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Zheng H, Mei H, Li X, Li D, Liu W. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Aspergillus fumigatus. Curr Microbiol 2024; 81:74. [PMID: 38253771 PMCID: PMC10803526 DOI: 10.1007/s00284-023-03565-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024]
Abstract
Aspergillus fumigatus is the significant causative agent in cases of invasive aspergillosis, leading to a high mortality rate in immunocompromised patients. A comprehensive understanding of its growth patterns and metabolic processes within the host is a critical prerequisite for the development of effective antifungal strategies. Lysine 2-hydroxyisobutyrylation (Khib) is a highly conserved protein posttranslational modifications (PTM) found in various organisms. In this study, we investigate the biological impact of Khib in A. fumigatus. Using a combination of antibody enrichment with the conventional LC-MS/MS method, the pattern of Khib-modification in proteins and their respective sites were analyzed in a wild type strain of A. fumigatus. Our findings revealed 3494 Khib-modified proteins with a total of 18,091 modified sites in this strain. Functional enrichment analysis indicated that these Khib-modified proteins participate in a diverse range of cellular functions, spanning various subcellular locations such as ribosome biosynthesis, protein synthesis and nucleocytoplasmic transport. Notably, when compared with other reported eukaryotes, A. fumigatus exhibited consistently higher numbers of Khib-modified proteins, suggesting the potential significance of this modification in this organism. An interesting observation is the prevalence of Khib modifications in most enzymes involved in the ergosterol synthesis pathway. The insights gathered from this study provide new avenue for studying PTM-associated mechanisms in fungal growth and offer potential implication for antifungal drug development.
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Affiliation(s)
- Hailin Zheng
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, 210042, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, Jiangsu, People's Republic of China
| | - Huan Mei
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, 210042, Jiangsu, People's Republic of China
| | - Xiaofang Li
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, 210042, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, Jiangsu, People's Republic of China
| | - Dongmei Li
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Weida Liu
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, 210042, Jiangsu, People's Republic of China.
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, Jiangsu, People's Republic of China.
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Deng B, Vanagas L, Alonso AM, Angel SO. Proteomics Applications in Toxoplasma gondii: Unveiling the Host-Parasite Interactions and Therapeutic Target Discovery. Pathogens 2023; 13:33. [PMID: 38251340 PMCID: PMC10821451 DOI: 10.3390/pathogens13010033] [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: 11/13/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
Toxoplasma gondii, a protozoan parasite with the ability to infect various warm-blooded vertebrates, including humans, is the causative agent of toxoplasmosis. This infection poses significant risks, leading to severe complications in immunocompromised individuals and potentially affecting the fetus through congenital transmission. A comprehensive understanding of the intricate molecular interactions between T. gondii and its host is pivotal for the development of effective therapeutic strategies. This review emphasizes the crucial role of proteomics in T. gondii research, with a specific focus on host-parasite interactions, post-translational modifications (PTMs), PTM crosstalk, and ongoing efforts in drug discovery. Additionally, we provide an overview of recent advancements in proteomics techniques, encompassing interactome sample preparation methods such as BioID (BirA*-mediated proximity-dependent biotin identification), APEX (ascorbate peroxidase-mediated proximity labeling), and Y2H (yeast two hybrid), as well as various proteomics approaches, including single-cell analysis, DIA (data-independent acquisition), targeted, top-down, and plasma proteomics. Furthermore, we discuss bioinformatics and the integration of proteomics with other omics technologies, highlighting its potential in unraveling the intricate mechanisms of T. gondii pathogenesis and identifying novel therapeutic targets.
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Affiliation(s)
- Bin Deng
- Department of Biology and VBRN Proteomics Facility, University of Vermont, Burlington, VT 05405, USA
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
| | - Andres M. Alonso
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
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Yin D, Jiang N, Cheng C, Sang X, Feng Y, Chen R, Chen Q. Protein Lactylation and Metabolic Regulation of the Zoonotic Parasite Toxoplasma gondii. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1163-1181. [PMID: 36216028 PMCID: PMC11082259 DOI: 10.1016/j.gpb.2022.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 09/06/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
The biology of Toxoplasma gondii, the causative pathogen of one of the most widespread parasitic diseases (toxoplasmosis), remains poorly understood. Lactate, which is derived from glucose metabolism, is not only an energy source in a variety of organisms, including T. gondii, but also a regulatory molecule that participates in gene activation and protein function. Lysine lactylation (Kla) is a type of post-translational modifications (PTMs) that has been recently associated with chromatin remodeling; however, Kla of histone and non-histone proteins has not yet been studied in T. gondii. To examine the prevalence and function of lactylation in T. gondii parasites, we mapped the lactylome of proliferating tachyzoite cells and identified 1964 Kla sites on 955 proteins in the T. gondii RH strain. Lactylated proteins were distributed in multiple subcellular compartments and were closely related to a wide variety of biological processes, including mRNA splicing, glycolysis, aminoacyl-tRNA biosynthesis, RNA transport, and many signaling pathways. We also performed a chromatin immunoprecipitation sequencing (ChIP-seq) analysis using a lactylation-specific antibody and found that the histones H4K12la and H3K14la were enriched in the promoter and exon regions of T. gondii associated with microtubule-based movement and cell invasion. We further confirmed the delactylase activity of histone deacetylases TgHDAC2-4, and found that treatment with anti-histone acetyltransferase (TgMYST-A) antibodies profoundly reduced protein lactylation in T. gondii. This study offers the first dataset of the global lactylation proteome and provides a basis for further dissecting the functional biology of T. gondii.
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Affiliation(s)
- Deqi Yin
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110166, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang 110866, China
| | - Ning Jiang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110166, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang 110866, China
| | - Chang Cheng
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110166, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang 110866, China
| | - Xiaoyu Sang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110166, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang 110866, China
| | - Ying Feng
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110166, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang 110866, China
| | - Ran Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110166, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang 110866, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110166, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang 110866, China.
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Zhang N, Wang S, Tian H, Li S, Liu L, Li J, Chen D, Zhao S, Yan X, Niaz M, Zhao L, Ren Y, Chen F. Functions of lysine 2-hydroxyisobutyrylation and future perspectives on plants. Proteomics 2023; 23:e2300045. [PMID: 37338329 DOI: 10.1002/pmic.202300045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel protein post-translational modifications (PTMs) observed in both eukaryotes and prokaryotes. Recent studies suggested that this novel PTM has the potential to regulate different proteins in various pathways. Khib is regulated by lysine acyltransferases and deacylases. This novel PTM reveals interesting connections between modifications and protein physiological functions, including gene transcription, glycolysis and cell growth, enzymic activity, sperm motility, and aging. Here, we review the discovery and the current understanding of this PTM. Then, we outline the networks of complexity of interactions among PTMs in plants, and raise possible directions of this novel PTM for future investigations in plants.
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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
| | - 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
| | - 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
| | - Lulu 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
| | - Jiaqi 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
| | - 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
| | - 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
| | - Xiangning Yan
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Mohsin Niaz
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lei 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
| | - 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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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] [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 W, Ren TH, Zhou YZ, Liu SB, Huang XY, Ning TY, Li G. Proteomic analysis of protein lysine 2-hydroxyisobutyrylation (K hib) in soybean leaves. BMC PLANT BIOLOGY 2023; 23:23. [PMID: 36631736 PMCID: PMC9835227 DOI: 10.1186/s12870-022-04033-6] [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: 09/14/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Protein lysine 2-hydroxyisobutyrylation (Khib) is a novel post-translational modification (PTM) discovered in cells or tissues of animals, microorganisms and plants in recent years. Proteome-wide identification of Khib-modified proteins has been performed in several plant species, suggesting that Khib-modified proteins are involved in a variety of biological processes and metabolic pathways. However, the protein Khib modification in soybean, a globally important legume crop that provides the rich source of plant protein and oil, remains unclear. RESULTS In this study, the Khib-modified proteins in soybean leaves were identified for the first time using affinity enrichment and high-resolution mass spectrometry-based proteomic techniques, and a systematic bioinformatics analysis of these Khib-modified proteins was performed. Our results showed that a total of 4251 Khib sites in 1532 proteins were identified as overlapping in three replicates (the raw mass spectrometry data are available via ProteomeXchange with the identifier of PXD03650). These Khib-modified proteins are involved in a wide range of cellular processes, particularly enriched in biosynthesis, central carbon metabolism and photosynthesis, and are widely distributed in subcellular locations, mainly in chloroplasts, cytoplasm and nucleus. In addition, a total of 12 sequence motifs were extracted from all identified Khib peptides, and a basic amino acid residue (K), an acidic amino acid residue (E) and three aliphatic amino acid residues with small side chains (G/A/V) were found to be more preferred around the Khib site. Furthermore, 16 highly-connected clusters of Khib proteins were retrieved from the global PPI network, which suggest that Khib modifications tend to occur in proteins associated with specific functional clusters. CONCLUSIONS These findings suggest that Khib modification is an abundant and conserved PTM in soybean and that this modification may play an important role in regulating physiological processes in soybean leaves. The Khib proteomic data obtained in this study will help to further elucidate the regulatory mechanisms of Khib modification in soybean in the future.
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Affiliation(s)
- Wei Zhao
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Ting-Hu Ren
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Yan-Zheng Zhou
- Jining Academy of Agricultural Sciences, Jining, Shandong 272075 People’s Republic of China
| | - Sheng-Bo Liu
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Xin-Yang Huang
- Jining Academy of Agricultural Sciences, Jining, Shandong 272075 People’s Republic of China
| | - Tang-Yuan Ning
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Geng Li
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
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Wang J, Liang L, Wei S, Zhang S, Hu Y, Lv Y. Histone 2-Hydroxyisobutyryltransferase Encoded by Afngg1 Is Involved in Pathogenicity and Aflatoxin Biosynthesis in Aspergillus flavus. Toxins (Basel) 2022; 15:7. [PMID: 36668827 PMCID: PMC9861817 DOI: 10.3390/toxins15010007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Aflatoxin, a carcinogenic secondary metabolite produced by Aspergillus flavus, is a significant threat to human health and agricultural production. Histone 2-hydroxyisobutyrylation is a novel post-translational modification that regulates various biological processes, including secondary metabolism. In this study, we identified the novel histone 2-hydroxyisobutyryltransferase Afngg1 in A. flavus, and explored its role in cell growth, development and aflatoxin biosynthesis. Afngg1 gene deletion markedly decreased lysine 2-hydroxyisobutyrylation modification of histones H4K5 and H4K8 compared with the control strain. Additionally, Afngg1 deletion inhibited mycelial growth of A. flavus, and the number of conidia and hydrophobicity were significantly decreased. Notably, aflatoxin B1 biosynthesis and sclerotia production were completely inhibited in the ΔAfngg1 strain. Furthermore, the pathogenicity of the ΔAfngg1 strain infecting peanut and corn grains was also diminished, including reduced spore production and aflatoxin biosynthesis compared with A. flavus control and Afngg1 complementation strains. Transcriptome analysis showed that, compared with control strains, differentially expressed genes in ΔAfngg1 were mainly involved in chromatin remodelling, cell development, secondary metabolism and oxidative stress. These results suggest that Afngg1 is involved in histone 2-hydroxyisobutyrylation and chromatin modification, and thus affects cell development and aflatoxin biosynthesis in A. flavus. Our results lay a foundation for in-depth research on the 2-hydroxyisobutyrylation modification in A. flavus, and may provide a novel target for aflatoxin contamination prevention.
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Affiliation(s)
- Jing Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Liuke Liang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Shan Wei
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Shuaibing Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Yuansen Hu
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
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Zhang K, Xu X, Guo X, Ding S, Gu T, Qin L, He Z. Sugarcane Streak Mosaic Virus P1 Attenuates Plant Antiviral Immunity and Enhances Potato Virus X Infection in Nicotiana benthamiana. Cells 2022; 11:cells11182870. [PMID: 36139443 PMCID: PMC9497147 DOI: 10.3390/cells11182870] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/06/2022] [Accepted: 09/10/2022] [Indexed: 12/05/2022] Open
Abstract
The sugarcane streak mosaic virus (SCSMV) is the most important disease in sugarcane produced in southern China. The SCSMV encoded protein 1 (P1SCSMV) is important in disease development, but little is known about its detailed functions in plant–virus interactions. Here, the differential accumulated proteins (DAPs) were identified in the heterologous expression of P1SCSMV via a potato virus X (PVX)-based expression system, using a newly developed four-dimensional proteomics approach. The data were evaluated for credibility and reliability using qRT-RCR and Western blot analyses. The physiological response caused by host factors that directly interacted with the PVX-encoded proteins was more pronounced for enhancing the PVX accumulation and pathogenesis in Nicotiana benthamiana. P1SCSMV reduced photosynthesis by damaging the photosystem II (PSII). Overall, P1SCSMV promotes changes in the physiological status of its host by up- or downregulating the expression of host factors that directly interact with the viral proteins. This creates optimal conditions for PVX replication and movement, thereby enhancing its accumulation levels and pathogenesis. Our investigation is the first to supply detailed evidence of the pathogenesis-enhancing role of P1SCSMV, which provides a deeper understanding of the mechanisms behind virus–host interactions.
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Affiliation(s)
- Kun Zhang
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Xiaowei Xu
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Xiao Guo
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Shiwen Ding
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Tianxiao Gu
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Lang Qin
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Zhen He
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-1529-8450-157
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Ding C, Song L, Li Y, Shen L, Liu D, Wang F, Lin Z, Yang J. Proteome-wide analysis of lysine 2-hydroxyisobutyrylation in Frankliniella occidentalis. BMC Genomics 2022; 23:621. [PMID: 36038823 PMCID: PMC9422105 DOI: 10.1186/s12864-022-08841-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lysine 2-hydroxyisobutyrylation (Khib) is a novel and conserved post-translational modification (PTM). Frankliniella occidentalis are economically important agricultural pests globally and also notorious for vectoring destructive plant viruses. To better study the disease transmission mechanism of F. occidentalis, it is necessary to conduct in-depth analysis of it. So far, no Khib modification of insects has been reported. RESULTS In this study, a proteome-wide analysis of Khib modifications in F. occidentalis was analyzed for the first time through the combination of high performance liquid chromatography fractionation technology and 2-hydroxyisobutyrylated peptide enrichment and other advanced technologies, 4093 Khib sites were identified on 1125 modified proteins. Bioinformatics and functional enrichment analyses showed that Khib-modified proteins were significantly enriched in many cell compartments and pathways, especially related to various cellular components and biological processes, and were more concentrated in ribosomes and proteasome subunits, involved in energy metabolism, protein synthesis and degradation, compared to the other nine species including Japonica rice, Homo sapiens, P. patens, Botrytis, Ustilaginoidea virens, Saccharomyces cerevisiae, T. gondii, C. albicans, and F. oxysporum. And Khib sites on virus-interacting insect proteins were discovered for the first time, such as cyclophilin and endoCP-GN. CONCLUSIONS After three repeated experiments, we found a total of 4093 Khib sites on 1125 proteins. These modified proteins are mainly concentrated in ribosomes and proteasome subunits, and are widely involved in a variety of critical biological activities and metabolic processes of F. occidentalis. In addition, for the first time, Khib modification sites are found on the proteome of F. occidentalis, and these sites could be acted as for the virus interaction, including cyclophilin and endoCP-GN. The global map of 2-hydroxyisobutyrylation in thrips is an invaluable resource to better understand the biological processes of thrips and provide new means for disease control and mitigation of pest damage to crops.
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Affiliation(s)
- Chengying Ding
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Liyun Song
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Dongyang Liu
- Liangshan State Company of Sichuan Province Tobacco Company, Liangshan, 615000, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhonglong Lin
- Country Yunnan Province Company of China Tobacco Corporation, Kunming, 650001, China.
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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10
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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; 43:1484-1494. [PMID: 34497374 PMCID: PMC9160025 DOI: 10.1038/s41401-021-00765-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [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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11
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Lv Y, Wang J, Yang H, Li N, Farzaneh M, Wei S, Zhai H, Zhang S, Hu Y. Lysine 2-hydroxyisobutyrylation orchestrates cell development and aflatoxin biosynthesis in Aspergillus flavus. Environ Microbiol 2022; 24:4356-4368. [PMID: 35621059 DOI: 10.1111/1462-2920.16077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib ) is a recently identified post-translational modifications (PTM) that regulates numerous cellular metabolic processes. In pathogenic microorganism, although glycolysis and fungal virulence are regulated by Khib , its potential roles in fungi remains to be elusive. Our preliminary results showed that levels of Khib fluctuate over time in Aspergillus flavus, which frequently contaminates crops and produces carcinogenic aflatoxins. However, the perception of Khib function in A. flavus is limited, especially in mycotoxin-producing strains. Here, we performed a comprehensive analysis of Khib in A. flavus, and 7156 Khib sites were identified in 1473 proteins. Notably, we demonstrated that Khib of AflM, a key enzyme in aflatoxin biosynthesis, affected conidia production and sclerotia formation. Furthermore, aflM deletion impaired aflatoxin biosynthesis, and more importantly, strains in which Khib was mimicked by K to T mutation at K49, K179 and K180 sites showed reduced aflatoxin production compared with wild type and ΔaflM complementation strains. These results indicate that Khib at these sites of AflM negatively regulates aflatoxin biosynthesis in A. flavus. In summary, our study revealed the potential roles of Khib in A. flavus, and particularly shed light on a new way to regulate aflatoxin production via Khib . This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Jing Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Haojie Yang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Na Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Mohsen Farzaneh
- Department of Agriculture, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, 1983969411, Tehran, Iran
| | - Shan Wei
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Huanchen Zhai
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Shuaibing Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Yuansen Hu
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
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12
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Protein Lipidation Types: Current Strategies for Enrichment and Characterization. Int J Mol Sci 2022; 23:ijms23042365. [PMID: 35216483 PMCID: PMC8880637 DOI: 10.3390/ijms23042365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications regulate diverse activities of a colossal number of proteins. For example, various types of lipids can be covalently linked to proteins enzymatically or non-enzymatically. Protein lipidation is perhaps not as extensively studied as protein phosphorylation, ubiquitination, or glycosylation although it is no less significant than these modifications. Evidence suggests that proteins can be attached by at least seven types of lipids, including fatty acids, lipoic acids, isoprenoids, sterols, phospholipids, glycosylphosphatidylinositol anchors, and lipid-derived electrophiles. In this review, we summarize types of protein lipidation and methods used for their detection, with an emphasis on the conjugation of proteins with polyunsaturated fatty acids (PUFAs). We discuss possible reasons for the scarcity of reports on PUFA-modified proteins, limitations in current methodology, and potential approaches in detecting PUFA modifications.
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Zhao Y, Zhang L, Ju C, Zhang X, Huang J. Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole. BMC Genomics 2022; 23:145. [PMID: 35180840 PMCID: PMC8855566 DOI: 10.1186/s12864-022-08372-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 02/04/2022] [Indexed: 11/30/2022] Open
Abstract
Backgrounds Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered posttranslational modification (PTM) and has been identified in several prokaryotic and eukaryotic organisms. Fusarium graminearum, a major pathogen of Fusarium head blight (FHB) in cereal crops, can cause considerable yield loss and produce various mycotoxins that threaten human health. The application of chemical fungicides such as tebuconazole (TEC) remains the major method to control this pathogen. However, the distribution of Khib in F. graminearum and whether Khib is remodified in response to fungicide stress remain unknown. Results Here, we carried out a proteome-wide analysis of Khib in F. graminearum, identifying the reshaping of the lysine 2-hydroxyisobutyrylome by tebuconazole, using the most recently developed high-resolution LC–MS/MS technique in combination with high-specific affinity enrichment. Specifically, 3501 Khib sites on 1049 proteins were identified, and 1083 Khib sites on 556 modified proteins normalized to the total protein content were changed significantly after TEC treatment. Bioinformatics analysis showed that Khib proteins are involved in a wide range of biological processes and may be involved in virulence and deoxynivalenol (DON) production, as well as sterol biosynthesis, in F. graminearum. Conclusions Here, we provided a wealth of resources for further study of the roles of Khib in the fungicide resistance of F. graminearum. The results enhanced our understanding of this PTM in filamentous ascomycete fungi and provided insight into the remodification of Khib sites during azole fungicide challenge in F. graminearum. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08372-4.
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Affiliation(s)
- Yanxiang Zhao
- College of Plant Health and Medicine and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China
| | - Limin Zhang
- College of Plant Health and Medicine and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China
| | - Chao Ju
- College of Plant Health and Medicine and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China
| | - Xiaoyan Zhang
- College of Agriculture, Ludong University, Yantai, 264025, Shandong Province, China
| | - Jinguang Huang
- College of Plant Health and Medicine and Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China.
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14
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Hong G, Su X, Xu K, Liu B, Wang G, Li J, Wang R, Zhu M, Li G. Salt stress downregulates 2-hydroxybutyrylation in Arabidopsis siliques. J Proteomics 2022; 250:104383. [PMID: 34562664 DOI: 10.1016/j.jprot.2021.104383] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/26/2021] [Accepted: 09/12/2021] [Indexed: 12/16/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly discovered post-translational modifications (PTMs) through protein acylation. It has been reported to be widely distributed in both eukaryotes and prokaryotes, and plays an important role in chromatin conformation change, gene transcription, protein subcellular localization, protein-protein interaction, signal transduction, and cellular proliferation. In this study, the Khib modification proteome of siliques from A. thaliana under salt stress (Ss) and those in the control (Cs) were compared. The results showed that Khib modification was abundant in siliques. Totally 3810 normalized Khib sites on 1254 proteins were identified, and the Khib modification showed a downregulation trend dramatically: it was down-regulated at 282 sites on 205 proteins while was up-regulated at 96 sites on 78 proteins in Ss siliques (Data are available via ProteomeXchange with identifier PXD028116 and PXD026643). Among them, 13 proteins, including F4IVN6, Q9M1P5, and Q9LF33, had sites with the most significant regulation of Khib modification. Bioinformatics analysis suggested that the differentially Khib-regulated proteins mainly participated in glycolysis/gluconeogenesis and endocytosis. In particular, there were differentially117 Khib-regulated proteins that were mapped to the protein-protein interaction database. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism. Overall, our work reveals the first systematic analysis of Khib proteome in Arabidopsis siliques under salt stress, and sheds a light on the future studies on the regulatory mechanisms of Khib during the salt stress response of plants. SIGNIFICANCE: In this study, we found the Khib-modified proteins in silique under salt stress and described the enrichment of Khib-modified proteins involved in the biological processes and cellular localization. Proteins undergoing 2-hydroxyisobutylation were mainly involved in the gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism, suggesting that 2-hydroxyisobutylation affects the energy metabolic pathway, and thus the development of the plant. In addition, specific candidate proteins that may affect plant development under salt stress were selected. This study will provide a theoretical basis for revealing the function and mechanism of these proteins and their 2-hydroxyisobutyryl modifications during the development of silique under salt stress.
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Affiliation(s)
- Geriqiqige Hong
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoyi Su
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Ke Xu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Bin Liu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China; CAS Center of Excellence in Molecular Plant Science, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai 201602, China
| | - Guangxia Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Li
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruigang Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China.
| | - Mulan Zhu
- CAS Center of Excellence in Molecular Plant Science, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai 201602, China.
| | - Guojing Li
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China.
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Abstract
Protozoan parasites continue to cause a significant health and economic burden worldwide. As infectious organisms, they pose unique and difficult challenges due to a level of conservation of critical eukaryotic cellular pathways with their hosts. Gene regulation has been pinpointed as an essential pathway with enough divergence to warrant investigation into therapeutically targeting. Examination of human parasites such as Plasmodium falciparum, Toxoplasma gondii, and kinetoplastids have revealed that epigenetic mechanisms play a key role in their gene regulation. The enzymes involved in adding and removing epigenetic posttranslational modifications (PTMs) have historically been the focus of study. However, the reader proteins that recognize and bind PTMs, initiating recruitment of chromatin-modifying and transcription complexes, are now being realized for their critical role in regulation and their potential as drug targets. In this review, we highlight the current knowledge on epigenetic reader proteins in model parasitic protozoa, focusing on the histone acyl- and methyl-reading domains. With this knowledge base, we compare differences between medically relevant parasites, discuss conceivable functions of these understudied proteins, indicate gaps in knowledge, and provide current progress in drug development.
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Affiliation(s)
- Krista Fleck
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Malorie Nitz
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Victoria Jeffers
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
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16
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Zheng C, Sun L. Qualitative lysine crotonylome analysis in the ovarian tissue of Harmonia axyridis (Pallas). PLoS One 2021; 16:e0258371. [PMID: 34662345 PMCID: PMC8523065 DOI: 10.1371/journal.pone.0258371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/24/2021] [Indexed: 11/19/2022] Open
Abstract
Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which has been studied at the proteomics level in a few species, with the study of Kcr in female fertility and in insect species is still lacking. Harmonia axyridis (Pallas) is a well-known beneficial insect used as a natural biological control agent against aphids in agriculture. Here, global Kcr identification in ovarian tissue of H. axyridis at diapause stage was performed to reveal potential roles for Kcr in H. axyridis ovarian cellular processes, female fertility and diapause regulation. In total, 3084 Kcr sites in 920 proteins were identified. Bioinformatic analyses revealed the distribution of these proteins in multiple subcellular localization categories and their involvement in diverse biological processes and metabolism pathways. Carbohydrate and energy metabolism related cellular processes including citric acid cycle, glycolysis and oxidative phosphorylation appeared be affected by Kcr modification. In addition, regulation of translation and protein biosynthesis may reflect Kcr involvement in diapause in H. axyridis, with Kcr affecting ribosome activities and amino acid metabolism. Moreover, Kcr modulation H. axyridis ovary development regulation may share some common mechanism with Kcr participation in some disease progression. These processes and pathways were uncovered under diapause stage, but possibly not enriched/specific for diapause stage due to limitations of qualitative proteomics experimental design. Our results informs on the potential for Kcr modifications to regulate female fertility and insect physiology.
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Affiliation(s)
- Changying Zheng
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao City, Shandong Province, P. R. China
| | - Lijuan Sun
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao City, Shandong Province, P. R. China
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Xu M, Zhang X, Yu J, Guo Z, Li Y, Song X, He K, Li G, Chi Y. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Aspergillus niger in Peanuts. Front Microbiol 2021; 12:719337. [PMID: 34489910 PMCID: PMC8418202 DOI: 10.3389/fmicb.2021.719337] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/30/2021] [Indexed: 01/10/2023] Open
Abstract
Aspergillus niger is a very destructive pathogen causing severe peanut root rot, especially in the seeding stage of peanuts (Arachis hypogaea), and often leading to the death of the plant. Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly detected post-translational modification identified in several species. In this study, we identified 5041 Khib sites on 1,453 modified proteins in A. niger. Compared with five other species, A. niger has conserved and novel proteins. Bioinformatics analysis showed that Khib proteins are widely distributed in A. niger and are involved in many biological processes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that Khib proteins were significantly enriched in many cellular compartments and pathways, such as ribosomes and proteasome subunits. A total of 223 Khib proteins were part of the PPI network, thus, suggesting that Khib proteins are associated with a large range of protein interactions and diverse pathways in the life processes of A. niger. Several identified proteins are involved in pathogenesis regulation. Our research provides the first comprehensive report of Khib and an extensive database for potential functional studies on Khib proteins in this economically important fungus.
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Affiliation(s)
- Manlin Xu
- Shandong Peanut Research Institute, Qingdao, China
| | - Xia Zhang
- Shandong Peanut Research Institute, Qingdao, China
| | - Jing Yu
- Shandong Peanut Research Institute, Qingdao, China
| | - Zhiqing Guo
- Shandong Peanut Research Institute, Qingdao, China
| | - Ying Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Xinying Song
- Shandong Peanut Research Institute, Qingdao, China
| | - Kang He
- Shandong Peanut Research Institute, Qingdao, China
| | - Guowei Li
- Institute of Crop Germplasm Resources, SAAS, Jinan, China
| | - Yucheng Chi
- Shandong Peanut Research Institute, Qingdao, China
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18
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Qi T, Li J, Wang H, Han X, Li J, Du J. Global analysis of protein lysine 2-hydroxyisobutyrylation (K hib) profiles in Chinese herb rhubarb (Dahuang). BMC Genomics 2021; 22:542. [PMID: 34266380 PMCID: PMC8283887 DOI: 10.1186/s12864-021-07847-0] [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: 03/23/2021] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered protein posttranslational modification (PTM) and is involved in the broad-spectrum regulation of cellular processes that are found in both prokaryotic and eukaryotic cells, including in plants. The Chinese herb rhubarb (Dahuang) is one of the most widely used traditional Chinese medicines in clinical applications. To better understand the physiological activities and mechanism of treating diseases with the herb, it is necessary to conduct intensive research on rhubarb. However, Khib modification has not been reported thus far in rhubarb. RESULTS In this study, we performed the first global analysis of Khib-modified proteins in rhubarb by using sensitive affinity enrichment combined with high-accuracy HPLC-MS/MS tandem spectrometry. A total of 4333 overlapping Khib modification peptides matched on 1525 Khib-containing proteins were identified in three independent tests. Bioinformatics analysis showed that these Khib-containing proteins are involved in a wide range of cellular processes, particularly in protein biosynthesis and central carbon metabolism and are distributed mainly in chloroplasts, cytoplasm, nucleus and mitochondria. In addition, the amino acid sequence motif analysis showed that a negatively charged side chain residue (E), a positively charged residue (K), and an uncharged residue with the smallest side chain (G) were strongly preferred around the Khib site, and a total of 13 Khib modification motifs were identified. These identified motifs can be classified into three motif patterns, and some motif patterns are unique to rhubarb and have not been identified in other plants to date. CONCLUSIONS A total of 4333 Khib-modified peptides on 1525 proteins were identified. The Khib-modified proteins are mainly distributed in the chloroplast, cytoplasm, nucleus and mitochondria, and involved in a wide range of cellular processes. Moreover, three types of amino acid sequence motif patterns, including EKhib/KhibE, GKhib and k.kkk….Khib….kkkkk, were extracted from a total of 13 Khib-modified peptides. This study provides comprehensive Khib-proteome resource of rhubarb. The findings from the study contribute to a better understanding of the physiological roles of Khib modification, and the Khib proteome data will facilitate further investigations of the roles and mechanisms of Khib modification in rhubarb.
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Affiliation(s)
- Tong Qi
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy,, Qingdao Agricultural University, Shandong, 266109, Qingdao, China
| | - Jinping Li
- International Cooperation Department of Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Huifang Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy,, Qingdao Agricultural University, Shandong, 266109, Qingdao, China
| | - Xiaofan Han
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy,, Qingdao Agricultural University, Shandong, 266109, Qingdao, China
| | - Junrong Li
- Bathurst Future Agri-Tech Institute of Qingdao Agricultural University, Qingdao, China
| | - Jinzhe Du
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy,, Qingdao Agricultural University, Shandong, 266109, Qingdao, China.
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19
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Yang J, He Z, Chen C, Li S, Qian J, Zhao J, Fang R. Toxoplasma gondii Infection Inhibits Histone Crotonylation to Regulate Immune Response of Porcine Alveolar Macrophages. Front Immunol 2021; 12:696061. [PMID: 34322124 PMCID: PMC8312545 DOI: 10.3389/fimmu.2021.696061] [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: 04/16/2021] [Accepted: 06/18/2021] [Indexed: 01/01/2023] Open
Abstract
Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that can infect almost all warm-blooded animals, causing serious public health problems. Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which is first identified on histones and has been proved relevant to procreation regulation, transcription activation, and cell signaling pathway. However, the biological functions of histone crotonylation have not yet been reported in macrophages infected with T. gondii. As a result, a total of 1,286 Kcr sites distributed in 414 proteins were identified and quantified, demonstrating the existence of crotonylation in porcine alveolar macrophages. According to our results, identified histones were overall downregulated. HDAC2, a histone decrotonylase, was found to be significantly increased, which might be the executor of histone Kcr after parasite infection. In addition, T. gondii infection inhibited the crotonylation of H2B on K12, contributing on the suppression of epigenetic regulation and NF-κB activation. Nevertheless, the reduction of histone crotonylation induced by parasite infection could promote macrophage proliferation via activating PI3K/Akt signaling pathway. The present findings point to a comprehensive understanding of the biological functions of histone crotonylation in porcine alveolar macrophages, thereby providing a certain research basis for the mechanism research on the immune response of host cells against T. gondii infection.
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Affiliation(s)
- Jing Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhengming He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chengjie Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Senyang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jiahui Qian
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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20
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Dong J, Li Y, Zheng F, Chen W, Huang S, Zhou X, Wang K, Cai W, Liu H, Yin L, Li Q, Tang D, Dai Y. Co-occurrence of Protein Crotonylation and 2-Hydroxyisobutyrylation in the Proteome of End-Stage Renal Disease. ACS OMEGA 2021; 6:15782-15793. [PMID: 34179622 PMCID: PMC8223210 DOI: 10.1021/acsomega.1c01161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/25/2021] [Indexed: 05/16/2023]
Abstract
End-stage renal disease (ESRD) is gradually becoming a major public healthcare burden worldwide. Post-translational modifications carrying epigenetic information play a crucial role in the pathogenesis of many chronic diseases. We performed lysine crotonylation (KCr) and lysine 2-hydroxyisobutyrylation (Khib) analyses with liquid chromatography-tandem mass spectrometry to obtain a comprehensive profile and reveal the specific pathogenesis of peripheral blood mononuclear cells in ESRD patients. 218 overlap proteins among differentially modified proteins (DMPs) of both 2-hydroxyisobutyrylation and crotonylation were identified. KEGG analysis enriched pathways of protein processing in endoplasmic reticulum (ER) and glycolysis/gluconeogenesis which is closely related with cell apoptosis. In Bip, a master regulator in the ER, eight sites were identified as having both KCr and Khib modifications. Five differentially KCr modification sites and three differentially Khib-modified sites were detected between ESRD patients and normal controls. Besides Bip, other proteins (GRP94, CNX, CRT, PDIs, GlcII, ERP57, Bap31, Hsp70, and Hsp90) happened both KCr and Khib modifications. Nine DMPs having both KCr and Khib modifications were related to the glycolysis/gluconeogenesis pathway containing two key regulatory enzymes of hexokinase-1 and pyruvate kinase. The two most abundant dual modification proteins were ENO1 and PGK1 with 15 sites and 8 sites, respectively. Lysine residue K228 with both KCr and Khib modifications in ENO1 was on its surface and made it accessible for p300 mediating dynamic modifications. Overall, we hypothesize that KCr and Khib comodifications may influence the number of immunocytes and further induce immune senescence in ESRD patients through the glycolysis/gluconeogenesis pathway and protein processing in the ER process, which may be a potential therapeutic direction in the future.
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Affiliation(s)
- Jingjing Dong
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Yixi Li
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Fengping Zheng
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Wenbiao Chen
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Shaoying Huang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Xianqing Zhou
- Guangxi
Key Laboratory of Metabolic Diseases Research, Affiliated No. 924
Hospital, Southern Medical University, Guilin 541002, China
| | - Kang Wang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Wanxia Cai
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - HaiPing Liu
- The
Second People’s Hospital of Lianping County, Heyuan517139, Guangdong , China
| | - Lianghong Yin
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
| | - Qiang Li
- Dongguan
Hospital of Guangzhou University of Traditional Chinese Medicine, Dongguan 523000, Guangdong, China
- . Phone: +86 0769 26385192
| | - Donge Tang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
- . Phone: +86 0755 22942106
| | - Yong Dai
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
- Guangxi
Key Laboratory of Metabolic Diseases Research, Affiliated No. 924
Hospital, Southern Medical University, Guilin 541002, China
- . Phone: +86 0755 22942780
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21
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Feng B, Li S, Wang Z, Cao F, Wang Z, Li G, Liu K. Systematic analysis of lysine 2-hydroxyisobutyrylation posttranslational modification in wheat leaves. PLoS One 2021; 16:e0253325. [PMID: 34138952 PMCID: PMC8211214 DOI: 10.1371/journal.pone.0253325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/02/2021] [Indexed: 01/15/2023] Open
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a recently discovered post-translational modification (PTM) showing diverse biological functions and effects in living organisms. However, the study of Khib in plant species is still relatively limited. Wheat (Triticum aestivum L.) is a global important cereal plant. In this study, the systematic Khib analysis was performed in wheat leave tissues. A total of 3004 Khib sites in 1104 proteins were repeatedly identified. Structure characterization of these Khib peptides revealed 12 conserved sequence motifs. Function classification and enrichment analysis indicated these Khib proteins showed a wide function and pathway distribution, of which ribosome activity, protein biosynthesis and photosynthesis were the preferred biological processes. Subcellular location predication indicated chloroplast was the dominant subcellular compartment where Khib was distributed. There may be some crosstalks among Khib, lysine acetylation and lysine succinylation modification because some proteins and sites were modified by all these three acylations. The present study demonstrated the critical role of Khib in wheat biological and physiology, which has expanded the scope of Khib in plant species. Our study is an available resource and reference of Khib function demonstration and structure characterization in cereal plant, as well as in plant kingdom.
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Affiliation(s)
- Bo Feng
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Shengdong Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Zongshuai Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Fang Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Zheng Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
| | - Geng Li
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, P. R. China
| | - Kaichang Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong, P. R. China
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22
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Role of chromatin modulation in the establishment of protozoan parasite infection for developing targeted chemotherapeutics. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00356-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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23
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Hou JY, Zhou L, Li JL, Wang DP, Cao JM. Emerging roles of non-histone protein crotonylation in biomedicine. Cell Biosci 2021; 11:101. [PMID: 34059135 PMCID: PMC8166067 DOI: 10.1186/s13578-021-00616-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 05/22/2021] [Indexed: 12/25/2022] Open
Abstract
Crotonylation of proteins is a newly found type of post-translational modifications (PTMs) which occurs leadingly on the lysine residue, namely, lysine crotonylation (Kcr). Kcr is conserved and is regulated by a series of enzymes and co-enzymes including lysine crotonyltransferase (writer), lysine decrotonylase (eraser), certain YEATS proteins (reader), and crotonyl-coenzyme A (donor). Histone Kcr has been substantially studied since 2011, but the Kcr of non-histone proteins is just an emerging field since its finding in 2017. Recent advances in the identification and quantification of non-histone protein Kcr by mass spectrometry have increased our understanding of Kcr. In this review, we summarized the main proteomic characteristics of non-histone protein Kcr and discussed its biological functions, including gene transcription, DNA damage response, enzymes regulation, metabolic pathways, cell cycle, and localization of heterochromatin in cells. We further proposed the performance of non-histone protein Kcr in diseases and the prospect of Kcr manipulators as potential therapeutic candidates in the diseases.
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Affiliation(s)
- Jia-Yi Hou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.,Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, China
| | - Lan Zhou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Jia-Lei Li
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - De-Ping Wang
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ji-Min Cao
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.
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24
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Bo F, Shengdong L, Zongshuai W, Fang C, Zheng W, Chunhua G, Geng L, Ling'an K. Global analysis of lysine 2-hydroxyisobutyrylation in wheat root. Sci Rep 2021; 11:6327. [PMID: 33737719 PMCID: PMC7973580 DOI: 10.1038/s41598-021-85879-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring post-translational modification. The system Khib identification at proteomics level has been performed in various species and tissues to characterize the role of Khib in biological activities. However, the study of Khib in plant species is relatively less. In the present study, the first plant root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat with antibody immunoprecipitation affinity, high resolution mass spectrometry-based proteomics and bioinformatics analysis. In total, 6328 Khib sites in 2186 proteins were repeatedly identified in three replicates. These Khib proteins showed a wide subcellular location distribution. Function and pathways characterization of these Khib proteins indicated that many cellular functions and metabolism pathways were potentially affected by this modification. Protein and amino acid metabolism related process may be regulated by Khib, especially ribosome activities and proteins biosynthesis process. Carbohydrate metabolism and energy production related processes including glycolysis/gluconeogenesis, TCA cycle and oxidative phosphorylation pathways were also affected by Khib modification. Besides, root sulfur assimilation and transformation related enzymes exhibited Khib modification. Our work illustrated the potential regulation role of Khib in wheat root physiology and biology, which could be used as a useful reference for Khib study in plant root.
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Affiliation(s)
- Feng Bo
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Li Shengdong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Wang Zongshuai
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Cao Fang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Wang Zheng
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Gao Chunhua
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China
| | - Li Geng
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China.
| | - Kong Ling'an
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250100, People's Republic of China.
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25
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Li FC, Nie LB, Elsheikha HM, Yin FY, Zhu XQ. Lysine crotonylation is widespread on proteins of diverse functions and localizations in Toxoplasma gondii. Parasitol Res 2021; 120:1617-1626. [PMID: 33655350 DOI: 10.1007/s00436-021-07057-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/17/2021] [Indexed: 12/27/2022]
Abstract
Lysine crotonylation (Kcr) is an evolutionally conserved post-translational modification (PTM) on histone proteins. However, information about Kcr and its involvement in the biology and metabolism of Toxoplasma gondii is limited. In the present study, a global Kcr proteome analysis using LC-MS/MS in combination with immune-affinity method was performed. A total of 12,152 Kcr sites distributed over 2719 crotonylated proteins were identified. Consistent with lysine acetylation and succinylation in Apicomplexa, Kcr was associated with various metabolic pathways, including carbon metabolism, pyrimidine metabolism, glycolysis, gluconeogenesis, and proteasome. Markedly, many stage-specific proteins, histones, and histone-modifying enzymes related to the stage transition were found to have Kcr sites, suggesting a potential involvement of Kcr in the parasite stage transformation. Most components of the apical secretory organelles were identified as crotonylated proteins which were associated with the attachment, invasion, and replication of T. gondii. These results expanded our understanding of Kcr proteome and proposed new hypotheses for further research of the Kcr roles in the pathobiology of T. gondii infection.
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Affiliation(s)
- Fa-Cai Li
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, People's Republic of China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China
| | - Lan-Bi Nie
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China.,College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Fang-Yuan Yin
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, People's Republic of China
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi Province, People's Republic of China. .,Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
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26
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Qian H, Wang L, Ma X, Yi X, Wang B, Liang W. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylated Proteins in Fusarium oxysporum. Front Microbiol 2021; 12:623735. [PMID: 33643252 PMCID: PMC7902869 DOI: 10.3389/fmicb.2021.623735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022] Open
Abstract
Protein lysine 2-hydroxyisobutyrylation (K hib ), a new type of post-translational modification, occurs in histones and non-histone proteins and plays an important role in almost all aspects of both eukaryotic and prokaryotic living cells. Fusarium oxysporum, a soil-borne fungal pathogen, can cause disease in more than 150 plants. However, little is currently known about the functions of K hib in this plant pathogenic fungus. Here, we report a systematic analysis of 2-hydroxyisobutyrylated proteins in F. oxysporum. In this study, 3782 K hib sites in 1299 proteins were identified in F. oxysporum. The bioinformatics analysis showed that 2-hydroxyisobutyrylated proteins are involved in different biological processes and functions and are located in diverse subcellular localizations. The enrichment analysis revealed that K hib participates in a variety of pathways, including the ribosome, oxidative phosphorylation, and proteasome pathways. The protein interaction network analysis showed that 2-hydroxyisobutyrylated protein complexes are involved in diverse interactions. Notably, several 2-hydroxyisobutyrylated proteins, including three kinds of protein kinases, were involved in the virulence or conidiation of F. oxysporum, suggesting that K hib plays regulatory roles in pathogenesis. Moreover, our study shows that there are different K hib levels of F. oxysporum in conidial and mycelial stages. These findings provide evidence of K hib in F. oxysporum, an important filamentous plant pathogenic fungus, and serve as a resource for further exploration of the potential functions of K hib in Fusarium species and other filamentous pathogenic fungi.
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Affiliation(s)
- Hengwei Qian
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Lulu Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | | | - Xingling Yi
- Micron Biotechnology Co., Ltd., Hangzhou, China
| | - Baoshan Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Wenxing Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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27
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Abstract
C. albicans is one of the most commonly reported fungal pathogens in mucosal and systemic infections. A better understanding of its growth habits and metabolic processes in the host should help improve defense strategies. Candida albicans is the most common human fungal pathogen, causing diseases ranging from mucosal to systemic infections for both immunocompetent and immunocompromised individuals. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we surveyed the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in C. albicans. Using an antibody enrichment approach along with the traditional liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, we analyzed the pattern of Khib-modified proteins and sites in one wild-type strain of C. albicans. We identified 1,438 Khib-modified proteins with 6,659 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of antibiotics, biosynthesis of secondary metabolites, biosynthesis of amino acids and carbon metabolism, of which the ribosome pathway is the most affected pathway. Even compared with the reported numbers of lysine acetylation (Kac) and succinylation (Ksuc) sites, the numbers of Khib-modified sites on ribosomal proteins remained the highest for C. albicans. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and protein translation. Findings in this study may provide new insights for studying posttranslational modification (PTM)-associated mechanisms in fungal development and pathogenicity. IMPORTANCEC. albicans is one of the most commonly reported fungal pathogens in mucosal and systemic infections. A better understanding of its growth habits and metabolic processes in the host should help improve defense strategies. The newly discovered protein posttranslational modification (PTM) on histones is one epigenetic mechanism which has been linked to many pathogenic events, including cancers. The types of PTM and their pathogenic roles in C. albicans are still somewhat poorly understood, even though studies of C. albicans based on acetylation inhibitors have shed some light on their function, and it seems that PTMs regulate pathogenic adhesion factors. Here, we quantified and analyzed the occurrence of lysine 2-hydroxyisobutyrylation (Khib) in C. albicans. The Khib-modified proteins are enriched with respect to carbon metabolism, ribosomal biogenesis, and protein translation in C. albicans.
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28
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Xu Y, Li X, Liang W, Liu M. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea. Front Microbiol 2020; 11:585614. [PMID: 33329453 PMCID: PMC7728723 DOI: 10.3389/fmicb.2020.585614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Posttranslational modifications (PTMs) of the whole proteome have become a hot topic in the research field of epigenetics, and an increasing number of PTM types have been identified and shown to play significant roles in different cellular processes. Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly detected PTM, and the 2-hydroxyisobutyrylome has been identified in several species. Botrytis cinerea is recognized as one of the most destructive pathogens due to its broad host distribution and very large economic losses; thus the many aspects of its pathogenesis have been continuously studied. However, distribution and function of Khib in this phytopathogenic fungus are not clear. In this study, a proteome-wide analysis of Khib in B. cinerea was performed, and 5,398 Khib sites on 1,181 proteins were identified. Bioinformatics analysis showed that the 2-hydroxyisobutyrylome in B. cinerea contains both conserved proteins and novel proteins when compared with Khib proteins in other species. Functional classification, functional enrichment and protein interaction network analyses showed that Khib proteins are widely distributed in cellular compartments and involved in diverse cellular processes. Significantly, 37 proteins involved in different aspects of regulating the pathogenicity of B. cinerea were detected as Khib proteins. Our results provide a comprehensive view of the 2-hydroxyisobutyrylome and lay a foundation for further studying the regulatory mechanism of Khib in both B. cinerea and other plant pathogens.
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Affiliation(s)
- Yang Xu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiaoxia Li
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenxing Liang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Mengjie Liu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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29
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Wang J, Jiang N, Sang X, Yang N, Feng Y, Chen R, Wang X, Chen Q. Protein Modification Characteristics of the Malaria Parasite Plasmodium falciparum and the Infected Erythrocytes. Mol Cell Proteomics 2020; 20:100001. [PMID: 33517144 PMCID: PMC7857547 DOI: 10.1074/mcp.ra120.002375] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Malaria elimination is still pending on the development of novel tools that rely on a deep understanding of parasite biology. Proteins of all living cells undergo myriad posttranslational modifications (PTMs) that are critical to multifarious life processes. An extensive proteome-wide dissection revealed a fine PTM map of most proteins in both Plasmodium falciparum, the causative agent of severe malaria, and the infected red blood cells. More than two-thirds of proteins of the parasite and its host cell underwent extensive and dynamic modification throughout the erythrocytic developmental stage. PTMs critically modulate the virulence factors involved in the host-parasite interaction and pathogenesis. Furthermore, P. falciparum stabilized the supporting proteins of erythrocyte origin by selective demodification. Collectively, our multiple omic analyses, apart from having furthered a deep understanding of the systems biology of P. falciparum and malaria pathogenesis, provide a valuable resource for mining new antimalarial targets.
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Affiliation(s)
- Jianhua Wang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China; College of Food Science, Shenyang Agricultural Sciences, Shenyang, China
| | - Ning Jiang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Xiaoyu Sang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Na Yang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ying Feng
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ran Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Xinyi Wang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; College of Basic Sciences, Shenyang Agricultural University, Shenyang, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China.
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30
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Nie LB, Liang QL, Elsheikha HM, Du R, Zhu XQ, Li FC. Global profiling of lysine 2-hydroxyisobutyrylome in Toxoplasma gondii using affinity purification mass spectrometry. Parasitol Res 2020; 119:4061-4071. [PMID: 33057814 DOI: 10.1007/s00436-020-06923-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/06/2020] [Indexed: 11/28/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a recently discovered and evolutionarily conserved form of protein post-translational modification (PTM) found in mammalian and yeast cells. Previous studies have shown that Khib plays roles in the activity of gene transcription and Khib-containing proteins are closely related to the cellular metabolism. In this study, a global Khib-containing analysis using the latest databases (ToxoDB 46, 8322 sequences, downloaded on April 16, 2020) and sensitive immune-affinity enrichment coupled with liquid chromatography-tandem mass spectrometry was performed. A total of 1078 Khib modification sites across 400 Khib-containing proteins were identified in tachyzoites of Toxoplasma gondii RH strain. Bioinformatics and functional enrichment analysis showed that Khib-modified proteins were associated with various biological processes, such as ribosome, glycolysis/gluconeogenesis, and central carbon metabolism. Interestingly, many proteins of the secretory organelles (e.g., microneme, rhoptry, and dense granule) that play roles in the infection cycle of T. gondii were found to be Khib-modified, suggesting the involvement of Khib in key biological process during T. gondii infection. We also found that histone proteins, key enzymes related to cellular metabolism, and several glideosome components had Khib sites. These results expanded our understanding of the roles of Khib in T. gondii and should promote further investigations of how Khib regulates gene expression and key biological functions in T. gondii.
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Affiliation(s)
- Lan-Bi Nie
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China
| | - Qin-Li Liang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China. .,College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi Province, People's Republic of China.
| | - Fa-Cai Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China.,College of Veterinary Medicine, Southwest University, Chongqing, 400715, People's Republic of China
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Zhang L, Zou Y, He N, Chen Y, Chen Z, Li L. DeepKhib: A Deep-Learning Framework for Lysine 2-Hydroxyisobutyrylation Sites Prediction. Front Cell Dev Biol 2020; 8:580217. [PMID: 33015075 PMCID: PMC7509169 DOI: 10.3389/fcell.2020.580217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 08/17/2020] [Indexed: 11/28/2022] Open
Abstract
As a novel type of post-translational modification, lysine 2-Hydroxyisobutyrylation (K hib ) plays an important role in gene transcription and signal transduction. In order to understand its regulatory mechanism, the essential step is the recognition of K hib sites. Thousands of K hib sites have been experimentally verified across five different species. However, there are only a couple traditional machine-learning algorithms developed to predict K hib sites for limited species, lacking a general prediction algorithm. We constructed a deep-learning algorithm based on convolutional neural network with the one-hot encoding approach, dubbed CNN OH . It performs favorably to the traditional machine-learning models and other deep-learning models across different species, in terms of cross-validation and independent test. The area under the ROC curve (AUC) values for CNN OH ranged from 0.82 to 0.87 for different organisms, which is superior to the currently available K hib predictors. Moreover, we developed the general model based on the integrated data from multiple species and it showed great universality and effectiveness with the AUC values in the range of 0.79-0.87. Accordingly, we constructed the on-line prediction tool dubbed DeepKhib for easily identifying K hib sites, which includes both species-specific and general models. DeepKhib is available at http://www.bioinfogo.org/DeepKhib.
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Affiliation(s)
- Luna Zhang
- School of Data Science and Software Engineering, Qingdao University, Qingdao, China
| | - Yang Zou
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ningning He
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yu Chen
- School of Data Science and Software Engineering, Qingdao University, Qingdao, China
| | - Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Lei Li
- School of Data Science and Software Engineering, Qingdao University, Qingdao, China
- School of Basic Medicine, Qingdao University, Qingdao, China
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