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Kangi E, Brzostek ER, Bills RJ, Callister SJ, Zink EM, Kim YM, Larsen PE, Cumming JR. A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency. FRONTIERS IN PLANT SCIENCE 2024; 15:1324608. [PMID: 38645387 PMCID: PMC11032019 DOI: 10.3389/fpls.2024.1324608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024]
Abstract
Introduction Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. Phosphorus deficiency is especially challenging for the production of bioenergy feedstock plantation species, such as poplars (Populus spp.), where fertilization may not be practically or economically feasible. While the phenotypic effects of P deficiency are well known, the molecular mechanisms underlying whole-plant and tissue-specific responses to P deficiency, and in particular the responses of commercially valuable hardwoods, are less studied. Methods We used a multi-tissue and multi-omics approach using transcriptomic, proteomic, and metabolomic analyses of the leaves and roots of black cottonwood (Populus trichocarpa) seedlings grown under P-deficient (5 µM P) and replete (100 µM P) conditions to assess this knowledge gap and to identify potential gene targets for selection for P efficiency. Results In comparison to seedlings grown at 100 µM P, P-deficient seedlings exhibited reduced dry biomass, altered chlorophyll fluorescence, and reduced tissue P concentrations. In line with these observations, growth, C metabolism, and photosynthesis pathways were downregulated in the transcriptome of the P-deficient plants. Additionally, we found evidence of strong lipid remodeling in the leaves. Metabolomic data showed that the roots of P-deficient plants had a greater relative abundance of phosphate ion, which may reflect extensive degradation of P-rich metabolites in plants exposed to long-term P-deficiency. With the notable exception of the KEGG pathway for Starch and Sucrose Metabolism (map00500), the responses of the transcriptome and the metabolome to P deficiency were consistent with one another. No significant changes in the proteome were detected in response to P deficiency. Discussion and conclusion Collectively, our multi-omic and multi-tissue approach enabled the identification of important metabolic and regulatory pathways regulated across tissues at the molecular level that will be important avenues to further evaluate for P efficiency. These included stress-mediating systems associated with reactive oxygen species maintenance, lipid remodeling within tissues, and systems involved in P scavenging from the rhizosphere.
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Affiliation(s)
- Emel Kangi
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Edward R. Brzostek
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Robert J. Bills
- Biology Department, Willamette University, Salem, OR, United States
| | - Stephen J. Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M. Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Peter E. Larsen
- Loyola Genomics Facility, Loyola University Chicago, Maywood, IL, United States
| | - Jonathan R. Cumming
- Department of Natural Sciences, University of Maryland Eastern Shore, Princess Anne, MD, United States
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Li P, Ma X, Wang J, Yao L, Li B, Meng Y, Si E, Yang K, Shang X, Zhang X, Wang H. Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Low Phosphorus Tolerance in Wheat Seedling. Int J Mol Sci 2023; 24:14840. [PMID: 37834288 PMCID: PMC10573437 DOI: 10.3390/ijms241914840] [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: 09/04/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Low phosphorus (LP) stress leads to a significant reduction in wheat yield, primarily in the reduction of biomass, the number of tillers and spike grains, the delay in heading and flowering, and the inhibition of starch synthesis and grouting. However, the differences in regulatory pathway responses to low phosphorus stress among different wheat genotypes are still largely unknown. In this study, metabolome and transcriptome analyses of G28 (LP-tolerant) and L143 (LP-sensitive) wheat varieties after 72 h of normal phosphorus (CK) and LP stress were performed. A total of 181 and 163 differentially accumulated metabolites (DAMs) were detected for G28CK vs. G28LP and L143CK vs. L143LP, respectively. Notably, the expression of pilocarpine (C07474) in G28CK vs. G28LP was significantly downregulated 4.77-fold, while the expression of neochlorogenic acid (C17147) in L143CK vs. L143LP was significantly upregulated 2.34-fold. A total of 4023 differentially expressed genes (DEGs) were acquired between G28 and L143, of which 1120 DEGs were considered as the core DEGs of LP tolerance of wheat after LP treatment. The integration of metabolomics and transcriptomic data further revealed that the LP tolerance of wheat was closely related to 15 metabolites and 18 key genes in the sugar and amino acid metabolism pathway. The oxidative phosphorylation pathway was enriched to four ATPases, two cytochrome c reductase genes, and fumaric acid under LP treatment. Moreover, PHT1;1, TFs (ARFA, WRKY40, MYB4, MYB85), and IAA20 genes were related to the Pi starvation stress of wheat roots. Therefore, the differences in LP tolerance of different wheat varieties were related to energy metabolism, amino acid metabolism, phytohormones, and PHT proteins, and precisely regulated by the levels of various molecular pathways to adapt to Pi starvation stress. Taken together, this study may help to reveal the complex regulatory process of wheat adaptation to Pi starvation and provide new genetic clues for further study on improving plant Pi utilization efficiency.
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Affiliation(s)
- Pengcheng Li
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaole Ma
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Juncheng Wang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Lirong Yao
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Baochun Li
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yaxiong Meng
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Erjing Si
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Ke Yang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xueyong Zhang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
| | - Huajun Wang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Ma Z, Yang K, Wang J, Ma J, Yao L, Si E, Li B, Ma X, Shang X, Meng Y, Wang H. Exogenous Melatonin Enhances the Low Phosphorus Tolerance of Barley Roots of Different Genotypes. Cells 2023; 12:1397. [PMID: 37408231 PMCID: PMC10217165 DOI: 10.3390/cells12101397] [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: 03/14/2023] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 07/07/2023] Open
Abstract
Melatonin (N-acetyl-5-methoxytryptamine) plays an important role in plant growth and development, and in the response to various abiotic stresses. However, its role in the responses of barley to low phosphorus (LP) stress remains largely unknown. In the present study, we investigated the root phenotypes and metabolic patterns of LP-tolerant (GN121) and LP-sensitive (GN42) barley genotypes under normal P, LP, and LP with exogenous melatonin (30 μM) conditions. We found that melatonin improved barley tolerance to LP mainly by increasing root length. Untargeted metabolomic analysis showed that metabolites such as carboxylic acids and derivatives, fatty acyls, organooxygen compounds, benzene and substituted derivatives were involved in the LP stress response of barley roots, while melatonin mainly regulated indoles and derivatives, organooxygen compounds, and glycerophospholipids to alleviate LP stress. Interestingly, exogenous melatonin showed different metabolic patterns in different genotypes of barley in response to LP stress. In GN42, exogenous melatonin mainly promotes hormone-mediated root growth and increases antioxidant capacity to cope with LP damage, while in GN121, it mainly promotes the P remobilization to supplement phosphate in roots. Our study revealed the protective mechanisms of exogenous MT in alleviating LP stress of different genotypes of barley, which can be used in the production of phosphorus-deficient crops.
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Affiliation(s)
- Zengke Ma
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Ke Yang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Juncheng Wang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jingwei Ma
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Lirong Yao
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Erjing Si
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Baochun Li
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaole Ma
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yaxiong Meng
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Huajun Wang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China; (Z.M.); (K.Y.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Li S, Zhou Y, Xu Y, Ran S, Hou M, Li Q, Zhong X, Zhong F. The analysis of lysine succinylation modification reveals the mechanism of oxybenzone damaging of pakchoi ( Brassica rapa L. ssp. chinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:1001935. [PMID: 36570927 PMCID: PMC9772522 DOI: 10.3389/fpls.2022.1001935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Oxybenzone (OBZ), one of a broad spectrum of ultraviolet (UV) absorbents, has been proven to be harmful to both plants and animals, while omics analysis of big data at the molecular level is still lacking. Lysine succinylation (Ksuc) is an important posttranslational modification of proteins that plays a crucial role in regulating the metabolic network in organisms under stress. Here, we report the changes in intracellular Ksuc modification in plants under OBZ stress. A total of 1276 succinylated sites on 507 proteins were identified. Among these sites, 181 modified proteins were hypersulfinylated/succinylated in OBZ-stressed pakchoi leaves. Differentially succinylated proteins (DSPs) are distributed mainly in the chloroplast, cytoplasm, and mitochondria and are distributed mainly in primary metabolic pathways, such as reactive oxygen species (ROS) scavenging, stress resistance, energy generation and transfer, photosynthetic carbon fixation, glycolysis, and the tricarboxylic acid (TCA) cycle. Comprehensive analysis shows that Ksuc mainly changes the carbon flow distribution, enhances the activity of the antioxidant system, affects the biosynthesis of amino acids, and increases the modification of histones. The results of this study first showed the profiling of the Kusc map under OBZ treatment and proposed the adaptive mechanism of pakchoi in response to pollutants and other abiotic stresses at the posttranslational level, which revealed the importance of Ksuc in the regulation of various life activities and provides a reference dataset for future research on molecular function.
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Affiliation(s)
- Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Yuqi Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Yang Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Shengxiang Ran
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Maomao Hou
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Qingming Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Cheng’du, China
| | - Xin Zhong
- Institute of Marine Science and Technology, Shandong University, Qing’dao, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
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5
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Chen Y, Wang J, Yao L, Li B, Ma X, Si E, Yang K, Li C, Shang X, Meng Y, Wang H. Combined Proteomic and Metabolomic Analysis of the Molecular Mechanism Underlying the Response to Salt Stress during Seed Germination in Barley. Int J Mol Sci 2022; 23:ijms231810515. [PMID: 36142428 PMCID: PMC9499682 DOI: 10.3390/ijms231810515] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
Salt stress is a major abiotic stress factor affecting crop production, and understanding of the response mechanisms of seed germination to salt stress can help to improve crop tolerance and yield. The differences in regulatory pathways during germination in different salt-tolerant barley seeds are not clear. Therefore, this study investigated the responses of different salt-tolerant barley seeds during germination to salt stress at the proteomic and metabolic levels. To do so, the proteomics and metabolomics of two barley seeds with different salt tolerances were comprehensively examined. Through comparative proteomic analysis, 778 differentially expressed proteins were identified, of which 335 were upregulated and 443 were downregulated. These proteins, were mainly involved in signal transduction, propanoate metabolism, phenylpropanoid biosynthesis, plant hormones and cell wall stress. In addition, a total of 187 salt-regulated metabolites were identified in this research, which were mainly related to ABC transporters, amino acid metabolism, carbohydrate metabolism and lipid metabolism; 72 were increased and 112 were decreased. Compared with salt-sensitive materials, salt-tolerant materials responded more positively to salt stress at the protein and metabolic levels. Taken together, these results suggest that salt-tolerant germplasm may enhance resilience by repairing intracellular structures, promoting lipid metabolism and increasing osmotic metabolites. These data not only provide new ideas for how seeds respond to salt stress but also provide new directions for studying the molecular mechanisms and the metabolic homeostasis of seeds in the early stages of germination under abiotic stresses.
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Affiliation(s)
- Yiyou Chen
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Juncheng Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Lirong Yao
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Baochun Li
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaole Ma
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Erjing Si
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Ke Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yaxiong Meng
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- Correspondence: (Y.M.); (H.W.)
| | - Huajun Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- Correspondence: (Y.M.); (H.W.)
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Wang J, Li C, Yao L, Ma Z, Ren P, Si E, Li B, Meng Y, Ma X, Yang K, Shang X, Wang H. Global proteome analyses of phosphorylation and succinylation of barley root proteins in response to phosphate starvation and recovery. FRONTIERS IN PLANT SCIENCE 2022; 13:917652. [PMID: 36061799 PMCID: PMC9433975 DOI: 10.3389/fpls.2022.917652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Phosphate (Pi) stress is an important environmental factor that limits plant growth and development. Of various posttranslational modifications (PTMs), protein phosphorylation and succinylation are the two most important PTMs that regulate multiple biological processes in response to Pi stress. However, these PTMs have been investigated individually but their interactions with proteins in response to Pi stress remain poorly understood. In this study, to elucidate the underlying mechanisms of protein phosphorylation and succinylation in response to Pi stress, we performed a global analysis of the barley root phosphorylome and succinylome in Pi starvation and recovery stages, respectively. A total of 3,634 and 884 unique phosphorylated and succinylated proteins, respectively, corresponding to 11,538 and 2,840 phospho- and succinyl-sites, were identified; of these, 275 proteins were found to be simultaneously phosphorylated and succinylated. Gene Set Enrichment Analysis was performed with a Kyoto Encyclopedia of Genes and Genomes pathway database revealing pathways that significantly enriched in the phosphorylome and succinylome. Such pathways, were dynamically regulated by Pi starvation and recovery treatments, and could be partitioned into distinct metabolic processes. In particular, phosphorylated proteins related to purine, the mitogen-activated protein kinase (MAPK) signaling pathway, pyrimidine, and ATP-binding cassette (ABC) transporters were upregulated in both Pi deprivation and recovery stages. Succinylated proteins, significantly upregulated by both Pi starvation and recovery, were enriched in nitrogen metabolism and phenylpropanoid biosynthesis. Meanwhile, succinylated proteins that were significantly downregulated by both Pi starvation and recovery were enriched in lysine degradation and tryptophan metabolism. This highlighted the importance of these metabolic pathways in regulating Pi homeostasis. Furthermore, protein-protein interaction network analyses showed that the response of central metabolic pathways to Pi starvation and recovery was significantly modulated by phosphorylation or succinylation, both individually and together. In addition, we discovered relevant proteins involved in MAPK signaling and phenylpropanoid biosynthetic pathways existing in interactions between phosphorylated and succinylated proteins in response to Pi recovery. The current study not only provides a comprehensive analysis of phosphorylated and succinylated proteins in plant responses to Pi starvation and recovery, but also reveals detailed interactions between phosphorylated and succinylated proteins in barley roots.
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Affiliation(s)
- Juncheng Wang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Lirong Yao
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zengke Ma
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Panrong Ren
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Erjing Si
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Baochun Li
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaxiong Meng
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaole Ma
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ke Yang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huajun Wang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
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Li X, Yang D, Yang Y, Jin G, Yin X, Zheng Y, Xu J, Yang Y. Quantitative Succinyl-Proteome Profiling of Turnip ( Brassica rapa var. rapa) in Response to Cadmium Stress. Cells 2022; 11:cells11121947. [PMID: 35741076 PMCID: PMC9221971 DOI: 10.3390/cells11121947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/30/2022] [Accepted: 06/15/2022] [Indexed: 01/25/2023] Open
Abstract
Protein post-translational modification (PTM) is an efficient biological mechanism to regulate protein structure and function, but its role in plant responses to heavy metal stress is poorly understood. The present study performed quantitative succinyl-proteome profiling using liquid chromatography−mass spectrometry analysis to explore the potential roles of lysine succinylation modification in turnip seedlings in response to cadmium (Cd) stress (20 μM) under hydroponic conditions over a short time period (0−8 h). A total of 547 succinylated sites on 256 proteins were identified in the shoots of turnip seedlings. These succinylated proteins participated in various biological processes (e.g., photosynthesis, tricarboxylic acid cycle, amino acid metabolism, and response to stimulation) that occurred in diverse cellular compartments according to the functional classification, subcellular localization, and protein interaction network analysis. Quantitative analysis showed that the intensities of nine succinylation sites on eight proteins were significantly altered (p < 0.05) in turnip shoots after 8 h of Cd stress. These differentially succinylated sites were highly conserved in Brassicaceae species and mostly located in the conserved domains of the proteins. Among them, a downregulated succinylation site (K150) in the glycolate oxidase protein (Gene0282600.1), an upregulated succinylation site (K396) in the catalase 3 protein (Gene0163880.1), and a downregulated succinylation site (K197) in the glutathione S-transferase protein (Gene0315380.1) may have contributed to the altered activity of the corresponding enzymes, which suggests that lysine succinylation affects the Cd detoxification process in turnip by regulating the H2O2 accumulation and glutathione metabolism. These results provide novel insights into understanding Cd response mechanisms in plants and important protein modification information for the molecular-assisted breeding of Brassica varieties with distinct Cd tolerance and accumulation capacities.
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Affiliation(s)
- Xiong Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Danni Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Yunqiang Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Xin Yin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Yan Zheng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Jianchu Xu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Correspondence: (J.X.); (Y.Y.)
| | - Yongping Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
- Correspondence: (J.X.); (Y.Y.)
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Zhou M, Zhu S, Mo X, Guo Q, Li Y, Tian J, Liang C. Proteomic Analysis Dissects Molecular Mechanisms Underlying Plant Responses to Phosphorus Deficiency. Cells 2022; 11:cells11040651. [PMID: 35203302 PMCID: PMC8870294 DOI: 10.3390/cells11040651] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/02/2022] [Accepted: 01/05/2022] [Indexed: 01/25/2023] Open
Abstract
Phosphorus (P) is an essential nutrient for plant growth. In recent decades, the application of phosphate (Pi) fertilizers has contributed to significant increases in crop yields all over the world. However, low efficiency of P utilization in crops leads to intensive application of Pi fertilizers, which consequently stimulates environmental pollution and exhaustion of P mineral resources. Therefore, in order to strengthen the sustainable development of agriculture, understandings of molecular mechanisms underlying P efficiency in plants are required to develop cultivars with high P utilization efficiency. Recently, a plant Pi-signaling network was established through forward and reverse genetic analysis, with the aid of the application of genomics, transcriptomics, proteomics, metabolomics, and ionomics. Among these, proteomics provides a powerful tool to investigate mechanisms underlying plant responses to Pi availability at the protein level. In this review, we summarize the recent progress of proteomic analysis in the identification of differential proteins that play roles in Pi acquisition, translocation, assimilation, and reutilization in plants. These findings could provide insights into molecular mechanisms underlying Pi acquisition and utilization efficiency, and offer new strategies in genetically engineering cultivars with high P utilization efficiency.
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Affiliation(s)
- Ming Zhou
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (X.M.); (Q.G.); (Y.L.)
| | - Shengnan Zhu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang 524048, China;
| | - Xiaohui Mo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (X.M.); (Q.G.); (Y.L.)
| | - Qi Guo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (X.M.); (Q.G.); (Y.L.)
| | - Yaxue Li
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (X.M.); (Q.G.); (Y.L.)
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (X.M.); (Q.G.); (Y.L.)
- Correspondence: (J.T.); (C.L.); Tel.: +86-2085283380 (J.T.); +86-2085280156 (C.L.)
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (X.M.); (Q.G.); (Y.L.)
- Correspondence: (J.T.); (C.L.); Tel.: +86-2085283380 (J.T.); +86-2085280156 (C.L.)
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Kosová K, Vítámvás P, Prášil IT, Klíma M, Renaut J. Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene. FRONTIERS IN PLANT SCIENCE 2021; 12:793113. [PMID: 34970290 PMCID: PMC8712444 DOI: 10.3389/fpls.2021.793113] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/16/2021] [Indexed: 05/30/2023]
Abstract
Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.
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Affiliation(s)
- Klára Kosová
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Pavel Vítámvás
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Ilja Tom Prášil
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Miroslav Klíma
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Jenny Renaut
- Biotechnologies and Environmental Analytics Platform (BEAP), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch-Sur-Alzette, Luxembourg
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Ma Z, Wang J, Li C, Ren P, Yao L, Li B, Meng Y, Ma X, Si E, Yang K, Shang X, Wang H. Global Profiling of Phosphorylation Reveals the Barley Roots Response to Phosphorus Starvation and Resupply. FRONTIERS IN PLANT SCIENCE 2021; 12:676432. [PMID: 34335649 PMCID: PMC8317692 DOI: 10.3389/fpls.2021.676432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/09/2021] [Indexed: 05/04/2023]
Abstract
Phosphorus (P) deficiency is a major threat to the crop production, and for understanding the response mechanism of plant roots, P stress may facilitate the development of crops with increased tolerance. Phosphorylation plays a critical role in the regulation of proteins for plant responses to biotic and abiotic stress; however, its functions in P starvation/resupply are largely unknown for barley (Hordeum vulgare) growth. Here, we performed a global review of phosphorylation in barley roots treated by P starvation/resupply. We identified 7,710 phosphorylation sites on 3,373 proteins, of which 76 types of conserved motifs were extracted from 10,428 phosphorylated peptides. Most phosphorylated proteins were located in the nucleus (36%) and chloroplast (32%). Compared with the control, 186 and 131 phosphorylated proteins under P starvation condition and 156 and 111 phosphorylated proteins under P resupply condition showed significant differences at 6 and 48 h, respectively. These proteins mainly participated in carbohydrate metabolism, phytohormones, signal transduction, cell wall stress, and oxidases stress. Moreover, the pathways of the ribosome, RNA binding, protein transport, and metal binding were significantly enriched under P starvation, and only two pathways of ribosome and RNA binding were greatly enriched under Pi resupply according to the protein-protein interaction analysis. The results suggested that the phosphorylation proteins might play important roles in the metabolic processes of barley roots in response to Pi deficiency/resupply. The data not only provide unique access to phosphorylation reprogramming of plant roots under deficiency/resupply but also demonstrate the close cooperation between these phosphorylation proteins and key metabolic functions.
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Affiliation(s)
- Zengke Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Panrong Ren
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lirong Yao
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Baochun Li
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaxiong Meng
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaole Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Erjing Si
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ke Yang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Huajun Wang
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