1
|
Hou X, Chen Y, Li X, Gu X, Dong W, Shi J, Ji S. Protein succinylation: regulating metabolism and beyond. Front Nutr 2024; 11:1336057. [PMID: 38379549 PMCID: PMC10876795 DOI: 10.3389/fnut.2024.1336057] [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: 11/10/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Modifications of protein post-translation are critical modulatory processes, which alters target protein biological activity,function and/or location, even involved in pathogenesis of some diseases. So far, there are at least 16 types of post-translation modifications identified, particularly through recent mass spectrometry analysis. Among them, succinylation (Ksuc) on protein lysine residues causes a variety of biological changes. Succinylation of proteins contributes to many cellular processes such as proliferation, growth, differentiation, metabolism and even tumorigenesis. Mechanically, Succinylation leads to conformation alteration of chromatin or remodeling. As a result, transcription/expression of target genes is changed accordingly. Recent research indicated that succinylation mainly contributes to metabolism modulations, from gene expression of metabolic enzymes to their activity modulation. In this review, we will conclude roles of succinylation in metabolic regulation of glucose, fat, amino acids and related metabolic disease launched by aberrant succinylation. Our goal is to stimulate extra attention to these still not well researched perhaps important succinylation modification on proteins and cell processes.
Collapse
Affiliation(s)
- Xiaoli Hou
- Department of Basic Medicine, Zhengzhou Shuqing Medical College, Zhengzhou, China
| | - Yiqiu Chen
- Department of Basic Medicine, Zhengzhou Shuqing Medical College, Zhengzhou, China
| | - Xiao Li
- Department of Basic Medicine, Zhengzhou Shuqing Medical College, Zhengzhou, China
| | - Xianliang Gu
- Department of Basic Medicine, Zhengzhou Shuqing Medical College, Zhengzhou, China
| | - Weixia Dong
- Department of Basic Medicine, Zhengzhou Shuqing Medical College, Zhengzhou, China
| | - Jie Shi
- Zhoukou Vocational and Technical College, Zhoukou, China
| | - Shaoping Ji
- Department of Basic Medicine, Zhengzhou Shuqing Medical College, Zhengzhou, China
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, China
| |
Collapse
|
2
|
Adejor J, Tumukunde E, Li G, Lin H, Xie R, Wang S. Impact of Lysine Succinylation on the Biology of Fungi. Curr Issues Mol Biol 2024; 46:1020-1046. [PMID: 38392183 PMCID: PMC10888112 DOI: 10.3390/cimb46020065] [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: 12/09/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/24/2024] Open
Abstract
Post-translational modifications (PTMs) play a crucial role in protein functionality and the control of various cellular processes and secondary metabolites (SMs) in fungi. Lysine succinylation (Ksuc) is an emerging protein PTM characterized by the addition of a succinyl group to a lysine residue, which induces substantial alteration in the chemical and structural properties of the affected protein. This chemical alteration is reversible, dynamic in nature, and evolutionarily conserved. Recent investigations of numerous proteins that undergo significant succinylation have underscored the potential significance of Ksuc in various biological processes, encompassing normal physiological functions and the development of certain pathological processes and metabolites. This review aims to elucidate the molecular mechanisms underlying Ksuc and its diverse functions in fungi. Both conventional investigation techniques and predictive tools for identifying Ksuc sites were also considered. A more profound comprehension of Ksuc and its impact on the biology of fungi have the potential to unveil new insights into post-translational modification and may pave the way for innovative approaches that can be applied across various clinical contexts in the management of mycotoxins.
Collapse
Affiliation(s)
- John Adejor
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Elisabeth Tumukunde
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guoqi Li
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Lin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Xie
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
3
|
Zhang L, Xiao J, Du M, Lei W, Yang W, Xue X. Post-translational modifications confer amphotericin B resistance in Candida krusei isolated from a neutropenic patient. Front Immunol 2023; 14:1148681. [PMID: 36936926 PMCID: PMC10015421 DOI: 10.3389/fimmu.2023.1148681] [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: 01/20/2023] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Neutropenia is a common complication in the treatment of hematological diseases and the most common predisposing factor for invasion by fungi, such as Candida krusei. Recent studies have shown that C. krusei, a life-threatening pathogen, has developed resistance to amphotericin B (AMB). However, the mechanisms that led to the rapid emergence of this AMB-resistant phenotype are unclear. In this study, we found the sensitivity for AMB could be promoted by inhibiting histone acyltransferase activity and western blot analysis revealed differences in the succinylation levels of C. krusei isolated from immunocompromised patients and of the corresponding AMB-resistant mutant. By comparative succinyl-proteome analysis, we identified a total of 383 differentially expressed succinylated sites in with 344 sites in 134 proteins being upregulated in the AMB-resistant mutant, compared to 39 sites in 23 proteins in the wild-type strain. These differentially succinylated proteins were concentrated in the ribosome and cell wall. The critical pathways associated with these proteins included those involved in glycolysis, gluconeogenesis, the ribosome, and fructose and mannose metabolism. In particular, AMB resistance was found to be associated with enhanced ergosterol synthesis and aberrant amino acid and glucose metabolism. Analysis of whole-cell proteomes, confirmed by parallel reaction monitoring, showed that the key enzyme facilitating lysine acylation was significantly upregulated in the AMB-resistant strain. Our results suggest that lysine succinylation may play an indispensable role in the development of AMB resistance in C. krusei. Our study provides mechanistic insights into the development of drug resistance in fungi and can aid in efforts to stifle the emergence of AMB-resistant pathogenic fungi.
Collapse
Affiliation(s)
- Li Zhang
- Institute of Dermatology, Naval Medical University, Shanghai, China
| | - Jinzhou Xiao
- Institute of Dermatology, Naval Medical University, Shanghai, China
| | - Mingwei Du
- Department of Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shanghai, China
| | - Wenzhi Lei
- Institute of Dermatology, Naval Medical University, Shanghai, China
- *Correspondence: Wenzhi Lei, ; Weiwei Yang, ; Xiaochun Xue,
| | - Weiwei Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
- *Correspondence: Wenzhi Lei, ; Weiwei Yang, ; Xiaochun Xue,
| | - Xiaochun Xue
- Department of Pharmacy, 905th Hospital of PLA Navy, Shanghai, China
- *Correspondence: Wenzhi Lei, ; Weiwei Yang, ; Xiaochun Xue,
| |
Collapse
|
4
|
Lu Y, Li X, Zhao K, Qiu P, Deng Z, Yao W, Wang J. Global landscape of 2-hydroxyisobutyrylation in human pancreatic cancer. Front Oncol 2022; 12:1001807. [PMID: 36249039 PMCID: PMC9563853 DOI: 10.3389/fonc.2022.1001807] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/12/2022] [Indexed: 11/26/2022] Open
Abstract
As a new type of post-translational modification (PTM), lysine 2-hydroxyisobutyrylation (Khib) was firstly identified in histones and functioned as a regulator of transactivation in mammals. However, the role of Khib proteins remains to be investigated. Here, we firstly identified 10,367 Khib sites on 2,325 modified proteins in seven patients with pancreatic cancer by applying liquid chromatography with tandem mass spectrometry (LC-MS/MS) qualitative proteomics techniques. Among them, 27 Khib-modified sites were identified in histones. Bioinformatics analysis revealed that the Khib-modified proteins were mainly distributed in the cytoplasm and enhanced in metabolic pathways, including glycolysis/gluconeogenesis, the tricarboxylic acid cycle (TCA cycle), and fatty acid degradation. In an overlapping comparison of lysine 2-hydroxyisobutyrylation, succinylation, and acetylation in humans, 105 proteins with 80 sites were modified by all three PTMs, suggesting there may be a complex network among the different modified proteins and sites. Furthermore, MG149, which was identified as a Tip60 inhibitor, significantly decreased the total Khib modification level in pancreatic cancer (PC) and strongly suppressed PC’s proliferation, migration, and invasion ability. Overall, our study is the first profiling of lysine 2-hydroxyisobutyrylome and provides a new database for better investigating Khib in PC.
Collapse
Affiliation(s)
- Yun Lu
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangyu Li
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Zhao
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Qiu
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhengdong Deng
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yao
- Department of Oncology Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Wei Yao, ; Jianming Wang,
| | - Jianming Wang
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Affiliated Tianyou Hospital, Wuhan University of Science & Technology, Wuhan, China
- *Correspondence: Wei Yao, ; Jianming Wang,
| |
Collapse
|
5
|
Xu X, Hu X, Dong J, Xue Y, Liu T, Jin Q. Proteome-Wide Identification and Functional Analysis of Lysine Crotonylation in Trichophyton rubrum Conidial and Mycelial Stages. Front Genet 2022; 13:832668. [PMID: 35356433 PMCID: PMC8960058 DOI: 10.3389/fgene.2022.832668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Lysine crotonylation is a newly discovered post-translational modification (PTM) with key roles in various important regulatory pathways. Despite its functional significance, there is limited knowledge about crotonylation in fungi. Trichophyton rubrum is the most common fungal pathogen in human infection and is considered a model organism of dermatophytes and human pathogenic filamentous fungi. In this study, we obtained a proteome-wide crotonylation profile of T. rubrum, leading to the identification of 14,019 crotonylated sites on 3144 proteins. The crotonylated proteins were significantly involved in translation and in various metabolic and biosynthetic processes. Some proteins related to fungal pathogenicity were also found to be targets of crotonylation. In addition, extensive crotonylation was found on histones, suggesting a role in epigenetic regulation. Furthermore, about half of the crotonylated proteins were specific to either the conidial or the mycelial stage, and functional enrichment analysis showed some differences between the two stages. The results suggest that the difference in crotonylation between the two stages is not due to differences in protein abundance. Crosstalk of crotonylation with acetylation, propionylation, and succinylation suggests distinct regulatory roles. This study is the first crotonylation analysis in dermatophytes and human pathogenic filamentous fungi. These results represent a solid foundation for further research on PTM regulatory mechanisms in fungi and should facilitate improved antifungal strategies against these medical important species.
Collapse
Affiliation(s)
| | | | | | | | - Tao Liu
- *Correspondence: Tao Liu, ; Qi Jin,
| | - Qi Jin
- *Correspondence: Tao Liu, ; Qi Jin,
| |
Collapse
|
6
|
iSuc-ChiDT: a computational method for identifying succinylation sites using statistical difference table encoding and the chi-square decision table classifier. BioData Min 2022; 15:3. [PMID: 35144656 PMCID: PMC8832670 DOI: 10.1186/s13040-022-00290-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background Lysine succinylation is a type of protein post-translational modification which is widely involved in cell differentiation, cell metabolism and other important physiological activities. To study the molecular mechanism of succinylation in depth, succinylation sites need to be accurately identified, and because experimental approaches are costly and time-consuming, there is a great demand for reliable computational methods. Feature extraction is a key step in building succinylation site prediction models, and the development of effective new features improves predictive accuracy. Because the number of false succinylation sites far exceeds that of true sites, traditional classifiers perform poorly, and designing a classifier to effectively handle highly imbalanced datasets has always been a challenge. Results A new computational method, iSuc-ChiDT, is proposed to identify succinylation sites in proteins. In iSuc-ChiDT, chi-square statistical difference table encoding is developed to extract positional features, and has a higher predictive accuracy and fewer features compared to common position-based encoding schemes such as binary encoding and physicochemical property encoding. Single amino acid and undirected pair-coupled amino acid composition features are supplemented to improve the fault tolerance for residue insertions and deletions. After feature selection by Chi-MIC-share algorithm, the chi-square decision table (ChiDT) classifier is constructed for imbalanced classification. With a training set of 4748:50,551(true: false sites), ChiDT clearly outperforms traditional classifiers in predictive accuracy, and runs fast. Using an independent testing set of experimentally identified succinylation sites, iSuc-ChiDT achieves a sensitivity of 70.47%, a specificity of 66.27%, a Matthews correlation coefficient of 0.205, and a global accuracy index Q9 of 0.683, showing a significant improvement in sensitivity and overall accuracy compared to PSuccE, Success, SuccinSite, and other existing succinylation site predictors. Conclusions iSuc-ChiDT shows great promise in predicting succinylation sites and is expected to facilitate further experimental investigation of protein succinylation. Supplementary Information The online version contains supplementary material available at 10.1186/s13040-022-00290-1.
Collapse
|
7
|
Cao X, Xu X, Dong J, Xue Y, Sun L, Zhu Y, Liu T, Jin Q. Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages. BMC Genomics 2022; 23:21. [PMID: 34983376 PMCID: PMC8725419 DOI: 10.1186/s12864-021-08184-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/18/2021] [Indexed: 12/28/2022] Open
Abstract
Background Circular RNAs (circRNAs) are a group of noncoding RNAs that participate in gene expression regulation in various pathways. The essential roles of circRNAs have been revealed in many species. However, knowledge of circRNAs in fungi is still not comprehensive. Results Trichophyton rubrum (T. rubrum) is considered a model organism of human pathogenic filamentous fungi and dermatophytes. In this study, we performed a genome-wide investigation of circRNAs in T. rubrum based on high-throughput sequencing and ultimately identified 4254 circRNAs. Most of these circRNAs were specific to the conidial or mycelial stage, revealing a developmental stage-specific expression pattern. In addition, 940 circRNAs were significantly differentially expressed between the conidial and mycelial stages. PCR experiments conducted on seven randomly selected differentially expressed (DE-) circRNAs confirmed the circularized structures and relative expression levels of these circRNAs. Based on their genome locations, most circRNAs originated from intergenic regions, unlike those in plants and animals. Furthermore, we constructed circRNA-miRNA-mRNA regulatory networks that included 661 DE-circRNAs targeting 140 miRNAs and further regulating 2753 mRNAs. The relative expression levels of two randomly selected circRNA-miRNA-mRNA axes were investigated by qRT-PCR, and the competing endogenous RNA (ceRNA) network theory was validated. Functional enrichment analysis of the target genes suggested that they were significantly involved in posttranscriptional processes and protein synthesis as well as some small-molecule metabolism processes. CircRNAs are relatively more conserved in closely related dermatophytes but rarely conserved in distantly related species. Tru_circ07138_001 is a highly conserved circRNA that was conserved in all ten dermatophytes analyzed in our study and three distantly related species. Its host gene TERG_07138 was also highly conserved in two of these distantly related species Gallus gallus and Caenorhabditis elegans. The specific role of this circRNA deserves further exploration. Conclusions Our study is the first to provide a global profile of circRNAs in T. rubrum as well as dermatophytes. These results could serve as valuable resources for research on circRNA regulatory mechanisms in fungi and reveal new insights for further investigation of the physical characteristics of these significant human fungal pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08184-y.
Collapse
Affiliation(s)
- Xingwei Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xingye Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Ying Xue
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Lilian Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yafang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Tao Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
| |
Collapse
|
8
|
OUP accepted manuscript. Brief Funct Genomics 2022; 21:243-269. [DOI: 10.1093/bfgp/elac007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
|
9
|
Deng YH, Zhang XX, Tao CY, Liang YJ, Yuan J, Yang SH, Yang YR, Xiong XY. Succinylation profiles of brain injury after intracerebral hemorrhage. PLoS One 2021; 16:e0259798. [PMID: 34780519 PMCID: PMC8592435 DOI: 10.1371/journal.pone.0259798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023] Open
Abstract
Protein posttranslational modifications (PTMs) regulate the biological processes of human diseases by genetic code expansion and cellular pathophysiology regulation; however, system-wide changes in PTM levels in the intracerebral hemorrhage (ICH) brain remain poorly understood. Succinylation refers to a major PTM during the regulation of multiple biological processes. In this study, according to the methods of quantitative succinyllysine proteomics based on high-resolution mass spectrometry, we investigated ICH-associated brain protein succinyllysine modifications and obtained 3,680 succinylated sites and quantified around 3,530 sites. Among them, 25 succinyllysine sites on 23 proteins were upregulated (hypersuccinylated), whereas 13 succinyllysine sites on 12 proteins were downregulated (hyposuccinylated) following ICH. The cell component enrichment analysis of these succinylproteins with significant changes showed that 58.3% of the hyposuccinylated proteins were observed in the mitochondria, while the hyper-succinylproteins located in mitochondria decreased in the percentage to about 35% in ICH brains with a concomitant increase in the percentage of cytoplasm to 30.4%. Further bioinformatic analysis showed that the succinylproteins were mostly mitochondria and synapse-related subcellular located and involved in many pathophysiological processes, like metabolism, synapse working, and ferroptosis. Moreover, the integrative analysis of our succinylproteomics data and previously published transcriptome data showed that the mRNAs matched by most differentially succinylated proteins were especially highly expressed in neurons, endothelial cells, and astrocytes. Our study uncovers some succinylation-affected processes and pathways in response to ICH brains and gives us novel insights into understanding pathophysiological processes of brain injury caused by ICH.
Collapse
Affiliation(s)
- Yuan-Hong Deng
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu, Sichuan Province, China
| | - Xin-Xiao Zhang
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu, Sichuan Province, China
| | - Chuan-Yuan Tao
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yan-Jing Liang
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu, Sichuan Province, China
| | - Jing Yuan
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu, Sichuan Province, China
| | - Su-Hao Yang
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu, Sichuan Province, China
| | - Yuan-Rui Yang
- Department of Geriatrics, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Xiao-Yi Xiong
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu, Sichuan Province, China
| |
Collapse
|
10
|
The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids. J Biol Chem 2021; 297:101155. [PMID: 34480900 PMCID: PMC8477199 DOI: 10.1016/j.jbc.2021.101155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 11/22/2022] Open
Abstract
Acylation modifications, such as the succinylation of lysine, are post-translational modifications and a powerful means of regulating protein activity. Some acylations occur nonenzymatically, driven by an increase in the concentration of acyl group donors. Lysine succinylation has a profound effect on the corresponding site within the protein, as it dramatically changes the charge of the residue. In eukaryotes, it predominantly affects mitochondrial proteins because the donor of succinate, succinyl-CoA, is primarily generated in the tricarboxylic acid cycle. Although numerous succinylated mitochondrial proteins have been identified in Saccharomyces cerevisiae, a more detailed characterization of the yeast mitochondrial succinylome is still lacking. Here, we performed a proteomic MS analysis of purified yeast mitochondria and detected 314 succinylated mitochondrial proteins with 1763 novel succinylation sites. The mitochondrial nucleoid, a complex of mitochondrial DNA and mitochondrial proteins, is one of the structures whose protein components are affected by succinylation. We found that Abf2p, the principal component of mitochondrial nucleoids responsible for compacting mitochondrial DNA in S. cerevisiae, can be succinylated in vivo on at least thirteen lysine residues. Abf2p succinylation in vitro inhibits its DNA-binding activity and reduces its sensitivity to digestion by the ATP-dependent ScLon protease. We conclude that changes in the metabolic state of a cell resulting in an increase in the concentration of tricarboxylic acid intermediates may affect mitochondrial functions.
Collapse
|
11
|
Huang Z, He L, Sang W, Wang L, Huang Q, Lei C. Potential role of lysine succinylation in the response of moths to artificial light at night stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112334. [PMID: 34020284 DOI: 10.1016/j.ecoenv.2021.112334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/14/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
Artificial light at night (ALAN) is a widespread environmental pollutant and stressor. Many nocturnal insects have been shown to experience ALAN stress. However, few studies have been conducted to uncover the mechanism by which nocturnal insects respond to ALAN stress. Previous studies suggest that lysine succinylation (Ksuc) is a potential mechanism that coordinates energy metabolism and antioxidant activity under stressful conditions. Mythimna separata (Walker) (M. separata) is a nocturnal insect that has been stressed by ALAN. In this study, we quantified the relative proteomic Ksuc levels in ALAN-stressed M. separata. Of the 466 identified Ksuc-modified proteins, 103 were hypersuccinylated/desuccinylated in ALAN-stressed moths. The hypersuccinylated/desuccinylated proteins were shown to be involved in various biological processes. In particular, they were enriched in metabolic processes, reactive oxygen species (ROS) homeostasis and the neuromuscular system. Furthermore, we demonstrated that Ksuc might affect moth locomotion by intervening with and coordinating these systems under ALAN stress. These findings suggest that Ksuc plays a vital role in the moth response to ALAN stress and moth locomotion behavior and provide a new perspective on the impact of ALAN on nocturnal insect populations and species communities.
Collapse
Affiliation(s)
- Zhijuan Huang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Li He
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wen Sang
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China.
| | - Lijun Wang
- College of Life Sciences, Yantai University, Yantai 264005, China.
| | - Qiuying Huang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chaoliang Lei
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
12
|
Li J, Pan H, Yang H, Wang C, Liu H, Zhou H, Li P, Li C, Lu X, Tian Y. Rhamnolipid Enhances the Nitrogen Fixation Activity of Azotobacter chroococcum by Influencing Lysine Succinylation. Front Microbiol 2021; 12:697963. [PMID: 34394039 PMCID: PMC8360865 DOI: 10.3389/fmicb.2021.697963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/28/2021] [Indexed: 11/23/2022] Open
Abstract
The enhancement of nitrogen fixation activity of diazotrophs is essential for safe crop production. Lysine succinylation (KSuc) is widely present in eukaryotes and prokaryotes and regulates various biological process. However, knowledge of the extent of KSuc in nitrogen fixation of Azotobacter chroococcum is scarce. In this study, we found that 250 mg/l of rhamnolipid (RL) significantly increased the nitrogen fixation activity of A. chroococcum by 39%, as compared with the control. Real-time quantitative reverse transcription PCR (qRT-PCR) confirmed that RL could remarkably increase the transcript levels of nifA and nifHDK genes. In addition, a global KSuc of A. chroococcum was profiled using a 4D label-free quantitative proteomic approach. In total, 5,008 KSuc sites were identified on 1,376 succinylated proteins. Bioinformatics analysis showed that the addition of RL influence on the KSuc level, and the succinylated proteins were involved in various metabolic processes, particularly enriched in oxidative phosphorylation, tricarboxylic acid cycle (TCA) cycle, and nitrogen metabolism. Meanwhile, multiple succinylation sites on MoFe protein (NifDK) may influence nitrogenase activity. These results would provide an experimental basis for the regulation of biological nitrogen fixation with KSuc and shed new light on the mechanistic study of nitrogen fixation.
Collapse
Affiliation(s)
- Jin Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Hu Pan
- Institute of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hui Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Huhu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Hui Zhou
- College of Food Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peiwang Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Xiangyang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| |
Collapse
|
13
|
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.
Collapse
|
14
|
Zhao Y, Han Y, Sun Y, Wei Z, Chen J, Niu X, An Q, Zhang L, Qi R, Gao X. Comprehensive Succinylome Profiling Reveals the Pivotal Role of Lysine Succinylation in Energy Metabolism and Quorum Sensing of Staphylococcus epidermidis. Front Microbiol 2021; 11:632367. [PMID: 33597936 PMCID: PMC7882547 DOI: 10.3389/fmicb.2020.632367] [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: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background Lysine succinylation is a newly identified posttranslational modification (PTM), which exists widely from prokaryotes to eukaryotes and participates in various cellular processes, especially in the metabolic processes. Staphylococcus epidermidis is a commensal bacterium in the skin, which attracts more attention as a pathogen, especially in immunocompromised patients and neonates by attaching to medical devices and forming biofilms. However, the significance of lysine succinylation in S. epidermidis proteins has not been investigated. Objectives The purpose of this study was to investigate the physiological and pathological processes of S. epidermidis at the level of PTM. Moreover, by analyzing previous succinylome datasets in various organisms, we tried to provide an in-depth understanding of lysine succinylation. Methods Using antibody affinity enrichment followed by LC-MS/MS analysis, we examined the succinylome of S. epidermidis (ATCC 12228). Then, bioinformatics analysis was performed, including Gene Ontology (GO), KEGG enrichment, motif characterization, secondary structure, protein–protein interaction, and BLAST analysis. Results A total of 1557 succinylated lysine sites in 649 proteins were identified in S. epidermidis (ATCC 12228). Among these succinylation proteins, GO annotation showed that proteins related to metabolic processes accounted for the most. KEGG pathway characterization indicated that proteins associated with the glycolysis/gluconeogenesis and citrate cycle (TCA cycle) pathway were more likely to be succinylated. Moreover, 13 conserved motifs were identified. The specific motif KsuD was conserved in model prokaryotes and eukaryotes. Succinylated proteins with this motif were highly enriched in the glycolysis/gluconeogenesis pathway. One succinylation site (K144) was identified in S-ribosylhomocysteine lyase, a key enzyme in the quorum sensing system, indicating the regulatory role succinylation may play in bacterial processes. Furthermore, 15 succinyltransferases and 18 desuccinylases (erasers) were predicted in S. epidermidis by BLAST analysis. Conclusion We performed the first comprehensive profile of succinylation in S. epidermidis and illustrated the significant role succinylation may play in energy metabolism, QS system, and other bacterial behaviors. This study may be a fundamental basis to investigate the underlying mechanisms of colonization, virulence, and infection of S. epidermidis, as well as provide a new insight into regulatory effects succinylation may lay on metabolic processes (Data are available via ProteomeXchange with identifier PXD022866).
Collapse
Affiliation(s)
- Yiping Zhao
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yang Han
- Department of Dermatology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Yuzhe Sun
- Department of Dermatology, Dermatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhendong Wei
- Department of Dermatology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jialong Chen
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xueli Niu
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Qian An
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Li Zhang
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ruiqun Qi
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xinghua Gao
- Key Laboratory of Immunodermatology, Department of Dermatology, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Ministry of Health and Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| |
Collapse
|
15
|
Shi R, Wang Y, Gao Y, Xu X, Mao S, Xiao Y, Song S, Wang L, Tian B, Zhao Y, Hua Y, Xu H. Succinylation at a key residue of FEN1 is involved in the DNA damage response to maintain genome stability. Am J Physiol Cell Physiol 2020; 319:C657-C666. [PMID: 32783654 DOI: 10.1152/ajpcell.00137.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human flap endonuclease 1 (FEN1) is a structure-specific, multifunctional endonuclease essential for DNA replication and repair. Our previous study showed that in response to DNA damage, FEN1 interacts with the PCNA-like Rad9-Rad1-Hus1 complex instead of PCNA to engage in DNA repair activities, such as stalled DNA replication fork repair, and undergoes SUMOylation by SUMO-1. Here, we report that succinylation of FEN1 was stimulated in response to DNA replication fork-stalling agents, such as ultraviolet (UV) irradiation, hydroxyurea, camptothecin, and mitomycin C. K200 is a key succinylation site of FEN1 that is essential for gap endonuclease activity and could be suppressed by methylation and stimulated by phosphorylation to promote SUMO-1 modification. Succinylation at K200 of FEN1 promoted the interaction of FEN1 with the Rad9-Rad1-Hus1 complex to rescue stalled replication forks. Impairment of FEN1 succinylation led to the accumulation of DNA damage and heightened sensitivity to fork-stalling agents. Altogether, our findings suggest an important role of FEN1 succinylation in regulating its roles in DNA replication and repair, thus maintaining genome stability.
Collapse
Affiliation(s)
- Rongyi Shi
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yiyi Wang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Ya Gao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Xiaoli Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Shuyu Mao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yue Xiao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Shuang Song
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| |
Collapse
|
16
|
Zhu Y, Jia C, Li F, Song J. Inspector: a lysine succinylation predictor based on edited nearest-neighbor undersampling and adaptive synthetic oversampling. Anal Biochem 2020; 593:113592. [DOI: 10.1016/j.ab.2020.113592] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 12/13/2022]
|
17
|
Xu X, Cao X, Yang J, Chen L, Liu B, Liu T, Jin Q. Proteome-Wide Identification of Lysine Propionylation in the Conidial and Mycelial Stages of Trichophyton rubrum. Front Microbiol 2019; 10:2613. [PMID: 31798556 PMCID: PMC6861857 DOI: 10.3389/fmicb.2019.02613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/28/2019] [Indexed: 01/05/2023] Open
Abstract
Posttranslational modifications (PTMs) exist in a wide variety of organisms and play key roles in regulating various essential biological processes. Lysine propionylation is a newly discovered PTM that has rarely been identified in fungi. Trichophyton rubrum (T. rubrum) is one of the most common fungal pathogens in the world and has been studied as an important model organism of anthropic pathogenic filamentous fungi. In this study, we performed a proteome-wide propionylation analysis in the conidial and mycelial stages of T. rubrum. A total of 157 propionylated sites on 115 proteins were identified, and the high confidence of propionylation identification was validated by parallel reaction monitoring (PRM) assay. The results show that the propionylated proteins were mostly involved in various metabolic pathways. Histones and 15 pathogenicity-related proteins were also targets for propionylation modification, suggesting their roles in epigenetic regulation and pathogenicity. A comparison of the conidial and mycelial stages revealed that most propionylated proteins and sites were growth-stage specific and independent of protein abundance. Based on the function classifications, the propionylated proteins had a similar distribution in both stages; however, some differences were also identified. Furthermore, our results show that the concentration of propionyl-CoA had a significant influence on the propionylation level. In addition to the acetylation, succinylation and propionylation identified in T. rubrum, 26 other PTMs were also found to exist in this fungus. Overall, our study provides the first global propionylation profile of a pathogenic fungus. These results would be a foundation for further research on the regulation mechanism of propionylation in T. rubrum, which will enhance our understanding of the physiological features of T. rubrum and provide some clues for the exploration of improved therapies to treat this medically important fungus.
Collapse
Affiliation(s)
- Xingye Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xingwei Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
18
|
Yuan H, Chen J, Yang Y, Shen C, Xu D, Wang J, Yan D, He Y, Zheng B. Quantitative succinyl-proteome profiling of Chinese hickory (Carya cathayensis) during the grafting process. BMC PLANT BIOLOGY 2019; 19:467. [PMID: 31684873 PMCID: PMC6829946 DOI: 10.1186/s12870-019-2072-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/14/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Chinese hickory (Carya cathayensis) is a popular nut plant having high economic value. Grafting is applied to accelerate the transition from vegetative phase to reproductive phase. Lysine succinylation occurs frequently in the proteins associated with metabolic pathways, which may participate in the regulation of the grafting process. However, the exact regulatory mechanism underlying grafting process in Chinese hickory has not been studied at post-translational modification level. RESULTS A comprehensive proteome-wide lysine succinylation profiling of Chinese hickory was explored by a newly developed method combining affinity enrichment and high-resolution LC-MS/MS. In total, 259 succinylation sites in 202 proteins were identified, representing the first comprehensive lysine succinylome in Chinese hickory. The succinylation was biased to occur in the cytosolic proteins of Chinese hickory. Moreover, four conserved succinylation motifs were identified in the succinylated peptides. Comparison of two grafting stages of Chinese hickory revealed that the differential expressed succinylated proteins were mainly involved in sugar metabolism, carbon fixation, amino acid metabolism and plant-pathogen interaction. Besides, seven heat shock proteins (HSPs) with 11 succinylation sites were also identified, all of which were observed to be up-regulated during the grafting process. CONCLUSIONS Succinylation of the proteins involved in amino acid biosynthesis might be required for a successful grafting. Succinylated HSPs might play a role in stress tolerance of the grafted Chinese hickory plants. Our results can be a good resource for functional validation of the succinylated proteins and a starting point for the investigation of molecular mechanisms during lysine succinylation occurring at grafting site.
Collapse
Affiliation(s)
- Huwei Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Juanjuan Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Ying Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Chenjia Shen
- College of Life and Environmental Sciences Hangzhou Normal University, Hangzhou, 310036 People’s Republic of China
| | - Dongbin Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Junfeng Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Daoliang Yan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Yi He
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| |
Collapse
|
19
|
Zhang LL, Li CW, Liu K, Liu Z, Liang BC, Yang YR, Shi XL. Discovery and Identification of Serum Succinyl-Proteome for Postmenopausal Women with Osteoporosis and Osteopenia. Orthop Surg 2019; 11:784-793. [PMID: 31663278 PMCID: PMC6819194 DOI: 10.1111/os.12519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/13/2019] [Accepted: 07/28/2019] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE For the purpose of providing evidence for the treatment of osteoporosis and osteopenia, this study retrospectively identified succinylation-modified sites and proteins in postmenopausal women, and bioinformatics analysis were performed. METHODS From January 2016 to June 2018, a total of 30 postmenopausal women aged from 55 to 70 years old were assigned to three groups: 10 cases with osteoporosis; 10 cases with osteopenia; and 10 cases with normal bone mass. Subsequently, the serum samples were collected from all cases for succinyl-proteome. Measures comprised label-free quantitative analysis, succinylation enrichment techniques, the liquid chromatograph-mass spectrometer/mass spectrometer (LC-MS/MS) methods, and bioinformatics. RESULTS A total of 113 succinylation sites on 35 proteins were identified based on quantitative information. The variation of the different multiple folds were more than 1.2 times as a significant increase for up-regulated and less than 1/1.2 times as a significant decrease for down-regulated. Among the quantified succinylation sites, 66 were up-regulated and 11 down-regulated in the Osteopenia/Normal comparison group, 24 were up-regulated and 44 down-regulated in the Osteoporosis/Osteopenia comparison group, 45 were up-regulated and 32 down-regulated in the Osteoporosis/Normal comparison group. Among the quantified succinylation proteins, 24 were up-regulated and 7 down-regulated in the Osteopenia/Normal comparison group, 15 were up-regulated and 20 down-regulated in the Osteoporosis/Osteopenia comparison group, 20 were up-regulated and 17 down-regulated in the Osteoporosis/Normal comparison group. The percentage of proteins differed in immune response, signaling pathway, proteolysis, lymphocyte, leukocyte, and cell activation. Four differentially expressed proteins (apolipoprotein A-I, apolipoprotein A-II, hemoglobin subunit alpha, and haptoglobin) contained quantitative information; they were mediated with receptors, factors, mechanisms, that related to bone metabolism. Hemoglobin subunit alpha was screened for diagnosis of osteopenia. CONCLUSIONS The succinyl-proteome experimental data indicated that apolipoprotein A-I, apolipoprotein A-II, hemoglobin subunit alpha, and haptoglobin were valuable for diagnosis and treatment in postmenopausal women with osteoporosis and osteopenia.
Collapse
Affiliation(s)
- Li-Li Zhang
- Department of Pathology, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Chun-Wen Li
- Department of Diagnostics of Traditional Chinese Medicine, College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Kang Liu
- Department of Osteology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhong Liu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bo-Cheng Liang
- Department of Osteology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Yi-Ran Yang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiao-Lin Shi
- Department of Osteology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| |
Collapse
|
20
|
Wang J, Li L, Chai R, Zhang Z, Qiu H, Mao X, Hao Z, Wang Y, Sun G. Succinyl-proteome profiling of Pyricularia oryzae, a devastating phytopathogenic fungus that causes rice blast disease. Sci Rep 2019; 9:3490. [PMID: 30837482 PMCID: PMC6401317 DOI: 10.1038/s41598-018-36852-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/27/2018] [Indexed: 11/21/2022] Open
Abstract
Pyricularia oryzae is the pathogen for rice blast disease, which is a devastating threat to rice production worldwide. Lysine succinylation, a newly identified post-translational modification, is associated with various cellular processes. Here, liquid chromatography tandem-mass spectrometry combined with a high-efficiency succinyl-lysine antibody was used to identify the succinylated peptides in P. oryzae. In total, 2109 lysine succinylation sites in 714 proteins were identified. Ten conserved succinylation sequence patterns were identified, among which, K*******Ksuc, and K**Ksuc, were two most preferred ones. The frequency of lysine succinylation sites, however, greatly varied among organisms, including plants, animals, and microbes. Interestingly, the numbers of succinylation site in each protein of P. oryzae were significantly greater than that of most previous published organisms. Gene ontology and KEGG analysis showed that these succinylated peptides are associated with a wide range of cellular functions, from metabolic processes to stimuli responses. Further analyses determined that lysine succinylation occurs on several key enzymes of the tricarboxylic acid cycle and glycolysis pathway, indicating that succinylation may play important roles in the regulation of basal metabolism in P. oryzae. Furthermore, more than 40 pathogenicity-related proteins were identified as succinylated proteins, suggesting an involvement of succinylation in pathogenicity. Our results provide the first comprehensive view of the P. oryzae succinylome and may aid to find potential pathogenicity-related proteins to control the rice blast disease. Significance Plant pathogens represent a great threat to world food security, and enormous reduction in the global yield of rice was caused by P. oryzae infection. Here, the succinylated proteins in P. oryzae were identified. Furthermore, comparison of succinylation sites among various species, indicating that different degrees of succinylation may be involved in the regulation of basal metabolism. This data facilitates our understanding of the metabolic pathways and proteins that are associated with pathogenicity.
Collapse
Affiliation(s)
- Jiaoyu Wang
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Ling Li
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
- The key laboratory for quality improvement of agricultural products of Zhejiang province, School of agricultural and food sciences, Zhejiang agriculture and forest university, Hangzhou, 311300, China
| | - Rongyao Chai
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Zhen Zhang
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Haiping Qiu
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Xueqin Mao
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Zhongna Hao
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Yanli Wang
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China
| | - Guochang Sun
- State key laboratory breeding base for Zhejiang sustainable pest and disease control, Institute of plant protection and microbiology, Zhejiang academy of agricultural sciences, Hangzhou, 310021, China.
| |
Collapse
|
21
|
Hasan MM, Khatun MS, Kurata H. Large-Scale Assessment of Bioinformatics Tools for Lysine Succinylation Sites. Cells 2019; 8:cells8020095. [PMID: 30696115 PMCID: PMC6406724 DOI: 10.3390/cells8020095] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 12/19/2022] Open
Abstract
Lysine succinylation is a form of posttranslational modification of the proteins that play an essential functional role in every aspect of cell metabolism in both prokaryotes and eukaryotes. Aside from experimental identification of succinylation sites, there has been an intense effort geared towards the development of sequence-based prediction through machine learning, due to its promising and essential properties of being highly accurate, robust and cost-effective. In spite of these advantages, there are several problems that are in need of attention in the design and development of succinylation site predictors. Notwithstanding of many studies on the employment of machine learning approaches, few articles have examined this bioinformatics field in a systematic manner. Thus, we review the advancements regarding the current state-of-the-art prediction models, datasets, and online resources and illustrate the challenges and limitations to present a useful guideline for developing powerful succinylation site prediction tools.
Collapse
Affiliation(s)
- Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
- Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| |
Collapse
|
22
|
Wang X, Chen X, Li J, Zhou X, Liu Y, Zhong L, Tang Y, Zheng H, Liu J, Zhan R, Chen L. Global analysis of lysine succinylation in patchouli plant leaves. HORTICULTURE RESEARCH 2019; 6:133. [PMID: 31814986 PMCID: PMC6885049 DOI: 10.1038/s41438-019-0216-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 09/25/2019] [Accepted: 10/23/2019] [Indexed: 05/03/2023]
Abstract
Lysine succinylation is a novel, naturally occurring posttranslational modification (PTM) in living organisms. Global lysine succinylation identification has been performed at the proteomic level in various species; however, the study of lysine succinylation in plant species is relatively limited. Patchouli plant (P. cablin (Blanco) Benth., Lamiaceae) is a globally important industrial plant and medicinal herb. In the present study, lysine succinylome analysis was carried out in patchouli plants to determine the potential regulatory role of lysine succinylation in patchouli growth, development, and physiology. The global succinylation sites and proteins in patchouli plants were screened with an immunoprecipitation affinity enrichment technique and advanced mass spectrometry-based proteomics. Several bioinformatic analyses, such as function classification and enrichment, subcellular location predication, metabolic pathway enrichment and protein-protein interaction networking, were conducted to characterize the functions of the identified sites and proteins. In total, 1097 succinylation sites in 493 proteins were detected in patchouli plants, among which 466 succinylation sites in 241 proteins were repeatedly identified within three independent experiments. The functional characterization of these proteins indicated that the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, photosynthesis processes, and amino acid biosynthesis may be regulated by lysine succinylation. In addition, these succinylated proteins showed a wide subcellular location distribution, although the chloroplast and cytoplasm were the top two preferred cellular components. Our study suggested the important role of lysine succinylation in patchouli plant physiology and biology and could serve as a useful reference for succinylation studies in other medicinal plants.
Collapse
Affiliation(s)
- Xiaobing Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Xiuzhen Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Junren Li
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Xuanxuan Zhou
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Yanting Liu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Liting Zhong
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Yun Tang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Hai Zheng
- Guangdong Institute of Traditional Chinese Medicine, Guangzhou, Guangdong, 510520 P. R. China
| | - Jiyun Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005 P.R. China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| | - Likai Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, Guangdong, 510006 P. R. China
| |
Collapse
|
23
|
Wang L, Xu X, Yang J, Chen L, Liu B, Liu T, Jin Q. Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum. BMC Genomics 2018; 19:933. [PMID: 30547762 PMCID: PMC6295003 DOI: 10.1186/s12864-018-5316-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Trichophyton rubrum (T. rubrum) is an important model organism of dermatophytes, which are the most common fungal pathogens worldwide. Despite the severity and prevalence of the infection caused by these pathogens, current therapies are not sufficient. MicroRNA (miRNA) is a class of small noncoding RNAs that are key factors in the regulation of gene expression. These miRNAs are reported to be highly conserved in different organisms and are involved in various essential cellular processes. In this study, we performed an integrated analysis of microRNA-like RNAs (milRNAs) and mRNAs between conidial and mycelial stages to investigate the roles of milRNAs in regulating the expression of target genes in T. rubrum. RESULTS A total of 158 conserved milRNAs and 12 novel milRNAs were identified in our study, corresponding to 5470 target genes, which were involved in various essential biological pathways. In addition, 137 target genes corresponding to 21 milRNAs were concurrent differentially expressed between the conidial and mycelial stages. Among these 137 target genes, 64 genes showed the opposite trend to their corresponding milRNAs in expression difference between the two stages, indicating possible negative regulation. Furthermore, 46% of differentially expressed target genes are involved in transcription, transcriptional and post-transcriptional regulation. Our results indicate that milRNAs might associate with other regulatory elements to control gene expression at both transcriptional and post-transcriptional level. CONCLUSIONS This study provides the first analysis of milRNA expression profile in T. rubrum as well as dermatophytes in general. The results revealed the roles of milRNAs in regulating gene expression between the two major growth stages of this fungus. Our study deepens our understanding of T. rubrum and will serve as a foundation for further investigations to combat this fungus.
Collapse
Affiliation(s)
- Lingling Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xingye Xu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| |
Collapse
|
24
|
Xu X, Liu T, Yang J, Chen L, Liu B, Wang L, Jin Q. The First Whole-Cell Proteome- and Lysine-Acetylome-Based Comparison between Trichophyton rubrum Conidial and Mycelial Stages. J Proteome Res 2018; 17:1436-1451. [PMID: 29564889 DOI: 10.1021/acs.jproteome.7b00793] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Trichophyton rubrum is the most common fungal pathogen in the world, which has been studied as an important dermatophyte model organism. Despite the prevalence of T. rubrum, the available antifungal therapies are not sufficiently efficient. In this study, we performed the first comparison between the two major growth stages of T. rubrum: conidial and mycelial stages, based on their whole-cell proteomes and lysine acetylomes. In total, 4343 proteins were identified in both stages, and 1879 proteins were identified as differentially expressed between the two stages. The results showed that secretory proteases were more abundant in conidia, while aerobic metabolism and protein synthesis were significantly activated in the mycelial stage. In addition, 386 acetylated sites on 285 proteins and 5414 acetylated sites on 2335 proteins were identified in conidia and mycelia, respectively. The acetylation modifications were highly involved in metabolism and protein synthesis in both stages but differentially involved in Kyoto Encyclopedia of Genes and Genomes pathways and in epigenetic regulation between the two stages. Furthermore, inhibition of acetyltransferases or deacetylases significantly inhibited fungal growth and induced apoptosis. These results will enhance our understanding of the biological and physiological characteristics of T. rubrum and facilitate the development of improved therapies targeting these medically important pathogenic fungi.
Collapse
Affiliation(s)
- Xingye Xu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730 , China
| | - Tao Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730 , China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730 , China
| | - Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730 , China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730 , China
| | - Lingling Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730 , China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730 , China
| |
Collapse
|