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Zha L, Wei S, Huang D, Zhang J. Multi-Omics Analyses of Lettuce ( Lactuca sativa) Reveals Primary Metabolism Reorganization Supporting Distinct Features of Secondary Metabolism Induced by Supplementing UV-A Radiation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38950542 DOI: 10.1021/acs.jafc.4c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
UV can serve as an effective light spectrum for regulating plant secondary metabolites, while relevant studies on UV-A are much less extensive than those on UV-B. A comprehensive understanding of the selective effects of UV-A on different secondary metabolites and the specific features of primary metabolism that drive these effects is still lacking. To address this knowledge gap, we conducted a study to analyze the dynamic changes in the metabolome and transcriptome of lettuce leaves irradiated with red plus UV-A light (monochromatic red light as control). Generally, UV-A promoted the synthesis of most phenylpropanoids and terpenoids originating from the shikimate and methylerythritol phosphate (MEP) pathway in plastids but sacrificed the synthesis of terpenoids derived from the mevalonate (MVA) pathway, particularly sesquiterpenes. Increased precursors supply for the shikimate and MEP pathway under UV-A was directly supported by the activation of the Calvin-Benson cycle and phosphoenolpyruvate transport. Whereas, along with phosphoenolpyruvate transport, the TCA cycle was restrained, causing deprivation of the MVA pathway precursor. In addition, UV-A also activated the plastidic oxidative branch of the pentose phosphate pathway, photorespiration, and malate shuttle, to ensure a sufficient supply of nitrogen, circulation homeostasis of the Calvin-Benson cycle, and energy balance, thus indirectly supporting UV-A-induced specific secondary metabolic output. This study provides a comprehensive framework for understanding the flexible primary-secondary metabolism interactions that are able to produce specific metabolites favorable for adaptation to environmental stimuli.
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Affiliation(s)
- Lingyan Zha
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiwei Wei
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Danfeng Huang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingjin Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Zhang X, Shan J, Wang J, Zhang Y, Yang F, Liu B, Zhang L, Li G, Wang R. Comprehensive Proteome and Acetylome Analysis of Needle Senescence in Larix gmelinii. Int J Mol Sci 2024; 25:6824. [PMID: 38999933 PMCID: PMC11241215 DOI: 10.3390/ijms25136824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Leaf senescence is essential for the growth and development of deciduous trees in the next season. Larix gmelinii, a deciduous coniferous tree, exhibits its most distinctive feature by turning yellow in the autumn and eventually shedding its leaves, resulting in significant changes in its appearance during the fall. Lysine acetylation plays an important role in diverse cellular processes; however, limited knowledge is available regarding acetylations in the needle senescence of L. gmelinii. In this study, the proteomics and acetylated modification omics of two phenotypic leaves, yellow and green (senescent and non-senescent) needles, were analyzed before autumn defoliation. In total, 5022 proteins and 4469 unique acetylation sites in 2414 lysine acylated proteins were identified, and this resulted in the discovery of 1335 differentially expressed proteins (DEPs) and 605 differentially expressed acetylated proteins (DAPs) in yellow versus green needles. There are significant differences between the proteome and acetylome; only 269 proteins were found to be DEP and DAP, of which 136 proteins were consistently expressed in both the DEP and DAP, 91 proteins were upregulated, and 45 proteins were down-regulated. The DEPs participate in the metabolism of starch and sucrose, while the DAPs are involved in glycolysis and the tricarboxylic acid cycle. Among them, DEPs underwent significant changes in glycolysis and citric acid cycling. Most of the enzymes involved in glycolysis and the citrate cycle were acetylated. DAPs were down-regulated in glycolysis and up-regulated in the citrate cycle. In all, the results of this study reveal the important role of lysine acetylation in the senescence of L. gmelinii needles and provide a new perspective for understanding the molecular mechanism of leaf senescence and tree seasonal growth.
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Affiliation(s)
- Xuting Zhang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jinyuan Shan
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jiaxiu Wang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yanxia Zhang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Feiyun Yang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Bin Liu
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lifeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Guojing Li
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ruigang Wang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
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Christianson DW. Chemical Versatility in Catalysis and Inhibition of the Class IIb Histone Deacetylases. Acc Chem Res 2024; 57:1135-1148. [PMID: 38530703 PMCID: PMC11021156 DOI: 10.1021/acs.accounts.3c00801] [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] [Indexed: 03/28/2024]
Abstract
The zinc-dependent histone deacetylases (HDACs 1-11) belong to the arginase-deacetylase superfamily of proteins, members of which share a common α/β fold and catalytic metal binding site. While several HDACs play a role in epigenetic regulation by catalyzing acetyllysine hydrolysis in histone proteins, the biological activities of HDACs extend far beyond histones. HDACs also deacetylate nonhistone proteins in the nucleus as well as the cytosol to regulate myriad cellular processes. The substrate pool is even more diverse in that certain HDACs can hydrolyze other covalent modifications. For example, HDAC6 is also a lysine decrotonylase, and HDAC11 is a lysine-fatty acid deacylase. Surprisingly, HDAC10 is not a lysine deacetylase but instead is a polyamine deacetylase. Thus, the HDACs are biologically and chemically versatile catalysts as they regulate the function of diverse protein and nonprotein substrates throughout the cell.Owing to their critical regulatory functions, HDACs serve as prominent targets for drug design. At present, four HDAC inhibitors are FDA-approved for cancer chemotherapy. However, these inhibitors are active against multiple HDAC isozymes, and a lack of selectivity is thought to contribute to undesirable side effects. Current medicinal chemistry campaigns focus on the development of isozyme-selective inhibitors, and many such studies largely focus on HDAC6 and HDAC10. HDAC6 is a target for therapeutic intervention due to its cellular role as a tubulin deacetylase and tau deacetylase, and selective inhibitors are being studied in cancer chemotherapy and the treatment of peripheral neuropathy. Crystal structures of enzyme-inhibitor complexes reveal how various features of inhibitor design, such as zinc-coordinating groups, bifurcated capping groups, and aromatic fluorination patterns, contribute to affinity and isozyme selectivity. The polyamine deacetylase HDAC10 is also an emerging target for cancer chemotherapy. Crystal structures of intact substrates trapped in the HDAC10 active site reveal the molecular basis of strikingly narrow substrate specificity for N8-acetylspermidine hydrolysis. Active site features responsible for substrate specificity have been successfully exploited in the design of potent and selective inhibitors.In this Account, I review the structural chemistry and inhibition of HDACs, highlighting recent X-ray crystallographic and functional studies of HDAC6 and HDAC10 in my laboratory. These studies have yielded fascinating snapshots of catalysis as well as novel chemical transformations involving bound inhibitors. The zinc-bound water molecule in the HDAC active site is the catalytic nucleophile in the deacetylation reaction, but this activated water molecule can also react with inhibitor C═O or C═N groups to yield unanticipated reaction products that bind exceptionally tightly. Versatile active site chemistry unleashes the full inhibitory potential of such compounds, and X-ray crystallography allows us to view this chemistry in action.
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Affiliation(s)
- David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323, USA
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4
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He C, Chen X, Chen Y, Sun J, Qi M, Rocha S, Wang M. Global acetylome profiling indicates EPA impedes but OA promotes prostate cancer motility through altered acetylation of PFN1 and FLNA. Proteomics 2024:e2300393. [PMID: 38430206 DOI: 10.1002/pmic.202300393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Prostate cancer (PCa) is one of the leading causes of cancer morbidity and mortality in men. Metastasis is the main cause of PCa-associated death. Recent evidence indicated a significant reduction in PCa mortality associated with higher ω-3 polyunsaturated fatty acids (PUFAs) consumption. However, the underlying mechanisms remained elusive. In this study, we applied global acetylome profiling to study the effect of fatty acids treatment. Results indicated that oleic acid (OA, monounsaturated fatty acid, MUFA, 100 µM) elevates while EPA (eicosapentaenoic acid, 100 µM) reduces the acetyl-CoA level, which alters the global acetylome. After treatment, two crucial cell motility regulators, PFN1 and FLNA, were found with altered acetylation levels. OA increased the acetylation of PFN1 and FLNA, whereas EPA decreased PFN1 acetylation level. Furthermore, OA promotes while EPA inhibits PCa migration and invasion. Immunofluorescence assay indicated that EPA impedes the formation of lamellipodia or filopodia through reduced localization of PFN1 and FLNA to the leading edge of cells. Therefore, perturbed acetylome may be one critical step in fatty acid-affected cancer cell motility. This study provides some new insights into the response of ω-3 PUFAs treatment and a better understanding of cancer cell migration and invasion modulation.
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Affiliation(s)
- Chao He
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Xiuyuan Chen
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Ying Chen
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Jianying Sun
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Manting Qi
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Sonia Rocha
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mu Wang
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
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Lv T, Lou Y, Yan Q, Nie L, Cheng Z, Zhou X. Phosphorylation: new star of pathogenesis and treatment in steatotic liver disease. Lipids Health Dis 2024; 23:50. [PMID: 38368351 PMCID: PMC10873984 DOI: 10.1186/s12944-024-02037-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/31/2024] [Indexed: 02/19/2024] Open
Abstract
Steatotic liver disease poses a serious threat to human health and has emerged as one of the most significant burdens of chronic liver disease worldwide. Currently, the research mechanism is not clear, and there is no specific targeted drug for direct treatment. Phosphorylation is widely regarded as the most common type of protein modification, closely linked to steatotic liver disease in previous studies. However, there is no systematic review to clarify the relationship and investigate from the perspective of phosphorylation. Phosphorylation has been found to mainly regulate molecule stability, affect localization, transform molecular function, and cooperate with other protein modifications. Among them, adenosine 5'-monophosphate-activated protein kinase (AMPK), serine/threonine kinase (AKT), and nuclear factor kappa-B (NF-kB) are considered the core mechanisms in steatotic liver disease. As to treatment, lifestyle changes, prescription drugs, and herbal ingredients can alleviate symptoms by influencing phosphorylation. It demonstrates the significant role of phosphorylation as a mechanism occurrence and a therapeutic target in steatotic liver disease, which could be a new star for future exploration.
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Affiliation(s)
- Tiansu Lv
- Department of Endocrinology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yan Lou
- Department of Endocrinology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Qianhua Yan
- Department of Endocrinology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lijuan Nie
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhe Cheng
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiqiao Zhou
- Department of Endocrinology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China.
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6
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Li XY, Yu JT, Dong YH, Shen XY, Hou R, Xie MM, Wei J, Hu XW, Dong ZH, Shan RR, Jin J, Shao W, Meng XM. Protein acetylation and related potential therapeutic strategies in kidney disease. Pharmacol Res 2023; 197:106950. [PMID: 37820854 DOI: 10.1016/j.phrs.2023.106950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/16/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Kidney disease can be caused by various internal and external factors that have led to a continual increase in global deaths. Current treatment methods can alleviate but do not markedly prevent disease development. Further research on kidney disease has revealed the crucial function of epigenetics, especially acetylation, in the pathology and physiology of the kidney. Histone acetyltransferases (HATs), histone deacetylases (HDACs), and acetyllysine readers jointly regulate acetylation, thus affecting kidney physiological homoeostasis. Recent studies have shown that acetylation improves mechanisms and pathways involved in various types of nephropathy. The discovery and application of novel inhibitors and activators have further confirmed the important role of acetylation. In this review, we provide insights into the physiological process of acetylation and summarise its specific mechanisms and potential therapeutic effects on renal pathology.
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Affiliation(s)
- Xiang-Yu Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ju-Tao Yu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Yu-Hang Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Xiao-Yu Shen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Rui Hou
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Man-Man Xie
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Jie Wei
- Department of Nephrology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei 230601, Anhui, China
| | - Xiao-Wei Hu
- Department of Clinical Pharmacy, Anhui Provincial Children's Hospital, Hefei 230051, China
| | - Ze-Hui Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Run-Run Shan
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Juan Jin
- Research Center for Translational Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Wei Shao
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China.
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Gao J, Li Z, Zhu B, Wang L, Xu J, Wang B, Fu X, Han H, Zhang W, Deng Y, Wang Y, Zuo Z, Peng R, Tian Y, Yao Q. Creation of Environmentally Friendly Super "Dinitrotoluene Scavenger" Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303785. [PMID: 37715295 PMCID: PMC10602510 DOI: 10.1002/advs.202303785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/15/2023] [Indexed: 09/17/2023]
Abstract
Pervasive environmental contamination due to the uncontrolled dispersal of 2,4-dinitrotoluene (2,4-DNT) represents a substantial global health risk, demanding urgent intervention for the removal of this detrimental compound from affected sites and the promotion of ecological restoration. Conventional methodologies, however, are energy-intensive, susceptible to secondary pollution, and may inadvertently increase carbon emissions. In this study, a 2,4-DNT degradation module is designed, assembled, and validated in rice plants. Consequently, the modified rice plants acquire the ability to counteract the phytotoxicity of 2,4-DNT. The most significant finding of this study is that these modified rice plants can completely degrade 2,4-DNT into innocuous substances and subsequently introduce them into the tricarboxylic acid cycle. Further, research reveals that the modified rice plants enable the rapid phytoremediation of 2,4-DNT-contaminated soil. This innovative, eco-friendly phytoremediation approach for dinitrotoluene-contaminated soil and water demonstrates significant potential across diverse regions, substantially contributing to carbon neutrality and sustainable development objectives by repurposing carbon and energy from organic contaminants.
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8
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Scandola S, Mehta D, Castillo B, Boyce N, Uhrig RG. Systems-level proteomics and metabolomics reveals the diel molecular landscape of diverse kale cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1170448. [PMID: 37575922 PMCID: PMC10421703 DOI: 10.3389/fpls.2023.1170448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/26/2023] [Indexed: 08/15/2023]
Abstract
Kale is a group of diverse Brassicaceae species that are nutritious leafy greens consumed for their abundance of vitamins and micronutrients. Typified by their curly, serrated and/or wavy leaves, kale varieties have been primarily defined based on their leaf morphology and geographic origin, despite having complex genetic backgrounds. Kale is a very promising crop for vertical farming due to its high nutritional content; however, being a non-model organism, foundational, systems-level analyses of kale are lacking. Previous studies in kale have shown that time-of-day harvesting can affect its nutritional composition. Therefore, to gain a systems-level diel understanding of kale across its wide-ranging and diverse genetic landscape, we selected nine publicly available and commercially grown kale cultivars for growth under near-sunlight LED light conditions ideal for vertical farming. We then analyzed changes in morphology, growth and nutrition using a combination of plant phenotyping, proteomics and metabolomics. As the diel molecular activities of plants drive their daily growth and development, ultimately determining their productivity as a crop, we harvested kale leaf tissue at both end-of-day (ED) and end-of-night (EN) time-points for all molecular analyses. Our results reveal that diel proteome and metabolome signatures divide the selected kale cultivars into two groups defined by their amino acid and sugar content, along with significant proteome differences involving carbon and nitrogen metabolism, mRNA splicing, protein translation and light harvesting. Together, our multi-cultivar, multi-omic analysis provides new insights into the molecular underpinnings of the diel growth and development landscape of kale, advancing our fundamental understanding of this nutritious leafy green super-food for horticulture/vertical farming applications.
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Affiliation(s)
| | | | | | | | - R. Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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9
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Fragoso MSI, de Siqueira CM, Vitorino FNL, Vieira AZ, Martins-Duarte ÉS, Faoro H, da Cunha JPC, Ávila AR, Nardelli SC. TgKDAC4: A Unique Deacetylase of Toxoplasma' s Apicoplast. Microorganisms 2023; 11:1558. [PMID: 37375060 DOI: 10.3390/microorganisms11061558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 06/29/2023] Open
Abstract
Toxoplasma gondii is an obligate intracellular parasite of the phylum Apicomplexa and causes toxoplasmosis infections, a disease that affects a quarter of the world's population and has no effective cure. Epigenetic regulation is one of the mechanisms controlling gene expression and plays an essential role in all organisms. Lysine deacetylases (KDACs) act as epigenetic regulators affecting gene silencing in many eukaryotes. Here, we focus on TgKDAC4, an enzyme unique to apicomplexan parasites, and a class IV KDAC, the least-studied class of deacetylases so far. This enzyme shares only a portion of the specific KDAC domain with other organisms. Phylogenetic analysis from the TgKDAC4 domain shows a putative prokaryotic origin. Surprisingly, TgKDAC4 is located in the apicoplast, making it the only KDAC found in this organelle to date. Transmission electron microscopy assays confirmed the presence of TgKDAC4 in the periphery of the apicoplast. We identified possible targets or/and partners of TgKDAC4 by immunoprecipitation assays followed by mass spectrometry analysis, including TgCPN60 and TgGAPDH2, both located at the apicoplast and containing acetylation sites. Understanding how the protein works could provide new insights into the metabolism of the apicoplast, an essential organelle for parasite survival.
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Affiliation(s)
| | | | - Francisca Nathália Luna Vitorino
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
| | | | - Érica Santos Martins-Duarte
- Department of Parasitology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81350-010, Brazil
| | - Júlia Pinheiro Chagas da Cunha
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
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Jeong BR, Jang J, Jin E. Genome engineering via gene editing technologies in microalgae. BIORESOURCE TECHNOLOGY 2023; 373:128701. [PMID: 36746216 DOI: 10.1016/j.biortech.2023.128701] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
CRISPR-Cas has revolutionized genetic modification with its comparative simplicity and accuracy, and it can be used even at the genomic level. Microalgae are excellent feedstocks for biofuels and nutraceuticals because they contain high levels of fatty acids, carotenoids, and other metabolites; however, genome engineering for microalgae is not yet as developed as for other model organisms. Microalgal engineering at the genetic and metabolic levels is relatively well established, and a few genomic resources are available. Their genomic information was used for a "safe harbor" site for stable transgene expression in microalgae. This review proposes further genome engineering schemes including the construction of sgRNA libraries, pan-genomic and epigenomic resources, and mini-genomes, which can together be developed into synthetic biology for carbon-based engineering in microalgae. Acetyl-CoA is at the center of carbon metabolic pathways and is further reviewed for the production of molecules including terpenoids in microalgae.
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Affiliation(s)
- Byeong-Ryool Jeong
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Junhwan Jang
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea; Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea.
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11
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Guo J, Ma Z, Deng C, Ding J, Chang Y. A comprehensive dynamic immune acetylproteomics profiling induced by Puccinia polysora in maize. BMC PLANT BIOLOGY 2022; 22:610. [PMID: 36564751 PMCID: PMC9789614 DOI: 10.1186/s12870-022-03964-4] [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: 08/29/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Lysine-ε-acetylation (Kac) is a reversible post-translational modification that plays important roles during plant-pathogen interactions. Some pathogens can deliver secreted effectors encoding acetyltransferases or deacetylases into host cell to directly modify acetylation of host proteins. However, the function of these acetylated host proteins in plant-pathogen defense remains to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein abundance and lysine acetylation changes in maize infected with Puccinia polysora (P. polysora) at 0 h, 12 h, 24 h, 48 h and 72 h. A total of 7412 Kac sites from 4697 proteins were identified, and 1732 Kac sites from 1006 proteins were quantified. Analyzed the features of lysine acetylation, we found that Kac is ubiquitous in cellular compartments and preferentially targets lysine residues in the -F/W/Y-X-X-K (ac)-N/S/T/P/Y/G- motif of the protein, this Kac motif contained proteins enriched in basic metabolism and defense-associated pathways during fungal infection. Further analysis of acetylproteomics data indicated that maize regulates cellular processes in response to P. polysora infection by altering Kac levels of histones and non-histones. In addition, acetylation of pathogen defense-related proteins presented converse patterns in signaling transduction, defense response, cell wall fortification, ROS scavenging, redox reaction and proteostasis. Our results provide informative resources for studying protein acetylation in plant-pathogen interactions, not only greatly extending the understanding on the roles of acetylation in vivo, but also providing a comprehensive dynamic pattern of Kac modifications in the process of plant immune response.
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Affiliation(s)
- Jianfei Guo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Zhigang Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan university, Shenzhen, 518000, China
| | - Ce Deng
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
- The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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12
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Li BB, Zhang W, Wei S, Lv YY, Shang JX, Hu YS. Comprehensive proteome and lysine acetylome analysis after artificial aging reveals the key acetylated proteins involved in wheat seed oxidative stress response and energy production. J Food Biochem 2022; 46:e14495. [PMID: 36322387 DOI: 10.1111/jfbc.14495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022]
Abstract
Lysine acetylation is a common post-translational modification of proteins within all organisms. However, quantitative acetylome characterization in wheat seed during aging in storage has not been reported. This study reports the first large-scale acetylome analysis of wheat seeds after artificial aging treatment, using the quantitative proteomic approach. In total, 11,002 acetylation sites, corresponding to 4262 acetylated proteins were identified, of which 1207 acetylated sites, representing 783 acetylated proteins, were significantly more or less acetylated after artificial aging. Functional analysis demonstrated that the majority of the acetylated proteins are closely involved with cellular and metabolic functions. In particular, key enzymes in the oxidative stress response and energy metabolism were significantly differentially acetylated and appear to be heavily involved in wheat seed aging. The acetylome analysis was verified by quantitative real-time PCR and enzyme activity determination. Lysine-acetylation results in a weaker oxidative stress response and lower energy production efficiency, resulting in the apoptosis of wheat seed cells, insufficient energy supply at the germination stage, and consequently, marked loss of seed vigor. PRACTICAL APPLICATIONS: It is known that the loss of protein function is an important reason for the decrease of seed vigor. Therefore, the change of protein function in the process of wheat seed aging was studied by proteome and lysine acetylome analysis technology. The results showed that the oxidation-reduction imbalance and the decrease of energy production efficiency of seeds were the important reasons for the decrease of their vigor. This will provide a new idea for green and safe storage of grain.
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Affiliation(s)
- Bang-Bang Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Wei Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Shan Wei
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Yang-Yong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Ji-Xu Shang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Yuan-Sen Hu
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
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13
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Wegener M, Dietz KJ. The mutual interaction of glycolytic enzymes and RNA in post-transcriptional regulation. RNA (NEW YORK, N.Y.) 2022; 28:1446-1468. [PMID: 35973722 PMCID: PMC9745834 DOI: 10.1261/rna.079210.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
About three decades ago, researchers suggested that metabolic enzymes participate in cellular processes that are unrelated to their catalytic activity, and the term "moonlighting functions" was proposed. Recently developed advanced technologies in the field of RNA interactome capture now unveil the unexpected RNA binding activity of many metabolic enzymes, as exemplified here for the enzymes of glycolysis. Although for most of these proteins a precise binding mechanism, binding conditions, and physiological relevance of the binding events still await in-depth clarification, several well explored examples demonstrate that metabolic enzymes hold crucial functions in post-transcriptional regulation of protein synthesis. This widely conserved RNA-binding function of glycolytic enzymes plays major roles in controlling cell activities. The best explored examples are glyceraldehyde 3-phosphate dehydrogenase, enolase, phosphoglycerate kinase, and pyruvate kinase. This review summarizes current knowledge about the RNA-binding activity of the ten core enzymes of glycolysis in plant, yeast, and animal cells, its regulation and physiological relevance. Apparently, a tight bidirectional regulation connects core metabolism and RNA biology, forcing us to rethink long established functional singularities.
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Affiliation(s)
- Melanie Wegener
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany
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14
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Du W, Ding J, Lu S, Wen X, Hu J, Ruan C. Identification of the key flavonoid and lipid synthesis proteins in the pulp of two sea buckthorn cultivars at different developmental stages. BMC PLANT BIOLOGY 2022; 22:299. [PMID: 35710338 PMCID: PMC9205118 DOI: 10.1186/s12870-022-03688-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Sea buckthorn is an economically important woody plant for desertification control and water soil conservation. Its berry pulp is rich in flavonoids and unsaturated fatty acids. Cultivars containing high oil and flavonoid contents have higher economic value and will increase in the planting area. However, the cause of the differences in oil and flavonoid contents among cultivars is still unclear. The influence of key enzymes in the lipid and flavonoid synthesis pathways on their content needs to be explored and clarified. RESULTS The flavonoid content in XE (Xin'e 3) was 54% higher than that in SJ (Suiji 1). Rutin was the main flavonoid in sea buckthorn pulp, and the differences in the rutin content could cause flavonoid differences between the two cultivars. The oil content of XE was 31.58% higher than that of SJ, and the difference in oil content was highest at 50-70 DAF. High-throughput proteomics was used to quantify key enzymes of flavonoid and lipid synthesis pathways in two cultivars at three developmental stages. By functional annotation and KEGG analysis, 41 key enzymes related to phenylpropanoid biosynthesis, flavonoid biosynthesis, flavone and flavonol biosynthesis, fatty acid biosynthesis and TAG biosynthesis were quantified. CHS, F3H, ANS, fabD, FATA, FAB2, LPIN and plcC showed significant differences between the two cultivars. In addition, we quantified 6 oleosins. With the exception of a 16 kDa oleosin, the other oleosins in the two cultivars were positively correlated with oil content. CONCLUSIONS In the flavonoid synthesis pathway, CHS and F3H were the main enzymes responsible for the difference in flavonoid content between the two cultivars. In the lipid synthesis pathway, LPIN, plcC and MGD were the main enzymes with different contents in the middle to late stages. Higher contents of LPIN and plcC in XE than in SJ could cause DAG to generate TAG from PC, since the difference in DGAT between the two cultivars was not significant. Investigating the causes of flavonoid and oil content differences among different cultivars from the perspective of proteomics, could provide a basis for understanding the regulatory mechanism of flavonoids and lipid synthesis in sea buckthorn pulp.
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Affiliation(s)
- Wei Du
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian, China
| | - Jian Ding
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian, China
| | - Shunguang Lu
- Management Center of Seabuckthorn Development, Ministry of Water Resources, Beijing, China
| | - Xiufeng Wen
- Management Center of Seabuckthorn Development, Ministry of Water Resources, Beijing, China
| | - Jianzhong Hu
- Management Center of Seabuckthorn Development, Ministry of Water Resources, Beijing, China
| | - Chengjiang Ruan
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian, China.
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15
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Liang D, Chen C, Huang S, Liu S, Fu L, Niu Y. Alterations of Lysine Acetylation Profile in Murine Skeletal Muscles Upon Exercise. Front Aging Neurosci 2022; 14:859313. [PMID: 35592697 PMCID: PMC9110802 DOI: 10.3389/fnagi.2022.859313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
Objective Regular exercise is a powerful tool that enhances skeletal muscle mass and strength. Lysine acetylation is an important post-translational modification (PTM) involved in a broad array of cellular functions. Skeletal muscle protein contains a considerable number of lysine-acetylated (Kac) sites, so we aimed to investigate the effects of exercise-induced lysine acetylation on skeletal muscle proteins. Methods We randomly divided 20 male C57BL/6 mice into exercise and control groups. After 6 weeks of treadmill exercise, a lysine acetylation proteomics analysis of the gastrocnemius muscles of mice was performed. Results A total of 2,254 lysine acetylation sites in 693 protein groups were identified, among which 1,916 sites in 528 proteins were quantified. The enrichment analysis suggested that protein acetylation could influence both structural and functional muscle protein properties. Moreover, molecular docking revealed that mimicking protein deacetylation primarily influenced the interaction between substrates and enzymes. Conclusion Exercise-induced lysine acetylation appears to be a crucial contributor to the alteration of skeletal muscle protein binding free energy, suggesting that its modulation is a potential approach for improving exercise performance.
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Affiliation(s)
- Dehuan Liang
- Department of Rehabilitation, School of Medical Technology, Tianjin Medical University, Tianjin, China
| | - Cheng Chen
- Department of Rehabilitation, School of Medical Technology, Tianjin Medical University, Tianjin, China
| | - Song Huang
- Department of Rehabilitation, School of Medical Technology, Tianjin Medical University, Tianjin, China
| | - Sujuan Liu
- Department of Anatomy and Histology, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Li Fu
- Department of Rehabilitation, School of Medical Technology, Tianjin Medical University, Tianjin, China
| | - Yanmei Niu
- Department of Rehabilitation, School of Medical Technology, Tianjin Medical University, Tianjin, China
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16
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Brand A, Tissier A. Control of resource allocation between primary and specialized metabolism in glandular trichomes. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102172. [PMID: 35144142 DOI: 10.1016/j.pbi.2022.102172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/07/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Plant specialized metabolites are often synthesized and stored in dedicated morphological structures such as glandular trichomes, resin ducts, or laticifers where they accumulate in large concentrations. How this high productivity is achieved is still elusive, in particular, with respect to the interface between primary and specialized metabolism. Here, we focus on glandular trichomes to survey recent progress in understanding how plant metabolic cell factories manage to balance homeostasis of essential central metabolites while producing large quantities of compounds that constitute a metabolic sink. In particular, we review the role of gene duplications, transcription factors and photosynthesis.
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Affiliation(s)
- Alejandro Brand
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - Alain Tissier
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany.
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17
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Xia L, Kong X, Song H, Han Q, Zhang S. Advances in proteome-wide analysis of plant lysine acetylation. PLANT COMMUNICATIONS 2022; 3:100266. [PMID: 35059632 PMCID: PMC8760137 DOI: 10.1016/j.xplc.2021.100266] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Lysine acetylation (LysAc) is a conserved and important post-translational modification (PTM) that plays a key role in plant physiological and metabolic processes. Based on advances in Lys-acetylated protein immunoenrichment and mass-spectrometric technology, LysAc proteomics studies have been performed in many species. Such studies have made substantial contributions to our understanding of plant LysAc, revealing that Lys-acetylated histones and nonhistones are involved in a broad spectrum of plant cellular processes. Here, we present an extensive overview of recent research on plant Lys-acetylproteomes. We provide in-depth insights into the characteristics of plant LysAc modifications and the mechanisms by which LysAc participates in cellular processes and regulates metabolism and physiology during plant growth and development. First, we summarize the characteristics of LysAc, including the properties of Lys-acetylated sites, the motifs that flank Lys-acetylated lysines, and the dynamic alterations in LysAc among different tissues and developmental stages. We also outline a map of Lys-acetylated proteins in the Calvin-Benson cycle and central carbon metabolism-related pathways. We then introduce some examples of the regulation of plant growth, development, and biotic and abiotic stress responses by LysAc. We discuss the interaction between LysAc and Nα-terminal acetylation and the crosstalk between LysAc and other PTMs, including phosphorylation and succinylation. Finally, we propose recommendations for future studies in the field. We conclude that LysAc of proteins plays an important role in the regulation of the plant life cycle.
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18
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Guo J, Chai X, Mei Y, Du J, Du H, Shi H, Zhu JK, Zhang H. Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response. STRESS BIOLOGY 2022; 2:1. [PMID: 37676343 PMCID: PMC10442023 DOI: 10.1007/s44154-021-00024-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/07/2021] [Indexed: 09/08/2023]
Abstract
Lysine-ε-acetylation (Kac) is a post-translational modification (PTM) that is critical for metabolic regulation and cell signaling in mammals. However, its prevalence and importance in plants remain to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein lysine acetylation in five representative Arabidopsis organs with 2 ~ 3 biological replicates per organ. A total of 2887 Kac proteins and 5929 Kac sites were identified. This comprehensive catalog allows us to analyze proteome-wide features of lysine acetylation. We found that Kac proteins tend to be more uniformly expressed in different organs, and the acetylation status exhibits little correlation with the gene expression level, indicating that acetylation is unlikely caused by stochastic processes. Kac preferentially targets evolutionarily conserved proteins and lysine residues, but only a small percentage of Kac proteins are orthologous between rat and Arabidopsis. A large portion of Kac proteins overlap with proteins modified by other PTMs including ubiquitination, SUMOylation and phosphorylation. Although acetylation, ubiquitination and SUMOylation all modify lysine residues, our analyses show that they rarely target the same sites. In addition, we found that "reader" proteins for acetylation and phosphorylation, i.e., bromodomain-containing proteins and GRF (General Regulatory Factor)/14-3-3 proteins, are intensively modified by the two PTMs, suggesting that they are main crosstalk nodes between acetylation and phosphorylation signaling. Analyses of GRF6/14-3-3λ reveal that the Kac level of GRF6 is decreased under alkaline stress, suggesting that acetylation represses plant alkaline response. Indeed, K56ac of GRF6 inhibits its binding to and subsequent activation of the plasma membrane H+-ATPase AHA2, leading to hypersensitivity to alkaline stress. These results provide valuable resources for protein acetylation studies in plants and reveal that protein acetylation suppresses phosphorylation output by acetylating GRF/14-3-3 proteins.
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Affiliation(s)
- Jianfei Guo
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoqiang Chai
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuchao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiamu Du
- Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Haining Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jian-Kang Zhu
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Heng Zhang
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
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19
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Lu L, Wei W, Tao J, Lu X, Bian X, Hu Y, Cheng T, Yin C, Zhang W, Chen S, Zhang J. Nuclear factor Y subunit GmNFYA competes with GmHDA13 for interaction with GmFVE to positively regulate salt tolerance in soybean. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2362-2379. [PMID: 34265872 PMCID: PMC8541785 DOI: 10.1111/pbi.13668] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 05/07/2023]
Abstract
Soybean is an important crop worldwide, but its production is severely affected by salt stress. Understanding the regulatory mechanism of salt response is crucial for improving the salt tolerance of soybean. Here, we reveal a role for nuclear factor Y subunit GmNFYA in salt tolerance of soybean likely through the regulation of histone acetylation. GmNFYA is induced by salt stress. Overexpression of GmNFYA significantly enhances salt tolerance in stable transgenic soybean plants by inducing salt-responsive genes. Analysis in soybean plants with transgenic hairy roots also supports the conclusion. GmNFYA interacts with GmFVE, which functions with putative histone deacetylase GmHDA13 in a complex for transcriptional repression possibly by reducing H3K9 acetylation at target loci. Under salt stress, GmNFYA likely accumulates and competes with GmHDA13 for interaction with GmFVE, leading to the derepression and maintenance of histone acetylation for activation of salt-responsive genes and finally conferring salt tolerance in soybean plants. In addition, a haplotype I GmNFYA promoter is identified with the highest self-activated promoter activity and may be selected during future breeding for salt-tolerant cultivars. Our study uncovers the epigenetic regulatory mechanism of GmNFYA in salt-stress response, and all the factors/elements identified may be potential targets for genetic manipulation of salt tolerance in soybean and other crops.
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Affiliation(s)
- Long Lu
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
- Key Lab of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsCollege of Crop SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wei Wei
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
| | - Jian‐Jun Tao
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
| | - Xiang Lu
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
| | - Xiao‐Hua Bian
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
| | - Yang Hu
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Tong Cheng
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Cui‐Cui Yin
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
| | - Wan‐Ke Zhang
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
| | - Shou‐Yi Chen
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
| | - Jin‐Song Zhang
- State Key Lab of Plant GenomicsInstitute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
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20
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Liu Z, Song J, Miao W, Yang B, Zhang Z, Chen W, Tan F, Suo H, Dai X, Zou X, Ou L. Comprehensive Proteome and Lysine Acetylome Analysis Reveals the Widespread Involvement of Acetylation in Cold Resistance of Pepper ( Capsicum annuum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:730489. [PMID: 34512705 PMCID: PMC8429487 DOI: 10.3389/fpls.2021.730489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Pepper is a typical warmth-loving vegetable that lacks a cold acclimation mechanism and is sensitive to cold stress. Lysine acetylation plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in the resistance of pepper plants to cold stress. In this study, the proteome and acetylome of two pepper varieties with different levels of cold resistance were investigated by subjecting them to cold treatments of varying durations followed by recovery periods. In total, 6,213 proteins and 4,574 lysine acetylation sites were identified, and this resulted in the discovery of 3,008 differentially expressed proteins and 768 differentially expressed acetylated proteins. A total of 1,988 proteins were identified in both the proteome and acetylome, and the functional differences in these co-identified proteins were elucidated through GO enrichment. KEGG analysis showed that 397 identified acetylated proteins were involved in 93 different metabolic pathways. The dynamic changes in the acetylated proteins in photosynthesis and the "carbon fixation in the photosynthetic organisms" pathway in pepper under low-temperature stress were further analyzed. It was found that acetylation of the PsbO and PsbR proteins in photosystem II and the PsaN protein in photosystem I could regulate the response of pepper leaves to cold stress. The acetylation levels of key carbon assimilation enzymes, such as ribulose bisphosphate carboxylase, fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, glyceraldehyde 3-phosphate dehydrogenase, phosphoribulokinase, and triosephosphate isomerase decreased, leading to decreases in carbon assimilation capacity and photosynthetic efficiency, reducing the cold tolerance of pepper leaves. This study is the first to identify the acetylome in pepper, and it greatly expands the catalog of lysine acetylation substrates and sites in Solanaceae crops, providing new insights for posttranslational modification studies.
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Affiliation(s)
- Zhoubin Liu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Jingshuang Song
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Wu Miao
- Hunan Xiangyan Seed Industry Co., Ltd, Changsha, China
| | - Bozhi Yang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Zhuqing Zhang
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Wenchao Chen
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Fangjun Tan
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Huan Suo
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Xiongze Dai
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Xuexiao Zou
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Lijun Ou
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
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21
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Yuan B, Liu T, Cheng Y, Gao S, Li L, Cai L, Yang J, Chen J, Zhong K. Comprehensive Proteomic Analysis of Lysine Acetylation in Nicotiana benthamiana After Sensing CWMV Infection. Front Microbiol 2021; 12:672559. [PMID: 34084157 PMCID: PMC8166574 DOI: 10.3389/fmicb.2021.672559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
Protein lysine acetylation (Kac) is an important post-translational modification mechanism in eukaryotes that is involved in cellular regulation. To investigate the role of Kac in virus-infected plants, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese wheat mosaic virus (CWMV) infection. We identified 4,803 acetylated lysine sites on 1,964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were upregulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were downregulated on 102 proteins. Nineteen conserved motifs were extracted and 51 percent of the acetylated proteins located on chloroplast. Nineteen Kac sites were located on histone proteins, including 10 Kac sites on histone 3. Bioinformatics analysis results indicated that lysine acetylation occurs on a large number of proteins involved in biological processes, especially photosynthesis. Furthermore, we found that the acetylation level of chloroplast proteins, histone 3 and some metabolic pathway-related proteins were significantly higher in CWMV-infected plants than in uninfected plants. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.
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Affiliation(s)
- Bowen Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tingting Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Ye Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shiqi Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China.,Yantai Academy of Agricultural Science, Yantai, China
| | - Linzhi Li
- Yantai Academy of Agricultural Science, Yantai, China
| | - Linna Cai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Kaili Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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Mehta D, Krahmer J, Uhrig RG. Closing the protein gap in plant chronobiology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1509-1522. [PMID: 33783885 DOI: 10.1111/tpj.15254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Our modern understanding of diel cell regulation in plants stems from foundational work in the late 1990s that analysed the dynamics of selected genes and mutants in Arabidopsis thaliana. The subsequent rise of transcriptomics technologies such as microarrays and RNA sequencing has substantially increased our understanding of anticipatory (circadian) and reactive (light- or dark-triggered) diel events in plants. However, it is also becoming clear that gene expression data fail to capture critical events in diel regulation that can only be explained by studying protein-level dynamics. Over the past decade, mass spectrometry technologies and quantitative proteomic workflows have significantly advanced, finally allowing scientists to characterise diel protein regulation at high throughput. Initial proteomic investigations suggest that the diel transcriptome and proteome generally lack synchrony and that the timing of daily regulatory events in plants is impacted by multiple levels of protein regulation (e.g., post-translational modifications [PTMs] and protein-protein interactions [PPIs]). Here, we highlight and summarise how the use of quantitative proteomics to elucidate diel plant cell regulation has advanced our understanding of these processes. We argue that this new understanding, coupled with the extraordinary developments in mass spectrometry technologies, demands greater focus on protein-level regulation of, and by, the circadian clock. This includes hitherto unexplored diel dynamics of protein turnover, PTMs, protein subcellular localisation and PPIs that can be masked by simple transcript- and protein-level changes. Finally, we propose new directions for how the latest advancements in quantitative proteomics can be utilised to answer outstanding questions in plant chronobiology.
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Affiliation(s)
- Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Johanna Krahmer
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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Su L, Liu S, Liu X, Zhang B, Li M, Zeng L, Li L. Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots. PeerJ 2021; 9:e10976. [PMID: 33777524 PMCID: PMC7977374 DOI: 10.7717/peerj.10976] [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: 07/09/2019] [Accepted: 01/29/2021] [Indexed: 11/20/2022] Open
Abstract
Background The peanut (Arachis hypogaea) is a crop plant of high economic importance, but the epigenetic regulation of its root growth and development has not received sufficient attention. Research on Arabidopsis thaliana has shown that histone deacetylases (HDACs) are involved in cell growth, cell differentiation, and stress response. Few studies have focused on the role of HDACs in the root development of other plants, particularly crop plants. In earlier studies, we found large accumulations of A. hypogaea histone deacetylase 1 (AhHDA1) mRNA in peanut roots. However, we did not explore the role of AhHDA1 in peanut root development. Methods In this paper, we investigated the role of the peanut AhHDA1 gene and focused on the effect of altered AhHDA1 expression in hairy roots at both the phenotypic and transcriptional levels. We analyzed the transformation of A. hypogaea hairy roots using Agrobacterium rhizogenes and RNA sequencing to identify differentially expressed genes that were assigned to specific metabolic pathways. Transgenic hairy roots were used as experimental material to analyze the downstream genes expression and histone acetylation levels. To thoroughly understand AhHDA1 function, we also simultaneously screened the AhHDA1-interacting proteins using a yeast two-hybrid system. Results AhHDA1-overexpressing hairy roots were growth-retarded after 20 d in vitro cultivation, and they had a greater accumulation of superoxide anions and hydrogen peroxide than the control and RNAi groups. AhHDA1 overexpression in hairy roots accelerated flux through various secondary synthetic metabolic pathways, as well as inhibited the primary metabolism process. AhHDA1 overexpression also caused a significant upregulation of genes encoding the critical enzyme chalcone synthase (Araip.B8TJ0, CHS) in the flavonoid biosynthesis pathway, hydroxyisoflavanone synthase (Araip.0P3RJ) in the isoflavonoid biosynthesis pathway, and caffeoyl-CoA O-methyltransferase (Aradu.M62BY, CCoAOMT) in the phenylpropanoid biosynthesis pathway. In contrast, ferredoxin 1 (Araip.327XS), the polypeptide of the oxygen-evolving complex of photosystem II (Araip.N6ZTJ), and ribulose bisphosphate carboxylase (Aradu.5IY98) in the photosynthetic pathway were significantly downregulated by AhHDA1 overexpression. The expression levels of these genes had a positive correlation with histone acetylation levels. Conclusion Our results revealed that the relationship between altered gene metabolism activities and AhHDA1 overexpression was mainly reflected in flavonoid, isoflavonoid, and phenylpropanoid metabolism. AhHDA1 overexpression retarded the growth of transgenic hairy roots and may be associated with cell metabolism status. Future studies should focus on the function of AhHDA1-interacting proteins and their effect on root development.
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Affiliation(s)
- Liangchen Su
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China.,Department of Bioengineering, Zunyi Medical University, Zhuhai, Guangdong, China
| | - Shuai Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Xing Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Baihong Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Meijuan Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Lidan Zeng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Ling Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
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Dewhirst RA, Lei J, Afseth CA, Castanha C, Wistrom CM, Mortimer JC, Jardine KJ. Are Methanol-Derived Foliar Methyl Acetate Emissions a Tracer of Acetate-Mediated Drought Survival in Plants? PLANTS (BASEL, SWITZERLAND) 2021; 10:411. [PMID: 33672332 PMCID: PMC7927132 DOI: 10.3390/plants10020411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/04/2022]
Abstract
Upregulation of acetate fermentation in plants has recently been described as an evolutionarily conserved drought survival strategy, with the amount of acetate produced directly correlating to survival. However, destructive measurements are required to evaluate acetate-linked drought responses, limiting the temporal and spatial scales that can be studied. Here, 13C-labeling studies with poplar (Populus trichocarpa) branches confirmed that methyl acetate is produced in plants from the acetate-linked acetylation of methanol. Methyl acetate emissions from detached leaves were strongly stimulated during desiccation, with total emissions decreasing with the leaf developmental stage. In addition, diurnal methyl acetate emissions from whole physiologically active poplar branches increased as a function of temperature, and light-dark transitions resulted in significant emission bursts lasting several hours. During experimental drought treatments of potted poplar saplings, light-dark methyl acetate emission bursts were eliminated while strong enhancements in methyl acetate emissions lasting > 6 days were observed with their initiation coinciding with the suppression of transpiration and photosynthesis. The results suggest that methyl acetate emissions represent a novel non-invasive tracer of acetate-mediated temperature and drought survival response in plants. The findings may have important implications for the future understanding of acetate-mediated drought responses to transcription, cellular metabolism, and hormone signaling, as well as its associated changes in carbon cycling and water use from individual plants to whole ecosystems.
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Affiliation(s)
- Rebecca A. Dewhirst
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (J.L.); (C.A.A.); (C.C.); (K.J.J.)
| | - Joseph Lei
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (J.L.); (C.A.A.); (C.C.); (K.J.J.)
| | - Cassandra A. Afseth
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (J.L.); (C.A.A.); (C.C.); (K.J.J.)
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Cristina Castanha
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (J.L.); (C.A.A.); (C.C.); (K.J.J.)
| | - Christina M. Wistrom
- College of Natural Resources, University of California, Berkeley, CA 94704, USA;
| | - Jenny C. Mortimer
- Environmental Genomics and Systems Biology, Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5005, Australia
| | - Kolby J. Jardine
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (J.L.); (C.A.A.); (C.C.); (K.J.J.)
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25
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Qaseem MF, Wu AM. Balanced Xylan Acetylation is the Key Regulator of Plant Growth and Development, and Cell Wall Structure and for Industrial Utilization. Int J Mol Sci 2020; 21:ijms21217875. [PMID: 33114198 PMCID: PMC7660596 DOI: 10.3390/ijms21217875] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
Xylan is the most abundant hemicellulose, constitutes about 25–35% of the dry biomass of woody and lignified tissues, and occurs up to 50% in some cereal grains. The accurate degree and position of xylan acetylation is necessary for xylan function and for plant growth and development. The post synthetic acetylation of cell wall xylan, mainly regulated by Reduced Wall Acetylation (RWA), Trichome Birefringence-Like (TBL), and Altered Xyloglucan 9 (AXY9) genes, is essential for effective bonding of xylan with cellulose. Recent studies have proven that not only xylan acetylation but also its deacetylation is vital for various plant functions. Thus, the present review focuses on the latest advances in understanding xylan acetylation and deacetylation and explores their effects on plant growth and development. Baseline knowledge about precise regulation of xylan acetylation and deacetylation is pivotal to developing plant biomass better suited for second-generation liquid biofuel production.
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Affiliation(s)
- Mirza Faisal Qaseem
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China;
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China;
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence:
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26
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Xiong Y, Zhang M, Li Y. Recent Advances in the Development of CBP/p300 Bromodomain Inhibitors. Curr Med Chem 2020; 27:5583-5598. [DOI: 10.2174/0929867326666190731141055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
CBP and p300 are two closely related Histone Acetyltransferases (HATs) that interact
with numerous transcription factors and act to increase the expression of their target genes. Both
proteins contain a bromodomain flanking the HAT catalytic domain that is important in binding of
CBP/p300 to chromatin, which offers an opportunity to develop protein-protein interaction inhibitors.
Since their discovery in 2006, CBP/p300 bromodomains have attracted much interest as promising
new epigenetic targets for diverse human diseases, including inflammation, cancer, autoimmune
disorders, and cardiovascular disease. Herein, we present a comprehensive review of the
structure, function, and inhibitors of CBP/p300 bromodomains developed in the last several years,
which is expected to be beneficial to relevant studies.
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Affiliation(s)
- Ying Xiong
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Mingming Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yingxia Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
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27
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Zhao H, Zhong S, Sang L, Zhang X, Chen Z, Wei Q, Chen G, Liu J, Yu Y. PaACL silencing accelerates flower senescence and changes the proteome to maintain metabolic homeostasis in Petunia hybrida. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4858-4876. [PMID: 32364241 PMCID: PMC7475263 DOI: 10.1093/jxb/eraa208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/25/2020] [Indexed: 06/07/2023]
Abstract
Cytosolic acetyl-CoA is an intermediate of the synthesis of most secondary metabolites and the source of acetyl for protein acetylation. The formation of cytosolic acetyl-CoA from citrate is catalysed by ATP-citrate lyase (ACL). However, the function of ACL in global metabolite synthesis and global protein acetylation is not well known. Here, four genes, PaACLA1, PaACLA2, PaACLB1, and PaACLB2, which encode the ACLA and ACLB subunits of ACL in Petunia axillaris, were identified as the same sequences in Petunia hybrida 'Ultra'. Silencing of PaACLA1-A2 and PaACLB1-B2 led to abnormal leaf and flower development, reduced total anthocyanin content, and accelerated flower senescence in petunia 'Ultra'. Metabolome and acetylome analysis revealed that PaACLB1-B2 silencing increased the content of many downstream metabolites of acetyl-CoA metabolism and the levels of acetylation of many proteins in petunia corollas. Mechanistically, the metabolic stress induced by reduction of acetyl-CoA in PaACL-silenced petunia corollas caused global and specific changes in the transcriptome, the proteome, and the acetylome, with the effect of maintaining metabolic homeostasis. In addition, the global proteome and acetylome were negatively correlated under acetyl-CoA deficiency. Together, our results suggest that ACL acts as an important metabolic regulator that maintains metabolic homeostasis by promoting changes in the transcriptome, proteome. and acetylome.
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Affiliation(s)
- Huina Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Shiwei Zhong
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Lina Sang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xinyou Zhang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Zeyu Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Qian Wei
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guoju Chen
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yixun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
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Singh PK, Gao W, Liao P, Li Y, Xu FC, Ma XN, Long L, Song CP. Comparative acetylome analysis of wild-type and fuzzless-lintless mutant ovules of upland cotton (Gossypium hirsutum Cv. Xu142) unveils differential protein acetylation may regulate fiber development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 150:56-70. [PMID: 32114400 DOI: 10.1016/j.plaphy.2020.02.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
Protein acetylation (KAC) is a significant post-translational modification, which plays an essential role in the regulation of growth and development. Unfortunately, related studies are inadequately available in angiosperms, and to date, there is no report providing insight on the role of protein acetylation in cotton fiber development. Therefore, we first compared the lysine-acetylation proteome (acetylome) of upland cotton ovules in the early fiber development stages by using wild-type as well as its fuzzless-lintless mutant to identify the role of KAC in the fiber development. A total of 1696 proteins with 2754 acetylation sites identified with the different levels of acetylation belonging to separate subcellular compartments suggesting a large number of proteins differentially acetylated in two cotton cultivars. About 80% of the sites were predicted to localize in the cytoplasm, chloroplast, and mitochondria. Seventeen significantly enriched acetylation motifs were identified. Serine and threonine and cysteine located downstream and upstream to KAC sites. KEGG pathway enrichment analysis indicated oxidative phosphorylation, fatty acid, ribosome and protein, and folate biosynthesis pathways enriched significantly. To our knowledge, this is the first report of comparative acetylome analysis to compare the wild-type as well as its fuzzless-lintless mutant acetylome data to identify the differentially acetylated proteins, which may play a significant role in cotton fiber development.
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Affiliation(s)
- Prashant Kumar Singh
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Rishon LeZion, 7505101, Israel; State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China; Department of Biotechnology, Pachhunga University College, Mizoram University, Aizawl, 796001, India.
| | - Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Peng Liao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Yang Li
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Fu-Chun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Xiao-Nan Ma
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Chun-Peng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China.
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29
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Herr DJ, Singh T, Dhammu T, Menick DR. Regulation of metabolism by mitochondrial enzyme acetylation in cardiac ischemia-reperfusion injury. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165728. [PMID: 32068115 DOI: 10.1016/j.bbadis.2020.165728] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 01/21/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022]
Abstract
Ischemia reperfusion injury (I/R injury) contributes significantly to morbidity and mortality following myocardial infarction (MI). Although rapid reperfusion of the ischemic myocardium was established decades ago as a highly beneficial therapy for MI, significant cell death still occurs after the onset of reperfusion. Mitochondrial dysfunction is closely associated with I/R injury, resulting in the uncontrolled production of reactive oxygen species (ROS). Considerable efforts have gone into understanding the metabolic perturbations elicited by I/R injury. Recent work has identified the critical role of reversible protein acetylation in maintaining normal mitochondrial biologic function and energy metabolism both in the normal heart and during I/R injury. Several studies have shown that modification of class I HDAC and/or Sirtuin (Sirt) activity is cardioprotective in the setting of I/R injury. A better understanding of the role of these metabolic pathways in reperfusion injury and their regulation by reversible protein acetylation presents a promising way forward in improving the treatment of cardiac reperfusion injury. Here we briefly review some of what is known about how acetylation regulates mitochondrial metabolism and how it relates to I/R injury.
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Affiliation(s)
- Daniel J Herr
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC, United States of America
| | - Toolika Singh
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC, United States of America
| | - Tajinder Dhammu
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC, United States of America
| | - Donald R Menick
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC, United States of America; Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC, United States of America.
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30
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Zhong R, Cui D, Richardson EA, Phillips DR, Azadi P, Lu G, Ye ZH. Cytosolic Acetyl-CoA Generated by ATP-Citrate Lyase Is Essential for Acetylation of Cell Wall Polysaccharides. PLANT & CELL PHYSIOLOGY 2020; 61:64-75. [PMID: 31503286 DOI: 10.1093/pcp/pcz178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/04/2019] [Indexed: 05/12/2023]
Abstract
Plant cell wall polysaccharides, including xylan, glucomannan, xyloglucan and pectin, are often acetylated. Although a number of acetyltransferases responsible for the acetylation of some of these polysaccharides have been biochemically characterized, little is known about the source of acetyl donors and how acetyl donors are translocated into the Golgi, where these polysaccharides are synthesized. In this report, we investigated roles of ATP-citrate lyase (ACL) that generates cytosolic acetyl-CoA in cell wall polysaccharide acetylation and effects of simultaneous mutations of four Reduced Wall Acetylation (RWA) genes on acetyl-CoA transport into the Golgi in Arabidopsis thaliana. Expression analyses of genes involved in the generation of acetyl-CoA in different subcellular compartments showed that the expression of several ACL genes responsible for cytosolic acetyl-CoA synthesis was elevated in interfascicular fiber cells and induced by secondary wall-associated transcriptional activators. Simultaneous downregulation of the expression of ACL genes was demonstrated to result in a substantial decrease in the degree of xylan acetylation and a severe alteration in secondary wall structure in xylem vessels. In addition, the degree of acetylation of other cell wall polysaccharides, including glucomannan, xyloglucan and pectin, was also reduced. Moreover, Golgi-enriched membrane vesicles isolated from the rwa1/2/3/4 quadruple mutant were found to exhibit a drastic reduction in acetyl-CoA transport activity compared with the wild type. These findings indicate that cytosolic acetyl-CoA generated by ACL is essential for cell wall polysaccharide acetylation and RWAs are required for its transport from the cytosol into the Golgi.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Dongtao Cui
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | | | - Dennis R Phillips
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Grace Lu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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Popa SC, Shin JA. The Intrinsically Disordered Loop in the USF1 bHLHZ Domain Modulates Its DNA-Binding Sequence Specificity in Hereditary Asthma. J Phys Chem B 2019; 123:9862-9871. [PMID: 31670516 DOI: 10.1021/acs.jpcb.9b06719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
USF1, a basic region/helix-loop-helix/leucine zipper (bHLHZ) transcription factor, binds to the E-box in the PAI-1 (plasminogen activator inhibitor) promoter. Two alleles containing the E-box control PAI-1 transcription; these alleles are termed "4G" and "5G" based on the G tract flanking E-box. USF1-governed transcription of PAI-1 is elevated in heritable asthma sufferers: the 4G/4G genotype has the highest plasma levels of PAI-1. While USF1 uses its basic region to bind E-box, we found that it uses its 12 amino-acid loop to recognize the flanking sequence and discern the single-nucleotide difference between the alleles. We used the bacterial one-hybrid and electrophoretic mobility shift assays to assess protein-DNA recognition, and circular dichroism to examine protein secondary structure. We mutated Ser233 and Thr234 in the USF1 bHLHZ loop to Ala to generate S233A and T234A. Interestingly, USF1 bHLHZ, S233A, and T234A prefer the 5G sequence (USF1 bHLHZ Kd values 4.1 ± 0.3 nM and 7.0 ± 0.4 nM for 5G and 4G, respectively), whereas studies in stimulated human mast cells showed a preference for 4G. We replaced the 8 amino-acid loop of transcription factor Max bHLHZ with the 12 amino-acid USF1 loop: this mutant now distinguishes the 4G/5G polymorphism-while Max bHLHZ does not-confirming that USF1 differentiation of the 4G/5G is driven by the loop.
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Affiliation(s)
- Serban C Popa
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
| | - Jumi A Shin
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
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32
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Xue C, Liu S, Chen C, Zhu J, Yang X, Zhou Y, Guo R, Liu X, Gong Z. Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in Oryza Sativa. Proteomics 2019; 18. [PMID: 29106068 DOI: 10.1002/pmic.201700036] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 10/11/2017] [Indexed: 01/26/2023]
Abstract
Lysine acetylation (Kac) is an important protein post-translational modification in both eukaryotes and prokaryotes. Herein, we report the results of a global proteome analysis of Kac and its diverse functions in rice (Oryza sativa). We identified 1353 Kac sites in 866 proteins in rice seedlings. A total of 11 Kac motifs are conserved, and 45% of the identified proteins are localized to the chloroplast. Among all acetylated proteins, 38 Kac sites are combined in core histones. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Protein-protein interaction networks of the identified proteins provided further evidence that Kac contributes to a wide range of regulatory functions. Furthermore, we demonstrated that the acetylation level of histone H3 (lysine 27 and 36) is increased in response to cold stress. In summary, our approach comprehensively profiles the regulatory roles of Kac in the growth and development of rice.
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Affiliation(s)
- Chao Xue
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Shuai Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Jun Zhu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, P. R. China
| | - Xibin Yang
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, P. R. China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Rui Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Xiaoyu Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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Gakière B, Fernie AR, Pétriacq P. More to NAD + than meets the eye: A regulator of metabolic pools and gene expression in Arabidopsis. Free Radic Biol Med 2018; 122:86-95. [PMID: 29309893 DOI: 10.1016/j.freeradbiomed.2018.01.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
Abstract
Since its discovery more than a century ago, nicotinamide adenine dinucleotide (NAD+) is recognised as a fascinating cornerstone of cellular metabolism. This ubiquitous energy cofactor plays vital roles in metabolic pathways and regulatory processes, a fact emphasised by the essentiality of a balanced NAD+ metabolism for normal plant growth and development. Research on the role of NAD in plants has been predominantly carried out in the model plant Arabidopsis thaliana (Arabidopsis) with emphasis on the redox properties and cellular signalling functions of the metabolite. This review examines the current state of knowledge concerning how NAD can regulate both metabolic pools and gene expression in Arabidopsis. Particular focus is placed on recent studies highlighting the complexity of metabolic regulations involving NAD, more particularly in the mitochondrial compartment, and of signalling roles with respect to interactions with environmental fluctuations most specifically those involving plant immunity.
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Affiliation(s)
- Bertrand Gakière
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Diderot, Univ. Paris-Saclay, Bâtiment 630 Rue Noetzlin, 91192 Gif-sur-Yvette cedex, France; Plateforme Métabolisme Métabolome, Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Diderot, Univ. ParisSaclay, Bâtiment 630 Rue Noetzlin, 91192 Gif-sur-Yvette cedex, France
| | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, Wissenschaftspark Golm, 14476 Potsdam-Golm, Germany
| | - Pierre Pétriacq
- biOMICS Facility, Department of Animal and Plant Sciences, The University of Sheffield, S10 2TN Sheffield, United Kingdom; UMR 1332 Biologie du Fruit et Pathologie, INRA Bordeaux & Université de Bordeaux, F-33883 Villenave d'Ornon, France.
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Wang Y, Berkowitz O, Selinski J, Xu Y, Hartmann A, Whelan J. Stress responsive mitochondrial proteins in Arabidopsis thaliana. Free Radic Biol Med 2018; 122:28-39. [PMID: 29555593 DOI: 10.1016/j.freeradbiomed.2018.03.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/05/2018] [Accepted: 03/16/2018] [Indexed: 12/27/2022]
Abstract
In the last decade plant mitochondria have emerged as a target, sensor and initiator of signalling cascades to a variety of stress and adverse growth conditions. A combination of various 'omic profiling approaches combined with forward and reverse genetic studies have defined how mitochondria respond to stress and the signalling pathways and regulators of these responses. Reactive oxygen species (ROS)-dependent and -independent pathways, specific metabolites, complex I dysfunction, and the mitochondrial unfolded protein response (UPR) pathway have been proposed to date. These pathways are regulated by kinases (sucrose non-fermenting response like kinase; cyclin dependent protein kinase E 1) and transcription factors from the abscisic acid-related, WRKY and NAC families. A number of independent studies have revealed that these mitochondrial signalling pathways interact with a variety of phytohormone signalling pathways. While this represents significant progress in the last decade there are more pathways to be uncovered. Post-transcriptional/translational regulation is also a likely determinant of the mitochondrial stress response. Unbiased analyses of the expression of genes encoding mitochondrial proteins in a variety of stress conditions reveal a modular network exerting a high degree of anterograde control. As abiotic and biotic stresses have significant impact on the yield of important crops such as rice, wheat and barley we will give an outlook of how knowledge gained in Arabidopsis may help to increase crop production and how emerging technologies may contribute.
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Affiliation(s)
- Yan Wang
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.
| | - Jennifer Selinski
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Yue Xu
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Andreas Hartmann
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
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Pan D, Wang L, Chen S, Lv X, Lu S, Cheng CL, Tan F, Chen W. Protein acetylation as a mechanism for Kandelia candel's adaption to daily flooding. TREE PHYSIOLOGY 2018; 38:895-910. [PMID: 29301031 DOI: 10.1093/treephys/tpx162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 12/07/2017] [Indexed: 06/07/2023]
Abstract
To explore the adaptation mechanisms of Kandelia candel (L.) Druce in response to daily flooding, a large-scale quantitative lysine acetylome was carried out using immunoaffinity enrichment of Lys-acetylated peptides and liquid chromatography linked to tandem mass spectrometry. A total of 1041 lysine acetylation (LysAc) sites, 1021 Lys-acetylated peptides and 617 Lys-acetylated proteins were identified. Six conserved sequence motifs of the LysAc sites, including a new motif KxxxxK, were detected. Among these proteins, 260 were differentially acetylated in response to flooding, which were preferentially predicted to participate in carbon metabolism and photosynthesis pathways based on KEGG pathway category enrichment analysis. Consistently, the transcriptional level of acetyltransferase and the consumption of acetyl-CoA were up-regulated under flooding conditions. Most of physiological parameters and mRNA expression levels related to carbon metabolism and photosynthesis were found to be insignificantly affected by flooding. Taken together, reversible protein LysAc is likely to be a post-translational mechanism contributing to the mangrove K. candel's adaptation to daily flooding.
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Affiliation(s)
- Dezhuo Pan
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Lingxia Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
- College of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Xiaojie Lv
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Si Lu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Chi-Lien Cheng
- Department of Biology, The University of Iowa, 210 Biology Building, Iowa City, IA 52242, USA
| | - Fanlin Tan
- Fujian Academy of Forestry, Fuzhou 350012, PR China
| | - Wei Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
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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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Liu S, Yu F, Yang Z, Wang T, Xiong H, Chang C, Yu W, Li N. Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis. Mol Cell Proteomics 2018; 17:1010-1027. [PMID: 29440448 DOI: 10.1074/mcp.ra117.000530] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/18/2018] [Indexed: 12/19/2022] Open
Abstract
Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we applied both CsCl density gradient (CDG) centrifugation-based protein fractionation and a dimethyl-labeling-based 4C quantitative PTM proteomics workflow in the study of dynamic acetylproteomic changes in Arabidopsis. This workflow integrates the dimethyl chemical labeling with chromatography-based acetylpeptide separation and enrichment followed by mass spectrometry (MS) analysis, the extracted ion chromatogram (XIC) quantitation-based computational analysis of mass spectrometry data to measure dynamic changes of acetylpeptide level using an in-house software program, named Stable isotope-based Quantitation-Dimethyl labeling (SQUA-D), and finally the confirmation of ethylene hormone-regulated acetylation using immunoblot analysis. Eventually, using this proteomic approach, 7456 unambiguous acetylation sites were found from 2638 different acetylproteins, and 5250 acetylation sites, including 5233 sites on lysine side chain and 17 sites on protein N termini, were identified repetitively. Out of these repetitively discovered acetylation sites, 4228 sites on lysine side chain (i.e. 80.5%) are novel. These acetylproteins are exemplified by the histone superfamily, ribosomal and heat shock proteins, and proteins related to stress/stimulus responses and energy metabolism. The novel acetylproteins enriched by the CDG centrifugation fractionation contain many cellular trafficking proteins, membrane-bound receptors, and receptor-like kinases, which are mostly involved in brassinosteroid, light, gravity, and development signaling. In addition, we identified 12 highly conserved acetylation site motifs within histones, P-glycoproteins, actin depolymerizing factors, ATPases, transcription factors, and receptor-like kinases. Using SQUA-D software, we have quantified 33 ethylene hormone-enhanced and 31 hormone-suppressed acetylpeptide groups or called unique PTM peptide arrays (UPAs) that share the identical unique PTM site pattern (UPSP). This CDG centrifugation protein fractionation in combination with dimethyl labeling-based quantitative PTM proteomics, and SQUA-D may be applied in the quantitation of any PTM proteins in any model eukaryotes and agricultural crops as well as tissue samples of animals and human beings.
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Affiliation(s)
- Shichang Liu
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Zhu Yang
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
| | - Tingliang Wang
- **Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hairong Xiong
- ‡‡College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Caren Chang
- §§Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland 20742-5815
| | - Weichuan Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ning Li
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
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Abstract
RNA-binding proteins (RBPs) are typically thought of as proteins that bind RNA through one or multiple globular RNA-binding domains (RBDs) and change the fate or function of the bound RNAs. Several hundred such RBPs have been discovered and investigated over the years. Recent proteome-wide studies have more than doubled the number of proteins implicated in RNA binding and uncovered hundreds of additional RBPs lacking conventional RBDs. In this Review, we discuss these new RBPs and the emerging understanding of their unexpected modes of RNA binding, which can be mediated by intrinsically disordered regions, protein-protein interaction interfaces and enzymatic cores, among others. We also discuss the RNA targets and molecular and cellular functions of the new RBPs, as well as the possibility that some RBPs may be regulated by RNA rather than regulate RNA.
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A Quantitative Acetylomic Analysis of Early Seed Development in Rice (Oryza sativa L.). Int J Mol Sci 2017; 18:ijms18071376. [PMID: 28654018 PMCID: PMC5535869 DOI: 10.3390/ijms18071376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 11/20/2022] Open
Abstract
PKA (protein lysine acetylation) is a critical post-translational modification that regulates various developmental processes, including seed development. However, the acetylation events and dynamics on a proteomic scale in this process remain largely unknown, especially in rice early seed development. We report the first quantitative acetylproteomic study focused on rice early seed development by employing a mass spectral-based (MS-based), label-free approach. A total of 1817 acetylsites on 1688 acetylpeptides from 972 acetylproteins were identified in pistils and seeds at three and seven days after pollination, including 268 acetyproteins differentially acetylated among the three stages. Motif-X analysis revealed that six significantly enriched motifs, such as (DxkK), (kH) and (kY) around the acetylsites of the identified rice seed acetylproteins. Differentially acetylated proteins among the three stages, including adenosine diphosphate (ADP) -glucose pyrophosphorylases (AGPs), PDIL1-1 (protein disulfide isomerase like 1-1), hexokinases, pyruvate dehydrogenase complex (PDC) and numerous other regulators that are extensively involved in the starch and sucrose metabolism, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle and photosynthesis pathways during early seed development. This study greatly expanded the rice acetylome dataset, and shed novel insight into the regulatory roles of PKA in rice early seed development.
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Lv Y. Proteome-wide profiling of protein lysine acetylation in Aspergillus flavus. PLoS One 2017; 12:e0178603. [PMID: 28582408 PMCID: PMC5459447 DOI: 10.1371/journal.pone.0178603] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 05/16/2017] [Indexed: 01/18/2023] Open
Abstract
Protein lysine acetylation is a prevalent post-translational modification that plays pivotal roles in various biological processes in both prokaryotes and eukaryotes. Aspergillus flavus, as an aflatoxin-producing fungus, has attracted tremendous attention due to its health impact on agricultural commodities. Here, we performed the first lysine-acetylome mapping in this filamentous fungus using immune-affinity-based purification integrated with high-resolution mass spectrometry. Overall, we identified 1383 lysine-acetylation sites in 652 acetylated proteins, which account for 5.18% of the total proteins in A. flavus. According to bioinformatics analysis, the acetylated proteins are involved in various cellular processes involving the ribosome, carbon metabolism, antibiotic biosynthesis, secondary metabolites, and the citrate cycle and are distributed in diverse subcellular locations. Additionally, we demonstrated for the first time the acetylation of fatty acid synthase α and β encoded by aflA and aflB involved in the aflatoxin-biosynthesis pathway (cluster 54), as well as backbone enzymes from secondary metabolite clusters 20 and 21 encoded by AFLA_062860 and AFLA_064240, suggesting important roles for acetylation associated with these processes. Our findings illustrating abundant lysine acetylation in A. flavus expand our understanding of the fungal acetylome and provided insight into the regulatory roles of acetylation in secondary metabolism.
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Affiliation(s)
- Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
- * E-mail:
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Pütter KM, van Deenen N, Unland K, Prüfer D, Schulze Gronover C. Isoprenoid biosynthesis in dandelion latex is enhanced by the overexpression of three key enzymes involved in the mevalonate pathway. BMC PLANT BIOLOGY 2017; 17:88. [PMID: 28532507 PMCID: PMC5441070 DOI: 10.1186/s12870-017-1036-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/10/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Latex from the dandelion species Taraxacum brevicorniculatum contains many high-value isoprenoid end products, e.g. triterpenes and polyisoprenes such as natural rubber. The isopentenyl pyrophosphate units required as precursors for these isoprenoids are provided by the mevalonate (MVA) pathway. The key enzyme in this pathway is 3-hydroxy-methyl-glutaryl-CoA reductase (HMGR) and its activity has been thoroughly characterized in many plant species including dandelion. However, two enzymes acting upstream of HMGR have not been characterized in dandelion latex: ATP citrate lyase (ACL), which provides the acetyl-CoA utilized in the MVA pathway, and acetoacetyl-CoA thiolase (AACT), which catalyzes the first step in the pathway to produce acetoacetyl-CoA. Here we isolated ACL and AACT genes from T. brevicorniculatum latex and characterized their expression profiles. We also overexpressed the well-characterized HMGR, ACL and AACT genes from Arabidopsis thaliana in T. brevicorniculatum to determine their impact on isoprenoid end products in the latex. RESULTS The spatial and temporal expression profiles of T. brevicorniculatum ACL and AACT revealed their pivotal role in the synthesis of precursors necessary for isoprenoid biosynthesis in latex. The overexpression of A. thaliana ACL and AACT and HMGR in T. brevicorniculatum latex resulted in the accumulation of all three enzymes, increased the corresponding enzymatic activities and ultimately increased sterol levels by ~5-fold and pentacyclic triterpene and cis-1,4-isoprene levels by ~2-fold. Remarkably high levels of the triterpene precursor squalene were also detected in the triple-transgenic lines (up to 32 mg/g root dry weight) leading to the formation of numerous lipid droplets which were observed in root cross-sections. CONCLUSIONS We could show the effective expression of up to three transgenes in T. brevicorniculatum latex which led to increased enzymatic activity and resulted in high level squalene accumulation in the dandelion roots up to an industrially relevant amount. Our data provide insight into the regulation of the MVA pathway in dandelion latex and can be used as a basis for metabolic engineering to enhance the production of isoprenoid end products in this specialized tissue.
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Affiliation(s)
- Katharina M. Pütter
- Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143 Muenster, Germany
| | - Nicole van Deenen
- Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143 Muenster, Germany
| | - Kristina Unland
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Schlossplatz 8, 48143 Muenster, Germany
| | - Dirk Prüfer
- Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143 Muenster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Schlossplatz 8, 48143 Muenster, Germany
| | - Christian Schulze Gronover
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Schlossplatz 8, 48143 Muenster, Germany
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Xia Y, Jing D, Kong L, Zhang J, OuYang F, Zhang H, Wang J, Zhang S. Global Lysine Acetylome Analysis of Desiccated Somatic Embryos of Picea asperata. FRONTIERS IN PLANT SCIENCE 2016; 7:1927. [PMID: 28066480 PMCID: PMC5179564 DOI: 10.3389/fpls.2016.01927] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/05/2016] [Indexed: 05/22/2023]
Abstract
Partial desiccation treatment (PDT) promotes the germination capacity of conifer somatic embryos. Lysine acetylation (LysAc) is a dynamic and reversible post-translational modification that plays a key role in many biological processes including metabolic pathways and stress response. To investigate the functional impact of LysAc in the response of Picea asperata somatic embryos to PDT, we performed a global lysine acetylome analysis. Here, combining antibody-based affinity enrichment and high-resolution mass spectrometry, we identified and validated 1079 acetylation sites in 556 acetylated proteins from P. asperata somatic embryos during PDT. These data represent a novel large-scale dataset of lysine-acetylated proteins from the conifer family. Intensive bioinformatics analysis of the Gene Ontology of molecular functions demonstrated that lysine-acetylated proteins were mainly associated with binding, catalytic activities, and structural molecular activities. Functional characterization of the acetylated proteins revealed that in the desiccated somatic embryos, LysAc is mainly involved in the response to stress and central metabolism. Accordingly, the majority of these interacting proteins were also highly enriched in ribosome, proteasome, spliceosome, and carbon metabolism clusters. This work provides the most comprehensive profile of LysAc for a coniferous species obtained to date and facilitates the systematic study of the physiological role of LysAc in desiccated somatic embryos of P. asperata.
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Affiliation(s)
- Yan Xia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Danlong Jing
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Lisheng Kong
- Centre for Forest Biology, Department of Biology, University of VictoriaVictoria, BC, Canada
| | - Jianwei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Fangqun OuYang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
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First Comprehensive Proteome Analyses of Lysine Acetylation and Succinylation in Seedling Leaves of Brachypodium distachyon L. Sci Rep 2016; 6:31576. [PMID: 27515067 PMCID: PMC4981852 DOI: 10.1038/srep31576] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/26/2016] [Indexed: 01/23/2023] Open
Abstract
Protein acetylation and succinylation are the most crucial protein post-translational modifications (PTMs) involved in the regulation of plant growth and development. In this study, we present the first lysine-acetylation and lysine-succinylation proteome analysis of seedling leaves in Brachypodium distachyon L (Bd). Using high accuracy nano LC-MS/MS combined with affinity purification, we identified a total of 636 lysine-acetylated sites in 353 proteins and 605 lysine-succinylated sites in 262 proteins. These proteins participated in many biology processes, with various molecular functions. In particular, 119 proteins and 115 sites were found to be both acetylated and succinylated, simultaneously. Among the 353 acetylated proteins, 148 had acetylation orthologs in Oryza sativa L., Arabidopsis thaliana, Synechocystis sp. PCC 6803, and Glycine max L. Among the 262 succinylated proteins, 170 of them were found to have homologous proteins in Oryza sativa L., Escherichia coli, Sacchayromyces cerevisiae, or Homo sapiens. Motif-X analysis of the acetylated and succinylated sites identified two new acetylated motifs (K---K and K-I-K) and twelve significantly enriched succinylated motifs for the first time, which could serve as possible binding loci for future studies in plants. Our comprehensive dataset provides a promising starting point for further functional analysis of acetylation and succinylation in Bd and other plant species.
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Kentache T, Jouenne T, Dé E, Hardouin J. Proteomic characterization of Nα- and Nε-acetylation in Acinetobacter baumannii. J Proteomics 2016; 144:148-58. [PMID: 27222042 DOI: 10.1016/j.jprot.2016.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/12/2016] [Accepted: 05/18/2016] [Indexed: 12/25/2022]
Abstract
Nα- and Nε-acetylation represent a pivotal post-translational modification used by both eukaryotes and prokaryotes to modulate diverse biological processes. Acinetobacter baumannii has been described as an important nosocomial pathogen for the past 30 years, frequently involved in ventilator-associated pneumonia, bloodstream and urinary tract infections. Many aspects of the biology of A. baumannii remain elusive, in particular the extent and function of N-acetylation. We investigated here N-acetylation in A. baumannii strain ATCC 17978 by proteomic analysis, and we showed the usefulness of using different analytical approaches. Overall, we identified 525 N-acetylated proteins in which, 145 were Nα-acetylated and 411 were Nε-acetylated. Among them, 41 proteins carried both types of N-acetylation. We found that N-acetylation may play a role in biofilm formation, bacterial virulence (e.g. in several iron acquisition pathways), as well as a number of phenotypes, such as, stress adaptation and drug resistance. BIOLOGICAL SIGNIFICANCE This study is the first to perform the N-acetylome of A. baumannii using different analytical approaches. Each analytical tool permitted to characterize distinctive modified peptides. The combination of all these methods allowed us to identify 145 and 411 Nα- and Nε-acetylated proteins. Besides the fact that acetylation was involved in central metabolism as previously described in other bacteria, some N-acetylated proteins showed interesting role in bacterial virulence (iron acquisition), biofilm formation, stress adaptation and drug resistance of A. baumannii.
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Affiliation(s)
- Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France.
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Zheng Y, Ding Y, Sun X, Xie S, Wang D, Liu X, Su L, Wei W, Pan L, Zhou DX. Histone deacetylase HDA9 negatively regulates salt and drought stress responsiveness in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1703-13. [PMID: 26733691 DOI: 10.1093/jxb/erv562] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Histone modification is an important epigenetic regulation in higher plants adapting to environment changes including salt and drought stresses. In this report, we show that the Arabidopsis RPD3-type histone deacetylase HDA9 is involved in modulating plant responses to salt and drought stresses in Arabidopsis. Loss-of-function mutants of the gene displayed phenotypes (such as seedling root growth and seed germination) insensitive to NaCl and polyethylene glycol (PEG) treatments. HDA9 mutation led to up-regulation of many genes, among which those involved in response to water deprivation stress (GO: 0009414) were enriched. These genes were much more induced in the mutants than wild-type plants when treated with PEG and NaCl. In addition, we found that in the mutants, salt and drought stresses led to much higher levels of histone H3K9 acetylation at promoters of 14 genes randomly selected from those that respond to water-deprivation stress than in wild-type plants. Our study suggested that HDA9 might be a novel chromatin protein that negatively regulates plant sensitivity to salt and drought stresses by regulating histone acetylation levels of a large number of stress-responsive genes in Arabidopsis.
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Affiliation(s)
- Yu Zheng
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Yue Ding
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Xuan Sun
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Sisi Xie
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Dan Wang
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Lufang Su
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Wei Wei
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Lei Pan
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
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Ouidir T, Kentache T, Hardouin J. Protein lysine acetylation in bacteria: Current state of the art. Proteomics 2015; 16:301-9. [DOI: 10.1002/pmic.201500258] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/11/2015] [Accepted: 09/15/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
| | - Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
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Castello A, Hentze MW, Preiss T. Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins. Trends Endocrinol Metab 2015; 26:746-757. [PMID: 26520658 PMCID: PMC4671484 DOI: 10.1016/j.tem.2015.09.012] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 12/21/2022]
Abstract
In the past century, few areas of biology advanced as much as our understanding of the pathways of intermediary metabolism. Initially considered unimportant in terms of gene regulation, crucial cellular fate changes, cell differentiation, or malignant transformation are now known to involve 'metabolic remodeling' with profound changes in the expression of many metabolic enzyme genes. This review focuses on the recent identification of RNA-binding activity of numerous metabolic enzymes. We discuss possible roles of this unexpected second activity in feedback gene regulation ('moonlighting') and/or in the control of enzymatic function. We also consider how metabolism-driven post-translational modifications could regulate enzyme-RNA interactions. Thus, RNA emerges as a new partner of metabolic enzymes with far-reaching possible consequences to be unraveled in the future.
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Affiliation(s)
- Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), ACT 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
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Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG. A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Structure 2015; 23:1801-1814. [PMID: 26365797 DOI: 10.1016/j.str.2015.08.004] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 01/09/2023]
Abstract
Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.
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Affiliation(s)
- E Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Oscar W Huang
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Florence Poy
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steve F Bellon
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Yong Tang
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA.
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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Hentchel KL, Escalante-Semerena JC. Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress. Microbiol Mol Biol Rev 2015; 79:321-46. [PMID: 26179745 PMCID: PMC4503791 DOI: 10.1128/mmbr.00020-15] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. Although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic acids (e.g., short-, medium-, and long-chain mono- and dicarboxylic aliphatics and aromatics) to modify a large suite of targets. Acetylation of biomolecules has been studied for decades within the context of histone-dependent regulation of gene expression and antibiotic resistance. It was not until the early 2000s that the connection between metabolism, physiology, and protein acetylation was reported. This was the first instance of a metabolic enzyme (acetyl coenzyme A [acetyl-CoA] synthetase) whose activity was controlled by acetylation via a regulatory system responsive to physiological cues. The above-mentioned system was comprised of an acyltransferase and a partner deacylase. Given the reversibility of the acylation process, this system is also referred to as reversible lysine acylation (RLA). A wealth of information has been obtained since the discovery of RLA in prokaryotes, and we are just beginning to visualize the extent of the impact that this regulatory system has on cell function.
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Affiliation(s)
- Kristy L Hentchel
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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