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Yan Y, Li M, Ding Z, Yang J, Xie Z, Ye X, Tie W, Tao X, Chen G, Huo K, Ma J, Ye J, Hu W. The regulation mechanism of ethephon-mediated delaying of postharvest physiological deterioration in cassava storage roots based on quantitative acetylproteomes analysis. Food Chem 2024; 458:140252. [PMID: 38964113 DOI: 10.1016/j.foodchem.2024.140252] [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: 01/26/2024] [Revised: 06/05/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Ethylene plays diverse roles in post-harvest processes of horticultural crops. However, its impact and regulation mechanism on the postharvest physiological deterioration (PPD) of cassava storage roots is unknown. In this study, a notable delay in PPD of cassava storage roots was observed when ethephon was utilized as an ethylene source. Physiological analyses and quantitative acetylproteomes were employed to investigate the regulation mechanism regulating cassava PPD under ethephon treatment. Ethephon was found to enhance the reactive oxygen species (ROS) scavenging system, resulting in a significant decrease in H2O2 and malondialdehyde (MDA) content. The comprehensive acetylome analysis identified 12,095 acetylation sites on 4403 proteins. Subsequent analysis demonstrated that ethephon can regulate the acetylation levels of antioxidant enzymes and members of the energy metabolism pathways. In summary, ethephon could enhance the antioxidant properties and regulate energy metabolism pathways, leading to the delayed PPD of cassava.
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Affiliation(s)
- Yan Yan
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Meiying Li
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Zehong Ding
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Jinghao Yang
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhengnan Xie
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoxue Ye
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Weiwei Tie
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Xiangru Tao
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ganlu Chen
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kaisen Huo
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Jianxiang Ma
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wei Hu
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
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2
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Zhang X, Shan J, Wang J, Zhang Y, Yang F, Liu B, Zhang L, Li G, Wang R. Comprehensive Proteome and Acetylome Analysis of Needle Senescence in Larix gmelinii. Int J Mol Sci 2024; 25:6824. [PMID: 38999933 PMCID: PMC11241215 DOI: 10.3390/ijms25136824] [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: 04/16/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Leaf senescence is essential for the growth and development of deciduous trees in the next season. Larix gmelinii, a deciduous coniferous tree, exhibits its most distinctive feature by turning yellow in the autumn and eventually shedding its leaves, resulting in significant changes in its appearance during the fall. Lysine acetylation plays an important role in diverse cellular processes; however, limited knowledge is available regarding acetylations in the needle senescence of L. gmelinii. In this study, the proteomics and acetylated modification omics of two phenotypic leaves, yellow and green (senescent and non-senescent) needles, were analyzed before autumn defoliation. In total, 5022 proteins and 4469 unique acetylation sites in 2414 lysine acylated proteins were identified, and this resulted in the discovery of 1335 differentially expressed proteins (DEPs) and 605 differentially expressed acetylated proteins (DAPs) in yellow versus green needles. There are significant differences between the proteome and acetylome; only 269 proteins were found to be DEP and DAP, of which 136 proteins were consistently expressed in both the DEP and DAP, 91 proteins were upregulated, and 45 proteins were down-regulated. The DEPs participate in the metabolism of starch and sucrose, while the DAPs are involved in glycolysis and the tricarboxylic acid cycle. Among them, DEPs underwent significant changes in glycolysis and citric acid cycling. Most of the enzymes involved in glycolysis and the citrate cycle were acetylated. DAPs were down-regulated in glycolysis and up-regulated in the citrate cycle. In all, the results of this study reveal the important role of lysine acetylation in the senescence of L. gmelinii needles and provide a new perspective for understanding the molecular mechanism of leaf senescence and tree seasonal growth.
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Affiliation(s)
- Xuting Zhang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jinyuan Shan
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jiaxiu Wang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yanxia Zhang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Feiyun Yang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Bin Liu
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lifeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Guojing Li
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ruigang Wang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
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Liu M, Gong F, Yu W, Cao K, Xu H, Zhou X. The Rhododendron Chrysanthum Pall.s' Acetylation Modification of Rubisco Enzymes Controls Carbon Cycling to Withstand UV-B Stress. Biomolecules 2024; 14:732. [PMID: 38927135 PMCID: PMC11201758 DOI: 10.3390/biom14060732] [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: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Lysine acetylation of proteins plays a critical regulatory function in plants. A few advances have been made in the study of plant acetylproteome. However, until now, there have been few data on Rhododendron chrysanthum Pall. (R. chrysanthum). We analyzed the molecular mechanisms of photosynthesis and stress resistance in R. chrysanthum under UV-B stress. We measured chlorophyll fluorescence parameters of R. chrysanthum under UV-B stress and performed a multi-omics analysis. Based on the determination of chlorophyll fluorescence parameters, R. chrysanthum Y(NO) (Quantum yield of non-photochemical quenching) increased under UV-B stress, indicating that the plant was damaged and photosynthesis decreased. In the analysis of acetylated proteomics data, acetylated proteins were found to be involved in a variety of biological processes. Notably, acetylated proteins were significantly enriched in the pathways of photosynthesis and carbon fixation, suggesting that lysine acetylation modifications have an important role in these activities. Our findings suggest that R. chrysanthum has decreased photosynthesis and impaired photosystems under UV-B stress, but NPQ shows that plants are resistant to UV-B. Acetylation proteomics revealed that up- or down-regulation of acetylation modification levels alters protein expression. Acetylation modification of key enzymes of the Calvin cycle (Rubisco, GAPDH) regulates protein expression, making Rubisco and GAPDH proteins expressed as significantly different proteins, which in turn affects the carbon fixation capacity of R. chrysanthum. Thus, Rubisco and GAPDH are significantly differentially expressed after acetylation modification, which affects the carbon fixation capacity and thus makes the plant resistant to UV-B stress. Lysine acetylation modification affects biological processes by regulating the expression of key enzymes in photosynthesis and carbon fixation, making plants resistant to UV-B stress.
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Affiliation(s)
| | | | | | | | - Hongwei Xu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
| | - Xiaofu Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
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4
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Wang S, Gu H, Chen S, Li Y, Shen J, Wang Y, Ding Z. Proteomics and phosphoproteomics reveal the different drought-responsive mechanisms of priming with (Z)-3-hexenyl acetate in two tea cultivars. J Proteomics 2023; 289:105010. [PMID: 37797878 DOI: 10.1016/j.jprot.2023.105010] [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: 06/15/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Drought is an important abiotic stress that constrains the quality and quantity of tea plants. The green leaf volatiles Z-3-hexenyl acetate (Z-3-HAC) have been reported to play an essential role in stress responses. However, the underlying mechanisms of drought tolerance in tea plants remain elusive. This study investigated the physiological, proteomic, and phosphoproteomic profiling of two tea plant varieties of Longjingchangye (LJCY) and Zhongcha 108 (ZC108) with contrasting drought tolerance characteristics under drought stress. Physiological data showed that spraying Z-3-HAC exhibited higher activities of superoxide dismutase (SOD) and catalase (CAT) in both LJCY and ZC108 but lower content of malondialdehyde (MDA) in LJCY under drought stress. The proteomic and phosphoproteomic analysis suggested that the drought tolerance mechanism of Z-3-HAC in LJCY and ZC108 was different. Proteomic analyses revealed that Z-3-HAC enhanced the drought tolerance of LJCY by fructose metabolism while enhancing the drought tolerance of ZC108 by promoting glucan biosynthesis and galactose metabolism. Furthermore, the differential abundance phosphoproteins (DAPPs) related to intracellular protein transmembrane transport and protein transmembrane transport were enriched in LJCY, and the regulation of response to osmotic stress and regulation of mRNA processing were enriched in ZC108. In addition, protein-phosphoprotein interactions (PPI) analyses suggested that energy metabolism and starch and sucrose metabolic processes might play critical roles in LJCY and ZC108, respectively. These results will help to understand the mechanisms by which Z-3-HAC enhances the drought resistance of tea plants at the protein level. SIGNIFICANT: Green leaf volatiles (GLVs) are important volatile organic compounds that play essential roles in plant defense against biotic and abiotic stresses. To understand the mechanisms of Z-3-HAC in improving the drought tolerance of tea plants, two contrasting drought tolerance varieties (LJCY and ZC108) were comparatively evaluated by proteomics and phosphoproteomics. This analysis evidenced changes in the abundance of proteins involved in energy metabolism and starch and sucrose metabolic processes in LJCY and ZC108, respectively. These proteins may elucidate new molecular aspects of the drought resistance mechanism of Z-3-HAC, providing a theoretical basis for drought resistance breeding of tea plants.
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Affiliation(s)
- Shuangshuang Wang
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Honglian Gu
- Tea Research Institute, Qingdao Agriculture University, Qingdao, China
| | - Sizhou Chen
- Tea Research Institute, Qingdao Agriculture University, Qingdao, China
| | - Yuchen Li
- Tea Research Institute, Qingdao Agriculture University, Qingdao, China
| | - Jiazhi Shen
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agriculture University, Qingdao, China
| | - Zhaotang Ding
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China.
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5
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Zhang W, Ni K, Long L, Ruan J. Nitrogen transport and assimilation in tea plant ( Camellia sinensis): a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1249202. [PMID: 37810380 PMCID: PMC10556680 DOI: 10.3389/fpls.2023.1249202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Nitrogen is one of the most important nutrients for tea plants, as it contributes significantly to tea yield and serves as the component of amino acids, which in turn affects the quality of tea produced. To achieve higher yields, excessive amounts of N fertilizers mainly in the form of urea have been applied in tea plantations where N fertilizer is prone to convert to nitrate and be lost by leaching in the acid soils. This usually results in elevated costs and environmental pollution. A comprehensive understanding of N metabolism in tea plants and the underlying mechanisms is necessary to identify the key regulators, characterize the functional phenotypes, and finally improve nitrogen use efficiency (NUE). Tea plants absorb and utilize ammonium as the preferred N source, thus a large amount of nitrate remains activated in soils. The improvement of nitrate utilization by tea plants is going to be an alternative aspect for NUE with great potentiality. In the process of N assimilation, nitrate is reduced to ammonium and subsequently derived to the GS-GOGAT pathway, involving the participation of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Additionally, theanine, a unique amino acid responsible for umami taste, is biosynthesized by the catalysis of theanine synthetase (TS). In this review, we summarize what is known about the regulation and functioning of the enzymes and transporters implicated in N acquisition and metabolism in tea plants and the current methods for assessing NUE in this species. The challenges and prospects to expand our knowledge on N metabolism and related molecular mechanisms in tea plants which could be a model for woody perennial plant used for vegetative harvest are also discussed to provide the theoretical basis for future research to assess NUE traits more precisely among the vast germplasm resources, thus achieving NUE improvement.
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Affiliation(s)
- Wenjing Zhang
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kang Ni
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Xihu National Agricultural Experimental Station for Soil Quality, Hangzhou, China
| | - Lizhi Long
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianyun Ruan
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Xihu National Agricultural Experimental Station for Soil Quality, Hangzhou, China
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6
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Liang L, Xie A, Yang H, Li N, Ma P, Wei S, Zhang S, Lv Y, Hu Y. Quantitative Acetylome Analysis of Soft Wheat Seeds during Artificial Ageing. Foods 2022; 11:foods11223611. [PMID: 36429203 PMCID: PMC9689531 DOI: 10.3390/foods11223611] [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: 10/21/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Lysine acetylation (Kac) is a protein post-translational modification (PTM) widely found in plants that plays vital roles in metabolic pathways. Although seed germination and development are regulated by Kac, its potential function in seed ageing remains to be investigated. Our preliminary study demonstrated that Kac levels were altered during wheat seed artificial ageing. However, its specific role in this process still needs to be elucidated. Here, we performed quantitative acetylation proteomics analysis of soft wheat seeds with different germination rates during artificial ageing. A total of 175 acetylation proteins and 255 acetylation modification sites were remarkably changed. The differentially acetylated proteins were enriched in metabolism; response to harsh intracellular environment, such as ROS; protein storage and processing. Notably, expression, point mutation to mimic Kac by K to Q mutation at K80 and K138, protein purification and enzyme activity detection revealed that the Kac of ROS-scavenging glutathione transferase attenuated its activity, indicating that the defense ability of wheat seeds to stress gradually diminished, and the ageing process was inevitable. Collectively, our data provide a basis for further understanding the roles of Kac in seed ageing and might aid in the development of new techniques to prolong seed viability and food quality.
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Affiliation(s)
- Liuke Liang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Aowen Xie
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Haojie Yang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Na Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Ping’an Ma
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shan Wei
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shuaibing Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- Correspondence:
| | - Yuansen Hu
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
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Ng JWX, Chua SK, Mutwil M. Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:944992. [PMID: 36212273 PMCID: PMC9539877 DOI: 10.3389/fpls.2022.944992] [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: 05/16/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Understanding how the different cellular components are working together to form a living cell requires multidisciplinary approaches combining molecular and computational biology. Machine learning shows great potential in life sciences, as it can find novel relationships between biological features. Here, we constructed a dataset of 11,801 gene features for 31,522 Arabidopsis thaliana genes and developed a machine learning workflow to identify linked features. The detected linked features are visualised as a Feature Important Network (FIN), which can be mined to reveal a variety of novel biological insights pertaining to gene function. We demonstrate how FIN can be used to generate novel insights into gene function. To make this network easily accessible to the scientific community, we present the FINder database, available at finder.plant.tools.
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Song L, Zhan H, Wang Y, Lin Z, Li B, Shen L, Jiao Y, Li Y, Wang F, Yang J. Cross-Talk of Protein Expression and Lysine Acetylation in Response to TMV Infection in Nicotiana benthamiana. ACS OMEGA 2022; 7:32496-32511. [PMID: 36120045 PMCID: PMC9475610 DOI: 10.1021/acsomega.2c03917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Lysine acetylation (Kac), a reversible PTM, plays an essential role in various biological processes, including those involving metabolic pathways, pathogen resistance, and transcription, in both prokaryotes and eukaryotes. TMV, the major factor that causes the poor quality of Solanaceae crops worldwide, directly alters many metabolic processes in tobacco. However, the extent and function of Kac during TMV infection have not been determined. The validation test to detect Kac level and viral expression after TMV infection and Nicotinamide (NAM) treatment clarified that acetylation was involved in TMV infection. Furthermore, we comprehensively analyzed the changes in the proteome and acetylome of TMV-infected tobacco (Nicotiana benthamiana) seedlings via LC-MS/MS in conjunction with highly sensitive immune-affinity purification. In total, 2082 lysine-acetylated sites on 1319 proteins differentially expressed in response to TMV infection were identified. Extensive bioinformatic studies disclosed changes in acetylation of proteins engaged in cellular metabolism and biological processes. The vital influence of Kac in fatty acid degradation and alpha-linolenic acid metabolism was also revealed in TMV-infected seedlings. This study first revealed Kac information in N. benthamiana under TMV infection and expanded upon the existing landscape of acetylation in pathogen infection.
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Affiliation(s)
- Liyun Song
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Huaixu Zhan
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Graduate
School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yujie Wang
- Luoyang
Branch of Henan Tobacco Company, Luoyang 471000, China
| | - Zhonglong Lin
- Yunnan
Tobacco Company of the China National Tobacco Corporation, Kunming 650011, China
| | - Bin Li
- Sichuan
Tobacco Company, Chengdu 610017, China
| | - Lili Shen
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yubing Jiao
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ying Li
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fenglong Wang
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jinguang Yang
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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9
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Tantray AY, Hazzazi Y, Ahmad A. Physiological, Agronomical, and Proteomic Studies Reveal Crucial Players in Rice Nitrogen Use Efficiency under Low Nitrogen Supply. Int J Mol Sci 2022; 23:6410. [PMID: 35742855 PMCID: PMC9224494 DOI: 10.3390/ijms23126410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
Excessive use of nitrogenous fertilizers to enhance rice productivity has become a significant source of nitrogen (N) pollution and reduced sustainable agriculture. However, little information about the physiology of different growth stages, agronomic traits, and associated genetic bases of N use efficiency (NUE) are available at low-N supply. Two rice (Oryza sativa L.) cultivars were grown with optimum N (120 kg ha-1) and low N (60 kg ha-1) supply. Six growth stages were analyzed to measure the growth and physiological traits, as well as the differential proteomic profiles, of the rice cultivars. Cultivar Panvel outclassed Nagina 22 at low-N supply and exhibited improved growth and physiology at most of the growth stages and agronomic efficiency due to higher N uptake and utilization at low-N supply. On average, photosynthetic rate, chlorophyll content, plant biomass, leaf N content, and grain yield were decreased in cultivar Nagina 22 than Panvel was 8%, 11%, 21%, 19%, and 22%, respectively, under low-N supply. Furthermore, proteome analyses revealed that many proteins were upregulated and downregulated at the different growth stages under low-N supply. These proteins are associated with N and carbon metabolism and other physiological processes. This supports the genotypic differences in photosynthesis, N assimilation, energy stabilization, and rice-protein yield. Our study suggests that enhancing NUE at low-N supply demands distinct modifications in N metabolism and physiological assimilation. The NUE may be regulated by key identified differentially expressed proteins. These proteins might be the targets for improving crop NUE at low-N supply.
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Affiliation(s)
- Aadil Yousuf Tantray
- Department of Botany, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India;
| | - Yehia Hazzazi
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK;
- Biology Department, Faculty of Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India;
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Zhao S, Cheng H, Xu P, Wang Y. Regulation of biosynthesis of the main flavor-contributing metabolites in tea plant ( Camellia sinensis): A review. Crit Rev Food Sci Nutr 2022; 63:10520-10535. [PMID: 35608014 DOI: 10.1080/10408398.2022.2078787] [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] [Indexed: 11/03/2022]
Abstract
In the process of adapting to the environment, tea plants (Camellia sinensis) endow tea with unique flavor and health functions, which should be attributed to secondary metabolites, including catechins, L-theanine, caffeine and terpene volatiles. Since the content of these flavor-contributing metabolites are mainly determined by the growth of tea plant, it is very important to understand their alteration and regulation mechanisms. In the present work, we first summarize the distribution, change characteristics of the main flavor-contributing metabolites in different cultivars, organs and under environmental stresses of tea plant. Subsequently, we discuss the regulating mechanisms involved in the biosynthesis of these metabolites based on the existing evidence. Finally, we propose the remarks and perspectives on the future study relating flavor-contributing metabolites. This review would contribute to the acceleration of research on the characteristic secondary metabolites and the breeding programs in tea plants.
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Affiliation(s)
- Shiqi Zhao
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Haiyan Cheng
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Ping Xu
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Yuefei Wang
- Tea Research Institute, Zhejiang University, Hangzhou, China
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11
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Ruan L, Wei K, Li J, He M, Wu L, Aktar S, Wang L, Cheng H. Responses of tea plants (Camellia sinensis) with different low-nitrogen tolerances during recovery from nitrogen deficiency. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:1405-1414. [PMID: 34374435 DOI: 10.1002/jsfa.11473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/09/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Tea plants have high nitrogen (N) consumptions, whereas molecular and physiological responses of tea plants to N recovery are still unclear. RESULTS By using non-invasive micro-test technology (NMT), 15 N tracer technique, ultra-performance liquid chromatography (UPLC), and transcriptome sequencing technology, we investigated the N recovery-induced changes in N absorptions, N tissue distributions, contents of free amino acids (FAAs), and global transcription of the low-N tolerant and intolerant tea genotypes [i.e. Wuniuzao (W) and Longjing43 (L)]. The results showed that the phenotype of Wuniuzao was better than that of Longjing43 under low-N condition. The N absorption and utilization of Wuniuzao were superior to Longjing43 under N recovery. The γ-aminobutyric acid (GABA) ratio (N recovery/N deficiency) in the root of Wuniuzao was significantly higher than that of Longjing43, while the glutamic acid ratio in the root of Wuniuzao was significantly lower than that of Longjing43. This findings suggested that Wuniuzao tended to enhance the GABA synthesis, while Longjing43 tended to inhibit the GABA synthesis under N recovery. The key genes in response to N recovery in Wuniuzao included N transport (AMT and NRT), N transformation (NR, NirA, and GAD), and amino acid transport (GAT) genes. In addition, some ribosome and flavonoid biosynthesis genes might help to maintain proteome homeostasis. CONCLUSION The N absorption and transport, and the conversion abilities of key amino acids (Glu and GABA) might improve the adaptability of tea plants to N recovery, which provided a basis for the breeding of N efficient tea varieties. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Li Ruan
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Kang Wei
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Jianwu Li
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Mengdi He
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Liyun Wu
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Shirin Aktar
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Liyuan Wang
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Hao Cheng
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
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12
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Xia L, Kong X, Song H, Han Q, Zhang S. Advances in proteome-wide analysis of plant lysine acetylation. PLANT COMMUNICATIONS 2022; 3:100266. [PMID: 35059632 PMCID: PMC8760137 DOI: 10.1016/j.xplc.2021.100266] [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] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Lysine acetylation (LysAc) is a conserved and important post-translational modification (PTM) that plays a key role in plant physiological and metabolic processes. Based on advances in Lys-acetylated protein immunoenrichment and mass-spectrometric technology, LysAc proteomics studies have been performed in many species. Such studies have made substantial contributions to our understanding of plant LysAc, revealing that Lys-acetylated histones and nonhistones are involved in a broad spectrum of plant cellular processes. Here, we present an extensive overview of recent research on plant Lys-acetylproteomes. We provide in-depth insights into the characteristics of plant LysAc modifications and the mechanisms by which LysAc participates in cellular processes and regulates metabolism and physiology during plant growth and development. First, we summarize the characteristics of LysAc, including the properties of Lys-acetylated sites, the motifs that flank Lys-acetylated lysines, and the dynamic alterations in LysAc among different tissues and developmental stages. We also outline a map of Lys-acetylated proteins in the Calvin-Benson cycle and central carbon metabolism-related pathways. We then introduce some examples of the regulation of plant growth, development, and biotic and abiotic stress responses by LysAc. We discuss the interaction between LysAc and Nα-terminal acetylation and the crosstalk between LysAc and other PTMs, including phosphorylation and succinylation. Finally, we propose recommendations for future studies in the field. We conclude that LysAc of proteins plays an important role in the regulation of the plant life cycle.
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Affiliation(s)
- Linchao Xia
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xiangge Kong
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haifeng Song
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Qingquan Han
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Sheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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13
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Hong G, Su X, Xu K, Liu B, Wang G, Li J, Wang R, Zhu M, Li G. Salt stress downregulates 2-hydroxybutyrylation in Arabidopsis siliques. J Proteomics 2022; 250:104383. [PMID: 34562664 DOI: 10.1016/j.jprot.2021.104383] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/26/2021] [Accepted: 09/12/2021] [Indexed: 12/16/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly discovered post-translational modifications (PTMs) through protein acylation. It has been reported to be widely distributed in both eukaryotes and prokaryotes, and plays an important role in chromatin conformation change, gene transcription, protein subcellular localization, protein-protein interaction, signal transduction, and cellular proliferation. In this study, the Khib modification proteome of siliques from A. thaliana under salt stress (Ss) and those in the control (Cs) were compared. The results showed that Khib modification was abundant in siliques. Totally 3810 normalized Khib sites on 1254 proteins were identified, and the Khib modification showed a downregulation trend dramatically: it was down-regulated at 282 sites on 205 proteins while was up-regulated at 96 sites on 78 proteins in Ss siliques (Data are available via ProteomeXchange with identifier PXD028116 and PXD026643). Among them, 13 proteins, including F4IVN6, Q9M1P5, and Q9LF33, had sites with the most significant regulation of Khib modification. Bioinformatics analysis suggested that the differentially Khib-regulated proteins mainly participated in glycolysis/gluconeogenesis and endocytosis. In particular, there were differentially117 Khib-regulated proteins that were mapped to the protein-protein interaction database. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism. Overall, our work reveals the first systematic analysis of Khib proteome in Arabidopsis siliques under salt stress, and sheds a light on the future studies on the regulatory mechanisms of Khib during the salt stress response of plants. SIGNIFICANCE: In this study, we found the Khib-modified proteins in silique under salt stress and described the enrichment of Khib-modified proteins involved in the biological processes and cellular localization. Proteins undergoing 2-hydroxyisobutylation were mainly involved in the gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism, suggesting that 2-hydroxyisobutylation affects the energy metabolic pathway, and thus the development of the plant. In addition, specific candidate proteins that may affect plant development under salt stress were selected. This study will provide a theoretical basis for revealing the function and mechanism of these proteins and their 2-hydroxyisobutyryl modifications during the development of silique under salt stress.
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Affiliation(s)
- Geriqiqige Hong
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoyi Su
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Ke Xu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Bin Liu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China; CAS Center of Excellence in Molecular Plant Science, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai 201602, China
| | - Guangxia Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Li
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruigang Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China.
| | - Mulan Zhu
- CAS Center of Excellence in Molecular Plant Science, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai 201602, China.
| | - Guojing Li
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China.
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14
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Balparda M, Elsässer M, Badia MB, Giese J, Bovdilova A, Hüdig M, Reinmuth L, Eirich J, Schwarzländer M, Finkemeier I, Schallenberg-Rüdinger M, Maurino VG. Acetylation of conserved lysines fine-tunes mitochondrial malate dehydrogenase activity in land plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:92-111. [PMID: 34713507 DOI: 10.1111/tpj.15556] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Plants need to rapidly and flexibly adjust their metabolism to changes of their immediate environment. Since this necessity results from the sessile lifestyle of land plants, key mechanisms for orchestrating central metabolic acclimation are likely to have evolved early. Here, we explore the role of lysine acetylation as a post-translational modification to directly modulate metabolic function. We generated a lysine acetylome of the moss Physcomitrium patens and identified 638 lysine acetylation sites, mostly found in mitochondrial and plastidial proteins. A comparison with available angiosperm data pinpointed lysine acetylation as a conserved regulatory strategy in land plants. Focusing on mitochondrial central metabolism, we functionally analyzed acetylation of mitochondrial malate dehydrogenase (mMDH), which acts as a hub of plant metabolic flexibility. In P. patens mMDH1, we detected a single acetylated lysine located next to one of the four acetylation sites detected in Arabidopsis thaliana mMDH1. We assessed the kinetic behavior of recombinant A. thaliana and P. patens mMDH1 with site-specifically incorporated acetyl-lysines. Acetylation of A. thaliana mMDH1 at K169, K170, and K334 decreases its oxaloacetate reduction activity, while acetylation of P. patens mMDH1 at K172 increases this activity. We found modulation of the malate oxidation activity only in A. thaliana mMDH1, where acetylation of K334 strongly activated it. Comparative homology modeling of MDH proteins revealed that evolutionarily conserved lysines serve as hotspots of acetylation. Our combined analyses indicate lysine acetylation as a common strategy to fine-tune the activity of central metabolic enzymes with likely impact on plant acclimation capacity.
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Affiliation(s)
- Manuel Balparda
- Molecular Plant Physiology, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Marlene Elsässer
- Molecular Evolution, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Mariana B Badia
- Plant Molecular Physiology and Biotechnology, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
- Facultad de Quı́mica e Ingenierı́a del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO, Rosario, Argentina
| | - Jonas Giese
- Plant Physiology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7, 48149, Münster, Germany
| | - Anastasiia Bovdilova
- Plant Molecular Physiology and Biotechnology, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
| | - Meike Hüdig
- Molecular Plant Physiology, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Plant Molecular Physiology and Biotechnology, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
| | - Lisa Reinmuth
- Molecular Evolution, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7, 48149, Münster, Germany
| | - Markus Schwarzländer
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7, 48149, Münster, Germany
| | - Mareike Schallenberg-Rüdinger
- Molecular Evolution, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Veronica G Maurino
- Molecular Plant Physiology, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Plant Molecular Physiology and Biotechnology, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
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15
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Yang J, Gu D, Wu S, Zhou X, Chen J, Liao Y, Zeng L, Yang Z. Feasible strategies for studying the involvement of DNA methylation and histone acetylation in the stress-induced formation of quality-related metabolites in tea (Camellia sinensis). HORTICULTURE RESEARCH 2021; 8:253. [PMID: 34848699 PMCID: PMC8632975 DOI: 10.1038/s41438-021-00679-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 08/17/2021] [Indexed: 05/26/2023]
Abstract
Tea plants are subjected to multiple stresses during growth, development, and postharvest processing, which affects levels of secondary metabolites in leaves and influences tea functional properties and quality. Most studies on secondary metabolism in tea have focused on gene, protein, and metabolite levels, whereas upstream regulatory mechanisms remain unclear. In this review, we exemplify DNA methylation and histone acetylation, summarize the important regulatory effects that epigenetic modifications have on plant secondary metabolism, and discuss feasible research strategies to elucidate the underlying specific epigenetic mechanisms of secondary metabolism regulation in tea. This information will help researchers investigate the epigenetic regulation of secondary metabolism in tea, providing key epigenetic data that can be used for future tea genetic breeding.
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Affiliation(s)
- Jie Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Dachuan Gu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Shuhua Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Xiaochen Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Jiaming Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yinyin Liao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Lanting Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Ziyin Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China.
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16
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Rodriguez MC, Mehta D, Tan M, Uhrig RG. Quantitative Proteome and PTMome Analysis of Arabidopsis thaliana Root Responses to Persistent Osmotic and Salinity Stress. PLANT & CELL PHYSIOLOGY 2021; 62:1012-1029. [PMID: 34059891 DOI: 10.1093/pcp/pcab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h to d) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while post-translational modifications (PTMs) do not. Further, we find significant changes in PTMs, and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulfur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.
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Affiliation(s)
- Maria C Rodriguez
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Richard G Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
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17
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Li G, Zheng B, Zhao W, Ren T, Zhang X, Ning T, Liu P. Global analysis of lysine acetylation in soybean leaves. Sci Rep 2021; 11:17858. [PMID: 34504199 PMCID: PMC8429545 DOI: 10.1038/s41598-021-97338-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 08/23/2021] [Indexed: 01/16/2023] Open
Abstract
Protein lysine acetylation (Kac) is an important post-translational modification in both animal and plant cells. Global Kac identification has been performed at the proteomic level in various species. However, the study of Kac in oil and resource plant species is relatively limited. Soybean is a globally important oil crop and resouce plant. In the present study, lysine acetylome analysis was performed in soybean leaves with proteomics techniques. Various bioinformatics analyses were performed to illustrate the structure and function of these Kac sites and proteins. Totally, 3148 acetylation sites in 1538 proteins were detected. Motif analysis of these Kac modified peptides extracted 17 conserved motifs. These Kac modified protein showed a wide subcellular location and functional distribution. Chloroplast is the primary subcellular location and cellular component where Kac proteins were localized. Function and pathways analyses indicated a plenty of biological processes and metabolism pathways potentially be influenced by Kac modification. Ribosome activity and protein biosynthesis, carbohydrate and energy metabolism, photosynthesis and fatty acid metabolism may be regulated by Kac modification in soybean leaves. Our study suggests Kac plays an important role in soybean physiology and biology, which is an available resource and reference of Kac function and structure characterization in oil crop and resource plant, as well as in plant kingdom.
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Affiliation(s)
- Geng Li
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Bin Zheng
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Wei Zhao
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Tinghu Ren
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xinghui Zhang
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Tangyuan Ning
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| | - Peng Liu
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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18
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Li J, Pan H, Yang H, Wang C, Liu H, Zhou H, Li P, Li C, Lu X, Tian Y. Rhamnolipid Enhances the Nitrogen Fixation Activity of Azotobacter chroococcum by Influencing Lysine Succinylation. Front Microbiol 2021; 12:697963. [PMID: 34394039 PMCID: PMC8360865 DOI: 10.3389/fmicb.2021.697963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/28/2021] [Indexed: 11/23/2022] Open
Abstract
The enhancement of nitrogen fixation activity of diazotrophs is essential for safe crop production. Lysine succinylation (KSuc) is widely present in eukaryotes and prokaryotes and regulates various biological process. However, knowledge of the extent of KSuc in nitrogen fixation of Azotobacter chroococcum is scarce. In this study, we found that 250 mg/l of rhamnolipid (RL) significantly increased the nitrogen fixation activity of A. chroococcum by 39%, as compared with the control. Real-time quantitative reverse transcription PCR (qRT-PCR) confirmed that RL could remarkably increase the transcript levels of nifA and nifHDK genes. In addition, a global KSuc of A. chroococcum was profiled using a 4D label-free quantitative proteomic approach. In total, 5,008 KSuc sites were identified on 1,376 succinylated proteins. Bioinformatics analysis showed that the addition of RL influence on the KSuc level, and the succinylated proteins were involved in various metabolic processes, particularly enriched in oxidative phosphorylation, tricarboxylic acid cycle (TCA) cycle, and nitrogen metabolism. Meanwhile, multiple succinylation sites on MoFe protein (NifDK) may influence nitrogenase activity. These results would provide an experimental basis for the regulation of biological nitrogen fixation with KSuc and shed new light on the mechanistic study of nitrogen fixation.
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Affiliation(s)
- Jin Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Hu Pan
- Institute of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hui Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Huhu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Hui Zhou
- College of Food Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peiwang Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Xiangyang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
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19
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Dong Y, Li P, Li P, Chen C. First comprehensive analysis of lysine succinylation in paper mulberry (Broussonetia papyrifera). BMC Genomics 2021; 22:255. [PMID: 33838656 PMCID: PMC8035759 DOI: 10.1186/s12864-021-07567-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lysine succinylation is a naturally occurring post-translational modification (PTM) that is ubiquitous in organisms. Lysine succinylation plays important roles in regulating protein structure and function as well as cellular metabolism. Global lysine succinylation at the proteomic level has been identified in a variety of species; however, limited information on lysine succinylation in plant species, especially paper mulberry, is available. Paper mulberry is not only an important plant in traditional Chinese medicine, but it is also a tree species with significant economic value. Paper mulberry is found in the temperate and tropical zones of China. The present study analyzed the effects of lysine succinylation on the growth, development, and physiology of paper mulberry. RESULTS A total of 2097 lysine succinylation sites were identified in 935 proteins associated with the citric acid cycle (TCA cycle), glyoxylic acid and dicarboxylic acid metabolism, ribosomes and oxidative phosphorylation; these pathways play a role in carbon fixation in photosynthetic organisms and may be regulated by lysine succinylation. The modified proteins were distributed in multiple subcellular compartments and were involved in a wide variety of biological processes, such as photosynthesis and the Calvin-Benson cycle. CONCLUSION Lysine-succinylated proteins may play key regulatory roles in metabolism, primarily in photosynthesis and oxidative phosphorylation, as well as in many other cellular processes. In addition to the large number of succinylated proteins associated with photosynthesis and oxidative phosphorylation, some proteins associated with the TCA cycle are succinylated. Our study can serve as a reference for further proteomics studies of the downstream effects of succinylation on the physiology and biochemistry of paper mulberry.
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Affiliation(s)
- Yibo Dong
- College of Animal Science, Guizhou university, Guiyang, 550025, Guizhou, China
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Ping Li
- Institute of Grassland Research, Sichuan Academy of Grassland Science, Chengdu, 610000, Sichuan, China
| | - Ping Li
- College of Animal Science, Guizhou university, Guiyang, 550025, Guizhou, China
| | - Chao Chen
- College of Animal Science, Guizhou university, Guiyang, 550025, Guizhou, China.
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Li P, Chen C, Li P, Dong Y. A comprehensive examination of the lysine acetylation targets in paper mulberry based on proteomics analyses. PLoS One 2021; 16:e0240947. [PMID: 33705403 PMCID: PMC7951917 DOI: 10.1371/journal.pone.0240947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/12/2021] [Indexed: 11/19/2022] Open
Abstract
Rocky desertification is a bottleneck that reduces ecological and environmental security in karst areas. Paper mulberry, a unique deciduous tree, shows good performance in rocky desertification areas. Its resistance mechanisms are therefore of high interest. In this study, a lysine acetylation proteomics analysis of paper mulberry seedling leaves was conducted in combination with the purification of acetylated protein by high-precision nano LC-MS/MS. We identified a total of 7130 acetylation sites in 3179 proteins. Analysis of the modified sites showed a predominance of nine motifs. Six positively charged residues: lysine (K), arginine (R), and histidine (H), serine (S), threonine (T), and tyrosine (Y) occurred most frequently at the +1 position, phenylalanine (F) was both detected both upstream and downstream of the acetylated lysines; and the sequence logos showed a strong preference for lysine and arginine around acetylated lysines. Functional annotation revealed that the identified enzymes were mainly involved in translation, transcription, ribosomal structure and biological processes, showing that lysine acetylation can regulate various aspects of primary carbon and nitrogen metabolism and secondary metabolism. Acetylated proteins were enriched in the chloroplast, cytoplasm, and nucleus, and many stress response-related proteins were also discovered to be acetylated, including PAL, HSP70, and ERF. HSP70, an important protein involved in plant abiotic and disease stress responses, was identified in paper mulberry, although it is rarely found in woody plants. This may be further examined in research in other plants and could explain the good adaptation of paper mulberry to the karst environment. However, these hypotheses require further verification. Our data can provide a new starting point for the further analysis of the acetylation function in paper mulberry and other plants.
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Affiliation(s)
- Ping Li
- College of Animal Science, Guizhou university, Guiyang, Guizhou, China
| | - Chao Chen
- College of Animal Science, Guizhou university, Guiyang, Guizhou, China
| | - Ping Li
- Institute of Grassland Research, Sichuan Academy of Grassland Science, Cheng Du, Si Chuan, China
| | - Yibo Dong
- College of Animal Science, Guizhou university, Guiyang, Guizhou, China
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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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Jain A, Singh HB, Das S. Deciphering plant-microbe crosstalk through proteomics studies. Microbiol Res 2020; 242:126590. [PMID: 33022544 DOI: 10.1016/j.micres.2020.126590] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 11/25/2022]
Abstract
Proteomic approaches are being used to elucidate a better discretion of interactions occurring between host, pathogen, and/or beneficial microorganisms at the molecular level. Application of proteomic techniques, unravel pathogenicity, stress-related, and antioxidant proteins expressed amid plant-microbe interactions and good information have been generated. It is being perceived that a fine regulation of protein expression takes place for effective pathogen recognition, induction of resistance, and maintenance of host integrity. However, our knowledge of molecular plant-microbe interactions is still incomplete and inconsequential. This review aims to provide insight into numerous ways used for proteomic investigation including peptide/protein identification, separation, and quantification during host defense response. Here, we highlight the current progress in proteomics of defense responses elicited by bacterial, fungal, and viral pathogens in plants along with which the proteome level changes induced by beneficial microorganisms are also discussed.
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Affiliation(s)
- Akansha Jain
- Division of Plant Biology, Bose Institute Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, 700054, West Bengal, India.
| | - Harikesh Bahadur Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Sampa Das
- Division of Plant Biology, Bose Institute Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, 700054, West Bengal, India.
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23
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Gai Z, Wang Y, Ding Y, Qian W, Qiu C, Xie H, Sun L, Jiang Z, Ma Q, Wang L, Ding Z. Exogenous abscisic acid induces the lipid and flavonoid metabolism of tea plants under drought stress. Sci Rep 2020; 10:12275. [PMID: 32704005 PMCID: PMC7378251 DOI: 10.1038/s41598-020-69080-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/02/2020] [Indexed: 01/12/2023] Open
Abstract
Abscisic acid (ABA) is an important phytohormone responsible for activating drought resistance, but the regulation mechanism of exogenous ABA on tea plants under drought stress was rarely reported. Here, we analyzed the effects of exogenous ABA on genes and metabolites of tea leaves under drought stress using transcriptomic and metabolomic analysis. The results showed that the exogenous ABA significantly induced the metabolic pathways of tea leaves under drought stress, including energy metabolism, amino acid metabolism, lipid metabolism and flavonoids biosynthesis. In which, the exogenous ABA could clearly affect the expression of genes involved in lipid metabolism and flavonoid biosynthesis. Meanwhile, it also increased the contents of flavone, anthocyanins, flavonol, isoflavone of tea leaves under drought stress, including, kaempferitrin, sakuranetin, kaempferol, and decreased the contents of glycerophospholipids, glycerolipids and fatty acids of tea leaves under drought stress. The results suggested that the exogenous ABA could alleviate the damages of tea leaves under drought stress through inducing the expression of the genes and altering the contents of metabolites in response to drought stress. This study will be helpful to understand the mechanism of resilience to abiotic stress in tea plant and provide novel insights into enhancing drought tolerance in the future.
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Affiliation(s)
- Zhongshuai Gai
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
- College of Life Science, Yantai University, Yantai, 264005, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yiqian Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wenjun Qian
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chen Qiu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hui Xie
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhongwu Jiang
- College of Life Science, Yantai University, Yantai, 264005, Shandong, China
| | - Qingping Ma
- College of Agriculture, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Linjun Wang
- Fruit Tea Station of Weihai Agricultural and Rural Affairs Service Center, Weihai, 264200, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China.
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24
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Qiu C, Sun J, Wang Y, Sun L, Xie H, Ding Y, Qian W, Ding Z. First nitrosoproteomic profiling deciphers the cysteine S-nitrosylation involved in multiple metabolic pathways of tea leaves. Sci Rep 2019; 9:17525. [PMID: 31772286 PMCID: PMC6879589 DOI: 10.1038/s41598-019-54077-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/08/2019] [Indexed: 02/04/2023] Open
Abstract
Cysteine S-nitrosylation is a reversible protein post-translational modification and critically regulates the activity, localization and stability of proteins. Tea (Camellia sinensis (L.) O. Kuntze) is one of the most thoroughly studied evergreen crop due to its broad non-alcoholic beverage and huge economic impact in the world. However, little is known about the S-nitrosylome in this plant. Here, we performed a global analysis of cysteine S-nitrosylation in tea leaves. In total, 228 cysteine S-nitrosylation sites were identified in 191 proteins, representing the first extensive data on the S-nitrosylome in tea plants. These S-nitrosylated proteins were located in various subcellular compartments, especially in the chloroplast and cytoplasm. Furthermore, the analysis of functional enrichment and PPI network revealed that the S-nitrosylated proteins were mainly involved in multiple metabolic pathways, including glycolysis, pyruvate metabolism, Calvin cycle and TCA cycle. Overall, this study not only systematically identified the proteins of S-nitrosylation in cysteines of tea leaves, but also laid the solid foundation for further verifying the roles of S-nitrosylation in cysteines of tea plants.
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Affiliation(s)
- Chen Qiu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Jianhao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hui Xie
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yiqian Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wenjun Qian
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China.
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25
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Liu Y, Lu S, Liu K, Wang S, Huang L, Guo L. Proteomics: a powerful tool to study plant responses to biotic stress. PLANT METHODS 2019; 15:135. [PMID: 31832077 PMCID: PMC6859632 DOI: 10.1186/s13007-019-0515-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/29/2019] [Indexed: 05/08/2023]
Abstract
In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.
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Affiliation(s)
- Yahui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Metrology, Beijing, China
| | - Song Lu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kefu Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Xu D, Wang X. Lysine Acetylation is an Important Post-Translational Modification that Modulates Heat Shock Response in the Sea Cucumber Apostichopus japonicus. Int J Mol Sci 2019; 20:ijms20184423. [PMID: 31505730 PMCID: PMC6770049 DOI: 10.3390/ijms20184423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 12/19/2022] Open
Abstract
Heat stress (HS) is an important factor for the survival of the marine organism Apostichopus japonicus. Lysine acetylation is a pivotal post-translational modification that modulates diverse physiological processes including heat shock response (HSR). In this study, 4028 lysine acetylation sites in 1439 proteins were identified in A. japonicus by acetylproteome sequencing. A total of 13 motifs were characterized around the acetylated lysine sites. Gene Ontology analysis showed that major acetylated protein groups were involved in “oxidation–reduction process”, “ribosome”, and “protein binding” terms. Compared to the control group, the acetylation quantitation of 25 and 41 lysine sites changed after 6 and 48 h HS. Notably, lysine acetyltransferase CREB-binding protein (CBP) was identified to have differential acetylation quantitation at multiple lysine sites under HS. Various chaperones, such as caseinolytic peptidase B protein homolog (CLBP), T-complex protein 1 (TCP1), and cyclophilin A (CYP1), showed differential acetylation quantitation after 48 h HS. Additionally, many translation-associated proteins, such as ribosomal proteins, translation initiation factor (IF), and elongation factors (EFs), had differential acetylation quantitation under HS. These proteins represented specific interaction networks. Collectively, our results offer novel insight into the complex HSR in A. japonicus and provide a resource for further mechanistic studies examining the regulation of protein function by lysine acetylation.
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Affiliation(s)
- Dongxue Xu
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - Xuan Wang
- Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China.
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Sun J, Qiu C, Qian W, Wang Y, Sun L, Li Y, Ding Z. Ammonium triggered the response mechanism of lysine crotonylome in tea plants. BMC Genomics 2019; 20:340. [PMID: 31060518 PMCID: PMC6501322 DOI: 10.1186/s12864-019-5716-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Lysine crotonylation, as a novel evolutionarily conserved type of post-translational modifications, is ubiquitous and essential in cell biology. However, its functions in tea plants are largely unknown, and the full functions of lysine crotonylated proteins of tea plants in nitrogen absorption and assimilation remains unclear. Our study attempts to describe the global profiling of nonhistone lysine crotonylation in tea leaves and to explore how ammonium (NH4+) triggers the response mechanism of lysine crotonylome in tea plants. RESULTS Here, we performed the global analysis of crotonylome in tea leaves under NH4+ deficiency/resupply using high-resolution LC-MS/MS coupled with highly sensitive immune-antibody. A total of 2288 lysine crotonylation sites on 971 proteins were identified, of which contained in 15 types of crotonylated motifs. Most of crotonylated proteins were located in chloroplast (37%) and cytoplasm (33%). Compared with NH4+ deficiency, 120 and 151 crotonylated proteins were significantly changed at 3 h and 3 days of NH4+ resupply, respectively. Bioinformatics analysis showed that differentially expressed crotonylated proteins participated in diverse biological processes such as photosynthesis (PsbO, PsbP, PsbQ, Pbs27, PsaN, PsaF, FNR and ATPase), carbon fixation (rbcs, rbcl, TK, ALDO, PGK and PRK) and amino acid metabolism (SGAT, GGAT2, SHMT4 and GDC), suggesting that lysine crotonylation played important roles in these processes. Moreover, the protein-protein interaction analysis revealed that the interactions of identified crotonylated proteins diversely involved in photosynthesis, carbon fixation and amino acid metabolism. Interestingly, a large number of enzymes were crotonylated, such as Rubisco, TK, SGAT and GGAT, and their activities and crotonylation levels changed significantly by sensing ammonium, indicating a potential function of crotonylation in the regulation of enzyme activities. CONCLUSIONS The results indicated that the crotonylated proteins had a profound influence on metabolic process of tea leaves in response to NH4+ deficiency/resupply, which mainly involved in diverse aspects of primary metabolic processes by sensing NH4+, especially in photosynthesis, carbon fixation and amino acid metabolism. The data might serve as important resources for exploring the roles of lysine crotonylation in N metabolism of tea plants. Data were available via ProteomeXchange with identifier PXD011610.
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Affiliation(s)
- Jianhao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Chen Qiu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Wenjun Qian
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yusheng Li
- Fruit and Tea Technology Extension Station, Jinan, 250000, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.
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