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Liu S, Yang T, Jiang Q, Zhang L, Shi X, Liu X, Li X. Lactate and Lactylation in Sepsis: A Comprehensive Review. J Inflamm Res 2024; 17:4405-4417. [PMID: 39006496 PMCID: PMC11244620 DOI: 10.2147/jir.s459185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/02/2024] [Indexed: 07/16/2024] Open
Abstract
Sepsis is a disorder of the immune response to infection or infectious factors with high morbidity and mortality in clinical settings. The lactylation of lysine residues, fueled by lactate, plays a pivotal role in its pathophysiology. In conducting a literature review on sepsis-related research, we employed a systematic approach to ensure comprehensiveness and accuracy. Initially, we conducted an extensive literature search through the PubMed database, utilizing a range of keywords including "sepsis", "lactate", "lactylation", and "epigenetic modification". The aim was to capture the most recent research related to the pathophysiological mechanisms of sepsis, metabolic disorders, and the role of lactylation. The results of the literature review revealed a close link between sepsis and metabolic dysfunction, particularly the pivotal role of lactylation in regulating immune responses and inflammatory processes. Lactate, not only an energy metabolic byproduct produced during glycolysis, affects the activity of various proteins, including those involved in immune regulation and cell signaling, through lactylation. In the context of sepsis, changes in the levels of lactylation may be closely associated with the severity and prognosis of the disease. In summary, lactylation, as an emerging type of epigenetic modification, provides a new perspective for the diagnosis and treatment of sepsis. Future research needs to further elucidate the exact mechanisms of lactylation in sepsis and explore its potential as a therapeutic target.
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Affiliation(s)
- Sijia Liu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Ting Yang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Qingsong Jiang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Liang Zhang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Xinhui Shi
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
| | - Xin Liu
- Medical Research Center, Southwest Hospital, Third Military Medical University, Chongqing, People’s Republic of China
| | - Xiaoli Li
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, People’s Republic of China
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Li X, Zhu Y, Yao Z, Ge R. The lysine 2-hydroxyisobutyrylome of Helicobacter pylori: Indicating potential roles of lysine 2-hydroxyisobutyrylation in the bacterial metabolism. Microb Pathog 2024; 186:106510. [PMID: 38147967 DOI: 10.1016/j.micpath.2023.106510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023]
Abstract
Helicobacter pylori (H. pylori) is a pathogen which colonizes the stomach, causing ulcers, chronic gastritis and other related diseases. Protein post-translational modifications (PTMs) in bacteria mainly include glycosylation, ubiquitination, nitrosylation, methylation, phosphorylation and acetylation, all of which have divergent functions in the physiology and pathology of the bacterium. Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered type of PTM in recent years in some kinds of organisms, and this PTM is involved in the regulation of a variety of metabolic process, such as bacterial glucose metabolism, lipid metabolism and protein synthesis. This study performed the first qualitative lysine 2-hydroxyisobutyrylome in H. pylori, and a total of 4419 Khib sites in 812 proteins were identified. The results show that Khib sites are mainly located in the key functional regions or active domains of proteins involved in nickel-trafficking, energy production, virulence factors, anti-oxidation, metal resistance, and ribosome biosynthesis in H. pylori. The study presented here provides new hints in the metabolism and pathology of H. pylori and the proteins with Khib modification may be potentially promising targets for the further development of antibiotics, especially considering the high occurrence of treatment failure of H. pylori failure due to development of antibiotics-resistance.
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Affiliation(s)
- Xinhang Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yulin Zhu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zihui Yao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ruiguang Ge
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, 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: 0] [Impact Index Per Article: 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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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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Kausar R, Wang X, Komatsu S. Crop Proteomics under Abiotic Stress: From Data to Insights. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212877. [PMID: 36365330 PMCID: PMC9657731 DOI: 10.3390/plants11212877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/22/2022] [Indexed: 06/09/2023]
Abstract
Food security is a major challenge in the present world due to erratic weather and climatic changes. Environmental stress negatively affects plant growth and development which leads to reduced crop yields. Technological advancements have caused remarkable improvements in crop-breeding programs. Proteins have an indispensable role in developing stress resilience and tolerance in crops. Genomic and biotechnological advancements have made the process of crop improvement more accurate and targeted. Proteomic studies provide the information required for such targeted approaches. The crosstalk among cellular components is being analyzed by subcellular proteomics. Additionally, the functional diversity of proteins is being unraveled by post-translational modifications during abiotic stress. The exploration of precise cellular responses and the networking among different cellular organelles help in the prediction of signaling pathways and protein-protein interactions. High-throughput mass-spectrometry-based protein studies are now possible due to incremental advancements in mass-spectrometry techniques, sample protocols, and bioinformatic tools as well as the increasing availability of plant genome sequence information for multiple species. In this review, the key role of proteomic analysis in identifying the abiotic-stress-responsive mechanisms in various crops was summarized. The development and availability of advanced computational tools were discussed in detail. The highly variable protein responses among different crops have provided a wide avenue for molecular-marker-assisted genetic buildup studies to develop smart, high-yielding, and stress-tolerant varieties to cope with food-security challenges.
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Affiliation(s)
- Rehana Kausar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Zhang K, Cao H, Ma Y, Si H, Zang J, Bai H, Yu L, Pang X, Zhou F, Xing J, Dong J. Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:1000039. [PMID: 36186065 PMCID: PMC9521605 DOI: 10.3389/fpls.2022.1000039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Proteins post-translational modification (PTMs) is necessary in the whole life process of organisms. Among them, lysine 2-hydroxyisobutyrylation (Khib) plays an important role in protein synthesis, transcriptional regulation, and cell metabolism. Khib is a newly identified PTM in several plant species. However, the function of Khib in maize was unclear. In this study, western blotting results showed that Khib modification level increased significantly after Fusarium graminearum infection, and 2,066 Khib modified sites on 728 proteins were identified in maize, among which 24 Khib sites occurred on core histones. Subcellular localization results showed that these Khib modified proteins were localized in cytoplasm, chloroplast, and nucleus. Then, comparative proteomic analysis of the defense response to F. graminearum infection showed that Khib modification participated in plant resistance to pathogen infection by regulating glycolysis, TCA cycle, protein synthesis, peroxisome, and secondary metabolic processes, such as benzoxazinoid biosynthesis, phenylpropanoid biosynthesis, jasmonic acid synthesis, and tyrosine and tryptophan biosynthesis. In addition, we also demonstrated that lysine 2-hydroxyisobutyrylation sites on histones were involved in the gene expression of pathogenesis-related proteins. Our results provide a new perspective for the study of plant disease resistance, and had directive significance of maize disease resistance for molecular breeding.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Hongzhe Cao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Yuxin Ma
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Helong Si
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jinping Zang
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Hua Bai
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Lu Yu
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Xi Pang
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Fan Zhou
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jihong Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, 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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