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Zhang Z, Zeng Y, Hou J, Li L. Advances in understanding the roles of plant HAT and HDAC in non-histone protein acetylation and deacetylation. PLANTA 2024; 260:93. [PMID: 39264431 DOI: 10.1007/s00425-024-04518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024]
Abstract
MAIN CONCLUSION This review focuses on HATs and HDACs that modify non-histone proteins, summarizes functional mechanisms of non-histone acetylation as well as the roles of HATs and HDACs in rice and Arabidopsis. The growth and development of plants, as well as their responses to biotic and abiotic stresses, are governed by intricate gene and protein regulatory networks, in which epigenetic modifying enzymes play a crucial role. Histone lysine acetylation levels, modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), are well-studied in the realm of transcriptional regulation. However, the advent of advanced proteomics has unveiled that non-histone proteins also undergo acetylation, with its underlying mechanisms now being clarified. Indeed, non-histone acetylation influences protein functionality through diverse pathways, such as modulating protein stability, adjusting enzymatic activity, steering subcellular localization, influencing interactions with other post-translational modifications, and managing protein-protein and protein-DNA interactions. This review delves into the recent insights into the functional mechanisms of non-histone acetylation in plants. We also provide a summary of the roles of HATs and HDACs in rice and Arabidopsis, and explore their potential involvement in the regulation of non-histone proteins.
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Affiliation(s)
- Zihan Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Zeng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Zhou J, Zhao L, Wu Y, Zhang X, Cheng S, Wei F, Zhang Y, Zhu H, Zhou Y, Feng Z, Feng H. A DEK domain-containing protein GhDEK2D mediated Gossypium hirsutum enhanced resistance to Verticillium dahliae. PLANT SIGNALING & BEHAVIOR 2022; 17:2024738. [PMID: 35034577 PMCID: PMC9176258 DOI: 10.1080/15592324.2021.2024738] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DEK is associated with DNA replication and break repair, mRNA splicing, and transcriptional regulation, which had been studied in humans and mammals. The function of DEK in plants was poorly understood. In this study, GhDEK2D was identified in Gossypium hirsutum by genome-wide and post-translational modifications. GhDEK2D had been phosphorylated, acetylated and ubiquitylated under Verticillium dahliae (Vd) challenge. The GhDEK2D-silenced cotton decreased resistance against Vd. In GhDEK2D-silenced cotton plants, the reactive oxygen species was activated, the callose, xylogen, hypersensitive reaction (HR) and expression levels of defense-related genes were reduced. Homozygous overexpressing-GhDEK2D transgenic Arabidopsis lines were more resistant to Verticillium wilt (Vw). We propose that GhDEK2D was a potential molecular target for improving resistance to Vw in cotton.
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Affiliation(s)
- Jinglong Zhou
- College of Agriculture, Yangtze University, Jingzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Lihong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Yajie Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xiaojian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Sheng Cheng
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Feng Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yalin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Heqin Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yi Zhou
- College of Agriculture, Yangtze University, Jingzhou, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Zili Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zili Feng State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Hongjie Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- CONTACT Hongjie Feng
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Yang W, Li X, Jiang G, Long Y, Li H, Yu S, Zhao H, Liu J. Crotonylation versus acetylation in petunia corollas with reduced acetyl-CoA due to PaACL silencing. PHYSIOLOGIA PLANTARUM 2022; 174:e13794. [PMID: 36193016 DOI: 10.1111/ppl.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Protein acetylation and crotonylation are important posttranslational modifications of lysine. In animal cells, the correlation of acetylation and crotonylation has been well characterized and the lysines of some proteins are acetylated or crotonylated depending on the relative concentrations of acetyl-CoA and crotonyl-CoA. However, in plants, the correlation of acetylation and crotonylation and the effects of the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA on protein crotonylation and acetylation are not well known. In our previous study, PaACL silencing changed the content of acetyl-CoA in petunia (Petunia hybrida) corollas, and the effect of PaACL silencing on the global acetylation proteome in petunia was analyzed. In the present study, we found that PaACL silencing did not significantly alter the content of crotonyl-CoA. We performed a global crotonylation proteome analysis of the corollas of PaACL-silenced and control petunia plants; we found that protein crotonylation was closely related to protein acetylation and that proteins with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins were enriched in many common Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. However, PaACL silencing resulted in different KEGG pathway enrichments of proteins with different levels of crotonylation sites and acetylation sites. PaACLB1-B2 silencing did not led to changes in the opposite direction in crotonylation and acetylation levels at the same lysine site in cytoplasmic proteins, which indicated that cytoplasmic lysine acetylation and crotonylation might not depend on the relative concentrations of acetyl-CoA and crotonyl-CoA. Moreover, the global crotonylome and acetylome were weakly positively correlated in the corollas of PaACL-silenced and control plants.
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Affiliation(s)
- Weiyuan Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xin Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guiyun Jiang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yu Long
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Hui Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shujun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Huina Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- College of Horticulture, South China Agricultural University, Guangzhou, China
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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 proteinย 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.ย 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 Nฮฑ-terminal acetylationย and the crosstalk between LysAc and other PTMs, including phosphorylation and succinylation. Finally, we proposeย recommendations for future studies in the field. We conclude that LysAc of proteinsย 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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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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Guo J, Chai X, Mei Y, Du J, Du H, Shi H, Zhu JK, Zhang H. Acetylproteomics analyses reveal critical features of lysine-ฮต-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response. STRESS BIOLOGY 2022; 2:1. [PMID: 37676343 PMCID: PMC10442023 DOI: 10.1007/s44154-021-00024-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/07/2021] [Indexed: 09/08/2023]
Abstract
Lysine-ฮต-acetylation (Kac) is a post-translational modification (PTM) that is critical for metabolic regulation and cell signaling in mammals. However, its prevalence and importance in plants remain to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein lysine acetylation in five representative Arabidopsis organs with 2โ~โ3 biological replicates per organ. A total of 2887 Kac proteins and 5929 Kac sites were identified. This comprehensive catalog allows us to analyze proteome-wide features of lysine acetylation. We found that Kac proteins tend to be more uniformly expressed in different organs, and the acetylation status exhibits little correlation with the gene expression level, indicating that acetylation is unlikely caused by stochastic processes. Kac preferentially targets evolutionarily conserved proteins and lysine residues, but only a small percentage of Kac proteins are orthologous between rat and Arabidopsis. A large portion of Kac proteins overlap with proteins modified by other PTMs including ubiquitination, SUMOylation and phosphorylation. Although acetylation, ubiquitination and SUMOylation all modify lysine residues, our analyses show that they rarely target the same sites. In addition, we found that "reader" proteins for acetylation and phosphorylation, i.e., bromodomain-containing proteins and GRF (General Regulatory Factor)/14-3-3 proteins, are intensively modified by the two PTMs, suggesting that they are main crosstalk nodes between acetylation and phosphorylation signaling. Analyses of GRF6/14-3-3ฮป reveal that the Kac level of GRF6 is decreased under alkaline stress, suggesting that acetylation represses plant alkaline response. Indeed, K56ac of GRF6 inhibits its binding to and subsequent activation of the plasma membrane H+-ATPase AHA2, leading to hypersensitivity to alkaline stress. These results provide valuable resources for protein acetylation studies in plants and reveal that protein acetylation suppresses phosphorylation output by acetylating GRF/14-3-3 proteins.
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Affiliation(s)
- Jianfei Guo
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoqiang Chai
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuchao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiamu Du
- Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Haining Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jian-Kang Zhu
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Heng Zhang
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
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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 (24โh 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 300โmM mannitol and 150โmM NaCl for 24โh. 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 24โh 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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Yuan B, Liu T, Cheng Y, Gao S, Li L, Cai L, Yang J, Chen J, Zhong K. Comprehensive Proteomic Analysis of Lysine Acetylation in Nicotiana benthamiana After Sensing CWMV Infection. Front Microbiol 2021; 12:672559. [PMID: 34084157 PMCID: PMC8166574 DOI: 10.3389/fmicb.2021.672559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
Protein lysine acetylation (Kac) is an important post-translational modification mechanism in eukaryotes that is involved in cellular regulation. To investigate the role of Kac in virus-infected plants, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese wheat mosaic virus (CWMV) infection. We identified 4,803 acetylated lysine sites on 1,964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were upregulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were downregulated on 102 proteins. Nineteen conserved motifs were extracted and 51 percent of the acetylated proteins located on chloroplast. Nineteen Kac sites were located on histone proteins, including 10 Kac sites on histone 3. Bioinformatics analysis results indicated that lysine acetylation occurs on a large number of proteins involved in biological processes, especially photosynthesis. Furthermore, we found that the acetylation level of chloroplast proteins, histone 3 and some metabolic pathway-related proteins were significantly higher in CWMV-infected plants than in uninfected plants. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.
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Affiliation(s)
- Bowen Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tingting Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Ye Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shiqi Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China.,Yantai Academy of Agricultural Science, Yantai, China
| | - Linzhi Li
- Yantai Academy of Agricultural Science, Yantai, China
| | - Linna Cai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Kaili Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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9
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Wang J, Ma Z, Li C, Ren P, Yao L, Li B, Meng Y, Ma X, Si E, Yang K, Shang X, Wang H. Dynamic Responses of Barley Root Succinyl-Proteome to Short-Term Phosphate Starvation and Recovery. FRONTIERS IN PLANT SCIENCE 2021; 12:649147. [PMID: 33868348 PMCID: PMC8045032 DOI: 10.3389/fpls.2021.649147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 05/05/2023]
Abstract
Barley (Hordeum vulgare L.)-a major cereal crop-has low Pi demand, which is a distinct advantage for studying the tolerance mechanisms of phosphorus deficiency. We surveyed dynamic protein succinylation events in barley roots in response to and recovery from Pi starvation by firstly evaluating the impact of Pi starvation in a Pi-tolerant (GN121) and Pi-sensitive (GN42) barley genotype exposed to long-term low Pi (40 d) followed by a high-Pi recovery for 10 d. An integrated proteomics approach involving label-free, immune-affinity enrichment, and high-resolution LC-MS/MS spectrometric analysis was then used to quantify succinylome and proteome in GN121 roots under short-term Pi starvation (6, 48 h) and Pi recovery (6, 48 h). We identified 2,840 succinylation sites (Ksuc) across 884 proteins; of which, 11 representative Ksuc motifs had the preferred amino acid residue (lysine). Furthermore, there were 81 differentially abundant succinylated proteins (DFASPs) from 119 succinylated sites, 83 DFASPs from 110 succinylated sites, 93 DFASPs from 139 succinylated sites, and 91 DFASPs from 123 succinylated sites during Pi starvation for 6 and 48 h and during Pi recovery for 6 and 48 h, respectively. Pi starvation enriched ribosome pathways, glycolysis, and RNA degradation. Pi recovery enriched the TCA cycle, glycolysis, and oxidative phosphorylation. Importantly, many of the DFASPs identified during Pi starvation were significantly overexpressed during Pi recovery. These results suggest that barley roots can regulate specific Ksuc site changes in response to Pi stress as well as specific metabolic processes. Resolving the metabolic pathways of succinylated protein regulation characteristics will improve phosphate acquisition and utilization efficiency in crops.
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Affiliation(s)
- 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
| | - 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
| | - 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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10
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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11
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Rubisco lysine acetylation occurs at very low stoichiometry in mature Arabidopsis leaves: implications for regulation of enzyme function. Biochem J 2020; 477:3885-3896. [PMID: 32959870 PMCID: PMC7557146 DOI: 10.1042/bcj20200413] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022]
Abstract
Multiple studies have shown ribulose-1,5-bisphosphate carboxylase/oxygenase (E.C. 4.1.1.39; Rubisco) to be subject to Lys-acetylation at various residues; however, opposing reports exist about the biological significance of these post-translational modifications. One aspect of the Lys-acetylation that has not been addressed in plants generally, or with Rubisco specifically, is the stoichiometry at which these Lys-acetylation events occur. As a method to ascertain which Lys-acetylation sites on Arabidopsis Rubisco might be of regulatory importance to its catalytic function in the CalvinโBenson cycle, we purified Rubisco from leaves in both the day and night-time and performed independent mass spectrometry based methods to determine the stoichiometry of Rubisco Lys-acetylation events. The results indicate that Rubisco is acetylated at most Lys residues, but each acetylation event occurs at very low stoichiometry. Furthermore, in vitro treatments that increased the extent of Lys-acetylation on purified Rubisco had no effect on Rubisco maximal activity. Therefore, we are unable to confirm that Lys-acetylation at low stoichiometries can be a regulatory mechanism controlling Rubisco maximal activity. The results highlight the need for further use of stoichiometry measurements when determining the biological significance of reversible PTMs like acetylation.
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12
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Guo W, Han L, Li X, Wang H, Mu P, Lin Q, Liu Q, Zhang Y. Proteome and lysine acetylome analysis reveals insights into the molecular mechanism of seed germination in wheat. Sci Rep 2020; 10:13454. [PMID: 32778714 PMCID: PMC7418024 DOI: 10.1038/s41598-020-70230-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/13/2020] [Indexed: 12/19/2022] Open
Abstract
Seed germination is the first stage in wheat growth and development, directly affecting grain yield and quality. As an important post-translation modification, lysine acetylation participates in diverse biological functions. However, little is known regarding the quantitative acetylproteome characterization during wheat seed germination. In this study, we generated the first comparative proteomes and lysine acetylomes during wheat seed germination. In total, 5,639 proteins and 1,301 acetylated sites on 722 proteins were identified at 0, 12 and 24ย h after imbibitions. Several particularly preferred amino acids were found near acetylation sites, including KacS, KacT, KacK, KacR, KacH, KacF, KacN, Kac*E, FKac and Kac*D, in the embryos during seed germination. Among them, KacH, KacF, FKac and KacK were conserved in wheat. Biosynthetic process, transcriptional regulation, ribosome and proteasome pathway related proteins were significantly enriched in both differentially expressed proteins and differentially acetylated proteins through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. We also revealed that histone acetylation was differentially involved in epigenetic regulation during seed germination. Meanwhile, abscisic acid and stress related proteins were found with acetylation changes. In addition, we focused on 8 enzymes involved in carbohydrate metabolism, and found they were differentially acetylated during seed germination. Finally, a putative metabolic pathway was proposed to dissect the roles of protein acetylation during wheat seed germination. These results not only demonstrate that lysine acetylation may play key roles in seed germination of wheat but also reveal insights into the molecular mechanism of seed germination in this crop.
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Affiliation(s)
- Weiwei Guo
- Shandong Provincial Key Laboratory of Dryland Farming Technology/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Liping Han
- Shandong Provincial Key Laboratory of Dryland Farming Technology/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dryland Farming Technology/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Huifang Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Ping Mu
- Shandong Provincial Key Laboratory of Dryland Farming Technology/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Qi Lin
- Shandong Provincial Key Laboratory of Dryland Farming Technology/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Qingchang Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China.,Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dryland Farming Technology/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China.
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13
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Evaluation of sea cucumber peptides-assisted memory activity and acetylation modification in hippocampus of test mice based on scopolamine-induced experimental animal model of memory disorder. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.103909] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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14
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Song G, Montes C, Walley JW. Quantitative Profiling of Protein Abundance and Phosphorylation State in Plant Tissues Using Tandem Mass Tags. Methods Mol Biol 2020; 2139:147-156. [PMID: 32462584 DOI: 10.1007/978-1-0716-0528-8_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Proteins produce or regulate nearly every component of cells. Thus, the ability to quantitatively determine the protein abundance and posttranslational modification (PTM) state is a critical aspect toward our understanding of biological processes. In this chapter, we describe methods to globally quantify protein abundance and phosphorylation state using isobaric labeling with tandem mass tags followed by phosphopeptide enrichment.
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Affiliation(s)
- Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA.
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15
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Li Z, Wang Y, Bello BK, Ajadi AA, Tong X, Chang Y, Zhang J. Construction of a Quantitative Acetylomic Tissue Atlas in Rice ( Oryza sativa L.). Molecules 2018; 23:molecules23112843. [PMID: 30388832 PMCID: PMC6278296 DOI: 10.3390/molecules23112843] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues.
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Affiliation(s)
- Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Babatunde Kazeem Bello
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Abolore Adijat Ajadi
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yuxiao Chang
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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16
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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17
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Hui M, Cheng J, Sha Z. First comprehensive analysis of lysine acetylation in Alvinocaris longirostris from the deep-sea hydrothermal vents. BMC Genomics 2018; 19:352. [PMID: 29747590 PMCID: PMC5946511 DOI: 10.1186/s12864-018-4745-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/30/2018] [Indexed: 11/27/2022] Open
Abstract
Background Deep-sea hydrothermal vents are unique chemoautotrophic ecosystems with harsh conditions. Alvinocaris longirostris is one of the dominant crustacean species inhabiting in these extreme environments. It is significant to clarify mechanisms in their adaptation to the vents. Lysine acetylation has been known to play critical roles in the regulation of many cellular processes. However, its function in A. longirostris and even marine invertebrates remains elusive. Our study is the first, to our knowledge, to comprehensively investigate lysine acetylome in A. longirostris. Results In total, 501 unique acetylation sites from 206 proteins were identified by combination of affinity enrichment and high-sensitive-massspectrometer. It was revealed that Arg, His and Lys occurred most frequently at the +โ1 position downstream of the acetylation sites, which were all alkaline amino acids and positively charged. Functional analysis revealed that the protein acetylation was involved in diverse cellular processes, such as biosynthesis of amino acids, citrate cycle, fatty acid degradation and oxidative phosphorylation. Acetylated proteins were found enriched in mitochondrion and peroxisome, and many stress response related proteins were also discovered to be acetylated, like arginine kinases, heat shock protein 70, and hemocyanins. In the two hemocyanins, nine acetylation sites were identified, among which one acetylation site was unique in A. longirostris when compared with other shallow water shrimps. Further studies are warranted to verify its function. Conclusion The lysine acetylome of A. longirostris is investigated for the first time and brings new insights into the regulation function of the lysine acetylation. The results supply abundant resources for exploring the functions of acetylation in A. longirostris and other shrimps. Electronic supplementary material The online version of this article (10.1186/s12864-018-4745-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Hui
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiao Cheng
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongli Sha
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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18
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Zhou H, Finkemeier I, Guan W, Tossounian MA, Wei B, Young D, Huang J, Messens J, Yang X, Zhu J, Wilson MH, Shen W, Xie Y, Foyer CH. Oxidative stress-triggered interactions between the succinyl- and acetyl-proteomes of rice leaves. PLANT, CELL & ENVIRONMENT 2018; 41:1139-1153. [PMID: 29126343 DOI: 10.1111/pce.13100] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/19/2017] [Indexed: 05/20/2023]
Abstract
Protein lysine acylations, such as succinylation and acetylation, are important post-translational modification (PTM) mechanisms, with key roles in cellular regulation. Antibody-based affinity enrichment, high-resolution liquid chromatography mass spectrometry analysis, and integrated bioinformatics analysis were used to characterize the lysine succinylome (Ksuc ) and acetylome (Kace ) of rice leaves. In total, 2,593 succinylated and 1,024 acetylated proteins were identified, of which 723 were simultaneously acetylated and succinylated. Proteins involved in photosynthetic carbon metabolism such as the large and small subunits of RuBisCO, ribosomal functions, and other key processes were subject to both PTMs. Preliminary insights into oxidant-induced changes to the rice acetylome and succinylome were gained from treatments with hydrogen peroxide. Exposure to oxidative stress did not regulate global changes in the rice acetylome or succinylome but rather led to modifications on a specific subset of the identified sites. De-succinylation of recombinant catalase (CATA) and glutathione S-transferase (OsGSTU6) altered the activities of these enzymes showing that this PTM may have a regulatory function. These findings not only greatly extend the list of acetylated and/or succinylated proteins but they also demonstrate the close cooperation between these PTMs in leaf proteins with key metabolic functions.
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Affiliation(s)
- Heng Zhou
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, Westfaelische Wilhelms University Muenster, Muenster, 48149, Germany
| | - Wenxue Guan
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Maria-Armineh Tossounian
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium
- Brussels Center for Redox Biology, Brussels, B-1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Bo Wei
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium
- Brussels Center for Redox Biology, Brussels, B-1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 927, Ghent, B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, B-9052, Belgium
| | - David Young
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium
- Brussels Center for Redox Biology, Brussels, B-1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Jingjing Huang
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium
- Brussels Center for Redox Biology, Brussels, B-1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 927, Ghent, B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, B-9052, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium
- Brussels Center for Redox Biology, Brussels, B-1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Xibin Yang
- Jingjie PTM Biolab (Hangzhou) Co. Ltd., Hangzhou, 310018, China
| | - Jun Zhu
- Jingjie PTM Biolab (Hangzhou) Co. Ltd., Hangzhou, 310018, China
| | - Michael H Wilson
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Wenbiao Shen
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanjie Xie
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Christine H Foyer
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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19
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Li X, Ye J, Ma H, Lu P. Proteomic analysis of lysine acetylation provides strong evidence for involvement of acetylated proteins in plant meiosis and tapetum function. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:142-154. [PMID: 29124795 DOI: 10.1111/tpj.13766] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 05/18/2023]
Abstract
Protein lysine acetylation (KAC) is a dynamic and reversible post-translational modification that has important biological roles in many organisms. Although KAC has been shown to affect reproductive development and meiosis in yeast and animals, similar studies are largely lacking in flowering plants, especially proteome-scale investigations for particular reproductive stages. Here, we report results from a proteomic investigation to detect the KAC status of the developing rice anthers near the time of meiosis (RAM), providing strong biochemical evidence for roles of many KAC-affected proteins during anther development and meiosis in rice. We identified a total of 1354 KAC sites in 676 proteins. Among these, 421 acetylated proteins with 629 KAC sites are novel, greatly enriching our knowledge on KAC in flowering plants. Gene Ontology enrichment analysis showed chromatin silencing, protein folding, fatty acid biosynthetic process and response to stress to be over-represented. In addition, certain potentially specific KAC motifs in RAM were detected. Importantly, 357 rice meiocyte proteins were acetylated; and four proteins genetically identified to be important for rice tapetum and pollen development were acetylated on 14 KAC sites in total. Furthermore, 47 putative secretory proteins were detected to exhibit acetylated status in RAM. Moreover, by comparing our lysine acetylome with the RAM phosphoproteome we obtained previously, we proposed a correlation between KAC and phosphorylation as a potential modulatory mechanism in rice RAM. This study provides the first global survey of KAC in plant reproductive development, making a promising starting point for further functional analysis of KAC during rice anther development and meiosis.
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Affiliation(s)
- Xiaojing Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Juanying Ye
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Pingli Lu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
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20
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Uhrig RG, Schlรคpfer P, Mehta D, Hirsch-Hoffmann M, Gruissem W. Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes. BMC Genomics 2017; 18:514. [PMID: 28679357 PMCID: PMC5499015 DOI: 10.1186/s12864-017-3894-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/21/2017] [Indexed: 12/30/2022] Open
Abstract
Background Reversible protein acetylation occurring on Lys-Ne has emerged as a key regulatory post-translational modification in eukaryotes. It is mediated by two groups of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) that catalyze the addition and removal of acetyl groups from target proteins. Estimates indicate that protein acetylation is second to protein phosphorylation in abundance, with thousands of acetylated sites now identified in different subcellular compartments. Considering the important regulatory role of protein phosphorylation, elucidating the diversity of KATs and KDACs across photosynthetic eukaryotes is essential in furthering our understanding of the impact of reversible protein acetylation on plant cell processes. Results We report a genome-scale analysis of lysine acetyltransferase (KAT)- and lysine deacetylase (KDAC)-families from 53 photosynthetic eukaryotes. KAT and KDAC orthologs were identified in sequenced genomes ranging from glaucophytes and algae to land plants and then analyzed for evolutionary relationships. Based on consensus molecular phylogenetic and subcellular localization data we found new sub-classes of enzymes in established KAT- and KDAC-families. Specifically, we identified a non-photosynthetic origin of the HD-tuin family KDACs, a new monocot-specific Class I HDA-family sub-class, and a phylogenetically distinct Class II algal/heterokont sub-class which maintains an ankyrin domain not conserved in land plant Class II KDACs. Protein structure analysis showed that HDA- and SRT-KDACs exist as bare catalytic subunits with highly conserved median protein length, while all KATs maintained auxiliary domains, with CBP- and TAFII250-KATs displaying protein domain gain and loss over the course of photosynthetic eukaryote evolution in addition to variable protein length. Lastly, promoter element enrichment analyses across species revealed conserved cis-regulatory sequences that support KAT and KDAC involvement in the regulation of plant development, cold/drought stress response, as well as cellular processes such as the circadian clock. Conclusions Our results reveal new evolutionary, structural, and biological insights into the KAT- and KDAC-families of photosynthetic eukaryotes, including evolutionary parallels to protein kinases and protein phosphatases. Further, we provide a comprehensive annotation framework through our extensive phylogenetic analysis, from which future research investigating aspects of protein acetylation in plants can use to position new findings in a broader context. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3894-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R Glen Uhrig
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitรคtstrasse 2, 8092, Zurich, Switzerland.
| | - Pascal Schlรคpfer
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitรคtstrasse 2, 8092, Zurich, Switzerland.,Plant Biology Department, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Devang Mehta
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitรคtstrasse 2, 8092, Zurich, Switzerland
| | - Matthias Hirsch-Hoffmann
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitรคtstrasse 2, 8092, Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitรคtstrasse 2, 8092, Zurich, Switzerland
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A Quantitative Acetylomic Analysis of Early Seed Development in Rice (Oryza sativa L.). Int J Mol Sci 2017; 18:ijms18071376. [PMID: 28654018 PMCID: PMC5535869 DOI: 10.3390/ijms18071376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 11/20/2022] Open
Abstract
PKA (protein lysine acetylation) is a critical post-translational modification that regulates various developmental processes, including seed development. However, the acetylation events and dynamics on a proteomic scale in this process remain largely unknown, especially in rice early seed development. We report the first quantitative acetylproteomic study focused on rice early seed development by employing a mass spectral-based (MS-based), label-free approach. A total of 1817 acetylsites on 1688 acetylpeptides from 972 acetylproteins were identified in pistils and seeds at three and seven days after pollination, including 268 acetyproteins differentially acetylated among the three stages. Motif-X analysis revealed that six significantly enriched motifs, such as (DxkK), (kH) and (kY) around the acetylsites of the identified rice seed acetylproteins. Differentially acetylated proteins among the three stages, including adenosine diphosphate (ADP) -glucose pyrophosphorylases (AGPs), PDIL1-1 (protein disulfide isomerase like 1-1), hexokinases, pyruvate dehydrogenase complex (PDC) and numerous other regulators that are extensively involved in the starch and sucrose metabolism, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle and photosynthesis pathways during early seed development. This study greatly expanded the rice acetylome dataset, and shed novel insight into the regulatory roles of PKA in rice early seed development.
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22
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OโLeary BM, Plaxton WC. Mechanisms and Functions of Post-translational Enzyme Modifications in the Organization and Control of Plant Respiratory Metabolism. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2017. [DOI: 10.1007/978-3-319-68703-2_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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23
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First Comprehensive Proteome Analyses of Lysine Acetylation and Succinylation in Seedling Leaves of Brachypodium distachyon L. Sci Rep 2016; 6:31576. [PMID: 27515067 PMCID: PMC4981852 DOI: 10.1038/srep31576] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/26/2016] [Indexed: 01/23/2023] Open
Abstract
Protein acetylation and succinylation are the most crucial protein post-translational modifications (PTMs) involved in the regulation of plant growth and development. In this study, we present the first lysine-acetylation and lysine-succinylation proteome analysis of seedling leaves in Brachypodium distachyon L (Bd). Using high accuracy nano LC-MS/MS combined with affinity purification, we identified a total of 636 lysine-acetylated sites in 353 proteins and 605 lysine-succinylated sites in 262 proteins. These proteins participated in many biology processes, with various molecular functions. In particular, 119 proteins and 115 sites were found to be both acetylated and succinylated, simultaneously. Among the 353 acetylated proteins, 148 had acetylation orthologs in Oryza sativa L., Arabidopsis thaliana, Synechocystis sp. PCC 6803, and Glycine max L. Among the 262 succinylated proteins, 170 of them were found to have homologous proteins in Oryza sativa L., Escherichia coli, Sacchayromyces cerevisiae, or Homo sapiens. Motif-X analysis of the acetylated and succinylated sites identified two new acetylated motifs (K---K and K-I-K) and twelve significantly enriched succinylated motifs for the first time, which could serve as possible binding loci for future studies in plants. Our comprehensive dataset provides a promising starting point for further functional analysis of acetylation and succinylation in Bd and other plant species.
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24
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Kentache T, Jouenne T, Dรฉ E, Hardouin J. Proteomic characterization of Nฮฑ- and Nฮต-acetylation in Acinetobacter baumannii. J Proteomics 2016; 144:148-58. [PMID: 27222042 DOI: 10.1016/j.jprot.2016.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/12/2016] [Accepted: 05/18/2016] [Indexed: 12/25/2022]
Abstract
Nฮฑ- and Nฮต-acetylation represent a pivotal post-translational modification used by both eukaryotes and prokaryotes to modulate diverse biological processes. Acinetobacter baumannii has been described as an important nosocomial pathogen for the past 30 years, frequently involved in ventilator-associated pneumonia, bloodstream and urinary tract infections. Many aspects of the biology of A. baumannii remain elusive, in particular the extent and function of N-acetylation. We investigated here N-acetylation in A. baumannii strain ATCC 17978 by proteomic analysis, and we showed the usefulness of using different analytical approaches. Overall, we identified 525 N-acetylated proteins in which, 145 were Nฮฑ-acetylated and 411 were Nฮต-acetylated. Among them, 41 proteins carried both types of N-acetylation. We found that N-acetylation may play a role in biofilm formation, bacterial virulence (e.g. in several iron acquisition pathways), as well as a number of phenotypes, such as, stress adaptation and drug resistance. BIOLOGICAL SIGNIFICANCE This study is the first to perform the N-acetylome of A. baumannii using different analytical approaches. Each analytical tool permitted to characterize distinctive modified peptides. The combination of all these methods allowed us to identify 145 and 411 Nฮฑ- and Nฮต-acetylated proteins. Besides the fact that acetylation was involved in central metabolism as previously described in other bacteria, some N-acetylated proteins showed interesting role in bacterial virulence (iron acquisition), biofilm formation, stress adaptation and drug resistance of A. baumannii.
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Affiliation(s)
- Takfarinas Kentache
- CNRS, UMR 6270, Polymรจres, Biopolymรจres, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymรจres, Biopolymรจres, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dรฉ
- CNRS, UMR 6270, Polymรจres, Biopolymรจres, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymรจres, Biopolymรจres, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France.
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25
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He D, Wang Q, Li M, Damaris RN, Yi X, Cheng Z, Yang P. Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed. J Proteome Res 2016; 15:879-90. [PMID: 26767346 DOI: 10.1021/acs.jproteome.5b00805] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Regulation of rice seed germination has been shown to mainly occur at post-transcriptional levels, of which the changes on proteome status is a major one. Lysine acetylation and succinylation are two prevalent protein post-translational modifications (PTMs) involved in multiple biological processes, especially for metabolism regulation. To investigate the potential mechanism controlling metabolism regulation in rice seed germination, we performed the lysine acetylation and succinylation analyses simultaneously. Using high-accuracy nano-LC-MS/MS in combination with the enrichment of lysine acetylated or succinylated peptides from digested embryonic proteins of 24 h after imbibition (HAI) rice seed, a total of 699 acetylated sites from 389 proteins and 665 succinylated sites from 261 proteins were identified. Among these modified lysine sites, 133 sites on 78 proteins were commonly modified by two PTMs. The overlapped PTM sites were more likely to be in polar acidic/basic amino acid regions and exposed on the protein surface. Both of the acetylated and succinylated proteins cover nearly all aspects of cellular functions. Ribosome complex and glycolysis/gluconeogenesis-related proteins were significantly enriched in both acetylated and succinylated protein profiles through KEGG enrichment and protein-protein interaction network analyses. The acetyl-CoA and succinyl-CoA metabolism-related enzymes were found to be extensively modified by both modifications, implying the functional interaction between the two PTMs. This study provides a rich resource to examine the modulation of the two PTMs on the metabolism pathway and other biological processes in germinating rice seed.
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Affiliation(s)
- Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| | - Qiong Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Ming Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xingling Yi
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China
| | - Zhongyi Cheng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
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26
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Bouchut A, Chawla AR, Jeffers V, Hudmon A, Sullivan WJ. Proteome-wide lysine acetylation in cortical astrocytes and alterations that occur during infection with brain parasite Toxoplasma gondii. PLoS One 2015; 10:e0117966. [PMID: 25786129 PMCID: PMC4364782 DOI: 10.1371/journal.pone.0117966] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/20/2014] [Indexed: 01/22/2023] Open
Abstract
Lysine acetylation is a reversible post-translational modification (PTM) that has been detected on thousands of proteins in nearly all cellular compartments. The role of this widespread PTM has yet to be fully elucidated, but can impact protein localization, interactions, activity, and stability. Here we present the first proteome-wide survey of lysine acetylation in cortical astrocytes, a subtype of glia that is a component of the blood-brain barrier and a key regulator of neuronal function and plasticity. We identified 529 lysine acetylation sites across 304 proteins found in multiple cellular compartments that largely function in RNA processing/transcription, metabolism, chromatin biology, and translation. Two hundred and seventy-seven of the acetylated lysines we identified on 186 proteins have not been reported previously in any other cell type. We also mapped an acetylome of astrocytes infected with the brain parasite, Toxoplasma gondii. It has been shown that infection with T. gondii modulates host cell gene expression, including several lysine acetyltransferase (KAT) and deacetylase (KDAC) genes, suggesting that the host acetylome may also be altered during infection. In the T. gondii-infected astrocytes, we identified 34 proteins exhibiting a level of acetylation >2-fold and 24 with a level of acetylation <2-fold relative to uninfected astrocytes. Our study documents the first acetylome map for cortical astrocytes, uncovers novel lysine acetylation sites, and demonstrates that T. gondii infection produces an altered acetylome.
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Affiliation(s)
- Anne Bouchut
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Aarti R. Chawla
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Victoria Jeffers
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Andy Hudmon
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - William J. Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
- * E-mail:
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27
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Fang X, Chen W, Zhao Y, Ruan S, Zhang H, Yan C, Jin L, Cao L, Zhu J, Ma H, Cheng Z. Global analysis of lysine acetylation in strawberry leaves. FRONTIERS IN PLANT SCIENCE 2015; 6:739. [PMID: 26442052 PMCID: PMC4569977 DOI: 10.3389/fpls.2015.00739] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/31/2015] [Indexed: 05/08/2023]
Abstract
Protein lysine acetylation is a reversible and dynamic post-translational modification. It plays an important role in regulating diverse cellular processes including chromatin dynamic, metabolic pathways, and transcription in both prokaryotes and eukaryotes. Although studies of lysine acetylome in plants have been reported, the throughput was not high enough, hindering the deep understanding of lysine acetylation in plant physiology and pathology. In this study, taking advantages of anti-acetyllysine-based enrichment and high-sensitive-mass spectrometer, we applied an integrated proteomic approach to comprehensively investigate lysine acetylome in strawberry. In total, we identified 1392 acetylation sites in 684 proteins, representing the largest dataset of acetylome in plants to date. To reveal the functional impacts of lysine acetylation in strawberry, intensive bioinformatic analysis was performed. The results significantly expanded our current understanding of plant acetylome and demonstrated that lysine acetylation is involved in multiple cellular metabolism and cellular processes. More interestingly, nearly 50% of all acetylated proteins identified in this work were localized in chloroplast and the vital role of lysine acetylation in photosynthesis was also revealed. Taken together, this study not only established the most extensive lysine acetylome in plants to date, but also systematically suggests the significant and unique roles of lysine acetylation in plants.
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Affiliation(s)
- Xianping Fang
- Institute of Biology, Hangzhou Academy of Agricultural SciencesHangzhou, China
| | - Wenyue Chen
- Institute of Biology, Hangzhou Academy of Agricultural SciencesHangzhou, China
| | - Yun Zhao
- Experiment Center, Hangzhou Academy of Agricultural SciencesHangzhou, China
| | - Songlin Ruan
- Institute of Biology, Hangzhou Academy of Agricultural SciencesHangzhou, China
| | - Hengmu Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Chengqi Yan
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Liang Jin
- Research and Development Center of Flower, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | | | - Jun Zhu
- Jingjie PTM BiolabsHangzhou, China
| | - Huasheng Ma
- Institute of Biology, Hangzhou Academy of Agricultural SciencesHangzhou, China
- *Correspondence: Huasheng Ma, Hangzhou Academy of Agricultural Sciences, Institute of Biology, East Hangxin Road 1, Hangzhou 310024, China
| | - Zhongyi Cheng
- Institute for Advanced Study of Translational Medicine, Tongji UniversityShanghai, China
- Zhongyi Cheng, Institute for Advanced Study of Translational Medicine, Tongji University, Siping Road 1239, Shanghai 200092, China
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28
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Rao RSP, Thelen JJ, Miernyk JA. In silico analysis of protein Lys-N(๐)-acetylation in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:381. [PMID: 25136347 PMCID: PMC4120686 DOI: 10.3389/fpls.2014.00381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/17/2014] [Indexed: 05/08/2023]
Abstract
Among post-translational modifications, there are some conceptual similarities between Lys-N(๐)-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. The study of Lys-acetylation of plant proteins has lagged behind studies of mammalian and microbial cells; 1000s of acetylation sites have been identified in mammalian proteins compared with only hundreds of sites in plant proteins. While most previous emphasis was focused on post-translational modifications of histones, more recent studies have addressed metabolic regulation. Being directly coupled with cellular CoA/acetyl-CoA and NAD/NADH, reversible Lys-N(๐)-acetylation has the potential to control, or contribute to control, of primary metabolism, signaling, and growth and development.
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Affiliation(s)
- R. Shyama Prasad Rao
- Division of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
| | - Jay J. Thelen
- Division of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
| | - Jรกn A. Miernyk
- Division of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
- Plant Genetics Research Unit, United States Department of Agriculture โ Agricultural Research ServiceColumbia, MO, USA
- *Correspondence: Jan A. Miernyk, Division of Biochemistry, University of Missouri, 102 Curtis Hall, Columbia, MO 65211, USA e-mail:
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