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Han Y, Zhao H, Li G, Jia J, Guo H, Tan J, Sun X, Li S, Ran Q, Bai C, Gu Y, Li Z, Guan H, Gao S, Zhou PK. GCN5 mediates DNA-PKcs crotonylation for DNA double-strand break repair and determining cancer radiosensitivity. Br J Cancer 2024; 130:1621-1634. [PMID: 38575732 PMCID: PMC11091118 DOI: 10.1038/s41416-024-02636-4] [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: 12/12/2023] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND DNA double-strand break (DSB) induction and repair are important events for determining cell survival and the outcome of cancer radiotherapy. The DNA-dependent protein kinase (DNA-PK) complex functions at the apex of DSBs repair, and its assembly and activity are strictly regulated by post-translation modifications (PTMs)-associated interactions. However, the PTMs of the catalytic subunit DNA-PKcs and how they affect DNA-PKcs's functions are not fully understood. METHODS Mass spectrometry analyses were performed to identify the crotonylation sites of DNA-PKcs in response to γ-ray irradiation. Co-immunoprecipitation (Co-IP), western blotting, in vitro crotonylation assays, laser microirradiation assays, in vitro DNA binding assays, in vitro DNA-PK assembly assays and IF assays were employed to confirm the crotonylation, identify the crotonylase and decrotonylase, and elucidate how crotonylation regulates the activity and function of DNA-PKcs. Subcutaneous xenografts of human HeLa GCN5 WT or HeLa GCN5 siRNA cells in BALB/c nude mice were generated and utilized to assess tumor proliferation in vivo after radiotherapy. RESULTS Here, we reveal that K525 is an important site of DNA-PKcs for crotonylation, and whose level is sharply increased by irradiation. The histone acetyltransferase GCN5 functions as the crotonylase for K525-Kcr, while HDAC3 serves as its dedicated decrotonylase. K525 crotonylation enhances DNA binding activity of DNA-PKcs, and facilitates assembly of the DNA-PK complex. Furthermore, GCN5-mediated K525 crotonylation is indispensable for DNA-PKcs autophosphorylation and the repair of double-strand breaks in the NHEJ pathway. GCN5 suppression significantly sensitizes xenograft tumors of mice to radiotherapy. CONCLUSIONS Our study defines K525 crotonylation of DNA-PKcs is important for the DNA-PK complex assembly and DSBs repair activity via NHEJ pathway. Targeting GCN5-mediated K525 Kcr of DNA-PKcs may be a promising therapeutic strategy for improving the outcome of cancer radiotherapy.
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Affiliation(s)
- Yang Han
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hongling Zhao
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Gang Li
- School of Public Health, Institute for Environmental Medicine and Radiation Hygiene, University of South China, Hengyang, China
- Department of Hospital Infection Control, Shenzhen Luohu Peoples Hospital, Shenzhen, China
| | - Jin Jia
- School of Medicine, University of South China, Hengyang, China
| | - Hejiang Guo
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jinpeng Tan
- School of Medicine, University of South China, Hengyang, China
| | - Xingyao Sun
- School of Medicine, University of South China, Hengyang, China
| | - Saiyu Li
- School of life Sciences, Hebei University, Baoding, China
| | - Qian Ran
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Chenjun Bai
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yongqing Gu
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - ZhongJun Li
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China.
| | - Hua Guan
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Shanshan Gao
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
- School of Public Health, Institute for Environmental Medicine and Radiation Hygiene, University of South China, Hengyang, China.
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Zhuang J, Liu S, Du GF, Fang Z, Wu J, Li N, Zhong T, Xu J, He QY, Sun X. YjgM is a crotonyltransferase critical for polymyxin resistance of Escherichia coli. Cell Rep 2024; 43:114161. [PMID: 38678561 DOI: 10.1016/j.celrep.2024.114161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Lysine crotonylation has attracted widespread attention in recent years. However, little is known about bacterial crotonylation, particularly crotonyltransferase and decrotonylase, and its effects on antibiotic resistance. Our study demonstrates the ubiquitous presence of crotonylation in E. coli, which promotes bacterial resistance to polymyxin. We identify the crotonyltransferase YjgM and its regulatory pathways in E. coli with a focus on crotonylation. Further studies show that YjgM upregulates the crotonylation of the substrate protein PmrA, thereby boosting PmrA's affinity for binding to the promoter of eptA, which, in turn, promotes EptA expression and confers polymyxin resistance in E. coli. Additionally, we discover that PmrA's crucial crotonylation site and functional site is Lys 164. These significant discoveries highlight the role of crotonylation in bacterial drug resistance and offer a fresh perspective on creating antibacterial compounds.
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Affiliation(s)
- Jianpeng Zhuang
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Shiqin Liu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Gao-Fei Du
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China; Key Laboratory of Laboratory Diagnostics, Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zuye Fang
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jiayi Wu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Nan Li
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Tairan Zhong
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jiayi Xu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Xuesong Sun
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.
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3
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Zhang L, Wang H, Xue C, Liu Y, Zhang Y, Liu Z, Meng X, Liu M, Zhao J. The crotonylated and succinylated proteins of jujube involved in phytoplasma-stress responses. BMC Biol 2024; 22:113. [PMID: 38750524 PMCID: PMC11094900 DOI: 10.1186/s12915-024-01917-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/10/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Protein posttranslational modifications (PTMs) are fast and early responses to environmental changes, including pathogen infection. Jujube witches' broom (JWB) is a phytoplasma disease causing great economic loss in jujube production. After phytoplasma infection, the transcriptional, translational, and metabolic levels in jujube were activated, enabling it to survive during phytoplasma invasion. However, no study has yet reported on PTMs in jujube. Lysine crotonylation (Kcr) and lysine succinylation (Ksu) have been popular studies in recent years and their function in plant phytoplasma-stress responses remains unclear. RESULTS Here, 1656 crotonylated and 282 succinylated jujube proteins were first identified under phytoplasma-stress, of which 198 were simultaneously crotonylated and succinylated. Comparative analysis revealed that 656 proteins, 137 crotonylated and 43 succinylated proteins in jujube were regulated by phytoplasma infection, suggesting that Kcr was more universal than Ksu. Kcr differentially expressed proteins (DEPs) were related to ribosomes, photosynthetic and carbon metabolism, while Ksu DEPs were mainly involved in carbon metabolism, the TCA cycle and secondary metabolite biosynthesis. The crosstalk network among proteome, crotonylome and succinylome showed that DEPs related to ribosomal, peroxidases and glutathione redox were enriched. Among them, ZjPOD51 and ZjPHGPX2 significantly increased at the protein and Kcr level under phytoplasma-stress. Notably, 7 Kcr sites were identified in ZjPHGPX2, a unique antioxidant enzyme. After inhibitor nicotinamide (NAM) treatment, GPX enzyme activity in jujube seedlings was reduced. Further, site-directed mutagenesis of key Kcr modification sites K130 and/or K135 in ZjPHGPX2 significantly reduced its activity. CONCLUSIONS This study firstly provided large-scale datasets of Kcr and Ksu in phytoplasma-infected jujube and revealed that Kcr modification in ZjPHGPX2 positively regulates its activity.
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Affiliation(s)
- Liman Zhang
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Huibin Wang
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Yin Liu
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiangrui Meng
- College of Life Science, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China.
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.
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Foyer CH, Kunert K. The ascorbate-glutathione cycle coming of age. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2682-2699. [PMID: 38243395 PMCID: PMC11066808 DOI: 10.1093/jxb/erae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Concepts regarding the operation of the ascorbate-glutathione cycle and the associated water/water cycle in the processing of metabolically generated hydrogen peroxide and other forms of reactive oxygen species (ROS) are well established in the literature. However, our knowledge of the functions of these cycles and their component enzymes continues to grow and evolve. Recent insights include participation in the intrinsic environmental and developmental signalling pathways that regulate plant growth, development, and defence. In addition to ROS processing, the enzymes of the two cycles not only support the functions of ascorbate and glutathione, they also have 'moonlighting' functions. They are subject to post-translational modifications and have an extensive interactome, particularly with other signalling proteins. In this assessment of current knowledge, we highlight the central position of the ascorbate-glutathione cycle in the network of cellular redox systems that underpin the energy-sensitive communication within the different cellular compartments and integrate plant signalling pathways.
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Affiliation(s)
- Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Karl Kunert
- Department of Plant and Soil Sciences, FABI, University of Pretoria, Pretoria, 2001, South Africa
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5
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Haber Z, Sharma D, Selvaraj KSV, Sade N. Is CRISPR/Cas9-based multi-trait enhancement of wheat forthcoming? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112021. [PMID: 38311249 DOI: 10.1016/j.plantsci.2024.112021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have been implemented in recent years in the genome editing of eukaryotes, including plants. The original system of knocking out a single gene by causing a double-strand break (DSB), followed by non-homologous end joining (NHEJ) or Homology-directed repair (HDR) has undergone many adaptations. These adaptations include employing CRISPR/Cas9 to upregulate gene expression or to cause specific small changes to the DNA sequence of the gene-of-interest. In plants, multiplexing, i.e., inducing multiple changes by CRISPR/Cas9, is extremely relevant due to the redundancy of many plant genes, and the time- and labor-consuming generation of stable transgenic plant lines via crossing. Here we discuss relevant examples of various traits, such as yield, biofortification, gluten content, abiotic stress tolerance, and biotic stress resistance, which have been successfully manipulated using CRISPR/Cas9 in plants. While existing studies have primarily focused on proving the impact of CRISPR/Cas9 on a single trait, there is a growing interest among researchers in creating a multi-stress tolerant wheat cultivar 'super wheat', to commercially and sustainably enhance wheat yields under climate change. Due to the complexity of the technical difficulties in generating multi-target CRISPR/Cas9 lines and of the interactions between stress responses, we propose enhancing already commercial local landraces with higher yield traits along with stress tolerances specific to the respective localities, instead of generating a general 'super wheat'. We hope this will serve as the sustainable solution to commercially enhancing crop yields under both stable and challenging environmental conditions.
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Affiliation(s)
- Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - K S Vijai Selvaraj
- Vegetable Research Station, Tamil Nadu Agricultural University, Palur 607102, Tamil Nadu, India
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel.
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6
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Jiang Y, Yan R, Wang X. PlantNh-Kcr: a deep learning model for predicting non-histone crotonylation sites in plants. PLANT METHODS 2024; 20:28. [PMID: 38360730 PMCID: PMC10870457 DOI: 10.1186/s13007-024-01157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Lysine crotonylation (Kcr) is a crucial protein post-translational modification found in histone and non-histone proteins. It plays a pivotal role in regulating diverse biological processes in both animals and plants, including gene transcription and replication, cell metabolism and differentiation, as well as photosynthesis. Despite the significance of Kcr, detection of Kcr sites through biological experiments is often time-consuming, expensive, and only a fraction of crotonylated peptides can be identified. This reality highlights the need for efficient and rapid prediction of Kcr sites through computational methods. Currently, several machine learning models exist for predicting Kcr sites in humans, yet models tailored for plants are rare. Furthermore, no downloadable Kcr site predictors or datasets have been developed specifically for plants. To address this gap, it is imperative to integrate existing Kcr sites detected in plant experiments and establish a dedicated computational model for plants. RESULTS Most plant Kcr sites are located on non-histones. In this study, we collected non-histone Kcr sites from five plants, including wheat, tabacum, rice, peanut, and papaya. We then conducted a comprehensive analysis of the amino acid distribution surrounding these sites. To develop a predictive model for plant non-histone Kcr sites, we combined a convolutional neural network (CNN), a bidirectional long short-term memory network (BiLSTM), and attention mechanism to build a deep learning model called PlantNh-Kcr. On both five-fold cross-validation and independent tests, PlantNh-Kcr outperformed multiple conventional machine learning models and other deep learning models. Furthermore, we conducted an analysis of species-specific effect on the PlantNh-Kcr model and found that a general model trained using data from multiple species outperforms species-specific models. CONCLUSION PlantNh-Kcr represents a valuable tool for predicting plant non-histone Kcr sites. We expect that this model will aid in addressing key challenges and tasks in the study of plant crotonylation sites.
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Affiliation(s)
- Yanming Jiang
- College of Mathematics and Computer Sciences, Shanxi Normal University, Taiyuan, 030031, China
| | - Renxiang Yan
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, 350002, China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350002, China
| | - Xiaofeng Wang
- College of Mathematics and Computer Sciences, Shanxi Normal University, Taiyuan, 030031, China.
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7
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Xie Y, Chen S, Guo Z, Tian Y, Hong X, Feng P, Xie Q, Yu Q. Down-regulation of Lon protease 1 lysine crotonylation aggravates mitochondrial dysfunction in polycystic ovary syndrome. MedComm (Beijing) 2023; 4:e396. [PMID: 37817894 PMCID: PMC10560969 DOI: 10.1002/mco2.396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a prevalent reproductive endocrine disorder, with metabolic abnormalities and ovulation disorders. The post-translational modifications (PTMs) are functionally relevant and strengthen the link between metabolism and cellular functions. Lysine crotonylation is a newly identified PTM, the function of which in PCOS has not yet been reported. To explore the molecular mechanisms of crotonylation involved in the abnormalities of metabolic homeostasis and oocyte maturation in PCOS, by using liquid chromatography-tandem mass spectrometry analysis, we constructed a comprehensive map of crotonylation modifications in ovarian tissue of PCOS-like mouse model established by dehydroepiandrosterone induction. The crotonylation levels of proteins involved in metabolic processes were significantly decreased in PCOS ovaries compared to control samples. Further investigation showed that decrotonylation of Lon protease 1 (LONP1) at lysine 390 was associated with mitochondrial dysfunction in PCOS. Moreover, LONP1 crotonylation levels in PCOS were correlated with ovarian tissue oxidative stress levels, androgen levels, and oocyte development. Consistently, down-regulation of LONP1 and LONP1 crotonylation levels were also observed in the blood samples of PCOS patients. Collectively, our study revealed a mechanism by which the decrotonylation of LONP1 may attenuate its activity and alter follicular microenvironment to affect oocyte maturation in PCOS.
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Affiliation(s)
- Yuan Xie
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Shuwen Chen
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Zaixin Guo
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Ying Tian
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Xinyu Hong
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Penghui Feng
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Qiu Xie
- Department of Medical Research CenterState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina
| | - Qi Yu
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
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8
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Li S. Novel insight into functions of ascorbate peroxidase in higher plants: More than a simple antioxidant enzyme. Redox Biol 2023; 64:102789. [PMID: 37352686 DOI: 10.1016/j.redox.2023.102789] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/01/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
As plants are sessile organisms, they are inevitably exposed to a variety of environmental stimuli that trigger rapid changes in the generation and disposal of reactive oxygen species such as hydrogen peroxide (H2O2). A major H2O2 scavenging system in plant cells is the ascorbate-glutathione cycle, in which ascorbate peroxidase (APX) catalyzes the conversion of H2O2 into water employing ascorbate as specific electron donor. In higher plants, distinct APX isoforms can occur in multiple subcellular compartments, including chloroplasts, mitochondria, and peroxisomes and the cytosol, to modulate organellar and cellular levels of H2O2. It is well established that APX plays crucial roles in protecting plant cells against diverse environmental stresses, as well as in plant growth and development. Apart from ascorbate, recently, APXs have been found to have a broader substrate specificity and possess chaperone activity, hence participating various biological processes. In this review, we describe the antioxidant properties of APXs and highlight their novel roles beyond 'ascorbate peroxidases'.
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Affiliation(s)
- Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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9
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Zhang N, Wang S, Zhao S, Chen D, Tian H, Li J, Zhang L, Li S, Liu L, Shi C, Yu X, Ren Y, Chen F. Global crotonylatome and GWAS revealed a TaSRT1- TaPGK model regulating wheat cold tolerance through mediating pyruvate. SCIENCE ADVANCES 2023; 9:eadg1012. [PMID: 37163591 PMCID: PMC10171821 DOI: 10.1126/sciadv.adg1012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we reported the complete profiling of the crotonylation proteome in common wheat. Through a combination of crotonylation and multi-omics analysis, we identified a TaPGK associated with wheat cold stress. Then, we confirmed the positive role of TaPGK-modulating wheat cold tolerance. Meanwhile, we found that cold stress induced lysine crotonylation of TaPGK. Moreover, we screened a lysine decrotonylase TaSRT1 interacting with TaPGK and found that TaSRT1 negatively regulated wheat cold tolerance. We subsequently demonstrated TaSRT1 inhibiting the accumulation of TaPGK protein, and this inhibition was possibly resulted from decrotonylation of TaPGK by TaSRT1. Transcriptome sequencing indicated that overexpression of TaPGK activated glycolytic key genes and thereby increased pyruvate content. Moreover, we found that exogenous application of pyruvate sharply enhanced wheat cold tolerance. These findings suggest that the TaSRT1-TaPGK model regulating wheat cold tolerance is possibly through mediating pyruvate. This study provided two valuable cold tolerance genes and dissected diverse mechanism of glycolytic pathway involving in wheat cold stress.
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Affiliation(s)
- Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Sisheng Wang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Simin Zhao
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Daiying Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Hongyan Tian
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Jia Li
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lingran Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Songgang Li
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lu Liu
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Chaonan Shi
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Xiaodong Yu
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
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10
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Guo W, Han J, Li X, He Z, Zhang Y. Large-scale analysis of protein crotonylation reveals its diverse functions in Pinellia ternata. BMC PLANT BIOLOGY 2022; 22:457. [PMID: 36151520 PMCID: PMC9502611 DOI: 10.1186/s12870-022-03835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pinellia ternata is an important traditional medicine in China, and its growth is regulated by the transcriptome or proteome. Lysine crotonylation, a newly identified and important type of posttranslational modification, plays a key role in many aspects of cell metabolism. However, little is known about its functions in Pinellia ternata. RESULTS In this study, we generated a global crotonylome analysis of Pinellia ternata and examined its overlap with lysine succinylation. A total of 2106 crotonylated sites matched on 1006 proteins overlapping in three independent tests were identified, and we found three specific amino acids surrounding crotonylation sites in Pinellia ternata: KcrF, K***Y**Kcr and Kcr****R. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that two crucial alkaloid biosynthesis-related enzymes and many stress-related proteins were also highly crotonylated. Furthermore, several enzymes participating in carbohydrate metabolism pathways were found to exhibit both lysine crotonylation and succinylation modifications. CONCLUSIONS These results indicate that lysine crotonylation performs important functions in many biological processes in Pinellia ternata, especially in the biosynthesis of alkaloids, and some metabolic pathways are simultaneously regulated by lysine crotonylation and succinylation.
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Affiliation(s)
- Weiwei Guo
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Jiayi Han
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Zihan He
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China.
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11
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Yang W, Li X, Jiang G, Long Y, Li H, Yu S, Zhao H, Liu J. Crotonylation versus acetylation in petunia corollas with reduced acetyl-CoA due to PaACL silencing. PHYSIOLOGIA PLANTARUM 2022; 174:e13794. [PMID: 36193016 DOI: 10.1111/ppl.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Protein acetylation and crotonylation are important posttranslational modifications of lysine. In animal cells, the correlation of acetylation and crotonylation has been well characterized and the lysines of some proteins are acetylated or crotonylated depending on the relative concentrations of acetyl-CoA and crotonyl-CoA. However, in plants, the correlation of acetylation and crotonylation and the effects of the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA on protein crotonylation and acetylation are not well known. In our previous study, PaACL silencing changed the content of acetyl-CoA in petunia (Petunia hybrida) corollas, and the effect of PaACL silencing on the global acetylation proteome in petunia was analyzed. In the present study, we found that PaACL silencing did not significantly alter the content of crotonyl-CoA. We performed a global crotonylation proteome analysis of the corollas of PaACL-silenced and control petunia plants; we found that protein crotonylation was closely related to protein acetylation and that proteins with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins were enriched in many common Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. However, PaACL silencing resulted in different KEGG pathway enrichments of proteins with different levels of crotonylation sites and acetylation sites. PaACLB1-B2 silencing did not led to changes in the opposite direction in crotonylation and acetylation levels at the same lysine site in cytoplasmic proteins, which indicated that cytoplasmic lysine acetylation and crotonylation might not depend on the relative concentrations of acetyl-CoA and crotonyl-CoA. Moreover, the global crotonylome and acetylome were weakly positively correlated in the corollas of PaACL-silenced and control plants.
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Affiliation(s)
- Weiyuan Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xin Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guiyun Jiang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yu Long
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Hui Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shujun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Huina Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- College of Horticulture, South China Agricultural University, Guangzhou, China
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12
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Yang X, Lin P, Luo Y, Bai H, Liao X, Li X, Tian Y, Jiang B, Pan Y, Zhang F, Zhang L, Jia Y, Li Y, Liu Q. Lysine decrotonylation of glutathione peroxidase at lysine 220 site increases glutathione peroxidase activity to resist cold stress in chrysanthemum. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113295. [PMID: 35151212 DOI: 10.1016/j.ecoenv.2022.113295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
Lysine crotonylation is a protein post-translational modification that has been newly discovered in recent years. There are few studies on the lysine crotonylation of proteins in plants, and their functions in response to cold stress are still unclear. In this study, the chrysanthemum (Chrysanthemum morifolium Ramat.) glutathione peroxidase (GPX) gene was selected and named DgGPX1, and was found to be responsive to low temperature. Overexpression of DgGPX1 improved the cold resistance of transgenic chrysanthemum by increasing GPX activity to reduce the accumulation of reactive oxygen species (ROS) under low-temperature conditions. Furthermore, the level of DgGPX1 lysine crotonylation at lysine (K) 220 decreased under low temperature in chrysanthemum. Lysine decrotonylation of DgGPX1 at K220 further increased GPX activity to reduce ROS accumulation under cold stress, and thereby enhanced the cold resistance of chrysanthemum. The above results show that lysine decrotonylation of DgGPX1 at K220 increases GPX activity to resist cold stress in chrysanthemum.
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Affiliation(s)
- Xiaohan Yang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Ping Lin
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Yunchen Luo
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Huiru Bai
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Xiaoqin Liao
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Xin Li
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Yuchen Tian
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Beibei Jiang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Yuanzhi Pan
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Fan Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Yin Jia
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
| | - Yan Li
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou, China.
| | - Qinglin Liu
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China.
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13
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Wu J, Meng X, Jiang W, Wang Z, Zhang J, Meng F, Yao X, Ye M, Yao L, Wang L, Yu N, Peng D, Xing S. Qualitative Proteome-Wide Analysis Reveals the Diverse Functions of Lysine Crotonylation in Dendrobium huoshanense. FRONTIERS IN PLANT SCIENCE 2022; 13:822374. [PMID: 35251091 PMCID: PMC8888884 DOI: 10.3389/fpls.2022.822374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
The lysine crotonylation of histone proteins is a newly identified posttranslational modification with diversified cellular functions. However, there are few reports on lysine crotonylation of non-histone proteins in medicinal plant cells. By using high-resolution liquid chromatography-mass spectrometry (LC-MS) coupled with highly sensitive-specific immune-affinity antibody analysis, a whole crotonylation proteome analysis of Dendrobium huoshanense was performed. In total, 1,591 proteins with 4,726 lysine crotonylation sites were identified; among them, 11 conserved motifs were identified. Bioinformatic analyses linked crotonylated proteins to the drought stress response and multiple metabolic pathways, including secondary metabolite biosynthesis, transport and catabolism, energy production and conversion, carbohydrate transport and metabolism, translation, and ribosomal structure and biogenesis. This study contributes toward understanding the regulatory mechanism of polysaccharide biosynthesis at the crotonylation level even under abiotic stress.
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Affiliation(s)
- Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, United States
| | - Weimin Jiang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, China
| | - Zhaojian Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jing Zhang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaoyan Yao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Mengjuan Ye
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Liang Yao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Longhai Wang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Nianjun Yu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, China
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14
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Chen Y, Zou H, Yan B, Wu X, Cao W, Qian Y, Zheng L, Yang G. Atomically Dispersed Cu Nanozyme with Intensive Ascorbate Peroxidase Mimic Activity Capable of Alleviating ROS-Mediated Oxidation Damage. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103977. [PMID: 34951150 PMCID: PMC8844488 DOI: 10.1002/advs.202103977] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/08/2021] [Indexed: 05/03/2023]
Abstract
Ascorbate peroxidase (APX) as a crucial antioxidant enzyme has drawn attentions for its utilization in preventing cells from oxidative stress responses by efficiently scavenging H2 O2 in plants. For eliminating the specific inactivation of natural APXs and regulating the catalytic activity, single-atom nanozymes are considered as promising classes of alternatives with similar active sites and maximal atomic utilization efficiency to natural APXs. Herein, graphitic carbon nitride (g-C3 N4 ) anchored with isolated single copper atoms (Cu SAs/CN) is designed as an efficient nanozyme with intrinsic APX mimetic behavior. The engineered Cu SAs/CN exhibits comparable specific activity and kinetics to the natural APXs. Based on the density functional theory (DFT), Cu-N4 moieties in the active center of Cu SAs/CN are determined to exert such favorable APX catalytic performance, in which the electron transfer between Cu and coordinated N atoms facilitates the activation and cleavage of the adsorbed H2 O2 molecules and results in fast kinetics. The constructed Cu SAs/CN nanozyme with superior APX-like performance and high biocompatibility can be applied for effectively protecting the H2 O2 -treated cells against oxidative injury in vitro. These findings report the single-atom nanozymes as a successful paradigm for guiding nanozymes to implement APX mimetic performance for reactive oxygen species-related biotherapeutic.
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Affiliation(s)
- Yuan Chen
- State Key Laboratory of Optoelectronic Materials and TechnologiesNanotechnology Research CenterSchool of Materials Science and EngineeringSchool of PhysicsSun Yat‐sen UniversityGuangzhouGuangdong510275P. R. China
| | - Hang Zou
- Department of Laboratory MedicineNanfang Hospital, Southern Medical University/The First School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdong510515P. R. China
| | - Bo Yan
- State Key Laboratory of Optoelectronic Materials and TechnologiesNanotechnology Research CenterSchool of Materials Science and EngineeringSchool of PhysicsSun Yat‐sen UniversityGuangzhouGuangdong510275P. R. China
| | - Xiaoju Wu
- State Key Laboratory of Optoelectronic Materials and TechnologiesNanotechnology Research CenterSchool of Materials Science and EngineeringSchool of PhysicsSun Yat‐sen UniversityGuangzhouGuangdong510275P. R. China
| | - Weiwei Cao
- State Key Laboratory of Optoelectronic Materials and TechnologiesNanotechnology Research CenterSchool of Materials Science and EngineeringSchool of PhysicsSun Yat‐sen UniversityGuangzhouGuangdong510275P. R. China
| | - Yihang Qian
- State Key Laboratory of Optoelectronic Materials and TechnologiesNanotechnology Research CenterSchool of Materials Science and EngineeringSchool of PhysicsSun Yat‐sen UniversityGuangzhouGuangdong510275P. R. China
| | - Lei Zheng
- Department of Laboratory MedicineNanfang Hospital, Southern Medical University/The First School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdong510515P. R. China
| | - Guowei Yang
- State Key Laboratory of Optoelectronic Materials and TechnologiesNanotechnology Research CenterSchool of Materials Science and EngineeringSchool of PhysicsSun Yat‐sen UniversityGuangzhouGuangdong510275P. R. China
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15
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Comprehensive Profiling of Paper Mulberry ( Broussonetia papyrifera) Crotonylome Reveals the Significance of Lysine Crotonylation in Young Leaves. Int J Mol Sci 2022; 23:ijms23031173. [PMID: 35163093 PMCID: PMC8834973 DOI: 10.3390/ijms23031173] [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: 12/16/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/01/2023] Open
Abstract
Lysine crotonylation is a newly discovered and reversible posttranslational modification involved in various biological processes, especially metabolism regulation. A total of 5159 lysine crotonylation sites in 2272 protein groups were identified. Twenty-seven motifs were found to be the preferred amino acid sequences for crotonylation sites. Functional annotation analyses revealed that most crotonylated proteins play important roles in metabolic processes and photosynthesis. Bioinformatics analysis suggested that lysine crotonylation preferentially targets a variety of important biological processes, including ribosome, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, proteasome and the TCA cycle, indicating lysine crotonylation is involved in the common mechanism of metabolic regulation. A protein interaction network analysis revealed that diverse interactions are modulated by protein crotonylation. These results suggest that lysine crotonylation is involved in a variety of biological processes. HSP70 is a crucial protein involved in protecting plant cells and tissues from thermal or abiotic stress responses, and HSP70 protein was found to be crotonylated in paper mulberry. This systematic analysis provides the first comprehensive analysis of lysine crotonylation in paper mulberry and provides important resources for further study on the regulatory mechanism and function of the lysine crotonylated proteome.
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Lysine crotonylation: A challenging new player in the epigenetic regulation of plants. J Proteomics 2022; 255:104488. [DOI: 10.1016/j.jprot.2022.104488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/20/2022]
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17
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Jiang G, Li C, Lu M, Lu K, Li H. Protein lysine crotonylation: past, present, perspective. Cell Death Dis 2021; 12:703. [PMID: 34262024 PMCID: PMC8280118 DOI: 10.1038/s41419-021-03987-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 02/08/2023]
Abstract
Lysine crotonylation has been discovered in histone and non-histone proteins and found to be involved in diverse diseases and biological processes, such as neuropsychiatric disease, carcinogenesis, spermatogenesis, tissue injury, and inflammation. The unique carbon–carbon π-bond structure indicates that lysine crotonylation may use distinct regulatory mechanisms from the widely studied other types of lysine acylation. In this review, we discussed the regulation of lysine crotonylation by enzymatic and non-enzymatic mechanisms, the recognition of substrate proteins, the physiological functions of lysine crotonylation and its cross-talk with other types of modification. The tools and methods for prediction and detection of lysine crotonylation were also described.
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Affiliation(s)
- Gaoyue Jiang
- West China Second University Hospital, State Key Laboratory of Biotherapy, and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China
| | - Chunxia Li
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Meng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China.
| | - Huihui Li
- West China Second University Hospital, State Key Laboratory of Biotherapy, and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China.
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