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Abstract
Lysine acylation, a type of posttranslational protein modification sensitive to cellular metabolic states, influences the functions of target proteins involved in diverse cellular processes. Particularly, lysine butyrylation, crotonylation, β-hydroxybutyrylation, and 2-hydroxyisobutyrylation, four types of four-carbon acylations, are modulated by intracellular concentrations of their respective acyl-CoAs and sensitive to alterations of nutrient metabolism induced by cellular and/or environmental signals. In this review, we discussed the metabolic pathways producing these four-carbon acyl-CoAs, the regulation of lysine acylation and deacylation, and the functions of individual lysine acylation.
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Affiliation(s)
- Yi Fang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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Yang D, Li X, Yu B, Peng H. Qualitative lysine crotonylation and 2-hydroxyisobutyrylation analysis in the ovarian tissue proteome of piglets. Front Cell Dev Biol 2023; 11:1176212. [PMID: 37255595 PMCID: PMC10225730 DOI: 10.3389/fcell.2023.1176212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023] Open
Abstract
Ovarian function influences diverse aspects of fertility and reproductive lifespan by regulating oocyte supply and hormone secretion. Lysine crotonylation (Kcr) and lysine 2-hydroxyisobutyryllysine (Khib) are newly identified post-translational modifications and function as regulators of transactivation in mammals. In this study, we investigated protein post-translational Kcr and 2-hydroxyisobutyrylation in the ovarian tissues of piglets. A total of 653 overlapping proteins among differentially modified proteins were identified for both crotonylation and 2-hydroxyisobutyrylation. Gene Ontology enrichment analysis indicated that 653 DMPs were significantly enriched in nucleosome organization, chromatin assembly, DNA packaging, peptide biosynthetic process and peptide metabolic process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed enrichment in proteasome, ribosome, fatty acid elongation, pyruvate metabolism and pentose phosphate pathway. Fifteen DMPs were identified in the proteasome pathway, of which PSMC6 and PSMB7 were the core proteins. In addition, the significant changes in Kcr and Khib in the complex subunits of the proteasome may be involved in cell cycle processes during oocyte development. Forty-four DMPs with both Kcr and Khib modifications were related to the ribosome pathway. The regulated ribosome pathway may indicate that Kcr and Khib comodified proteins participate in protein synthesis during oocyte development. Western blot and immunofluorescence staining results supported the reliability of the sequencing results. Our results may provide a valuable resource to help illuminate the roles of Kcr and Khib in ovarian development and may serve as new tools to better control diseases.
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Zhao LN, Yuan HF, Wang YF, Yun HL, Zheng W, Yuan Y, Geng Y, Zhao M, Feng LY, Zhang XD. IFN-α inhibits HBV transcription and replication by promoting HDAC3-mediated de- 2-hydroxyisobutyrylation of histone H4K8 on HBV cccDNA minichromosome in liver. Acta Pharmacol Sin 2022; 43:1484-94. [PMID: 34497374 DOI: 10.1038/s41401-021-00765-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
The epigenetic modification of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) plays a crucial role in cccDNA transcription and viral persistence. Interferon-α (IFN-α) is a pivotal agent against HBV cccDNA. However, the mechanism by which IFN-α modulates the epigenetic regulation of cccDNA remains poorly understood. In this study, we report that IFN-α2b enhances the histone deacetylase 3 (HDAC3)-mediated de-2-hydroxyisobutyrylation of histone H4 lysine 8 (H4K8) on HBV cccDNA minichromosome to restrict the cccDNA transcription in liver. By screening acetyltransferases and deacetylases, we identified that HDAC3 was an effective restrictor of HBV transcription and replication. Moreover, we found that HDAC3 was able to mediate the de-2-hydroxyisobutyrylation of H4K8 in HBV-expressing hepatoma cells. Then, the 2-hydroxyisobutyrylation of histone H4K8 (H4K8hib) was identified on the HBV cccDNA minichromosome, promoting the HBV transcription and replication. The H4K8hib was regulated by HDAC3 depending on its deacetylase domain in the system. The low level of HDAC3 and high level of H4K8hib were observed in the liver tissues from HBV-infected human liver-chimeric mice. The levels of H4K8hib on HBV cccDNA minichromosome were significantly elevated in the liver biopsy specimens from clinical hepatitis B patients, which was consistent with the high transcriptional activity of cccDNA. Strikingly, IFN-α2b effectively facilitated the histone H4K8 de-2-hydroxyisobutyrylation mediated by HDAC3 on the HBV cccDNA minichromosome in primary human hepatocytes and hepatoma cells, leading to the inhibition of HBV transcription and replication. Our finding provides new insights into the mechanism by which IFN-α modulates the epigenetic regulation of HBV cccDNA minichromosome.
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Zhang X, Chen J, Dong Q, Zhu J, Peng R, He C, Li Y, Lin R, Jiang P, Zheng M, Zhang H, Liu S, Chen Z. Lysine Acylation Modification Landscape of Brucella abortus Proteome and its Virulent Proteins. Front Cell Dev Biol 2022; 10:839822. [PMID: 35300419 PMCID: PMC8921143 DOI: 10.3389/fcell.2022.839822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The myriad of posttranslational modifications (PTMs) of proteins that occur in all living cells are crucial to all kinds of biological processes. Brucella is an intracellular parasitic bacterium that can cause chronic diseases in both humans and livestock. To reveal the relationship between PTMs and the virulence and survival of Brucella, we described the first comprehensive multiple PTM-omics atlas of B. abortus 2308. Five PTMs involving lysine, namely 2-hydroxyisobutyrylation, succinylation, crotonylation, acetylation, and malonylation were identified. Nearly 2,000 modified proteins were observed, and these proteins took part in many biological processes, with a variety of molecular functions. In addition, we detected many significant virulence factors of Brucella among the modified proteins. 10 of the 15 T4SS effector proteins were detected with one or more PTMs. Moreover, abundant PTMs were detected in other typical virulence factors. Considering the role of PTMs in various biological processes of Brucella virulence and survival, we propose that the virulence of Brucella is associated with the PTMs of proteins. Taken together, this study provides the first global survey of PTMs in Brucella. This is a prospective starting point for further functional analysis of PTMs during the survival of Brucella in hosts, interpretation of the function of Brucella proteins, and elucidation of the pathogenic mechanism of Brucella.
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Affiliation(s)
- Xi Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Jingjing Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Qiao Dong
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Jinying Zhu
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Ruihao Peng
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Chuanyu He
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Yuzhuo Li
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Ruiqi Lin
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Pengfei Jiang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Min Zheng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Huan Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Shiwei Liu
- Department of Nephrology and Endocrinology, Wangjing Hospital, Chinese Academy of Chinese Medical Science, Beijing, China
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China.,Department of Nephrology and Endocrinology, Wangjing Hospital, Chinese Academy of Chinese Medical Science, Beijing, China.,Innovative Institute of Zoonoses, Medical College, Inner Mongolia Minzu University, Tongliao, China
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Zhu W, Jiang X, Sun H, Li Y, Shi W, Zheng M, Liu D, Ma A, Feng X. Global Lysine Acetylation and 2-Hydroxyisobutyrylation Profiling Reveals the Metabolism Conversion Mechanism in Giardia lamblia. Mol Cell Proteomics 2021; 20:100043. [PMID: 33376196 PMCID: PMC8724866 DOI: 10.1074/mcp.ra120.002353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/01/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022] Open
Abstract
Giardia lamblia (G. lamblia) is the cause of giardiasis, a common infection that affects the general population of the world. Despite the constant possibility of damage because of their own metabolism, G. lamblia has survived and evolved to adapt to various environments. However, research on energy-metabolism conversion in G. lamblia is limited. This study aimed to reveal the dynamic metabolism conversion mechanism in G. lamblia under sugar starvation by detecting global lysine acetylation (Kac) and 2-hydroxyisobutyrylation (Khib) sites combined with quantitative proteome analyses. A total of 2999 acetylation sites on 956 proteins and 8877 2-hydroxyisobutyryl sites on 1546 proteins were quantified under sugar starvation. Integrated Kac and Khib data revealed that modified proteins were associated with arginine biosynthesis, glycolysis/gluconeogenesis, and alanine, aspartate, and glutamate metabolisms. These findings suggest that Kac and Khib were ubiquitous and provide deep insight into the metabolism conversion mechanism in G. lamblia under sugar starvation. Overall, these results can help delineate the biology of G. lamblia infections and reveal the evolutionary rule from prokaryote to eukaryote.
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Affiliation(s)
- Wenhe Zhu
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Xiaoming Jiang
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Hongyu Sun
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Yawei Li
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Wenyan Shi
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Meiyu Zheng
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Di Liu
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Aixin Ma
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Xianmin Feng
- Academy of Basic Medicine, Jilin Medical University, Jilin, China.
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Ou M, Li C, Tang D, Xue W, Xu Y, Zhu P, Li B, Xie J, Chen J, Sui W, Yin L, Dai Y. Genotyping, generation and proteomic profiling of the first human autosomal dominant osteopetrosis type II-specific induced pluripotent stem cells. Stem Cell Res Ther 2019; 10:251. [PMID: 31412925 PMCID: PMC6693165 DOI: 10.1186/s13287-019-1369-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022] Open
Abstract
Background Autosomal dominant osteopetrosis type II (ADO2) is a rare human genetic disease that has been broadly studied as an important osteopetrosis model; however, there are no disease-specific induced pluripotent stem cells (ADO2-iPSCs) that may be valuable for understanding the pathogenesis and may be a potential source of cells for autologous cell-based therapies. Methods To generate the first human ADO2-iPSCs from a Chinese family with ADO2 and to identify their characteristics, blood samples were collected from the proband and his parents and were used for genotyping by whole-exome sequencing (WES); the urine-derived cells of the proband were reprogrammed with episomal plasmids that contained transcription factors, such as KLF4, OCT4, c-MYC, and SOX2. The proteome-wide protein quantification and lysine 2-hydroxyisobutyrylation detection of the ADO2-iPSCs and normal control iPSCs (NC-iPSCs) were performed by high-resolution LC-MS/MS and bioinformatics analysis. Results WES with filtering strategies identified a mutation in CLCN7 (R286W) in the proband and his father, which was absent in the proband’s mother and the healthy controls; this was confirmed by Sanger sequencing. The ADO2-iPSCs were successfully generated, which carried a normal male karyotype (46, XY) and the mutation of CLCN7 (R286W); the ADO2-iPSCs positively expressed alkaline phosphatase and other surface markers; and no vector and transgene were detected. The ADO2-iPSCs could differentiate into all three germ cell layers, both in vitro and in vivo. The proteomic profiling revealed similar expression of pluripotency markers in the two cell lines and identified 7405 proteins and 3664 2-hydroxyisobutyrylated peptides in 1036 proteins in the ADO2-iPSCs. Conclusions Our data indicated that the mutation CLCN7 (R286W) may be a cause of the osteopetrosis family. The generated vector-free and transgene-free ADO2-iPSCs with known proteomic characteristics may be valuable for personalized and cell-based regenerative medicine in the future. Electronic supplementary material The online version of this article (10.1186/s13287-019-1369-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Minglin Ou
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, China.,Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin No. 181 Hospital, No. 1, Xinqiaoyuan Road, Guilin, 541002, China
| | - Chunhong Li
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, China.,Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin No. 181 Hospital, No. 1, Xinqiaoyuan Road, Guilin, 541002, China.,College of Life Science, Guangxi Normal University, Guilin, 541004, China
| | - Donge Tang
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, China.,Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin No. 181 Hospital, No. 1, Xinqiaoyuan Road, Guilin, 541002, China
| | - Wen Xue
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin No. 181 Hospital, No. 1, Xinqiaoyuan Road, Guilin, 541002, China
| | - Yong Xu
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, China
| | - Peng Zhu
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, China
| | - Bo Li
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, China
| | - Jiansheng Xie
- Shenzen Maternity & Child Healthcare Hospital, Shenzhen, 518017, China
| | - Jiejing Chen
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin No. 181 Hospital, No. 1, Xinqiaoyuan Road, Guilin, 541002, China
| | - Weiguo Sui
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin No. 181 Hospital, No. 1, Xinqiaoyuan Road, Guilin, 541002, China
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Yong Dai
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, China. .,Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin No. 181 Hospital, No. 1, Xinqiaoyuan Road, Guilin, 541002, China.
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Wu Q, Ke L, Wang C, Fan P, Wu Z, Xu X. Global Analysis of Lysine 2-Hydroxyisobutyrylome upon SAHA Treatment and Its Relationship with Acetylation and Crotonylation. J Proteome Res 2018; 17:3176-3183. [PMID: 30109935 DOI: 10.1021/acs.jproteome.8b00289] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysine 2-hydroxyisobutyrylation is a newly discovered protein acylation and was reported to share acyltransferases and deacylases with the widely studied lysine acetylation. The well-known acetyltransferase Tip60 and histone deacetylases HDAC 2 and HDAC 3 were discovered to be "writer" and "eraser" of this new PTM on histones. However, the acyltransferases and deacylases for nonhistone proteins are still unclear. In this work, lysine 2-hydroxyisobutyrylome on both histones and nonhistone proteins upon SAHA treatment were intensively studied and 8765 lysine 2-hydroxyisobutyrylation sites on 2484 proteins were identified in A549 cells. This is the largest data set of lysine 2-hydroxyisobutyrylome in mammalian cells to date. It was found that lysine 2-hydroxyisobutyrylation participates in varieties of biological functions and processes including ribosome, glycolysis/gluconeogenesis, and transcription. More importantly, it was found that most quantified sites on core histones were up-regulated upon SAHA treatment for all 2-hydroxyisobutyrylation, crotonylation, and acetylation and the fold changes upon SAHA of 2-hydroxyisobutyrylation and crotonylation on nonhistone proteins were highly correlated, while their fold changes have little correlations with acetylation on nonhistone proteins.
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Affiliation(s)
- Quan Wu
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China.,Department of Microbiology and Immunobiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Li Ke
- Department of Thoracic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Chi Wang
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Pingsheng Fan
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Zhiwei Wu
- Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
| | - Xiaoling Xu
- Department of Respiration, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine , University of Science and Technology of China , Hefei , Anhui 230001 , P. R. China
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