 up regulated, 259 down regulated genes in the three stress conditions) and unique sets of up regulated (1337 genes by drought, 516 genes by heat, and 97 genes by salt stress) and down regulated (2445 genes by drought, 678 genes by heat, and 204 genes by salt stress) differentially expressed genes (DEGs) suggesting common, yet stress-specific transcriptional responses to these three abiotic stressors. Gene Ontology analysis of down regulated DEGs common to both heat and salt stress revealed enrichment of terms associated with "cell population proliferation" suggestive of an impact on the cell cycle by the two stress conditions. To identify shared and unique gene co-expression networks under multiple abiotic stress conditions, weighted gene co-expression network analysis was performed using gene expression profiles from heat, salt, and drought stress treated 'Beauregard' leaves yielding 18 co-expression modules. One module was enriched for "response to water deprivation," "response to abscisic acid," and "nitrate transport" indicating synergetic crosstalk between nitrogen, water, and phytohormones with genes encoding osmotin, cell expansion, and cell wall modification proteins present as key hub genes in this drought-associated module. This research lays the groundwork for exploring to a further degree, mechanisms for abiotic stress tolerance in sweetpotato.
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Affiliation(s)
- Mercy Kitavi
- Research Technology Support Facility (RTSF)Michigan State UniversityEast LansingMichiganUSA
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
| | - Dorcus C. Gemenet
- International Potato CenterLimaPeru
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF HouseNairobiKenya
| | - Joshua C. Wood
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
| | - John P. Hamilton
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Crop & Soil SciencesUniversity of GeorgiaAthensGeorgiaUSA
| | - Shan Wu
- Boyce Thompson InstituteCornell UniversityIthacaNew YorkUSA
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNew YorkUSA
| | - Awais Khan
- International Potato CenterLimaPeru
- Present address:
Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant ScienceCornell UniversityGenevaNew YorkUSA
| | - C. Robin Buell
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Crop & Soil SciencesUniversity of GeorgiaAthensGeorgiaUSA
- Institute of Plant Breeding, Genetics, & GenomicsUniversity of GeorgiaAthensGeorgiaUSA
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Zuo ZF, Li Y, Mi XF, Li YL, Zhai CY, Yang GF, Wang ZY, Zhang K. Physiological and lipidomic response of exogenous choline chloride alleviating salt stress injury in Kentucky bluegrass ( Poa pratensis). FRONTIERS IN PLANT SCIENCE 2023; 14:1269286. [PMID: 37719216 PMCID: PMC10501137 DOI: 10.3389/fpls.2023.1269286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023]
Abstract
Introduction Choline participates in plant stress tolerance through glycine betaine (GB) and phospholipid metabolism. As a salt-sensitive turfgrass species, Kentucky bluegrass (Poa pratensis) is the main turfgrass species in cool-season areas. Methods To improve salinity tolerance and investigate the effects of choline on the physiological and lipidomic responses of turfgrass plants under salinity stress conditions, exogenous choline chloride was applied to Kentucky bluegrass exposed to salt stress. Results From physiological indicators, exogenous choline chloride could alleviate salt stress injury in Kentucky bluegrass. Lipid analysis showed that exogenous choline chloride under salt-stress conditions remodeled the content of phospholipids, glycolipids, and lysophospholipids. Monogalactosyl diacylglycerol, digalactosyl diacylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and lysophosphatidylcholine content were increased and phosphatidic acid content were decreased in plants after exogenous choline chloride under salt treatment. Plant leaf choline content increased, but GB was not detected in exogenous choline chloride treatment plants under nonstress or salt-stress conditions. Discussion GB synthesis pathway related genes showed no clear change to choline chloride treatment, whereas cytidyldiphosphate-choline (CDP-choline) pathway genes were upregulated by choline chloride treatment. These results reveal that lipid remodeling through choline metabolism plays an important role in the salt tolerance mechanism of Kentucky bluegrass. Furthermore, the lipids selected in this study could serve as biomarkers for further improvement of salt-sensitive grass species.
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Affiliation(s)
| | | | | | | | | | | | | | - Kun Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
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Zhuang X, Liu Y, Fang N, Bai Z, Gao J. Quorum sensing improves the plant growth-promoting ability of Stenotrophomonas rhizophila under saline-alkaline stress by enhancing its environmental adaptability. Front Microbiol 2023; 14:1155081. [PMID: 37113227 PMCID: PMC10126360 DOI: 10.3389/fmicb.2023.1155081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Quorum sensing (QS) system has an essential function in plant growth-promoting rhizobacteria (PGPR) response to environmental stress and PGPR induction of plant tolerance to saline-alkaline stress. Nevertheless, there is a lack of understanding about how QS influences the growth-promoting effects of PGPR on plants. Stenotrophomonas rhizophila DSM14405T is a PGPR with a QS system, which can secrete diffusible signal factor (DSF), one of the QS signal molecules. In this study, we used the S. rhizophila wild type (WT) and an incompetent DSF production rpfF-knockout mutant strain to explore whether DSF-QS could affect the growth-promoting ability of PGPR in Brassica napus L. By measuring the seed germination rate, plant fresh weight, biomass, the total antioxidant capacity (T-AOC) level, and the content of chlorophyll in leaves, we found that DSF was unable to enhance the growth-promoting capacity of ΔrpfF and did not directly assist the plants in tolerating saline-alkaline stress. However, DSF aided S. rhizophila ΔrpfF in resisting stress during its effective period, and QS represents a continuous and precise regulatory mechanism. Altogether, our results show that DSF is helpful to improve the environmental adaptability and survival rate of S. rhizophila, thus indirectly improving the germination rate of seeds and helping plants grow under saline-alkaline stress. In this study, the mechanism of QS enhancing the environmental adaptability of PGPR was studied, which provided a theoretical basis for improving the application of PGPR to help plants better cope with saline-alkaline stress.
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Affiliation(s)
- Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, China
| | - Na Fang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Zhihui Bai
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Xiong’an Institute of Innovation, Xiong’an New Area, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Jie Gao,
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Yang L, Wu Q, Liang H, Yin L, Shen P. Integrated analyses of transcriptome and metabolome provides new insights into the primary and secondary metabolism in response to nitrogen deficiency and soil compaction stress in peanut roots. FRONTIERS IN PLANT SCIENCE 2022; 13:948742. [PMID: 36247623 PMCID: PMC9554563 DOI: 10.3389/fpls.2022.948742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
Abstract
Peanut (Arachis hypogaea L.) is an important oil crop globally because of its high edible and economic value. However, its yield and quality are often restricted by certain soil factors, especially nitrogen (N) deficiency, and soil compaction. To explore the molecular mechanisms and metabolic basis behind the peanut response to N deficiency and soil compaction stresses, transcriptome and metabolome analyses of peanut root were carried out. The results showed that N deficiency and soil compaction stresses clearly impaired the growth and development of peanut's aboveground and underground parts, as well as its root nodulation. A total of 18645 differentially expressed genes (DEGs) and 875 known differentially accumulated metabolites (DAMs) were identified in peanut root under differing soil compaction and N conditions. The transcriptome analysis revealed that DEGs related to N deficiency were mainly enriched in "amino acid metabolism", "starch and sucrose metabolism", and "TCA cycle" pathways, while DEGs related to soil compaction were mainly enriched in "oxidoreductase activity", "lipids metabolism", and "isoflavonoid biosynthesis" pathways. The metabolome analysis also showed significant differences in the accumulation of metabolisms in these pathways under different stress conditions. Then the involvement of genes and metabolites in pathways of "amino acid metabolism", "TCA cycle", "lipids metabolism", and "isoflavonoid biosynthesis" under different soil compaction and N deficiency stresses were well discussed. This integrated transcriptome and metabolome analysis study enhances our mechanistic knowledge of how peanut plants respond to N deficiency and soil compaction stresses. Moreover, it provides new leads to further investigate candidate functional genes and metabolic pathways for use in improving the adaptability of peanut to abiotic stress and accelerating its breeding process of new stress-resistant varieties.
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The Caucasian Clover Gene TaMYC2 Responds to Abiotic Stress and Improves Tolerance by Increasing the Activity of Antioxidant Enzymes. Genes (Basel) 2022; 13:genes13020329. [PMID: 35205373 PMCID: PMC8871790 DOI: 10.3390/genes13020329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 02/06/2023] Open
Abstract
Abiotic stress affects metabolic processes in plants and restricts plant growth and development. In this experiment, Caucasian clover (Trifolium ambiguum M. Bieb.) was used as a material, and the CDS of TaMYC2, which is involved in regulating the response to abiotic stress, was cloned. The CDS of TaMYC2 was 726 bp in length and encoded 241 amino acids. The protein encoded by TaMYC2 was determined to be unstable, be highly hydrophilic, and contain 23 phosphorylation sites. Subcellular localization results showed that TaMYC2 was localized in the nucleus. TaMYC2 responded to salt, alkali, cold, and drought stress and could be induced by IAA, GA3, and MeJA. By analyzing the gene expression and antioxidant enzyme activity in plants before and after stress, we found that drought and cold stress could induce the expression of TaMYC2 and increase the antioxidant enzyme activity. TaMYC2 could also induce the expression of ROS scavenging-related and stress-responsive genes and increase the activity of antioxidant enzymes, thus improving the ability of plants to resist stress. The results of this experiment provide references for subsequent in-depth exploration of both the function of TaMYC2 in and the molecular mechanism underlying the resistance of Caucasian clover.
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Han X, Yang Y. Phospholipids in Salt Stress Response. PLANTS 2021; 10:plants10102204. [PMID: 34686013 PMCID: PMC8540237 DOI: 10.3390/plants10102204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/25/2022]
Abstract
High salinity threatens crop production by harming plants and interfering with their development. Plant cells respond to salt stress in various ways, all of which involve multiple components such as proteins, peptides, lipids, sugars, and phytohormones. Phospholipids, important components of bio-membranes, are small amphoteric molecular compounds. These have attracted significant attention in recent years due to the regulatory effect they have on cellular activity. Over the past few decades, genetic and biochemical analyses have partly revealed that phospholipids regulate salt stress response by participating in salt stress signal transduction. In this review, we summarize the generation and metabolism of phospholipid phosphatidic acid (PA), phosphoinositides (PIs), phosphatidylserine (PS), phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG), as well as the regulatory role each phospholipid plays in the salt stress response. We also discuss the possible regulatory role based on how they act during other cellular activities.
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Affiliation(s)
- Xiuli Han
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China;
| | - Yongqing Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel./Fax: +86-10-62732030
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