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Zhang L, Wang H, Xue C, Liu Y, Zhang Y, Liu Z, Meng X, Liu M, Zhao J. The crotonylated and succinylated proteins of jujube involved in phytoplasma-stress responses. BMC Biol 2024; 22:113. [PMID: 38750524 PMCID: PMC11094900 DOI: 10.1186/s12915-024-01917-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/10/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Protein posttranslational modifications (PTMs) are fast and early responses to environmental changes, including pathogen infection. Jujube witches' broom (JWB) is a phytoplasma disease causing great economic loss in jujube production. After phytoplasma infection, the transcriptional, translational, and metabolic levels in jujube were activated, enabling it to survive during phytoplasma invasion. However, no study has yet reported on PTMs in jujube. Lysine crotonylation (Kcr) and lysine succinylation (Ksu) have been popular studies in recent years and their function in plant phytoplasma-stress responses remains unclear. RESULTS Here, 1656 crotonylated and 282 succinylated jujube proteins were first identified under phytoplasma-stress, of which 198 were simultaneously crotonylated and succinylated. Comparative analysis revealed that 656 proteins, 137 crotonylated and 43 succinylated proteins in jujube were regulated by phytoplasma infection, suggesting that Kcr was more universal than Ksu. Kcr differentially expressed proteins (DEPs) were related to ribosomes, photosynthetic and carbon metabolism, while Ksu DEPs were mainly involved in carbon metabolism, the TCA cycle and secondary metabolite biosynthesis. The crosstalk network among proteome, crotonylome and succinylome showed that DEPs related to ribosomal, peroxidases and glutathione redox were enriched. Among them, ZjPOD51 and ZjPHGPX2 significantly increased at the protein and Kcr level under phytoplasma-stress. Notably, 7 Kcr sites were identified in ZjPHGPX2, a unique antioxidant enzyme. After inhibitor nicotinamide (NAM) treatment, GPX enzyme activity in jujube seedlings was reduced. Further, site-directed mutagenesis of key Kcr modification sites K130 and/or K135 in ZjPHGPX2 significantly reduced its activity. CONCLUSIONS This study firstly provided large-scale datasets of Kcr and Ksu in phytoplasma-infected jujube and revealed that Kcr modification in ZjPHGPX2 positively regulates its activity.
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Affiliation(s)
- Liman Zhang
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Huibin Wang
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Yin Liu
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiangrui Meng
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China.
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.
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Ding Y, Liu Y, Yang K, Zhao Y, Wen C, Yang Y, Zhang W. Proteomic Analysis of Lysine Acetylation and Succinylation to Investigate the Pathogenicity of Virulent Pseudomonas syringae pv. tomato DC3000 and Avirulent Line Pseudomonas syringae pv. tomato DC3000 avrRpm1 on Arabidopsis thaliana. Genes (Basel) 2024; 15:499. [PMID: 38674433 PMCID: PMC11050401 DOI: 10.3390/genes15040499] [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: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) is able to infect many economically important crops and thus causes substantial losses in the global agricultural economy. Pst DC3000 can be divided into virulent lines and avirulent lines. For instance, the pathogen effector avrRPM1 of avirulent line Pst-avrRpm1 (Pst DC3000 avrRpm1) can be recognized and detoxified by the plant. To further compare the pathogenicity mechanisms of virulent and avirulent Pst DC3000, a comprehensive analysis of the acetylome and succinylome in Arabidopsis thaliana was conducted following infection with virulent line Pst DC3000 and avirulent line Pst-avrRpm1. In this study, a total of 1625 acetylated proteins encompassing 3423 distinct acetylation sites were successfully identified. Additionally, 229 succinylated proteins with 527 unique succinylation sites were detected. A comparison of these modification profiles between plants infected with Pst DC3000 and Pst-avrRpm1 revealed significant differences. Specifically, modification sites demonstrated inconsistencies, with a variance of up to 10% compared to the control group. Moreover, lysine acetylation (Kac) and lysine succinylation (Ksu) displayed distinct preferences in their modification patterns. Lysine acetylation is observed to exhibit a tendency towards up-regulation in Arabidopsis infected with Pst-avrRpm1. Conversely, the disparity in the number of Ksu up-regulated and down-regulated sites was not as pronounced. Motif enrichment analysis disclosed that acetylation modification sequences are relatively conserved, and regions rich in polar acidic/basic and non-polar hydrophobic amino acids are hotspots for acetylation modifications. Functional enrichment analysis indicated that the differentially modified proteins are primarily enriched in the photosynthesis pathway, particularly in relation to light-capturing proteins. In conclusion, this study provides an insightful profile of the lysine acetylome and succinylome in A. thaliana infected with virulent and avirulent lines of Pst DC3000. Our findings revealed the potential impact of these post-translational modifications (PTMs) on the physiological functions of the host plant during pathogen infection. This study offers valuable insights into the complex interactions between plant pathogens and their hosts, laying the groundwork for future research on disease resistance and pathogenesis mechanisms.
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Affiliation(s)
- Yongqiang Ding
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Yangxuan Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Kexin Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Yiran Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Chun Wen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Y.D.); (K.Y.); (Y.Z.); (C.W.); (Y.Y.)
| | - Wei Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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3
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Zeng K, Yin H. KAT2A changes the function of endometrial stromal cells via regulating the succinylation of ENO1. Open Life Sci 2024; 19:20220785. [PMID: 38585644 PMCID: PMC10997078 DOI: 10.1515/biol-2022-0785] [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: 08/03/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/09/2024] Open
Abstract
Endometriosis is increasingly affecting women worldwide and research is focusing on identifying key targets in its pathogenesis. Changes in succinylation genes regulate the function of this protein and further influence the development of the disease. However, the role of succinylation genes in endometriosis is not clear from current studies. The expression of succinylation genes was determined in ectopic endometrium (EC) and ectopic patients with uterine fibroids (EN) by real-time quantitative PCR (qRT-PCR) and Western blot. Cell Counting Kit-8, transwell assays, and flow cytometry were used to assess endometrial stromal cells (ESCs) proliferation, apoptosis, migration, and invasion. KAT2A and ENO1 association was detected by qRT-PCR, immunofluorescence, and CoIP. We found that gene and protein levels of KAT2A were significantly increased in the EC group compared to EN group tissues. KAT2A silencing inhibited cell proliferation, migration, and invasion and promoted apoptosis. Western blot results showed that the expression of ENO1 and its succinylation was significantly upregulated in ECSc after KAT2A overexpression. CoIP results showed that KAT2A is positively bound to ENO1. Immunofluorescence also showed co-localized expression of KAT2A with ENO1. Furthermore, ENO1 overexpression reversed the effects of KAT2A silencing on the malignant behavior of ESCs. In summary, we found that succinylation of ENO1 mediated by KAT2A played a role in promoting the progression of endometriosis.
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Affiliation(s)
- Kangkang Zeng
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, 32 Renmin South Road, Maojian District, Shiyan442000, Hubei, China
| | - Hao Yin
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, 32 Renmin South Road, Maojian District, Shiyan442000, Hubei, China
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Zhu J, Guo W, Lan Y. Global Analysis of Lysine Lactylation of Germinated Seeds in Wheat. Int J Mol Sci 2023; 24:16195. [PMID: 38003390 PMCID: PMC10671351 DOI: 10.3390/ijms242216195] [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: 08/30/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Protein lactylation is a newly discovered posttranslational modification (PTM) and is involved in multiple biological processes, both in mammalian cells and rice grains. However, the function of lysine lactylation remains unexplored in wheat. In this study, we performed the first comparative proteomes and lysine lactylomes during seed germination of wheat. In total, 8000 proteins and 927 lactylated sites in 394 proteins were identified at 0 and 12 h after imbibition (HAI). Functional enrichment analysis showed that glycolysis- and TCA-cycle-related proteins were significantly enriched, and more differentially lactylated proteins were enriched in up-regulated lactylated proteins at 12 HAI vs. 0 HAI through the KEGG pathway and protein domain enrichment analysis compared to down-regulated lactylated proteins. Meanwhile, ten particularly preferred amino acids near lactylation sites were found in the embryos of germinated seeds: AA*KlaT, A***KlaD********A, KlaA**T****K, K******A*Kla, K*Kla********K, KlaA******A, Kla*A, KD****Kla, K********Kla and KlaG. These results supplied a comprehensive profile of lysine lactylation of wheat and indicated that protein lysine lactylation played important functions in several biological processes.
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Affiliation(s)
- Junke Zhu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China;
| | - Weiwei Guo
- College of Agronomy, Qingdao Agricultural University/Shandong Key Laboratory of Dryland Farming Technology/Shandong Engineering Research Center of Germplasm, Innovation and Utilization of Salt-Tolerant Crops, Qingdao 266109, China
| | - Yubin Lan
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China;
- National Sub-Center for International Collaboration Research on Precision Agricultural Aviation Pesticide Spraying Technology, Shandong University of Technology, Zibo 255000, China
- Academy of Ecological Unmanned Farm, Shandong University of Technology, Zibo 255000, China
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5
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Jiang Y, He C, Ye H, Xu Q, Chen X, Chen Y, Sun J, Rocha S, Wang M. Comprehensive analysis of the lysine succinylome in fish oil-treated prostate cancer cells. Life Sci Alliance 2023; 6:e202302131. [PMID: 37684043 PMCID: PMC10487806 DOI: 10.26508/lsa.202302131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Prostate cancer (PCa) poses a significant health threat to males, and research has shown that fish oil (FO) can impede PCa progression by activating multiple mitochondria-related pathways. Our research is focused on investigating the impact of FO on succinylation, a posttranslational modification that is closely associated with mitochondria in PCa cells. This study employed a mass spectrometry-based approach to investigate succinylation in PCa cells. Bioinformatics analysis of these succinylated proteins identified glutamic-oxaloacetic transaminase 2 (GOT2) protein as a key player in PCa cell proliferation. Immunoprecipitation and RNA interference technologies validated the functional data. Further analyses revealed the significance of GOT2 protein in regulating nucleotide synthesis by providing aspartate, which is critical for the survival and proliferation of PCa cells. Our findings suggest that FO-dependent GOT2 succinylation status has the potential to inhibit building block generation. This study lays a solid foundation for future research into the role of succinylation in various biological processes. This study highlights the potential use of FO as a nutrition supplement for managing and slowing down PCa progression.
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Affiliation(s)
- Yifan Jiang
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Chao He
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Haokai Ye
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Qianhan Xu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Xiuyuan Chen
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Ying Chen
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Jianying Sun
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Sonia Rocha
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mu Wang
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
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6
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Chen B, Wang Z, Jiao M, Zhang J, Liu J, Zhang D, Li Y, Wang G, Ke H, Cui Q, Yang J, Sun Z, Gu Q, Wang X, Wu J, Wu L, Zhang G, Wang X, Ma Z, Zhang Y. Lysine 2-Hydroxyisobutyrylation- and Succinylation-Based Pathways Act Inside Chloroplasts to Modulate Plant Photosynthesis and Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301803. [PMID: 37492013 PMCID: PMC10520639 DOI: 10.1002/advs.202301803] [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: 03/20/2023] [Revised: 06/11/2023] [Indexed: 07/27/2023]
Abstract
Crops must efficiently allocate their limited energy resources to survival, growth and reproduction, including balancing growth and defense. Thus, investigating the underlying molecular mechanism of crop under stress is crucial for breeding. Chloroplasts immunity is an important facet involving in plant resistance and growth, however, whether and how crop immunity modulated by chloroplast is influenced by epigenetic regulation remains unclear. Here, the cotton lysine 2-hydroxyisobutyrylation (Khib) and succinylation (Ksuc) modifications are firstly identified and characterized, and discover that the chloroplast proteins are hit most. Both modifications are strongly associated with plant resistance to Verticillium dahliae, reflected by Khib specifically modulating PR and salicylic acid (SA) signal pathway and the identified GhHDA15 and GhSRT1 negatively regulating Verticillium wilt (VW) resistance via removing Khib and Ksuc. Further investigation uncovers that photosystem repair protein GhPSB27 situates in the core hub of both Khib- and Ksuc-modified proteins network. The acylated GhPSB27 regulated by GhHDA15 and GhSRT1 can raise the D1 protein content, further enhancing plant biomass- and seed-yield and disease resistance via increasing photosynthesis and by-products of chloroplast-derived reactive oxygen species (cROS). Therefore, this study reveals a mechanism balancing high disease resistance and high yield through epigenetic regulation of chloroplast protein, providing a novel strategy to crop improvements.
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Affiliation(s)
- Bin Chen
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Zhicheng Wang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Mengjia Jiao
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Jin Zhang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Jie Liu
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Dongmei Zhang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Yanbin Li
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Qiuxia Cui
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Qishen Gu
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Xingyi Wang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Jinhua Wu
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Germplasm Resources of Education MinistryHebei Agricultural UniversityBaoding071001China
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Zhang N, Wang S, Zhao S, Chen D, Tian H, Li J, Zhang L, Li S, Liu L, Shi C, Yu X, Ren Y, Chen F. Global crotonylatome and GWAS revealed a TaSRT1- TaPGK model regulating wheat cold tolerance through mediating pyruvate. SCIENCE ADVANCES 2023; 9:eadg1012. [PMID: 37163591 PMCID: PMC10171821 DOI: 10.1126/sciadv.adg1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we reported the complete profiling of the crotonylation proteome in common wheat. Through a combination of crotonylation and multi-omics analysis, we identified a TaPGK associated with wheat cold stress. Then, we confirmed the positive role of TaPGK-modulating wheat cold tolerance. Meanwhile, we found that cold stress induced lysine crotonylation of TaPGK. Moreover, we screened a lysine decrotonylase TaSRT1 interacting with TaPGK and found that TaSRT1 negatively regulated wheat cold tolerance. We subsequently demonstrated TaSRT1 inhibiting the accumulation of TaPGK protein, and this inhibition was possibly resulted from decrotonylation of TaPGK by TaSRT1. Transcriptome sequencing indicated that overexpression of TaPGK activated glycolytic key genes and thereby increased pyruvate content. Moreover, we found that exogenous application of pyruvate sharply enhanced wheat cold tolerance. These findings suggest that the TaSRT1-TaPGK model regulating wheat cold tolerance is possibly through mediating pyruvate. This study provided two valuable cold tolerance genes and dissected diverse mechanism of glycolytic pathway involving in wheat cold stress.
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Affiliation(s)
- Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Sisheng Wang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Simin Zhao
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Daiying Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Hongyan Tian
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Jia Li
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lingran Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Songgang Li
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lu Liu
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Chaonan Shi
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Xiaodong Yu
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
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8
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Baker A, Lin CC, Lett C, Karpinska B, Wright MH, Foyer CH. Catalase: A critical node in the regulation of cell fate. Free Radic Biol Med 2023; 199:56-66. [PMID: 36775107 DOI: 10.1016/j.freeradbiomed.2023.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Catalase (CAT) is an extensively studied if somewhat enigmatic enzyme that is at the heart of eukaryotic antioxidant systems with a canonical role in peroxisomal function. The CAT family of proteins exert control over a wide range of plant growth and defence processes. CAT proteins are subject to many types of post-translational modification (PTM), which modify activity, ligand binding, stability, compartmentation and function. The CAT interactome involves many cytosolic and nuclear proteins that appear to be essential for protein functions. Hence, the CAT network of roles extends far beyond those associated with peroxisomal metabolism. Some pathogen effector proteins are able to redirect CAT to the nucleus and recent evidence indicates CAT can traffic to the nucleus in the absence of exogenous proteins. While the mechanisms that target CAT to the nucleus are not understood, CAT activity in the cytosol and nucleus is promoted by interactions with nucleoredoxin. Here we discuss recent findings that have been pivotal in generating a step change in our understanding of CAT functions in plant cells.
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Affiliation(s)
- Alison Baker
- Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Chi-Chuan Lin
- Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Casey Lett
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Barbara Karpinska
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Megan H Wright
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Christine H Foyer
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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9
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Luo W, He M, Luo Q, Li Y. Proteome-wide analysis of lysine β-hydroxybutyrylation in the myocardium of diabetic rat model with cardiomyopathy. Front Cardiovasc Med 2023; 9:1066822. [PMID: 36698951 PMCID: PMC9868477 DOI: 10.3389/fcvm.2022.1066822] [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: 10/11/2022] [Accepted: 12/13/2022] [Indexed: 01/10/2023] Open
Abstract
Lysine ß-hydroxybutyrylation (kbhb), a novel modification of lysine residues with the ß-hydroxybuty group, is associated with ketone metabolism in numerous species. However, its potential role in diabetes, especially in diabetic cardiomyopathy (DCM), remains largely unexplored. In this study, using affinity enrichment and liquid chromatography-mass spectrometry (LC-MS/MS) method, we quantitatively analyze the kbhb residues on heart tissues of a DCM model rat. A total of 3,520 kbhb sites in 1,089 proteins were identified in this study. Further analysis showed that 336 kbhb sites in 143 proteins were differentially expressed between the heart tissues of DCM and wild-type rats. Among them, 284 kbhb sites in 96 proteins were upregulated, while 52 kbhb sites in 47 proteins were downregulated. Bioinformatic analysis of the proteomic results revealed that these kbhb-modified proteins were widely distributed in various components and involved in a wide range of cellular functions and biological processes (BPs). Functional analysis showed that the kbhb-modified proteins were involved in the tricarboxylic acid cycle, oxidative phosphorylation, and propanoate metabolism. Our findings demonstrated how kbhb is related to many metabolic pathways and is mainly involved in energy metabolism. These results provide the first global investigation of the kbhb profile in DCM progression and can be an essential resource to explore DCM's pathogenesis further.
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Affiliation(s)
- Weiguang Luo
- Department of Clinical Laboratory, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mei He
- Henan Medical Key Laboratory of Arrhythmia, The 7th People’s Hospital of Zhengzhou, Zhengzhou Cardiovascular Hospital, Zhengzhou, China
| | - Qizhi Luo
- Department of Immunology, Basic Medical School of Central South University, Changsha, Hunan, China
| | - Yi Li
- Department of Clinical Laboratory, Henan Provincial People’s Hospital, Henan University People’s Hospital, Zhengzhou, Henan, China,*Correspondence: Yi Li,
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Li S, Zhou Y, Xu Y, Ran S, Hou M, Li Q, Zhong X, Zhong F. The analysis of lysine succinylation modification reveals the mechanism of oxybenzone damaging of pakchoi ( Brassica rapa L. ssp. chinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:1001935. [PMID: 36570927 PMCID: PMC9772522 DOI: 10.3389/fpls.2022.1001935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Oxybenzone (OBZ), one of a broad spectrum of ultraviolet (UV) absorbents, has been proven to be harmful to both plants and animals, while omics analysis of big data at the molecular level is still lacking. Lysine succinylation (Ksuc) is an important posttranslational modification of proteins that plays a crucial role in regulating the metabolic network in organisms under stress. Here, we report the changes in intracellular Ksuc modification in plants under OBZ stress. A total of 1276 succinylated sites on 507 proteins were identified. Among these sites, 181 modified proteins were hypersulfinylated/succinylated in OBZ-stressed pakchoi leaves. Differentially succinylated proteins (DSPs) are distributed mainly in the chloroplast, cytoplasm, and mitochondria and are distributed mainly in primary metabolic pathways, such as reactive oxygen species (ROS) scavenging, stress resistance, energy generation and transfer, photosynthetic carbon fixation, glycolysis, and the tricarboxylic acid (TCA) cycle. Comprehensive analysis shows that Ksuc mainly changes the carbon flow distribution, enhances the activity of the antioxidant system, affects the biosynthesis of amino acids, and increases the modification of histones. The results of this study first showed the profiling of the Kusc map under OBZ treatment and proposed the adaptive mechanism of pakchoi in response to pollutants and other abiotic stresses at the posttranslational level, which revealed the importance of Ksuc in the regulation of various life activities and provides a reference dataset for future research on molecular function.
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Affiliation(s)
- Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Yuqi Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Yang Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Shengxiang Ran
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Maomao Hou
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Qingming Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Cheng’du, China
| | - Xin Zhong
- Institute of Marine Science and Technology, Shandong University, Qing’dao, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
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11
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Zhang B, Chen Z, Sun Q, Liu J. Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.). BMC PLANT BIOLOGY 2022; 22:503. [PMID: 36289454 PMCID: PMC9608919 DOI: 10.1186/s12870-022-03885-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Bermudagrass (Cynodon dactylon L.) is an important warm-season turfgrass species with well-developed stolons, which lay the foundation for the fast propagation of bermudagrass plants through asexual clonal growth. However, the growth and development of bermudagrass stolons are still poorly understood at the molecular level. RESULTS In this study, we comprehensively analyzed the acetylation and succinylation modifications of proteins in fast-growing stolons of the bermudagrass cultivar Yangjiang. A total of 4657 lysine acetylation sites on 1914 proteins and 226 lysine succinylation sites on 128 proteins were successfully identified using liquid chromatography coupled to tandem mass spectrometry, respectively. Furthermore, 78 proteins and 81 lysine sites were found to be both acetylated and succinylated. Functional enrichment analysis revealed that acetylated proteins regulate diverse reactions of carbohydrate metabolism and protein turnover, whereas succinylated proteins mainly regulate the citrate cycle. These results partly explained the different growth disturbances of bermudagrass stolons under treatment with sodium butyrate and sodium malonate, which interfere with protein acetylation and succinylation, respectively. Moreover, 140 acetylated proteins and 42 succinylated proteins were further characterized having similarly modified orthologs in other grass species. Site-specific mutations combined with enzymatic activity assays indicated that the conserved acetylation of catalase and succinylation of malate dehydrogenase both inhibited their activities, further implying important regulatory roles of the two modifications. CONCLUSION In summary, our study implied that lysine acetylation and succinylation of proteins possibly play important regulatory roles in the fast growth of bermudagrass stolons. The results not only provide new insights into clonal growth of bermudagrass but also offer a rich resource for functional analyses of protein lysine acetylation and succinylation in plants.
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Affiliation(s)
- Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Zhuoting Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qixue Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
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12
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Guo W, Han J, Li X, He Z, Zhang Y. Large-scale analysis of protein crotonylation reveals its diverse functions in Pinellia ternata. BMC PLANT BIOLOGY 2022; 22:457. [PMID: 36151520 PMCID: PMC9502611 DOI: 10.1186/s12870-022-03835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pinellia ternata is an important traditional medicine in China, and its growth is regulated by the transcriptome or proteome. Lysine crotonylation, a newly identified and important type of posttranslational modification, plays a key role in many aspects of cell metabolism. However, little is known about its functions in Pinellia ternata. RESULTS In this study, we generated a global crotonylome analysis of Pinellia ternata and examined its overlap with lysine succinylation. A total of 2106 crotonylated sites matched on 1006 proteins overlapping in three independent tests were identified, and we found three specific amino acids surrounding crotonylation sites in Pinellia ternata: KcrF, K***Y**Kcr and Kcr****R. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that two crucial alkaloid biosynthesis-related enzymes and many stress-related proteins were also highly crotonylated. Furthermore, several enzymes participating in carbohydrate metabolism pathways were found to exhibit both lysine crotonylation and succinylation modifications. CONCLUSIONS These results indicate that lysine crotonylation performs important functions in many biological processes in Pinellia ternata, especially in the biosynthesis of alkaloids, and some metabolic pathways are simultaneously regulated by lysine crotonylation and succinylation.
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Affiliation(s)
- Weiwei Guo
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Jiayi Han
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Zihan He
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China.
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13
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Li X, Yang D, Yang Y, Jin G, Yin X, Zheng Y, Xu J, Yang Y. Quantitative Succinyl-Proteome Profiling of Turnip ( Brassica rapa var. rapa) in Response to Cadmium Stress. Cells 2022; 11:cells11121947. [PMID: 35741076 PMCID: PMC9221971 DOI: 10.3390/cells11121947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/30/2022] [Accepted: 06/15/2022] [Indexed: 01/25/2023] Open
Abstract
Protein post-translational modification (PTM) is an efficient biological mechanism to regulate protein structure and function, but its role in plant responses to heavy metal stress is poorly understood. The present study performed quantitative succinyl-proteome profiling using liquid chromatography−mass spectrometry analysis to explore the potential roles of lysine succinylation modification in turnip seedlings in response to cadmium (Cd) stress (20 μM) under hydroponic conditions over a short time period (0−8 h). A total of 547 succinylated sites on 256 proteins were identified in the shoots of turnip seedlings. These succinylated proteins participated in various biological processes (e.g., photosynthesis, tricarboxylic acid cycle, amino acid metabolism, and response to stimulation) that occurred in diverse cellular compartments according to the functional classification, subcellular localization, and protein interaction network analysis. Quantitative analysis showed that the intensities of nine succinylation sites on eight proteins were significantly altered (p < 0.05) in turnip shoots after 8 h of Cd stress. These differentially succinylated sites were highly conserved in Brassicaceae species and mostly located in the conserved domains of the proteins. Among them, a downregulated succinylation site (K150) in the glycolate oxidase protein (Gene0282600.1), an upregulated succinylation site (K396) in the catalase 3 protein (Gene0163880.1), and a downregulated succinylation site (K197) in the glutathione S-transferase protein (Gene0315380.1) may have contributed to the altered activity of the corresponding enzymes, which suggests that lysine succinylation affects the Cd detoxification process in turnip by regulating the H2O2 accumulation and glutathione metabolism. These results provide novel insights into understanding Cd response mechanisms in plants and important protein modification information for the molecular-assisted breeding of Brassica varieties with distinct Cd tolerance and accumulation capacities.
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Affiliation(s)
- Xiong Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Danni Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Yunqiang Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Xin Yin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Yan Zheng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
| | - Jianchu Xu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Correspondence: (J.X.); (Y.Y.)
| | - Yongping Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.L.); (D.Y.); (Y.Y.); (G.J.); (X.Y.); (Y.Z.)
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
- Correspondence: (J.X.); (Y.Y.)
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14
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Wang X, Chen J, Ni H, Mustafa G, Yang Y, Wang Q, Fu H, Zhang L, Yang B. Use Chou's 5-steps rule to identify protein post-translational modification and its linkage to secondary metabolism during the floral development of Lonicera japonica Thunb. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:1035-1048. [PMID: 34600181 DOI: 10.1016/j.plaphy.2021.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/01/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Lonicera japonica Thunb. is widely used in traditional medicine systems of East Asian and attracts a large amount of studies on the biosynthesis of its active components. Currently, there is little understanding regarding the regulatory mechanisms behind the accumulation of secondary metabolites during its developmental stages. In this study, published transcriptomic and proteomic data were mined to evaluate potential linkage between protein modification and secondary metabolism during the floral development. Stronger correlations were observed between differentially expressed genes (DEGs) and their corresponding differentially abundant proteins (DAPs) in the comparison of juvenile bud stage (JBS)/third green stage (TGS) vs. silver flowering stage (SFS). Seventy-five and 76 cor-rDEGs and cor-rDAPs (CDDs) showed opposite trends at both transcriptional and translational levels when comparing their levels at JBS and TGS relative to those at SFS. CDDs were mainly involved in elements belonging to the protein metabolism and the TCA cycle. Protein-protein interaction analysis indicated that the interacting proteins in the major cluster were primarily involved in TCA cycle and protein metabolism. In the simple phenylpropanoids biosynthetic pathway of SFS, both phospho-2-dehydro-3-deoxyheptonate aldolase (PDA) and glutamate/aspartate-prephenate aminotransferase (AAT) were decreased at the protein level, but increased at the gene level. A confirmatory experiment indicated that protein ubiquitination and succinylation were more prominent during the early floral developmental stages, in correlation with simple phenylpropanoids accumulation. Taken together, those data indicates that phenylpropanoids metabolism and floral development are putatively regulated through the ubiquitination and succinylation modifications of PDA, AAT, and TCA cycle proteins in L. japonica.
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Affiliation(s)
- Xueqin Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jiaqi Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Haofu Ni
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ghazala Mustafa
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Yuling Yang
- Wenshan Academy of Agricultural Sciences, Wenshan, 663000, China
| | - Qi Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, School of Pharmacy, Shihezi University, Shihezi, 832002, China
| | - Hongwei Fu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Lin Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Bingxian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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15
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The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids. J Biol Chem 2021; 297:101155. [PMID: 34480900 PMCID: PMC8477199 DOI: 10.1016/j.jbc.2021.101155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 11/22/2022] Open
Abstract
Acylation modifications, such as the succinylation of lysine, are post-translational modifications and a powerful means of regulating protein activity. Some acylations occur nonenzymatically, driven by an increase in the concentration of acyl group donors. Lysine succinylation has a profound effect on the corresponding site within the protein, as it dramatically changes the charge of the residue. In eukaryotes, it predominantly affects mitochondrial proteins because the donor of succinate, succinyl-CoA, is primarily generated in the tricarboxylic acid cycle. Although numerous succinylated mitochondrial proteins have been identified in Saccharomyces cerevisiae, a more detailed characterization of the yeast mitochondrial succinylome is still lacking. Here, we performed a proteomic MS analysis of purified yeast mitochondria and detected 314 succinylated mitochondrial proteins with 1763 novel succinylation sites. The mitochondrial nucleoid, a complex of mitochondrial DNA and mitochondrial proteins, is one of the structures whose protein components are affected by succinylation. We found that Abf2p, the principal component of mitochondrial nucleoids responsible for compacting mitochondrial DNA in S. cerevisiae, can be succinylated in vivo on at least thirteen lysine residues. Abf2p succinylation in vitro inhibits its DNA-binding activity and reduces its sensitivity to digestion by the ATP-dependent ScLon protease. We conclude that changes in the metabolic state of a cell resulting in an increase in the concentration of tricarboxylic acid intermediates may affect mitochondrial functions.
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16
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Huang Z, He L, Sang W, Wang L, Huang Q, Lei C. Potential role of lysine succinylation in the response of moths to artificial light at night stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112334. [PMID: 34020284 DOI: 10.1016/j.ecoenv.2021.112334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/14/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
Artificial light at night (ALAN) is a widespread environmental pollutant and stressor. Many nocturnal insects have been shown to experience ALAN stress. However, few studies have been conducted to uncover the mechanism by which nocturnal insects respond to ALAN stress. Previous studies suggest that lysine succinylation (Ksuc) is a potential mechanism that coordinates energy metabolism and antioxidant activity under stressful conditions. Mythimna separata (Walker) (M. separata) is a nocturnal insect that has been stressed by ALAN. In this study, we quantified the relative proteomic Ksuc levels in ALAN-stressed M. separata. Of the 466 identified Ksuc-modified proteins, 103 were hypersuccinylated/desuccinylated in ALAN-stressed moths. The hypersuccinylated/desuccinylated proteins were shown to be involved in various biological processes. In particular, they were enriched in metabolic processes, reactive oxygen species (ROS) homeostasis and the neuromuscular system. Furthermore, we demonstrated that Ksuc might affect moth locomotion by intervening with and coordinating these systems under ALAN stress. These findings suggest that Ksuc plays a vital role in the moth response to ALAN stress and moth locomotion behavior and provide a new perspective on the impact of ALAN on nocturnal insect populations and species communities.
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Affiliation(s)
- Zhijuan Huang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Li He
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wen Sang
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China.
| | - Lijun Wang
- College of Life Sciences, Yantai University, Yantai 264005, China.
| | - Qiuying Huang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chaoliang Lei
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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17
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Xu M, Tian X, Ku T, Wang G, Zhang E. Global Identification and Systematic Analysis of Lysine Malonylation in Maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2021; 12:728338. [PMID: 34490025 PMCID: PMC8417889 DOI: 10.3389/fpls.2021.728338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 05/27/2023]
Abstract
Lysine malonylation is a kind of post-translational modifications (PTMs) discovered in recent years, which plays an important regulatory role in plants. Maize (Zea mays L.) is a major global cereal crop. Immunoblotting revealed that maize was rich in malonylated proteins. We therefore performed a qualitative malonylome analysis to globally identify malonylated proteins in maize. In total, 1,722 uniquely malonylated lysine residues were obtained in 810 proteins. The modified proteins were involved in various biological processes such as photosynthesis, ribosome and oxidative phosphorylation. Notably, a large proportion of the modified proteins (45%) were located in chloroplast. Further functional analysis revealed that 30 proteins in photosynthesis and 15 key enzymes in the Calvin cycle were malonylated, suggesting an indispensable regulatory role of malonylation in photosynthesis and carbon fixation. This work represents the first comprehensive survey of malonylome in maize and provides an important resource for exploring the function of lysine malonylation in physiological regulation of maize.
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Affiliation(s)
- Min Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Xiaomin Tian
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Tingting Ku
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Guangyuan Wang
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Enying Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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18
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Feng B, Li S, Wang Z, Cao F, Wang Z, Li G, Liu K. Systematic analysis of lysine 2-hydroxyisobutyrylation posttranslational modification in wheat leaves. PLoS One 2021; 16:e0253325. [PMID: 34138952 PMCID: PMC8211214 DOI: 10.1371/journal.pone.0253325] [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: 11/19/2020] [Accepted: 06/02/2021] [Indexed: 01/15/2023] Open
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a recently discovered post-translational modification (PTM) showing diverse biological functions and effects in living organisms. However, the study of Khib in plant species is still relatively limited. Wheat (Triticum aestivum L.) is a global important cereal plant. In this study, the systematic Khib analysis was performed in wheat leave tissues. A total of 3004 Khib sites in 1104 proteins were repeatedly identified. Structure characterization of these Khib peptides revealed 12 conserved sequence motifs. Function classification and enrichment analysis indicated these Khib proteins showed a wide function and pathway distribution, of which ribosome activity, protein biosynthesis and photosynthesis were the preferred biological processes. Subcellular location predication indicated chloroplast was the dominant subcellular compartment where Khib was distributed. There may be some crosstalks among Khib, lysine acetylation and lysine succinylation modification because some proteins and sites were modified by all these three acylations. The present study demonstrated the critical role of Khib in wheat biological and physiology, which has expanded the scope of Khib in plant species. Our study is an available resource and reference of Khib function demonstration and structure characterization in cereal plant, as well as in plant kingdom.
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Affiliation(s)
- Bo Feng
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Shengdong Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Zongshuai Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Fang Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Zheng Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Geng Li
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, P. R. China
| | - Kaichang Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. 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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Bo F, Shengdong L, Zongshuai W, Fang C, Zheng W, Chunhua G, Geng L, Ling'an K. Global analysis of lysine 2-hydroxyisobutyrylation in wheat root. Sci Rep 2021; 11:6327. [PMID: 33737719 PMCID: PMC7973580 DOI: 10.1038/s41598-021-85879-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring post-translational modification. The system Khib identification at proteomics level has been performed in various species and tissues to characterize the role of Khib in biological activities. However, the study of Khib in plant species is relatively less. In the present study, the first plant root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat with antibody immunoprecipitation affinity, high resolution mass spectrometry-based proteomics and bioinformatics analysis. In total, 6328 Khib sites in 2186 proteins were repeatedly identified in three replicates. These Khib proteins showed a wide subcellular location distribution. Function and pathways characterization of these Khib proteins indicated that many cellular functions and metabolism pathways were potentially affected by this modification. Protein and amino acid metabolism related process may be regulated by Khib, especially ribosome activities and proteins biosynthesis process. Carbohydrate metabolism and energy production related processes including glycolysis/gluconeogenesis, TCA cycle and oxidative phosphorylation pathways were also affected by Khib modification. Besides, root sulfur assimilation and transformation related enzymes exhibited Khib modification. Our work illustrated the potential regulation role of Khib in wheat root physiology and biology, which could be used as a useful reference for Khib study in plant root.
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Affiliation(s)
- Feng Bo
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Li Shengdong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Wang Zongshuai
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Cao Fang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Wang Zheng
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Gao Chunhua
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Li Geng
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China.
| | - Kong Ling'an
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China.
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21
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Qian H, Wang L, Ma X, Yi X, Wang B, Liang W. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylated Proteins in Fusarium oxysporum. Front Microbiol 2021; 12:623735. [PMID: 33643252 PMCID: PMC7902869 DOI: 10.3389/fmicb.2021.623735] [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: 10/30/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022] Open
Abstract
Protein lysine 2-hydroxyisobutyrylation (K hib ), a new type of post-translational modification, occurs in histones and non-histone proteins and plays an important role in almost all aspects of both eukaryotic and prokaryotic living cells. Fusarium oxysporum, a soil-borne fungal pathogen, can cause disease in more than 150 plants. However, little is currently known about the functions of K hib in this plant pathogenic fungus. Here, we report a systematic analysis of 2-hydroxyisobutyrylated proteins in F. oxysporum. In this study, 3782 K hib sites in 1299 proteins were identified in F. oxysporum. The bioinformatics analysis showed that 2-hydroxyisobutyrylated proteins are involved in different biological processes and functions and are located in diverse subcellular localizations. The enrichment analysis revealed that K hib participates in a variety of pathways, including the ribosome, oxidative phosphorylation, and proteasome pathways. The protein interaction network analysis showed that 2-hydroxyisobutyrylated protein complexes are involved in diverse interactions. Notably, several 2-hydroxyisobutyrylated proteins, including three kinds of protein kinases, were involved in the virulence or conidiation of F. oxysporum, suggesting that K hib plays regulatory roles in pathogenesis. Moreover, our study shows that there are different K hib levels of F. oxysporum in conidial and mycelial stages. These findings provide evidence of K hib in F. oxysporum, an important filamentous plant pathogenic fungus, and serve as a resource for further exploration of the potential functions of K hib in Fusarium species and other filamentous pathogenic fungi.
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Affiliation(s)
- Hengwei Qian
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Lulu Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | | | - Xingling Yi
- Micron Biotechnology Co., Ltd., Hangzhou, China
| | - Baoshan Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Wenxing Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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22
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Li X, Wang L, Wang M, Zhang Z, Ma C, Ma X, Na X, Liang W. Global analysis of protein succinylation modification of Nostoc flagelliforme in response to dehydration. J Proteomics 2021; 237:104149. [PMID: 33588108 DOI: 10.1016/j.jprot.2021.104149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/13/2021] [Accepted: 02/02/2021] [Indexed: 11/29/2022]
Abstract
Nostoc flagelliforme is a type of terrestrial cyanobacteria that is distributed in arid or semi-arid steppes in China. To research the molecular mechanisms underlying the adaptation of N. flagelliforme to drought stress, the succinylated expression profile and changes in N. flagelliforme that resulted as a response to dehydration were analyzed by label-free proteomics. A total of 1149 succinylated sites, 1128 succinylated peptides, and 396 succinylated proteins were identified. Succinylated proteins were differentially involved in photosynthesis and energy metabolism, as well as in reactive oxygen species (ROS) scavenging. Motif-X analysis of succinylated sites determined a succinylation motif [KxxG]. N. flagelliforme adapts to dehydration by increasing glucose metabolism and pentose phosphate pathway flux, and decreasing photosynthetic rate, which some of the key proteins were succinylated. ROS scavenging was mainly involved in the regulation of the enzyme antioxidant defense system and non-enzymatic antioxidant defense system through succinylation modification, thus eliminating excessive ROS. Protein succinylation of N. flagelliforme may play an important regulatory role in response to dehydration. The results are foundational, as they can inform future research into the mechanisms involved in the succinylation regulation mechanism of N. flagelliforme in response to dehydration. SIGNIFICANCE: The global succinylation network involved in response to dehydration in N. flagelliforme has been established. We found that many succinylated proteins were involved in photosynthesis, glucose metabolism and antioxidation. The global survey of succinylated proteins and the changes of succinylated levels in response to dehydration provided effective information for the drought tolerance mechanism in N. flagelliforme.
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Affiliation(s)
- Xiaoxu Li
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Lingxia Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Meng Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Zheng Zhang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Caixia Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Xiaorong Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Xiaofan Na
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China.
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23
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Zeng F, Pang H, Chen Y, Zheng H, Li W, Ramanathan S, Hoare R, Monaghan SJ, Lin X, Jian J. First Succinylome Profiling of Vibrio alginolyticus Reveals Key Role of Lysine Succinylation in Cellular Metabolism and Virulence. Front Cell Infect Microbiol 2021; 10:626574. [PMID: 33614530 PMCID: PMC7892601 DOI: 10.3389/fcimb.2020.626574] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
Recent studies have shown that a key strategy of many pathogens is to use post-translational modification (PTMs) to modulate host factors critical for infection. Lysine succinylation (Ksuc) is a major PTM widespread in prokaryotic and eukaryotic cells, and is associated with the regulation of numerous important cellular processes. Vibrio alginolyticus is a common pathogen that causes serious disease problems in aquaculture. Here we used the affinity enrichment method with LC-MS/MS to report the first identification of 2082 lysine succinylation sites on 671 proteins in V. alginolyticus, and compared this with the lysine acetylation of V. alginolyticus in our previous work. The Ksuc modification of SodB and PEPCK proteins were further validated by Co-immunoprecipitation combined with Western blotting. Bioinformatics analysis showed that the identified lysine succinylated proteins are involved in various biological processes and central metabolism pathways. Moreover, a total of 1,005 (25.4%) succinyl sites on 502 (37.3%) proteins were also found to be acetylated, which indicated that an extensive crosstalk between acetylation and succinylation in V. alginolyticus occurs, especially in three central metabolic pathways: glycolysis/gluconeogenesis, TCA cycle, and pyruvate metabolism. Furthermore, we found at least 50 (7.45%) succinylated virulence factors, including LuxS, Tdh, SodB, PEPCK, ClpP, and the Sec system to play an important role in bacterial virulence. Taken together, this systematic analysis provides a basis for further study on the pathophysiological role of lysine succinylation in V. alginolyticus and provides targets for the development of attenuated vaccines.
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Affiliation(s)
- Fuyuan Zeng
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Huanying Pang
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China, Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Hongwei Zheng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Wanxin Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Srinivasan Ramanathan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rowena Hoare
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Sean J. Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jichang Jian
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China, Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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24
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Zhao Y, Han Y, Sun Y, Wei Z, Chen J, Niu X, An Q, Zhang L, Qi R, Gao X. Comprehensive Succinylome Profiling Reveals the Pivotal Role of Lysine Succinylation in Energy Metabolism and Quorum Sensing of Staphylococcus epidermidis. Front Microbiol 2021; 11:632367. [PMID: 33597936 PMCID: PMC7882547 DOI: 10.3389/fmicb.2020.632367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background Lysine succinylation is a newly identified posttranslational modification (PTM), which exists widely from prokaryotes to eukaryotes and participates in various cellular processes, especially in the metabolic processes. Staphylococcus epidermidis is a commensal bacterium in the skin, which attracts more attention as a pathogen, especially in immunocompromised patients and neonates by attaching to medical devices and forming biofilms. However, the significance of lysine succinylation in S. epidermidis proteins has not been investigated. Objectives The purpose of this study was to investigate the physiological and pathological processes of S. epidermidis at the level of PTM. Moreover, by analyzing previous succinylome datasets in various organisms, we tried to provide an in-depth understanding of lysine succinylation. Methods Using antibody affinity enrichment followed by LC-MS/MS analysis, we examined the succinylome of S. epidermidis (ATCC 12228). Then, bioinformatics analysis was performed, including Gene Ontology (GO), KEGG enrichment, motif characterization, secondary structure, protein–protein interaction, and BLAST analysis. Results A total of 1557 succinylated lysine sites in 649 proteins were identified in S. epidermidis (ATCC 12228). Among these succinylation proteins, GO annotation showed that proteins related to metabolic processes accounted for the most. KEGG pathway characterization indicated that proteins associated with the glycolysis/gluconeogenesis and citrate cycle (TCA cycle) pathway were more likely to be succinylated. Moreover, 13 conserved motifs were identified. The specific motif KsuD was conserved in model prokaryotes and eukaryotes. Succinylated proteins with this motif were highly enriched in the glycolysis/gluconeogenesis pathway. One succinylation site (K144) was identified in S-ribosylhomocysteine lyase, a key enzyme in the quorum sensing system, indicating the regulatory role succinylation may play in bacterial processes. Furthermore, 15 succinyltransferases and 18 desuccinylases (erasers) were predicted in S. epidermidis by BLAST analysis. Conclusion We performed the first comprehensive profile of succinylation in S. epidermidis and illustrated the significant role succinylation may play in energy metabolism, QS system, and other bacterial behaviors. This study may be a fundamental basis to investigate the underlying mechanisms of colonization, virulence, and infection of S. epidermidis, as well as provide a new insight into regulatory effects succinylation may lay on metabolic processes (Data are available via ProteomeXchange with identifier PXD022866).
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Affiliation(s)
- Yiping Zhao
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yang Han
- Department of Dermatology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Yuzhe Sun
- Department of Dermatology, Dermatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhendong Wei
- Department of Dermatology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jialong Chen
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xueli Niu
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Qian An
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Li Zhang
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ruiqun Qi
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xinghua Gao
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
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25
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Liu L, Wang H, Rao X, Yu Y, Li W, Zheng P, Zhao L, Zhou C, Pu J, Yang D, Fang L, Ji P, Song J, Wei H, Xie P. Comprehensive analysis of the lysine acetylome and succinylome in the hippocampus of gut microbiota-dysbiosis mice. J Adv Res 2020; 30:27-38. [PMID: 34026284 PMCID: PMC8132208 DOI: 10.1016/j.jare.2020.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/12/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Introduction Major depressive disorder is caused by gene–environment interactions, and the host microbiome has been recognized as an important environmental factor. However, the underlying mechanisms of the host–microbiota interactions that lead to depression are complex and remain poorly understood. Objectives The present study aimed to explore the possible mechanisms underlying gut microbiota dysbiosis-induced depressive-like behaviors. Methods We used high-performance liquid chromatography-tandem mass spectrometry to analyze alterations in the hippocampal lysine acetylome and succinylome in male mice that had received gut microbiota from fecal samples of either patients with major depressive disorder or healthy controls. This was followed by bioinformatic analyses. Results A total of 315 acetylation sites on 223 proteins and 624 succinylation sites on 494 proteins were differentially expressed in the gut microbiota-dysbiosis mice. The significantly acetylated proteins were primarily associated with carbon metabolism disruption and gene transcription suppression, while the synaptic vesicle cycle and protein translation were the most significantly altered functions for succinylated proteins. Additionally, our findings suggest that gut microbiota dysbiosis disturbs mitochondria-mediated biological processes and the MAPK signaling pathway through crosstalk between acetylation and succinylation on relevant proteins. Conclusions This is the first study to demonstrate modifications in acetylation and succinylation in gut microbiota-dysbiosis mice. Our findings provide new avenues for exploring the pathogenesis of gut microbiota dysbiosis-related depression, and highlight potential targets for depression treatment.
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Affiliation(s)
- Lanxiang Liu
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Haiyang Wang
- College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, 401147, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xuechen Rao
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Ying Yu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Wenxia Li
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Peng Zheng
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Libo Zhao
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Chanjuan Zhou
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Juncai Pu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Deyu Yang
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Liang Fang
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Ping Ji
- College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, 401147, China.,Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing 401147, China
| | - Jinlin Song
- College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, 401147, China.,Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing 401147, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Peng Xie
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China.,College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, 401147, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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26
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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 24 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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27
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Mao M, Xue Y, He Y, Zhou X, Rafique F, Hu H, Liu J, Feng L, Yang W, Li X, Sun L, Huang Z, Ma J. Systematic identification and comparative analysis of lysine succinylation between the green and white parts of chimeric leaves of Ananas comosus var. bracteatus. BMC Genomics 2020; 21:383. [PMID: 32493214 PMCID: PMC7268518 DOI: 10.1186/s12864-020-6750-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/21/2020] [Indexed: 01/26/2023] Open
Abstract
Background Lysine succinylation, an important protein posttranslational modification (PTM), is widespread and conservative. The regulatory functions of succinylation in leaf color has been reported. The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts and albino white parts. However, the extent and function of lysine succinylation in chimeric leaves of Ananas comosus var. bracteatus has yet to be investigated. Results Compared to the green (Gr) parts, the global succinylation level was increased in the white (Wh) parts of chimeric leaves according to the Western blot and immunohistochemistry analysis. Furthermore, we quantitated the change in the succinylation profiles between the Wh and Gr parts of chimeric leaves using label-free LFQ intensity. In total, 855 succinylated sites in 335 proteins were identified, and 593 succinylated sites in 237 proteins were quantified. Compared to the Gr parts, 232 (61.1%) sites in 128 proteins were quantified as upregulated targets, and 148 (38.9%) sites in 70 proteins were quantified as downregulated targets in the Wh parts of chimeric leaves using a 1.5-fold threshold (P < 0.05). These proteins with altered succinylation level were mainly involved in crassulacean acid metabolism (CAM) photosynthesis, photorespiration, glycolysis, the citric acid cycle (CAC) and pyruvate metabolism. Conclusions Our results suggested that the changed succinylation level in proteins might function in the main energy metabolism pathways—photosynthesis and respiration. Succinylation might provide a significant effect in the growth of chimeric leaves and the relationship between the Wh and Gr parts of chimeric leaves. This study not only provided a basis for further characterization on the function of succinylated proteins in chimeric leaves of Ananas comosus var. bracteatus but also provided a new insight into molecular breeding for leaf color chimera.
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Affiliation(s)
- Meiqin Mao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yanbin Xue
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yehua He
- Horticultural Biotechnology College, South China Agricultural University, Guangzhou, China
| | - Xuzixing Zhou
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Fatima Rafique
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Hao Hu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jiawen Liu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Lijun Feng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Wei Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Lingxia Sun
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Zhuo Huang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China.
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Dobolyi A, Bago A, Palkovits M, Nemeria NS, Jordan F, Doczi J, Ambrus A, Adam-Vizi V, Chinopoulos C. Exclusive neuronal detection of KGDHC-specific subunits in the adult human brain cortex despite pancellular protein lysine succinylation. Brain Struct Funct 2020; 225:639-667. [PMID: 31982949 PMCID: PMC7046601 DOI: 10.1007/s00429-020-02026-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 01/11/2020] [Indexed: 12/31/2022]
Abstract
The ketoglutarate dehydrogenase complex (KGDHC) consists of three different subunits encoded by OGDH (or OGDHL), DLST, and DLD, combined in different stoichiometries. DLD subunit is shared between KGDHC and pyruvate dehydrogenase complex, branched-chain alpha-keto acid dehydrogenase complex, and the glycine cleavage system. Despite KGDHC's implication in neurodegenerative diseases, cell-specific localization of its subunits in the adult human brain has never been investigated. Here, we show that immunoreactivity of all known isoforms of OGDHL, OGDH, and DLST was detected exclusively in neurons of surgical human cortical tissue samples identified by their morphology and visualized by double labeling with fluorescent Nissl, while being absent from glia expressing GFAP, Aldhl1, myelin basic protein, Olig2, or IBA1. In contrast, DLD immunoreactivity was evident in both neurons and glia. Specificity of anti-KGDHC subunits antisera was verified by a decrease in staining of siRNA-treated human cancer cell lines directed against the respective coding gene products; furthermore, immunoreactivity of KGDHC subunits in human fibroblasts co-localized > 99% with mitotracker orange, while western blotting of 63 post-mortem brain samples and purified recombinant proteins afforded further assurance regarding antisera monospecificity. KGDHC subunit immunoreactivity correlated with data from the Human Protein Atlas as well as RNA-Seq data from the Allen Brain Atlas corresponding to genes coding for KGDHC components. Protein lysine succinylation, however, was immunohistochemically evident in all cortical cells; this was unexpected, because this posttranslational modification requires succinyl-CoA, the product of KGDHC. In view of the fact that glia of the human brain cortex lack succinate-CoA ligase, an enzyme producing succinyl-CoA when operating in reverse, protein lysine succinylation in these cells must exclusively rely on propionate and/or ketone body metabolism or some other yet to be discovered pathway encompassing succinyl-CoA.
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Affiliation(s)
- Arpad Dobolyi
- MTA-ELTE Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Hungarian Academy of Sciences and Eotvos Lorand University, Budapest, 1117, Hungary
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, 1094, Hungary
| | - Attila Bago
- National Institute of Neurosurgery, Budapest, 1145, Hungary
| | - Miklos Palkovits
- MTA-ELTE Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Hungarian Academy of Sciences and Eotvos Lorand University, Budapest, 1117, Hungary
| | - Natalia S Nemeria
- Department of Chemistry, Rutgers University, Newark, NJ, 07102-1811, USA
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ, 07102-1811, USA
| | - Judit Doczi
- Department of Medical Biochemistry, Semmelweis University, Tuzolto st. 37-47, Budapest, 1094, Hungary
| | - Attila Ambrus
- Department of Medical Biochemistry, Semmelweis University, Tuzolto st. 37-47, Budapest, 1094, Hungary
- MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, Semmelweis University, Tuzolto st. 37-47, Budapest, 1094, Hungary
- MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Christos Chinopoulos
- Department of Medical Biochemistry, Semmelweis University, Tuzolto st. 37-47, Budapest, 1094, Hungary.
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Qiu C, Wang Y, Sun JH, Qian WJ, Xie H, Ding YQ, Ding ZT. A Qualitative Proteome-Wide Lysine Succinylation Profiling of Tea Revealed its Involvement in Primary Metabolism. Mol Biol 2020. [DOI: 10.1134/s0026893320010124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Meng X, Mujahid H, Zhang Y, Peng X, Redoña ED, Wang C, Peng Z. Comprehensive Analysis of the Lysine Succinylome and Protein Co-modifications in Developing Rice Seeds. Mol Cell Proteomics 2019; 18:2359-2372. [PMID: 31492684 PMCID: PMC6885699 DOI: 10.1074/mcp.ra119.001426] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/04/2019] [Indexed: 11/06/2022] Open
Abstract
Lysine succinylation has been recognized as a post-translational modification (PTM) in recent years. It is plausible that succinylation may have a vaster functional impact than acetylation because of bulkier structural changes and more significant charge differences on the modified lysine residue. Currently, however, the quantity and identity of succinylated proteins and their corresponding functions in cereal plants remain largely unknown. In this study, we estimated the native succinylation occupancy on lysine was between 2% to 10% in developing rice seeds. Eight hundred fifty-four lysine succinylation sites on 347 proteins have been identified by a thorough investigation in developing rice seeds. Six motifs were revealed as preferred amino acid sequence arrangements for succinylation sites, and a noteworthy motif preference was identified in proteins associated with different biological processes, molecular functions, pathways, and domains. Remarkably, heavy succinylation was detected on major seed storage proteins, in conjunction with critical enzymes involved in central carbon metabolism and starch biosynthetic pathways for rice seed development. Meanwhile, our results showed that the modification pattern of in vitro nonenzymatically succinylated proteins was different from those of the proteins isolated from cells in Western blots, suggesting that succinylation is not generated via nonenzymatic reaction in the cells, at least not completely. Using the acylation data obtained from the same rice tissue, we mapped many sites harboring lysine succinylation, acetylation, malonylation, crotonylation, and 2-hydroxisobutyrylation in rice seed proteins. A striking number of proteins with multiple modifications were shown to be involved in critical metabolic events. Given that these modification moieties are intermediate products of multiple cellular metabolic pathways, these targeted lysine residues may mediate the crosstalk between different metabolic pathways via modifications by different moieties. Our study exhibits a platform for extensive investigation of molecular networks administrating cereal seed development and metabolism via PTMs.
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Affiliation(s)
- Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762
| | - Hana Mujahid
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762
| | - Yadong Zhang
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762; Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing 210014, China
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab Co. Ltd, Hangzhou 310018, China
| | - Edilberto D Redoña
- Delta Research and Extension Center, Mississippi State University, Stoneville MS, 38776
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing 210014, China.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762.
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Yuan H, Chen J, Yang Y, Shen C, Xu D, Wang J, Yan D, He Y, Zheng B. Quantitative succinyl-proteome profiling of Chinese hickory (Carya cathayensis) during the grafting process. BMC PLANT BIOLOGY 2019; 19:467. [PMID: 31684873 PMCID: PMC6829946 DOI: 10.1186/s12870-019-2072-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/14/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Chinese hickory (Carya cathayensis) is a popular nut plant having high economic value. Grafting is applied to accelerate the transition from vegetative phase to reproductive phase. Lysine succinylation occurs frequently in the proteins associated with metabolic pathways, which may participate in the regulation of the grafting process. However, the exact regulatory mechanism underlying grafting process in Chinese hickory has not been studied at post-translational modification level. RESULTS A comprehensive proteome-wide lysine succinylation profiling of Chinese hickory was explored by a newly developed method combining affinity enrichment and high-resolution LC-MS/MS. In total, 259 succinylation sites in 202 proteins were identified, representing the first comprehensive lysine succinylome in Chinese hickory. The succinylation was biased to occur in the cytosolic proteins of Chinese hickory. Moreover, four conserved succinylation motifs were identified in the succinylated peptides. Comparison of two grafting stages of Chinese hickory revealed that the differential expressed succinylated proteins were mainly involved in sugar metabolism, carbon fixation, amino acid metabolism and plant-pathogen interaction. Besides, seven heat shock proteins (HSPs) with 11 succinylation sites were also identified, all of which were observed to be up-regulated during the grafting process. CONCLUSIONS Succinylation of the proteins involved in amino acid biosynthesis might be required for a successful grafting. Succinylated HSPs might play a role in stress tolerance of the grafted Chinese hickory plants. Our results can be a good resource for functional validation of the succinylated proteins and a starting point for the investigation of molecular mechanisms during lysine succinylation occurring at grafting site.
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Affiliation(s)
- Huwei Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Juanjuan Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Ying Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Chenjia Shen
- College of Life and Environmental Sciences Hangzhou Normal University, Hangzhou, 310036 People’s Republic of China
| | - Dongbin Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Junfeng Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Daoliang Yan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Yi He
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
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Gao Y, Lee H, Kwon OK, Tan M, Kim KT, Lee S. Global Proteomic Analysis of Lysine Succinylation in Zebrafish (Danio rerio). J Proteome Res 2019; 18:3762-3769. [DOI: 10.1021/acs.jproteome.9b00462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Gao
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | | | - Oh Kwang Kwon
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Minjia Tan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Sangkyu Lee
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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Wang G, Xu L, Yu H, Gao J, Guo L. Systematic analysis of the lysine succinylome in the model medicinal mushroom Ganoderma lucidum. BMC Genomics 2019; 20:585. [PMID: 31311503 PMCID: PMC6636155 DOI: 10.1186/s12864-019-5962-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 07/09/2019] [Indexed: 01/08/2023] Open
Abstract
Background Ganoderma lucidum, one of the best-known medicinal mushrooms in the world, produces more than 400 different bioactive compounds. However, the regulation of these bioactive compounds biosynthesis is still unclear. Lysine succinylation is a critical post-translational modification and has many important functions in all aspects of eukaryotic and prokaryotic cells. Although it has been studied for a long time, its function is still unclear in G. lucidum. In this study, a global investigation was carried out on the succinylome in G. lucidum. Results In total, 382 modified proteins which contain 742 lysine succinylated sites were obtained. The proteomics data are available through ProteomeXchange with the dataset accession number PXD013954. Bioinformatics analysis revealed that the succinylated proteins were distributed in various cellular biological processes and participated in a great variety of metabolic pathways including carbon metabolism and biosynthesis of secondary metabolites. Notably, a total of 47 enzymes associated with biosynthesis of triterpenoids and polysaccharides were found to be succinylated. Furthermore, two succinylated sites K90 and K106 were found in the conserved Fve region of immunomodulatory protein LZ8. These observations show that lysine succinylation plays an indispensable role in metabolic regulation of bioactive compounds in G. lucidum. Conclusions These findings indicate that lysine succinylation is related to many metabolic pathways, especially pharmacologically bioactive compounds metabolism. This study provides the first global investigation of lysine succinylation in G. lucidum and the succinylome dataset provided in this study serves as a resource to further explore the physiological roles of these modifications in secondary metabolism. Electronic supplementary material The online version of this article (10.1186/s12864-019-5962-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangyuan Wang
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Changcheng Road, No.700, Qingdao, 266109, China
| | - Lili Xu
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Changcheng Road, No.700, Qingdao, 266109, China
| | - Hao Yu
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Changcheng Road, No.700, Qingdao, 266109, China
| | - Jie Gao
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Changcheng Road, No.700, Qingdao, 266109, China
| | - Lizhong Guo
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Changcheng Road, No.700, Qingdao, 266109, China.
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Wang J, Li L, Chai R, Zhang Z, Qiu H, Mao X, Hao Z, Wang Y, Sun G. Succinyl-proteome profiling of Pyricularia oryzae, a devastating phytopathogenic fungus that causes rice blast disease. Sci Rep 2019; 9:3490. [PMID: 30837482 PMCID: PMC6401317 DOI: 10.1038/s41598-018-36852-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/27/2018] [Indexed: 11/21/2022] Open
Abstract
Pyricularia oryzae is the pathogen for rice blast disease, which is a devastating threat to rice production worldwide. Lysine succinylation, a newly identified post-translational modification, is associated with various cellular processes. Here, liquid chromatography tandem-mass spectrometry combined with a high-efficiency succinyl-lysine antibody was used to identify the succinylated peptides in P. oryzae. In total, 2109 lysine succinylation sites in 714 proteins were identified. Ten conserved succinylation sequence patterns were identified, among which, K*******Ksuc, and K**Ksuc, were two most preferred ones. The frequency of lysine succinylation sites, however, greatly varied among organisms, including plants, animals, and microbes. Interestingly, the numbers of succinylation site in each protein of P. oryzae were significantly greater than that of most previous published organisms. Gene ontology and KEGG analysis showed that these succinylated peptides are associated with a wide range of cellular functions, from metabolic processes to stimuli responses. Further analyses determined that lysine succinylation occurs on several key enzymes of the tricarboxylic acid cycle and glycolysis pathway, indicating that succinylation may play important roles in the regulation of basal metabolism in P. oryzae. Furthermore, more than 40 pathogenicity-related proteins were identified as succinylated proteins, suggesting an involvement of succinylation in pathogenicity. Our results provide the first comprehensive view of the P. oryzae succinylome and may aid to find potential pathogenicity-related proteins to control the rice blast disease. Significance Plant pathogens represent a great threat to world food security, and enormous reduction in the global yield of rice was caused by P. oryzae infection. Here, the succinylated proteins in P. oryzae were identified. Furthermore, comparison of succinylation sites among various species, indicating that different degrees of succinylation may be involved in the regulation of basal metabolism. This data facilitates our understanding of the metabolic pathways and proteins that are associated with pathogenicity.
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Affiliation(s)
- Jiaoyu Wang
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Ling Li
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
- The key laboratory for quality improvement of agricultural products of Zhejiang province, School of agricultural and food sciences, Zhejiang agriculture and forest university, Hangzhou, 311300, China
| | - Rongyao Chai
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Zhen Zhang
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Haiping Qiu
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Xueqin Mao
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Zhongna Hao
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Yanli Wang
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Guochang Sun
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China.
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Hasan MM, Khatun MS, Kurata H. Large-Scale Assessment of Bioinformatics Tools for Lysine Succinylation Sites. Cells 2019; 8:cells8020095. [PMID: 30696115 PMCID: PMC6406724 DOI: 10.3390/cells8020095] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 12/19/2022] Open
Abstract
Lysine succinylation is a form of posttranslational modification of the proteins that play an essential functional role in every aspect of cell metabolism in both prokaryotes and eukaryotes. Aside from experimental identification of succinylation sites, there has been an intense effort geared towards the development of sequence-based prediction through machine learning, due to its promising and essential properties of being highly accurate, robust and cost-effective. In spite of these advantages, there are several problems that are in need of attention in the design and development of succinylation site predictors. Notwithstanding of many studies on the employment of machine learning approaches, few articles have examined this bioinformatics field in a systematic manner. Thus, we review the advancements regarding the current state-of-the-art prediction models, datasets, and online resources and illustrate the challenges and limitations to present a useful guideline for developing powerful succinylation site prediction tools.
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Affiliation(s)
- Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
- Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
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Wang X, Chen X, Li J, Zhou X, Liu Y, Zhong L, Tang Y, Zheng H, Liu J, Zhan R, Chen L. Global analysis of lysine succinylation in patchouli plant leaves. HORTICULTURE RESEARCH 2019; 6:133. [PMID: 31814986 PMCID: PMC6885049 DOI: 10.1038/s41438-019-0216-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 09/25/2019] [Accepted: 10/23/2019] [Indexed: 05/03/2023]
Abstract
Lysine succinylation is a novel, naturally occurring posttranslational modification (PTM) in living organisms. Global lysine succinylation identification has been performed at the proteomic level in various species; however, the study of lysine succinylation in plant species is relatively limited. Patchouli plant (P. cablin (Blanco) Benth., Lamiaceae) is a globally important industrial plant and medicinal herb. In the present study, lysine succinylome analysis was carried out in patchouli plants to determine the potential regulatory role of lysine succinylation in patchouli growth, development, and physiology. The global succinylation sites and proteins in patchouli plants were screened with an immunoprecipitation affinity enrichment technique and advanced mass spectrometry-based proteomics. Several bioinformatic analyses, such as function classification and enrichment, subcellular location predication, metabolic pathway enrichment and protein-protein interaction networking, were conducted to characterize the functions of the identified sites and proteins. In total, 1097 succinylation sites in 493 proteins were detected in patchouli plants, among which 466 succinylation sites in 241 proteins were repeatedly identified within three independent experiments. The functional characterization of these proteins indicated that the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, photosynthesis processes, and amino acid biosynthesis may be regulated by lysine succinylation. In addition, these succinylated proteins showed a wide subcellular location distribution, although the chloroplast and cytoplasm were the top two preferred cellular components. Our study suggested the important role of lysine succinylation in patchouli plant physiology and biology and could serve as a useful reference for succinylation studies in other medicinal plants.
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Affiliation(s)
- Xiaobing Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Xiuzhen Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Junren Li
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Xuanxuan Zhou
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Yanting Liu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Liting Zhong
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Yun Tang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Hai Zheng
- Guangdong Institute of Traditional Chinese Medicine, Guangzhou, Guangdong, 510520 P. R. China
| | - Jiyun Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005 P.R. China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Likai Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
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Hasan MM, Kurata H. GPSuc: Global Prediction of Generic and Species-specific Succinylation Sites by aggregating multiple sequence features. PLoS One 2018; 13:e0200283. [PMID: 30312302 PMCID: PMC6193575 DOI: 10.1371/journal.pone.0200283] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/22/2018] [Indexed: 01/09/2023] Open
Abstract
Lysine succinylation is one of the dominant post-translational modification of the protein that contributes to many biological processes including cell cycle, growth and signal transduction pathways. Identification of succinylation sites is an important step for understanding the function of proteins. The complicated sequence patterns of protein succinylation revealed by proteomic studies highlight the necessity of developing effective species-specific in silico strategies for global prediction succinylation sites. Here we have developed the generic and nine species-specific succinylation site classifiers through aggregating multiple complementary features. We optimized the consecutive features using the Wilcoxon-rank feature selection scheme. The final feature vectors were trained by a random forest (RF) classifier. With an integration of RF scores via logistic regression, the resulting predictor termed GPSuc achieved better performance than other existing generic and species-specific succinylation site predictors. To reveal the mechanism of succinylation and assist hypothesis-driven experimental design, our predictor serves as a valuable resource. To provide a promising performance in large-scale datasets, a web application was developed at http://kurata14.bio.kyutech.ac.jp/GPSuc/.
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Affiliation(s)
- Md. Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu, Iizuka, Fukuoka, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu, Iizuka, Fukuoka, Japan
- Biomedi Informatics R&D Center, Kyushu Institute of Technology, Kawazu, Iizuka, Fukuoka, Japan
- * E-mail:
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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: 35] [Impact Index Per Article: 5.8] [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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Systematic analysis of the lysine malonylome in common wheat. BMC Genomics 2018; 19:209. [PMID: 29558883 PMCID: PMC5859436 DOI: 10.1186/s12864-018-4535-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 02/06/2018] [Indexed: 01/19/2023] Open
Abstract
Background Protein lysine malonylation, a newly discovered post-translational modification (PTM), plays an important role in diverse metabolic processes in both eukaryotes and prokaryotes. Common wheat is a major global cereal crop. However, the functions of lysine malonylation are relatively unknown in this crop. Here, a global analysis of lysine malonylation was performed in wheat. Results In total, 342 lysine malonylated sites were identified in 233 proteins. Bioinformatics analysis showed that the frequency of arginine (R) in position + 1 was highest, and a modification motif, KmaR, was identified. The malonylated proteins were located in multiple subcellular compartments, especially in the cytosol (45%) and chloroplast (30%). The identified proteins were found to be involved in diverse pathways, such as carbon metabolism, the Calvin cycle, and the biosynthesis of amino acids, suggesting an important role for lysine malonylation in these processes. Protein interaction network analysis revealed eight highly interconnected clusters of malonylated proteins, and 137 malonylated proteins were mapped to the protein network database. Moreover, five proteins were simultaneously modified by lysine malonylation, acetylation and succinylation, suggesting that these three PTMs may coordinately regulate the function of many proteins in common wheat. Conclusions Our results suggest that lysine malonylation is involved in a variety of biological processes, especially carbon fixation in photosynthetic organisms. These data represent the first report of the lysine malonylome in common wheat and provide an important dataset for further exploring the physiological role of lysine malonylation in wheat and likely all plants. Electronic supplementary material The online version of this article (10.1186/s12864-018-4535-y) contains supplementary material, which is available to authorized users.
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Wagner S, Van Aken O, Elsässer M, Schwarzländer M. Mitochondrial Energy Signaling and Its Role in the Low-Oxygen Stress Response of Plants. PLANT PHYSIOLOGY 2018; 176:1156-1170. [PMID: 29298823 PMCID: PMC5813528 DOI: 10.1104/pp.17.01387] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/29/2017] [Indexed: 05/07/2023]
Abstract
Cellular responses to low-oxygen stress and to respiratory inhibitors share common mitochondrial energy signaling pathways.
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Affiliation(s)
- Stephan Wagner
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany
| | | | - Marlene Elsässer
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany
- Institute for Cellular and Molecular Botany (IZMB), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany
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Hasan MM, Khatun MS, Mollah MNH, Yong C, Guo D. A systematic identification of species-specific protein succinylation sites using joint element features information. Int J Nanomedicine 2017; 12:6303-6315. [PMID: 28894368 PMCID: PMC5584904 DOI: 10.2147/ijn.s140875] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Lysine succinylation, an important type of protein posttranslational modification, plays significant roles in many cellular processes. Accurate identification of succinylation sites can facilitate our understanding about the molecular mechanism and potential roles of lysine succinylation. However, even in well-studied systems, a majority of the succinylation sites remain undetected because the traditional experimental approaches to succinylation site identification are often costly, time-consuming, and laborious. In silico approach, on the other hand, is potentially an alternative strategy to predict succinylation substrates. In this paper, a novel computational predictor SuccinSite2.0 was developed for predicting generic and species-specific protein succinylation sites. This predictor takes the composition of profile-based amino acid and orthogonal binary features, which were used to train a random forest classifier. We demonstrated that the proposed SuccinSite2.0 predictor outperformed other currently existing implementations on a complementarily independent dataset. Furthermore, the important features that make visible contributions to species-specific and cross-species-specific prediction of protein succinylation site were analyzed. The proposed predictor is anticipated to be a useful computational resource for lysine succinylation site prediction. The integrated species-specific online tool of SuccinSite2.0 is publicly accessible.
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Affiliation(s)
- Md Mehedi Hasan
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, People's Republic of China
| | - Mst Shamima Khatun
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Nurul Haque Mollah
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Cao Yong
- Department of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen Graduate School, Shenzhen, People's Republic of China
| | - Dianjing Guo
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, People's Republic of China
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