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Wang S, Jiang Y, Zhang W, Wei Y, Xiao X, Wei Z, Wen X, Dong Y, Jian J, Wang N, Pang H. The Effect of the Lysine Acetylation Modification of ClpP on the Virulence of Vibrio alginolyticus. Molecules 2024; 29:4278. [PMID: 39275125 PMCID: PMC11396845 DOI: 10.3390/molecules29174278] [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: 07/10/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 09/16/2024] Open
Abstract
Acetylation modification has become one of the most popular topics in protein post-translational modification (PTM) research and plays an important role in bacterial virulence. A previous study indicated that the virulence-associated caseinolytic protease proteolytic subunit (ClpP) is acetylated at the K165 site in Vibrio alginolyticus strain HY9901, but its regulation regarding the virulence of V. alginolyticus is still unknown. We further confirmed that ClpP undergoes lysine acetylation (Kace) modification by immunoprecipitation and Western blot analysis and constructed the complementation strain (C-clpP) and site-directed mutagenesis strains including K165Q and K165R. The K165R strain significantly increased biofilm formation at 36 h of incubation, and K165Q significantly decreased biofilm formation at 24 h of incubation. However, the acetylation modification of ClpP did not affect the extracellular protease (ECPase) activity. In addition, we found that the virulence of K165Q was significantly reduced in zebrafish by in vivo injection. To further study the effect of lysine acetylation on the pathogenicity of V. alginolyticus, GS cells were infected with four strains, namely HY9901, C-clpP, K165Q and K165R. This indicated that the effect of the K165Q strain on cytotoxicity was significantly reduced compared with the wild-type strain, while K165R showed similar levels to the wild-type strain. In summary, the results of this study indicate that the Kace of ClpP is involved in the regulation of the virulence of V. alginolyticus.
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Affiliation(s)
- Shi Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Yingying Jiang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Weijie Zhang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Yingzhu Wei
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Xing Xiao
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Zhiqing Wei
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Xiaoxin Wen
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Yuhang Dong
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Jichang Jian
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
| | - Na Wang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Huanying Pang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524025, China
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2
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Feng M, Yi X, Feng Y, He F, Xiao Z, Yao H. Acetyl-proteome profiling revealed the role of lysine acetylation in erythromycin resistance of Staphylococcus aureus. Heliyon 2024; 10:e35326. [PMID: 39170456 PMCID: PMC11336636 DOI: 10.1016/j.heliyon.2024.e35326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 07/21/2024] [Accepted: 07/26/2024] [Indexed: 08/23/2024] Open
Abstract
Background Staphylococcus aureus (S. aureus), a prevalent human pathogen known for its propensity to cause severe infections, has exhibited a growing resistance to antibiotics. Lysine acetylation (Kac) is a dynamic and reversible protein post-translational modification (PTM), played important roles in various physiological functions. Recent studies have shed light on the involvement of Kac modification in bacterial antibiotic resistance. However, the precise relationship between Kac modification and antibiotic resistance in S. aureus remains inadequately comprehended. Methods We compared the differential expression of acetylated proteins between erythromycin-resistant (Ery-R) and erythromycin-susceptible (Ery-S) strains of S. aureus by 4D label-free quantitative proteomics technology. Additionally, we employed motif analysis, functional annotation and PPI network to investigate the acetylome landscape and heterogeneity of S. aureus. Furthermore, polysome profiling experiments were performed to assess the translational status of ribosome. Results 6791 Kac sites were identified on 1808 proteins in S. aureus, among which 1907 sites in 483 proteins were quantified. A total of 548 Kac sites on 316 acetylated proteins were differentially expressed by erythromycin pressure. The differentially acetylated proteins were primarily enriched in ribosome assembly, glycolysis and lysine biosynthesis. Bioinformatic analyses implied that Kac modification of ribosomal proteins may play an important role in erythromycin resistance of S. aureus. Western bolt and polysome profiling experiments indicated that the increased Kac levels of ribosomal proteins in the resistant strain may partially offset the inhibitory effect of erythromycin on ribosome function. Conclusions Our findings confirm that Kac modification is related to erythromycin resistance in S. aureus and emphasize the potential roles of ribosomal proteins. These results expand our current knowledge of antibiotic resistance mechanisms, potentially guiding future research on PTM-mediated antibiotic resistance.
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Affiliation(s)
- Miao Feng
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Xiaoyu Yi
- Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Feng He
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zonghui Xiao
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Hailan Yao
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, Beijing, 100020, China
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3
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Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible N ε-Lysine Acylation in Bacteria. J Proteome Res 2024; 23:2733-2749. [PMID: 38442041 PMCID: PMC11296938 DOI: 10.1021/acs.jproteome.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Post-translational modifications (PTMs) have been extensively studied in both eukaryotes and prokaryotes. Lysine acetylation, originally thought to be a rare occurrence in bacteria, is now recognized as a prevalent and important PTM in more than 50 species. This expansion in interest in bacterial PTMs became possible with the advancement of mass spectrometry technology and improved reagents such as acyl-modification specific antibodies. In this Review, we discuss how mass spectrometry-based proteomic studies of lysine acetylation and other acyl modifications have contributed to our understanding of bacterial physiology, focusing on recently published studies from 2018 to 2023. We begin with a discussion of approaches used to study bacterial PTMs. Next, we discuss newly characterized acylomes, including acetylomes, succinylomes, and malonylomes, in different bacterial species. In addition, we examine proteomic contributions to our understanding of bacterial virulence and biofilm formation. Finally, we discuss the contributions of mass spectrometry to our understanding of the mechanisms of acetylation, both enzymatic and nonenzymatic. We end with a discussion of the current state of the field and possible future research avenues to explore.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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Guo Y, Wen H, Chen Z, Jiao M, Zhang Y, Ge D, Liu R, Gu J. Conjoint analysis of succinylome and phosphorylome reveals imbalanced HDAC phosphorylation-driven succinylayion dynamic contibutes to lung cancer. Brief Bioinform 2024; 25:bbae415. [PMID: 39179249 PMCID: PMC11343571 DOI: 10.1093/bib/bbae415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/17/2024] [Indexed: 08/26/2024] Open
Abstract
Cancerous genetic mutations result in a complex and comprehensive post-translational modification (PTM) dynamics, in which protein succinylation is well known for its ability to reprogram cell metabolism and is involved in the malignant evolution. Little is known about the regulatory interactions between succinylation and other PTMs in the PTM network. Here, we developed a conjoint analysis and systematic clustering method to explore the intermodification communications between succinylome and phosphorylome from eight lung cancer patients. We found that the intermodification coorperation in both parallel and series. Besides directly participating in metabolism pathways, some phosphosites out of mitochondria were identified as an upstream regulatory modification directing succinylome dynamics in cancer metabolism reprogramming. Phosphorylated activation of histone deacetylase (HDAC) in lung cancer resulted in the removal of acetylation and favored the occurrence of succinylation modification of mitochondrial proteins. These results suggest a tandem regulation between succinylation and phosphorylation in the PTM network and provide HDAC-related targets for intervening mitochondrial succinylation and cancer metabolism reprogramming.
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Affiliation(s)
- Yifan Guo
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Haoyu Wen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Zongwei Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Mengxia Jiao
- Shanghai Fifth People's Hospital and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Yuchen Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Ronghua Liu
- Shanghai Fifth People's Hospital and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Jie Gu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
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5
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Rizo J, Encarnación-Guevara S. Bacterial protein acetylation: mechanisms, functions, and methods for study. Front Cell Infect Microbiol 2024; 14:1408947. [PMID: 39027134 PMCID: PMC11254643 DOI: 10.3389/fcimb.2024.1408947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Lysine acetylation is an evolutionarily conserved protein modification that changes protein functions and plays an essential role in many cellular processes, such as central metabolism, transcriptional regulation, chemotaxis, and pathogen virulence. It can alter DNA binding, enzymatic activity, protein-protein interactions, protein stability, or protein localization. In prokaryotes, lysine acetylation occurs non-enzymatically and by the action of lysine acetyltransferases (KAT). In enzymatic acetylation, KAT transfers the acetyl group from acetyl-CoA (AcCoA) to the lysine side chain. In contrast, acetyl phosphate (AcP) is the acetyl donor of chemical acetylation. Regardless of the acetylation type, the removal of acetyl groups from acetyl lysines occurs only enzymatically by lysine deacetylases (KDAC). KATs are grouped into three main superfamilies based on their catalytic domain sequences and biochemical characteristics of catalysis. Specifically, members of the GNAT are found in eukaryotes and prokaryotes and have a core structural domain architecture. These enzymes can acetylate small molecules, metabolites, peptides, and proteins. This review presents current knowledge of acetylation mechanisms and functional implications in bacterial metabolism, pathogenicity, stress response, translation, and the emerging topic of protein acetylation in the gut microbiome. Additionally, the methods used to elucidate the biological significance of acetylation in bacteria, such as relative quantification and stoichiometry quantification, and the genetic code expansion tool (CGE), are reviewed.
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Affiliation(s)
| | - Sergio Encarnación-Guevara
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Lozano-Terol G, Chiozzi RZ, Gallego-Jara J, Sola-Martínez RA, Vivancos AM, Ortega Á, Heck AJ, Díaz MC, de Diego Puente T. Relative impact of three growth conditions on the Escherichia coli protein acetylome. iScience 2024; 27:109017. [PMID: 38333705 PMCID: PMC10850759 DOI: 10.1016/j.isci.2024.109017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
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Zheng J, Li Y, Liu N, Zhang J, Liu S, Tan H. Multi-omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1149-1162. [PMID: 36115661 PMCID: PMC11082262 DOI: 10.1016/j.gpb.2022.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Streptomycetes possess numerous gene clusters and the potential to produce a large amount of natural products. Histone deacetylase (HDAC) inhibitors play an important role in the regulation of histone modifications in fungi, but their roles in prokaryotes remain poorly understood. Here, we investigated the global effects of the HDAC inhibitor, sodium butyrate (SB), on marine-derived Streptomycesolivaceus FXJ 8.021, particularly focusing on the activation of secondary metabolite biosynthesis. The antiSMASH analysis revealed 33 secondary metabolite biosynthetic gene clusters (BGCs) in strain FXJ 8.021, among which the silent lobophorin BGC was activated by SB. Transcriptomic data showed that the expression of genes involved in lobophorin biosynthesis (ge00097-ge00139) and CoA-ester formation (e.g., ge02824), as well as the glycolysis/gluconeogenesis pathway (e.g., ge01661), was significantly up-regulated in the presence of SB. Intracellular CoA-ester analysis confirmed that SB triggered the biosynthesis of CoA-ester, thereby increasing the precursor supply for lobophorin biosynthesis. Further acetylomic analysis revealed that the acetylation levels on 218 sites of 190 proteins were up-regulated and those on 411 sites of 310 proteins were down-regulated. These acetylated proteins were particularly enriched in transcriptional and translational machinery components (e.g., elongation factor GE04399), and their correlations with the proteins involved in lobophorin biosynthesis were established by protein-protein interaction network analysis, suggesting that SB might function via a complex hierarchical regulation to activate the expression of lobophorin BGC. These findings provide solid evidence that acetylated proteins triggered by SB could affect the expression of genes involved in the biosynthesis of primary and secondary metabolites in prokaryotes.
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Affiliation(s)
- Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China.
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Dale AL, Man L, Cordwell SJ. Global Acetylomics of Campylobacter jejuni Shows Lysine Acetylation Regulates CadF Adhesin Processing and Human Fibronectin Binding. J Proteome Res 2023; 22:3519-3533. [PMID: 37830485 DOI: 10.1021/acs.jproteome.3c00391] [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] [Indexed: 10/14/2023]
Abstract
Lysine acetylation (KAc) is a reversible post-translational modification (PTM) that can alter protein structure and function; however, specific roles for KAc are largely undefined in bacteria. Acetyl-lysine immunoprecipitation and LC-MS/MS identified 5567 acetylated lysines on 1026 proteins from the gastrointestinal pathogen Campylobacter jejuni (∼63% of the predicted proteome). KAc was identified on proteins from all subcellular locations, including the outer membrane (OM) and extracellular proteins. Label-based LC-MS/MS identified proteins and KAc sites during growth in 0.1% sodium deoxycholate (DOC, a component of gut bile salts). 3410 acetylated peptides were quantified, and 784 (from 409 proteins) were differentially abundant in DOC growth. Changes in KAc involved multiple pathways, suggesting a dynamic role for this PTM in bile resistance. As observed elsewhere, we show KAc is primarily nonenzymatically mediated via acetyl-phosphate; however, the deacetylase CobB also contributes to a global elevation of this modification in DOC. We observed several multiply acetylated OM proteins and altered DOC abundance of acetylated peptides in the fibronectin (Fn)-binding adhesin CadF. We show KAc reduces CadF Fn binding and prevalence of lower mass variants. This study provides the first system-wide lysine acetylome of C. jejuni and contributes to our understanding of KAc as an emerging PTM in bacteria.
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Affiliation(s)
- Ashleigh L Dale
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
| | - Lok Man
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- Sydney Mass Spectrometry, The University of Sydney, New South Wales 2006, Australia
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9
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Watson PR, Christianson DW. Structure and Function of Kdac1, a Class II Deacetylase from the Multidrug-Resistant Pathogen Acinetobacter baumannii. Biochemistry 2023; 62:2689-2699. [PMID: 37624144 PMCID: PMC10528293 DOI: 10.1021/acs.biochem.3c00288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Proteomics studies indicate that 10% of proteins in the opportunistic pathogen Acinetobacter baumannii are acetylated, suggesting that lysine acetyltransferases and deacetylases function to maintain and regulate a robust bacterial acetylome. As the first step in exploring these fascinating prokaryotic enzymes, we now report the preparation and characterization of the lysine deacetylase Kdac1. We show that Kdac1 catalyzes the deacetylation of free acetyllysine and acetyllysine tetrapeptide assay substrates, and we also report the X-ray crystal structures of unliganded Kdac1 as well as its complex with the hydroxamate inhibitor Citarinostat. Kdac1 is a tetramer in solution and in the crystal; the crystal structure reveals that the L1 loop functions to stabilize quaternary structure, forming inter-subunit hydrogen bonds and salt bridges around a central arginine residue (R30). Surprisingly, the L1 loop partially blocks entry to the active site, but it is sufficiently flexible to allow for the binding of two Citarinostat molecules in the active site. The L12 loop is also important for maintaining quaternary structure; here, a conserved arginine (R278) accepts hydrogen bonds from the backbone carbonyl groups of residues in an adjacent monomer. Structural comparisons with two other prokaryotic lysine deacetylases reveal conserved residues in the L1 and L12 loops that similarly support tetramer assembly. These studies provide a structural foundation for understanding enzymes that regulate protein function in bacteria through reversible lysine acetylation, serving as a first step in the exploration of these enzymes as possible targets for the development of new antibiotics.
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Affiliation(s)
- Paris R. Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
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10
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Chen X, Wang S, Wu M, Zhao Y. Role of Succinylation in Pseudorabies Virus Infection. J Virol 2023; 97:e0179022. [PMID: 36975827 PMCID: PMC10134788 DOI: 10.1128/jvi.01790-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Affiliation(s)
- Xiaoyong Chen
- Institute of Animal Sciences, Wenzhou Academy of Agricultural Sciences, Zhejiang, People’s Republic of China
| | - Shuaiwei Wang
- Institute of Animal Sciences, Wenzhou Academy of Agricultural Sciences, Zhejiang, People’s Republic of China
| | - Mengzhe Wu
- Hangzhou Normal University, Hangzhou, People’s Republic of China
| | - Yan Zhao
- Institute of Animal Sciences, Wenzhou Academy of Agricultural Sciences, Zhejiang, People’s Republic of China
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11
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Duan H, Zhang X, Figeys D. An emerging field: Post-translational modification in microbiome. Proteomics 2023; 23:e2100389. [PMID: 36239139 DOI: 10.1002/pmic.202100389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
Post-translational modifications (PTMs) play an essential role in most biological processes. PTMs on human proteins have been extensively studied. Studies on bacterial PTMs are emerging, which demonstrate that bacterial PTMs are different from human PTMs in their types, mechanisms and functions. Few PTM studies have been done on the microbiome. Here, we reviewed several studied PTMs in bacteria including phosphorylation, acetylation, succinylation, glycosylation, and proteases. We discussed the enzymes responsible for each PTM and their functions. We also summarized the current methods used to study microbiome PTMs and the observations demonstrating the roles of PTM in the microbe-microbe interactions within the microbiome and their interactions with the environment or host. Although new methods and tools for PTM studies are still needed, the existing technologies have made great progress enabling a deeper understanding of the functional regulation of the microbiome. Large-scale application of these microbiome-wide PTM studies will provide a better understanding of the microbiome and its roles in the development of human diseases.
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Affiliation(s)
- Haonan Duan
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Xu Zhang
- Center for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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Tan L, Yang Y, Shang W, Hu Z, Peng H, Li S, Hu X, Rao X. Identification of Lysine Succinylome and Acetylome in the Vancomycin-Intermediate Staphylococcus aureus XN108. Microbiol Spectr 2022; 10:e0348122. [PMID: 36374118 PMCID: PMC9769639 DOI: 10.1128/spectrum.03481-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
Protein posttranslational modifications (PTMs) play important roles in regulating numerous biological functions of prokaryotic and eukaryotic organisms. Lysine succinylation (Ksucc) and acetylation (Kac) are two important PTMs that have been identified in various bacterial species. However, the biological functions of Ksucc and Kac in vancomycin-intermediate S. aureus (VISA) remain unclear. In this study, we systematically identified 3,260 Ksucc sites in 799 proteins and 7,935 Kac sites across 1,710 proteins in the VISA strain XN108. Functional analyses revealed that both Ksucc and Kac sites were highly enriched in several critical metabolic pathways, including ribosomal metabolism, tricarboxylic acid cycle, and glycolysis. Furthermore, a remarkable cross talk between Ksucc and Kac modifications was observed that almost 75% of the succinylated sites were also frequently acetylated. In addition, we identified SaCobB, a Sirtuin 2-like lysine deacetylase, as a bifunctional enzyme with both deacetylation and desuccinylation activities in S. aureus. We demonstrated the first lysine succinylome and acetylome in a VISA and identified SaCobB, a functional enzyme taking part in the regulation of Ksucc and Kac in S. aureus. Our findings provide valuable information for further study on the regulatory mechanisms of PTMs in S. aureus. IMPORTANCE Lysine succinylation (Ksucc) and acetylation (Kac) are two important protein posttranslational modifications (PTMs) that regulate numerous biological functions in prokaryotes and eukaryotes. However, the functions of Ksucc and Kac in Staphylococcus aureus are seldom described. Understanding of Ksucc and Kac modifications in S. aureus will facilitate the development of new strategies to control infections. Herein, we quantified both Ksucc and Kac in a vancomycin-intermediate S. aureus (VISA) strain XN108, analyzed the interaction between these two PTMs, and identified SaCobB as a bifunctional enzyme with both deacetylation and desuccinylation activities. This study is the first description of dual PTMs, Ksucc and Kac profiles, in the VISA. The findings could provide valuable information for the following researches on the regulatory roles of PTMs in S. aureus.
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Affiliation(s)
- Li Tan
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yi Yang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing, China
| | - Weilong Shang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhen Hu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing, China
| | - Huagang Peng
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shu Li
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xiaomei Hu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing, China
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13
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Umezawa K, Tsumoto H, Kawakami K, Miura Y. A chemical probe for proteomic analysis and visualization of intracellular localization of lysine-succinylated proteins. Analyst 2022; 148:95-104. [PMID: 36468704 DOI: 10.1039/d2an01370c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein acylation is a vital post-translational modification that regulates various protein functions. In particular, protein succinylation has attracted significant attention because of its potential relationship with various biological events and diseases. In this report, we establish a new method for the comprehensive detection and analysis of potentially succinylated proteins using a chemical tagging technology. The newly synthesized alkyne-containing succinyl substrate successfully labeled lysine residues of proteins through intracellular metabolic labeling independent of other acylation pathways such as protein malonylation. Furthermore, reporter molecules such as biotin moieties and fluorescent dyes were conjugated to alkyne-tagged succinylated proteins via Click reactions, permitting enrichment for proteomic analysis and fluorescence imaging of the labeled proteins. We successfully analyzed and identified numerous potential succinylated proteins associated with various biological processes using gel electrophoresis, proteomic and bioinformatic analyses, and their visualization in cells.
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Affiliation(s)
- Keitaro Umezawa
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, Japan.
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, Japan.
| | - Kyojiro Kawakami
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, Japan.
| | - Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, Japan.
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14
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Xiong L, Yi F, Yu Q, Huang X, Ao K, Wang Y, Xie Y. Transcriptomic analysis reveals the regulatory role of quorum sensing in the Acinetobacter baumannii ATCC 19606 via RNA-seq. BMC Microbiol 2022; 22:198. [PMID: 35971084 PMCID: PMC9380347 DOI: 10.1186/s12866-022-02612-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Background Acinetobacter baumannii has emerged as the major opportunistic pathogen in healthcare-associated infections with high-level antibiotic resistance and high mortality. Quorum sensing (QS) system is a cell-to-cell bacterial communication mediated by the synthesis, secretion, and binding of auto-inducer signals. It is a global regulatory system to coordinate the behavior of individual bacteria in a population. The present study focused on the QS system, aiming to investigate the regulatory role of QS in bacterial virulence and antibiotic resistance. Method The auto-inducer synthase gene abaI was deleted using the A. baumannii ATCC 19606 strain to interrupt the QS process. The RNA-seq was performed to identify the differentially expressed genes (DEGs) and pathways in the mutant (△abaI) strain compared with the wild-type (WT) strain. Results A total of 380 DEGs [the adjusted P value < 0.05 and the absolute value of log2(fold change) > log21.5] were identified, including 256 upregulated genes and 124 downregulated genes in the △abaI strain. The enrichment analysis indicated that the DEGs involved in arginine biosynthesis, purine metabolism, biofilm formation, and type VI secretion system (T6SS) were downregulated, while the DEGs involved in pathways related to fatty acid metabolism and amino acid metabolism were upregulated. Consistent with the expression change of the DEGs, a decrease in biofilm formation was observed in the △abaI strain compared with the WT strain. On the contrary, no obvious changes were found in antimicrobial resistance following the deletion of abaI. Conclusions The present study demonstrated the transcriptomic profile of A. baumannii after the deletion of abaI, revealing an important regulatory role of the QS system in bacterial virulence. The deletion of abaI suppressed the biofilm formation in A. baumannii ATCC 19606, leading to decreased pathogenicity. Further studies on the role of abaR, encoding the receptor of auto-inducer in the QS circuit, are required for a better understanding of the regulation of bacterial virulence and pathogenicity in the QS network. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02612-z.
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Affiliation(s)
- Li Xiong
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Fanli Yi
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Qiuju Yu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xiyue Huang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Keping Ao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanfang Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Xie
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.
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15
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Dade CM, Douzi B, Cambillau C, Ball G, Voulhoux R, Forest KT. The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases. Acta Crystallogr D Struct Biol 2022; 78:1064-1078. [PMID: 35916229 PMCID: PMC9344471 DOI: 10.1107/s2059798322007033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022] Open
Abstract
Pseudomonas aeruginosa secretes diverse proteins via its type 2 secretion system, including a 39 kDa chitin-binding protein, CbpD. CbpD has recently been shown to be a lytic polysaccharide monooxygenase active on chitin and to contribute substantially to virulence. To date, no structure of this virulence factor has been reported. Its first two domains are homologous to those found in the crystal structure of Vibrio cholerae GbpA, while the third domain is homologous to the NMR structure of the CBM73 domain of Cellvibrio japonicus CjLPMO10A. Here, the 3.0 Å resolution crystal structure of CbpD solved by molecular replacement is reported, which required ab initio models of each CbpD domain generated by the artificial intelligence deep-learning structure-prediction algorithm RoseTTAFold. The structure of CbpD confirms some previously reported substrate-specificity motifs among LPMOAA10s, while challenging the predictive power of others. Additionally, the structure of CbpD shows that post-translational modifications occur on the chitin-binding surface. Moreover, the structure raises interesting possibilities about how type 2 secretion-system substrates may interact with the secretion machinery and demonstrates the utility of new artificial intelligence protein structure-prediction algorithms in making challenging structural targets tractable.
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Affiliation(s)
- Christopher M. Dade
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Badreddine Douzi
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
- Aix-Marseille University, CNRS, AFMB, Marseille, France
| | | | - Genevieve Ball
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
| | - Romé Voulhoux
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
| | - Katrina T. Forest
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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16
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Acetylation of CspC Controls the Las Quorum-Sensing System through Translational Regulation of rsaL in Pseudomonas aeruginosa. mBio 2022; 13:e0054722. [PMID: 35467416 PMCID: PMC9239060 DOI: 10.1128/mbio.00547-22] [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] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous pathogenic bacterium that can adapt to a variety environments. The ability to effectively sense and respond to host local nutrients is critical for the infection of P. aeruginosa. However, the mechanisms employed by the bacterium to respond to nutrients remain to be explored. CspA family proteins are RNA binding proteins that are involved in gene regulation. We previously demonstrated that the P. aeruginosa CspA family protein CspC regulates the type III secretion system in response to temperature shift. In this study, we found that CspC regulates the quorum-sensing (QS) systems by repressing the translation of a QS negative regulatory gene, rsaL. Through RNA immunoprecipitation coupled with real-time quantitative reverse transcription-PCR (RIP-qRT-PCR) and electrophoretic mobility shift assays (EMSAs), we found that CspC binds to the 5′ untranslated region of the rsaL mRNA. Unlike glucose, itaconate (a metabolite generated by macrophages during infection) reduces the acetylation of CspC, which increases the affinity between CspC and the rsaL mRNA, leading to upregulation of the QS systems. Our results revealed a novel regulatory mechanism of the QS systems in response to a host-generated metabolite.
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17
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Fu Y, Zhang L, Song H, Liao J, Lin L, Jiang W, Wu X, Wang G. Acetylome and Succinylome Profiling of Edwardsiella tarda Reveals Key Roles of Both Lysine Acylations in Bacterial Antibiotic Resistance. Antibiotics (Basel) 2022; 11:841. [PMID: 35884095 PMCID: PMC9312108 DOI: 10.3390/antibiotics11070841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
The antibiotic resistance of Edwardsiella tarda is becoming increasingly prevalent, and thus novel antimicrobial strategies are being sought. Lysine acylation has been demonstrated to play an important role in bacterial physiological functions, while its role in bacterial antibiotic resistance remains largely unclear. In this study, we investigated the lysine acetylation and succinylation profiles of E. tarda strain EIB202 using affinity antibody purification combined with LC-MS/MS. A total of 1511 lysine-acetylation sites were identified on 589 proteins, and 2346 lysine-succinylation sites were further identified on 692 proteins of this pathogen. Further bioinformatic analysis showed that both post-translational modifications (PTMs) were enriched in the tricarboxylic acid (TCA) cycle, pyruvate metabolism, biosynthesis, and carbon metabolism. In addition, 948 peptides of 437 proteins had overlapping associations with multiple metabolic pathways. Moreover, both acetylation and succinylation were found in many antimicrobial resistance (AMR) proteins, suggesting their potentially vital roles in antibiotic resistance. In general, our work provides insights into the acetylome and succinylome features responsible for the antibiotic resistance mechanism of E. tarda, and the results may facilitate future investigations into the pathogenesis of this bacterium.
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Affiliation(s)
- Yuying Fu
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (H.S.)
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huanhuan Song
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (H.S.)
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junyan Liao
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Li Lin
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Wenjia Jiang
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Xiaoyun Wu
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Guibin Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (H.S.)
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing 102206, China
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18
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Sauvage S, Gaviard C, Tahrioui A, Coquet L, Le H, Alexandre S, Ben Abdelkrim A, Bouffartigues E, Lesouhaitier O, Chevalier S, Jouenne T, Hardouin J. Impact of Carbon Source Supplementations on Pseudomonas aeruginosa Physiology. J Proteome Res 2022; 21:1392-1407. [PMID: 35482949 DOI: 10.1021/acs.jproteome.1c00936] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen highly resistant to a wide range of antimicrobial agents, making its infections very difficult to treat. Since microorganisms need to perpetually adapt to their surrounding environment, understanding the effect of carbon sources on P. aeruginosa physiology is therefore essential to avoid increasing drug-resistance and better fight this pathogen. By a global proteomic approach and phenotypic assays, we investigated the impact of various carbon source supplementations (glucose, glutamate, succinate, and citrate) on the physiology of the P. aeruginosa PA14 strain. A total of 581 proteins were identified as differentially expressed in the 4 conditions. Most of them were more abundant in citrate supplementation and were involved in virulence, motility, biofilm development, and antibiotic resistance. Phenotypic assays were performed to check these hypotheses. By coupling all this data, we highlight the importance of the environment in which the bacterium evolves on its metabolism, and thus the necessity to better understand the metabolic pathways implied in its adaptative response according to the nutrient availability.
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Affiliation(s)
- Salomé Sauvage
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Charlotte Gaviard
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Ali Tahrioui
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Laurent Coquet
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Hung Le
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France
| | - Stéphane Alexandre
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France
| | - Ahmed Ben Abdelkrim
- Lactanet, Valacta, 555 Boul des Anciens-Combattants, Sainte-Anne-de-Bellevue, Québec H9X 3R4, Canada
| | - Emeline Bouffartigues
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Sylvie Chevalier
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Thierry Jouenne
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
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Sirt5-mediated desuccinylation of OPTN protects retinal ganglion cells from autophagic flux blockade in diabetic retinopathy. Cell Death Dis 2022; 8:63. [PMID: 35165261 PMCID: PMC8844082 DOI: 10.1038/s41420-022-00861-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/05/2022] [Accepted: 01/27/2022] [Indexed: 01/06/2023]
Abstract
Retinal neurodegeneration develops early in the course of diabetic retinopathy (DR), and our previous research showed that succinate accumulation results in retinal ganglion cells (RGCs) dysfunction in the retinas of rats with DR. Succinate can enhance lysine succinylation, but the succinylation of DR is not well understood. In this study, we investigated the role of the succinylome in DR and identified the key factor in this process. TMT labeling and LC–MS/MS analysis were combined to quantify the differentially succinylated proteins between vitreous humor (VH) samples from DR and non-DR patients. A total of 74 sites in 35 proteins were differentially succinylated between DR and non-DR vitreous humor samples, among which succinylation of the K108 site of optineurin (OPTN K108su) in the defense response was enriched by GO analysis based on the biological process category. Then, using a streptozotocin (STZ)-induced diabetic rat model, R28 cells and primary rat RGCs (rRGCs), we demonstrated that OPTN underwent lysine succinylation in the retinas of rats with DR and that OPTN K108su mediated autophagic flux blockade under high-glucose (HG) conditions. Sirt5 can desuccinylate OPTN K108su, thus protecting RGCs function from high glucose-induced RGCs autophagic flux blockade in the diabetic retina. Overall, desuccinylation of OPTN is an essential adaptive mechanism for ameliorating autophagic flux blockade in RGCs under DR conditions, and targeting the Sirt5-desuccK108-OPTN axis may thus open an avenue for therapeutic intervention in RCGs dysfunction. ![]()
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20
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Ye J, Li J. First analyses of lysine succinylation proteome and overlap between succinylation and acetylation in Solenopsis invicta Buren (Hymenoptera: Formicidae). BMC Genomics 2022; 23:61. [PMID: 35039013 PMCID: PMC8764763 DOI: 10.1186/s12864-021-08285-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/28/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Lysine succinylation (Ksu) exists in both eukaryotes and prokaryotes, and influences a variety of metabolism processes. However, little attention has been paid to Ksu in insects, especially the notorious invasive pest Solenopsis invicta. RESULTS In this study, the first analyses of Ksu proteome and overlap between Ksu and lysine acetylation (Kac) in S. invicta were presented. 3753 succinylated sites in 893 succinylated proteins were tested. The dihydrolipoyl dehydrogenase, V-type proton ATPase subunit G, and tubulin alpha chain all had evolutionary conservatism among diverse ant or bee species. Immunoblotting validation showed that there were many Ksu protein bands with a wide range of molecular mass. In addition, 1230 sites in 439 proteins were highly overlapped between Ksu and Kac. 54.05% of Ksu proteins in cytoplasm were acetylated. The results demonstrated that Ksu may play a vital part in the allergization, redox metabolism, sugar, fat, and protein metabolism, energy production, immune response, and biosynthesis of various secondary metabolites. CONCLUSIONS Ksu and Kac were two ubiquitous protein post-translational modifications participated in a variety of biological processes. Our results may supply rich resources and a starting point for the molecular basic research of regulation on metabolic pathways and other biological processes by succinylation and acetylation.
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Affiliation(s)
- Jingwen Ye
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of zoology, Guangdong Academy of Sciences, Xingang West Road 105, Guangzhou, Guangdong Province, 510260, People's Republic of China
| | - Jun Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of zoology, Guangdong Academy of Sciences, Xingang West Road 105, Guangzhou, Guangdong Province, 510260, People's Republic of China.
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21
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Ning Q, Ma Z, Zhao X, Yin M. SSKM_Succ: A Novel Succinylation Sites Prediction Method Incorporating K-Means Clustering With a New Semi-Supervised Learning Algorithm. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:643-652. [PMID: 32750881 DOI: 10.1109/tcbb.2020.3006144] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein succinylation is a type of post-translational modification (PTM) that occurs on lysine sites and plays a key role in protein conformation regulation and cellular function control. When training in computational method, it is difficult to designate negative samples because of the uncertainty of non-succinylation lysine sites, and if not handled properly, it may affect the performance of computational models dramatically. Therefore, we propose a new semi-supervised learning method to identify reliable non-succinylation lysine sites as negative samples. This method, named SSKM_Succ, also employs K-means clustering to divide data into 5 clusters. Besides, information of proximal PTMs and three kinds of sequence features (grey pseudo amino acid composition, K-space and position-special amino acid propensity) are utilized to formulate protein. Then, we perform a two-step feature selection to remove redundant features and construct the optimization model for each cluster. Finally, support vector machine is applied to construct a prediction model for each cluster. Promising results are obtained by this method with an accuracy of 80.18 percent for succinylation sites on the independent testing dataset. Meanwhile, we compare the result with other existing tools, and it shows that our method is promising for predicting succinylation sites. Through analysis, we further verify that succinylated protein has potential effects on amino acid degradation and fatty acid metabolism, and speculate that protein succinylation may be closely related to neurodegenerative diseases. The code of SSKM_Succ is available on the web https://github.com/yangyq505/SSKM_Succ.git.
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22
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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Yang Y, Zhang H, Guo Z, Zou S, Long F, Wu J, Li P, Zhao GP, Zhao W. Global Insights Into Lysine Acylomes Reveal Crosstalk Between Lysine Acetylation and Succinylation in Streptomyces coelicolor Metabolic Pathways. Mol Cell Proteomics 2021; 20:100148. [PMID: 34530157 PMCID: PMC8498004 DOI: 10.1016/j.mcpro.2021.100148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/08/2021] [Indexed: 02/09/2023] Open
Abstract
Lysine acylations are reversible and ubiquitous post-translational modifications that play critical roles in regulating multiple cellular processes. In the current study, highly abundant and dynamic acetylation, besides succinylation, was uncovered in a soil bacterium, Streptomyces coelicolor. By affinity enrichment using anti–acetyl-lysine antibody and the following LC−MS/MS analysis, a total of 1298 acetylation sites among 601 proteins were identified. Bioinformatics analyses suggested that these acetylated proteins have diverse subcellular localization and were enriched in a wide range of biological functions. Specifically, a majority of the acetylated proteins were also succinylated in the tricarboxylic acid cycle and protein translation pathways, and the bimodification occurred at the same sites in some proteins. The acetylation and succinylation sites were quantified by knocking out either the deacetylase ScCobB1 or the desuccinylase ScCobB2, demonstrating a possible competitive relationship between the two acylations. Moreover, in vitro experiments using synthetically modified peptides confirmed the regulatory crosstalk between the two sirtuins, which may be involved in the collaborative regulation of cell physiology. Collectively, these results provided global insights into the S. coelicolor acylomes and laid a foundation for characterizing the regulatory roles of the crosstalk between lysine acetylation and succinylation in the future. A highly abundant and dynamic acetylation is discovered in Streptomyces coelicolor. Quantitative acetylome and succinylome analyses in Streptomyces coelicolor. The bimodification proteins are enriched in multiple metabolic pathways.
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Affiliation(s)
- Yujiao Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Key Laboratory of Synthetic Biology, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhenyang Guo
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Siwei Zou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Fei Long
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiacheng Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Key Laboratory of Synthetic Biology, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Li
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China.
| | - Guo-Ping Zhao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Key Laboratory of Synthetic Biology, University of Chinese Academy of Sciences, Beijing, China.
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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24
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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: 6] [Impact Index Per Article: 2.0] [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.
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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: 8] [Impact Index Per Article: 2.7] [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.
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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.
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Abstract
Nε-lysine acetylation is an important, dynamic regulatory posttranslational modification (PTM) that is common in bacteria. Protein acetylomes have been characterized for more than 30 different species, and it is known that acetylation plays important regulatory roles in many essential biological processes. The levels of acetylation are enzymatically controlled by the opposing actions of lysine acetyltransferases and deacetylases. In bacteria, a second mechanism of acetylation exists and occurs via an enzyme-independent manner using the secondary metabolite acetyl-phosphate. Nonenzymatic acetylation accounts for global low levels of acetylation. Recently, studies concerning the role of protein acetylation in bacterial virulence have begun. Acetylated virulence factors have been identified and further characterized. The roles of the enzymes that acetylate and deacetylate proteins in the establishment of infection and biofilm formation have also been investigated. In this review, we discuss the acetylomes of human bacterial pathogens. We highlight examples of known acetylated virulence proteins and examine how they affect survival in the host. Finally, we discuss how acetylation might influence host-pathogen interactions and look at the contribution of acetylation to antimicrobial resistance.
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27
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Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence. Biochem Soc Trans 2021; 49:1905-1926. [PMID: 34374408 DOI: 10.1042/bst20191088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
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Li S, Weng Y, Li X, Yue Z, Chai Z, Zhang X, Gong X, Pan X, Jin Y, Bai F, Cheng Z, Wu W. Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa. Nucleic Acids Res 2021; 49:6756-6770. [PMID: 34139014 PMCID: PMC8266623 DOI: 10.1093/nar/gkab506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/25/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
The ability to fine tune global gene expression in response to host environment is critical for the virulence of pathogenic bacteria. The host temperature is exploited by the bacteria as a cue for triggering virulence gene expression. However, little is known about the mechanism employed by Pseudomonas aeruginosa to response to host body temperature. CspA family proteins are RNA chaperones that modulate gene expression. Here we explored the functions of P. aeruginosa CspA family proteins and found that CspC (PA0456) controls the bacterial virulence. Combining transcriptomic analyses, RNA-immunoprecipitation and high-throughput sequencing (RIP-Seq), we demonstrated that CspC represses the type III secretion system (T3SS) by binding to the 5' untranslated region of the mRNA of exsA, which encodes the T3SS master regulatory protein. We further demonstrated that acetylation at K41 of the CspC reduces its affinity to nucleic acids. Shifting the culture temperature from 25°C to 37°C or infection of mouse lung increased the CspC acetylation, which derepressed the expression of the T3SS genes, resulting in elevated virulence. Overall, our results identified the regulatory targets of CspC and revealed a regulatory mechanism of the T3SS in response to temperature shift and host in vivo environment.
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Affiliation(s)
- Shouyi Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuding Weng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaoxiao Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhuo Yue
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhouyi Chai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xinxin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xuetao Gong
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
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Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics. mBio 2021; 12:e0053021. [PMID: 34182779 PMCID: PMC8437408 DOI: 10.1128/mbio.00530-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Penicillin binding protein 2a (PBP2a)-dependent resistance to β-lactam antibiotics in methicillin-resistant Staphylococcus aureus (MRSA) is regulated by the activity of the tricarboxylic acid (TCA) cycle via a poorly understood mechanism. We report that mutations in sucC and sucD, but not other TCA cycle enzymes, negatively impact β-lactam resistance without changing PBP2a expression. Increased intracellular levels of succinyl coenzyme A (succinyl-CoA) in the sucC mutant significantly perturbed lysine succinylation in the MRSA proteome. Suppressor mutations in sucA or sucB, responsible for succinyl-CoA biosynthesis, reversed sucC mutant phenotypes. The major autolysin (Atl) was the most succinylated protein in the proteome, and increased Atl succinylation in the sucC mutant was associated with loss of autolytic activity. Although PBP2a and PBP2 were also among the most succinylated proteins in the MRSA proteome, peptidoglycan architecture and cross-linking were unchanged in the sucC mutant. These data reveal that perturbation of the MRSA succinylome impacts two interconnected cell wall phenotypes, leading to repression of autolytic activity and increased susceptibility to β-lactam antibiotics.
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30
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Miao Y, Wang Y, Huang D, Lin X, Lin Z, Lin X. Profile of protein lysine propionylation in Aeromonas hydrophila and its role in enzymatic regulation. Biochem Biophys Res Commun 2021; 562:1-8. [PMID: 34030039 DOI: 10.1016/j.bbrc.2021.05.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 11/18/2022]
Abstract
Protein lysine propionylation (Kpr) modification is a novel post-translational modification (PTM) of prokaryotic cells that was recently discovered; however, it is not clear how this modification regulates bacterial life. In this study, the protein Kpr modification profile in Aeromonas hydrophila was identified by high specificity antibody-based affinity enrichment combined with high resolution LC MS/MS. A total of 98 lysine-propionylated peptides with 59 Kpr proteins were identified, most of which were associated with energy metabolism, transcription and translation processes. To further understand the role of Kpr modified proteins, the K168 site on malate dehydrogenase (MDH) and K608 site on acetyl-coenzyme A synthetase (AcsA) were subjected to site-directed mutation to arginine (R) and glutamine (Q) to simulate deacylation and propionylation, respectively. Subsequent measurement of the enzymatic activity showed that the K168 site of Kpr modification on MDH may negatively regulate the MDH enzymatic activity while also affecting the survival of mdh derivatives when using glucose as the carbon source, whereas Kpr modification of K608 of AcsA does not. Overall, the results of this study indicate that protein Kpr modification plays an important role in bacterial biological functions, especially those involved in the activity of metabolic enzymes.
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Affiliation(s)
- Yuxuan Miao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Yuqian Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Dongping Huang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Xiaoke Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Zhenping Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
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31
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Le H, Arnoult C, Dé E, Schapman D, Galas L, Le Cerf D, Karakasyan C. Antibody-Conjugated Nanocarriers for Targeted Antibiotic Delivery: Application in the Treatment of Bacterial Biofilms. Biomacromolecules 2021; 22:1639-1653. [PMID: 33709706 DOI: 10.1021/acs.biomac.1c00082] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conventional antibiotic treatment is in most cases insufficient to eradicate biofilm-related infections, resulting in high risk of treatment failure and recurrent infections. Recent studies have shown that novel methods of antibiotic delivery can improve clinical outcomes and reduce the emergence of antibiotic resistance. The objectives of this work were to develop and evaluate a targeting nanocarrier system that enables effective delivery of antimicrobial drugs to Staphylococcus aureus, a commonly virulent human pathogen. For this purpose, we first prepared a formulation of polymeric nanoparticles (NPs) suitable for encapsulation and sustained release of antibiotics. A specific antibody against S. aureus was used as a targeting ligand and was covalently immobilized onto the surface of nanoparticulate materials. It was demonstrated that the targeting NPs preferentially bound S. aureus cells and presented an elevated accumulation in the S. aureus biofilm. Compared to free-form antibiotic, the antibiotic-loaded targeting NPs significantly enhanced in vitro bactericidal activity against S. aureus both in planktonic and biofilm forms. Using a mouse infection model, we observed improved therapeutic efficacy of these antibiotic-loaded NPs after a single intravenous administration. Taken together, our studies show that the targeting nanoparticulate system could be a promising strategy to enhance the biodistribution of antibiotics and thereby improve their efficacy.
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Affiliation(s)
- Hung Le
- Normandie Université, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
| | - Christophe Arnoult
- Normandie Université, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
| | - Emmanuelle Dé
- Normandie Université, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
| | - Damien Schapman
- Normandie Université, UNIROUEN, INSERM, PRIMACEN, 76000 Rouen, France
| | - Ludovic Galas
- Normandie Université, UNIROUEN, INSERM, PRIMACEN, 76000 Rouen, France
| | - Didier Le Cerf
- Normandie Université, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
| | - Carole Karakasyan
- Normandie Université, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
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Ofori S, Gukathasan S, Awuah SG. Gold-Based Pharmacophore Inhibits Intracellular MYC Protein. Chemistry 2021; 27:4168-4175. [PMID: 33275307 PMCID: PMC8605874 DOI: 10.1002/chem.202004962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/03/2020] [Indexed: 12/13/2022]
Abstract
Direct targeting of intrinsically disordered proteins, including MYC, by small molecules for biomedical applications would resolve a longstanding issue in chemical biology and medicine. Thus, we developed gold-based small-molecule MYC reagents that engage MYC inside cells and modulate MYC transcriptional activity. Lead compounds comprise an affinity ligand and a gold(I) or gold(III) warhead capable of protein chemical modification. Cell-based MYC target engagement studies via CETSA and co-immunoprecipitation reveal specific interaction of compounds with MYC in cells. The lead gold(I) reagent, 1, demonstrates superior cell-killing potential (up to 35-fold) in a MYC-dependent manner when compared to 10058-F4 in cells including the TNBC, MDA-MB-231. Subsequently, 1 suppresses MYC transcription factor activity via functional colorimetric assays, and gene-profiling using whole-cell transcriptomics reveals significant modulation of MYC target genes by 1. These findings point to metal-mediated ligand affinity chemistry (MLAC) based on gold as a promising strategy to develop chemical probes and anticancer therapeutics targeting MYC.
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Affiliation(s)
- Samuel Ofori
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington Kentucky, 40506
| | - Sailajah Gukathasan
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington Kentucky, 40506
| | - Samuel G. Awuah
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington Kentucky, 40506
- Center for Pharmaceutical and Research Innovation, College of Pharmacy, Department of Pharmaceutical Sciences, University of Kentucky, Lexington Kentucky, 40536
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33
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Askarian F, Uchiyama S, Masson H, Sørensen HV, Golten O, Bunæs AC, Mekasha S, Røhr ÅK, Kommedal E, Ludviksen JA, Arntzen MØ, Schmidt B, Zurich RH, van Sorge NM, Eijsink VGH, Krengel U, Mollnes TE, Lewis NE, Nizet V, Vaaje-Kolstad G. The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection. Nat Commun 2021; 12:1230. [PMID: 33623002 PMCID: PMC7902821 DOI: 10.1038/s41467-021-21473-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/29/2021] [Indexed: 12/20/2022] Open
Abstract
The recently discovered lytic polysaccharide monooxygenases (LPMOs), which cleave polysaccharides by oxidation, have been associated with bacterial virulence, but supporting functional data is scarce. Here we show that CbpD, the LPMO of Pseudomonas aeruginosa, is a chitin-oxidizing virulence factor that promotes survival of the bacterium in human blood. The catalytic activity of CbpD was promoted by azurin and pyocyanin, two redox-active virulence factors also secreted by P. aeruginosa. Homology modeling, molecular dynamics simulations, and small angle X-ray scattering indicated that CbpD is a monomeric tri-modular enzyme with flexible linkers. Deletion of cbpD rendered P. aeruginosa unable to establish a lethal systemic infection, associated with enhanced bacterial clearance in vivo. CbpD-dependent survival of the wild-type bacterium was not attributable to dampening of pro-inflammatory responses by CbpD ex vivo or in vivo. Rather, we found that CbpD attenuates the terminal complement cascade in human serum. Studies with an active site mutant of CbpD indicated that catalytic activity is crucial for virulence function. Finally, profiling of the bacterial and splenic proteomes showed that the lack of this single enzyme resulted in substantial re-organization of the bacterial and host proteomes. LPMOs similar to CbpD occur in other pathogens and may have similar immune evasive functions.
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Affiliation(s)
- Fatemeh Askarian
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
| | - Satoshi Uchiyama
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, UC San Diego, La Jolla, CA, USA
| | - Helen Masson
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | | | - Ole Golten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anne Cathrine Bunæs
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sophanit Mekasha
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Åsmund Kjendseth Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Eirik Kommedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | | | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Benjamin Schmidt
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, UC San Diego, La Jolla, CA, USA
| | - Raymond H Zurich
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, UC San Diego, La Jolla, CA, USA
| | - Nina M van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ute Krengel
- Department of Chemistry, University of Oslo, Oslo, Norway
| | - Tom Eirik Mollnes
- Research Laboratory, Nordland Hospital, Bodø, Norway
- K.G. Jebsen TREC, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- Department of Immunology, Oslo University Hospital, and K.G. Jebsen IRC, University of Oslo, Oslo, Norway
- Center of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - Nathan E Lewis
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, UC San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Victor Nizet
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, UC San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, CA, USA.
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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Li X, Wang L, Wang M, Zhang Z, Ma C, Ma X, Na X, Liang W. Global analysis of protein succinylation modification of Nostoc flagelliforme in response to dehydration. J Proteomics 2021; 237:104149. [PMID: 33588108 DOI: 10.1016/j.jprot.2021.104149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/13/2021] [Accepted: 02/02/2021] [Indexed: 11/29/2022]
Abstract
Nostoc flagelliforme is a type of terrestrial cyanobacteria that is distributed in arid or semi-arid steppes in China. To research the molecular mechanisms underlying the adaptation of N. flagelliforme to drought stress, the succinylated expression profile and changes in N. flagelliforme that resulted as a response to dehydration were analyzed by label-free proteomics. A total of 1149 succinylated sites, 1128 succinylated peptides, and 396 succinylated proteins were identified. Succinylated proteins were differentially involved in photosynthesis and energy metabolism, as well as in reactive oxygen species (ROS) scavenging. Motif-X analysis of succinylated sites determined a succinylation motif [KxxG]. N. flagelliforme adapts to dehydration by increasing glucose metabolism and pentose phosphate pathway flux, and decreasing photosynthetic rate, which some of the key proteins were succinylated. ROS scavenging was mainly involved in the regulation of the enzyme antioxidant defense system and non-enzymatic antioxidant defense system through succinylation modification, thus eliminating excessive ROS. Protein succinylation of N. flagelliforme may play an important regulatory role in response to dehydration. The results are foundational, as they can inform future research into the mechanisms involved in the succinylation regulation mechanism of N. flagelliforme in response to dehydration. SIGNIFICANCE: The global succinylation network involved in response to dehydration in N. flagelliforme has been established. We found that many succinylated proteins were involved in photosynthesis, glucose metabolism and antioxidation. The global survey of succinylated proteins and the changes of succinylated levels in response to dehydration provided effective information for the drought tolerance mechanism in N. flagelliforme.
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Affiliation(s)
- Xiaoxu Li
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Lingxia Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Meng Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Zheng Zhang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Caixia Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Xiaorong Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Xiaofan Na
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China.
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Zeng F, Pang H, Chen Y, Zheng H, Li W, Ramanathan S, Hoare R, Monaghan SJ, Lin X, Jian J. First Succinylome Profiling of Vibrio alginolyticus Reveals Key Role of Lysine Succinylation in Cellular Metabolism and Virulence. Front Cell Infect Microbiol 2021; 10:626574. [PMID: 33614530 PMCID: PMC7892601 DOI: 10.3389/fcimb.2020.626574] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
Recent studies have shown that a key strategy of many pathogens is to use post-translational modification (PTMs) to modulate host factors critical for infection. Lysine succinylation (Ksuc) is a major PTM widespread in prokaryotic and eukaryotic cells, and is associated with the regulation of numerous important cellular processes. Vibrio alginolyticus is a common pathogen that causes serious disease problems in aquaculture. Here we used the affinity enrichment method with LC-MS/MS to report the first identification of 2082 lysine succinylation sites on 671 proteins in V. alginolyticus, and compared this with the lysine acetylation of V. alginolyticus in our previous work. The Ksuc modification of SodB and PEPCK proteins were further validated by Co-immunoprecipitation combined with Western blotting. Bioinformatics analysis showed that the identified lysine succinylated proteins are involved in various biological processes and central metabolism pathways. Moreover, a total of 1,005 (25.4%) succinyl sites on 502 (37.3%) proteins were also found to be acetylated, which indicated that an extensive crosstalk between acetylation and succinylation in V. alginolyticus occurs, especially in three central metabolic pathways: glycolysis/gluconeogenesis, TCA cycle, and pyruvate metabolism. Furthermore, we found at least 50 (7.45%) succinylated virulence factors, including LuxS, Tdh, SodB, PEPCK, ClpP, and the Sec system to play an important role in bacterial virulence. Taken together, this systematic analysis provides a basis for further study on the pathophysiological role of lysine succinylation in V. alginolyticus and provides targets for the development of attenuated vaccines.
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Affiliation(s)
- Fuyuan Zeng
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Huanying Pang
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China, Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Hongwei Zheng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
| | - Wanxin Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Srinivasan Ramanathan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rowena Hoare
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Sean J. Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jichang Jian
- Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhan jiang), Zhanjiang, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China, Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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36
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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).
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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
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Pang R, Li Y, Liao K, Guo P, Li Y, Yang X, Zhang S, Lei T, Wang J, Chen M, Wu S, Xue L, Wu Q. Genome- and Proteome-Wide Analysis of Lysine Acetylation in Vibrio vulnificus Vv180806 Reveals Its Regulatory Roles in Virulence and Antibiotic Resistance. Front Microbiol 2020; 11:591287. [PMID: 33250879 PMCID: PMC7674927 DOI: 10.3389/fmicb.2020.591287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/15/2020] [Indexed: 12/31/2022] Open
Abstract
Infection with Vibrio vulnificus is notorious for its atypical clinical manifestations and irreversible disease progression. Lysine acetylation is a conserved post-translational modification (PTM) that plays a critical regulatory role in diverse cellular processes. However, little is known about the role of lysine acetylation on the pathogenesis of V. vulnificus. Here, we report the complete genome sequence and a global profile for protein lysine acetylation of V. vulnificus Vv180806, a highly cefoxitin resistant strain isolated from a mortality case. The assembled genome comprised two circular chromosomes and one circular plasmid; it contained 4,770 protein-coding genes and 153 RNA genes. Phylogenetic analysis revealed genetic homology of this strain with other V. vulnificus strains from food sources. Of all the proteins in this strain, 1,924 (40.34%) were identified to be acetylated at 6,626 sites. The acetylated proteins were enriched in metabolic processes, binding functions, cytoplasm, and multiple central metabolic pathways. Moreover, the acetylation was found in most identified virulence factors of this strain, suggesting its potentially important role in bacterial virulence. Our work provides insights into the genomic and acetylomic features responsible for the virulence and antibiotic resistance of V. vulnificus, which will facilitate future investigations on the pathogenesis of this bacterium.
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Affiliation(s)
- Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Penghao Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanping Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuhong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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38
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Zeng J, Wu L, Chen Q, Wang L, Qiu W, Zheng X, Yin X, Liu J, Ren Y, Li Y. Comprehensive profiling of protein lysine acetylation and its overlap with lysine succinylation in the Porphyromonas gingivalis fimbriated strain ATCC 33277. Mol Oral Microbiol 2020; 35:240-250. [PMID: 32939976 DOI: 10.1111/omi.12312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Porphyromonas gingivalis is a pathogen closely associated with periodontal and systemic infections. Recently, lysine acetylation (Kac) and lysine succinylation (Ksuc) have been identified in bacterial proteins with diverse biological and pathological functions. The Ksuc of P. gingivalis ATCC 33277 has been characterized in our previous work, and here, we report the systematic analysis of Kac and its crosstalk with Ksuc in this bacterium. A combination of the affinity enrichment by the acetyl-lysine antibody with highly sensitive LC-MS/MS was used to identify the lysine-acetylated proteins and sites in P. gingivalis ATCC 33277. A total of 1,112 lysine-acetylated sites matching 438 proteins were identified. These proteins involved in several cellular processes, especially those proteins related to protein biosynthesis and central metabolism had a high tendency to be lysine acetylated. Moreover, lysine sites flanked by tyrosine, phenylalanine, and histidine in the +1 position, as well as residue lysine in position +4 to +5, were the targets of Kac. Additionally, proteins involved in adhesins, gingipains, black pigmentation, and oxidative stress resistance were identified as substrates of Kac. Collectively, these results suggest Kac may play a critical role in the regulation of physiology and virulence of P. gingivalis. Furthermore, we discovered that, Ksuc and Kac were extensively overlapped in P. gingivalis ATCC 33277, especially in proteins related to ribosomes and metabolism. This study provides a significant beginning for further investigating the role of Kac and Ksuc in the pathogenicity of P. gingivalis.
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Affiliation(s)
- Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Leng Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiushi Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Lingyun Wang
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Qiu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xin Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoming Yin
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jie Liu
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yan Ren
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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Abstract
Acetylation was initially discovered as a post-translational modification (PTM) on the unstructured, highly basic N-terminal tails of eukaryotic histones in the 1960s. Histone acetylation constitutes part of the "histone code", which regulates chromosome compaction and various DNA processes such as gene expression, recombination, and DNA replication. In bacteria, nucleoid-associated proteins (NAPs) are responsible these functions in that they organize and compact the chromosome and regulate some DNA processes. The highly conserved DNABII family of proteins are considered functional homologues of eukaryotic histones despite having no sequence or structural conservation. Within the past decade, a growing interest in Nε-lysine acetylation led to the discovery that hundreds of bacterial proteins are acetylated with diverse cellular functions, in direct contrast to the original thought that this was a rare phenomenon. Similarly, other previously undiscovered bacterial PTMs, like serine, threonine, and tyrosine phosphorylation, have also been characterized. In this review, the various PTMs that were discovered among DNABII family proteins, specifically histone-like protein (HU) orthologues, from large-scale proteomic studies are discussed. The functional significance of these modifications and the enzymes involved are also addressed. The discovery of novel PTMs on these proteins begs this question: is there a histone-like code in bacteria?
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Affiliation(s)
- Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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40
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Forrest S, Welch M. Arming the troops: Post-translational modification of extracellular bacterial proteins. Sci Prog 2020; 103:36850420964317. [PMID: 33148128 PMCID: PMC10450907 DOI: 10.1177/0036850420964317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein secretion is almost universally employed by bacteria. Some proteins are retained on the cell surface, whereas others are released into the extracellular milieu, often playing a key role in virulence. In this review, we discuss the diverse types and potential functions of post-translational modifications (PTMs) occurring to extracellular bacterial proteins.
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Affiliation(s)
- Suzanne Forrest
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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41
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Sauvage S, Hardouin J. Exoproteomics for Better Understanding Pseudomonas aeruginosa Virulence. Toxins (Basel) 2020; 12:E571. [PMID: 32899849 PMCID: PMC7551764 DOI: 10.3390/toxins12090571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/25/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is the most common human opportunistic pathogen associated with nosocomial diseases. In 2017, the World Health Organization has classified P. aeruginosa as a critical agent threatening human health, and for which the development of new treatments is urgently necessary. One interesting avenue is to target virulence factors to understand P. aeruginosa pathogenicity. Thus, characterising exoproteins of P. aeruginosa is a hot research topic and proteomics is a powerful approach that provides important information to gain insights on bacterial virulence. The aim of this review is to focus on the contribution of proteomics to the studies of P. aeruginosa exoproteins, highlighting its relevance in the discovery of virulence factors, post-translational modifications on exoproteins and host-pathogen relationships.
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Affiliation(s)
- Salomé Sauvage
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, CEDEX, F-76821 Mont-Saint-Aignan, France;
- PISSARO Proteomics Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, CEDEX, F-76821 Mont-Saint-Aignan, France;
- PISSARO Proteomics Facility, IRIB, F-76820 Mont-Saint-Aignan, France
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42
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Ceyssens PJ, De Smet J, Wagemans J, Akulenko N, Klimuk E, Hedge S, Voet M, Hendrix H, Paeshuyse J, Landuyt B, Xu H, Blanchard J, Severinov K, Lavigne R. The Phage-Encoded N-Acetyltransferase Rac Mediates Inactivation of Pseudomonas aeruginosa Transcription by Cleavage of the RNA Polymerase Alpha Subunit. Viruses 2020; 12:v12090976. [PMID: 32887488 PMCID: PMC7552054 DOI: 10.3390/v12090976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/20/2022] Open
Abstract
In this study, we describe the biological function of the phage-encoded protein RNA polymerase alpha subunit cleavage protein (Rac), a predicted Gcn5-related acetyltransferase encoded by phiKMV-like viruses. These phages encode a single-subunit RNA polymerase for transcription of their late (structure- and lysis-associated) genes, whereas the bacterial RNA polymerase is used at the earlier stages of infection. Rac mediates the inactivation of bacterial transcription by introducing a specific cleavage in the α subunit of the bacterial RNA polymerase. This cleavage occurs within the flexible linker sequence and disconnects the C-terminal domain, required for transcription initiation from most highly active cellular promoters. To achieve this, Rac likely taps into a novel post-translational modification (PTM) mechanism within the host Pseudomonas aeruginosa. From an evolutionary perspective, this novel phage-encoded regulation mechanism confirms the importance of PTMs in the prokaryotic metabolism and represents a new way by which phages can hijack the bacterial host metabolism.
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Affiliation(s)
- Pieter-Jan Ceyssens
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jeroen De Smet
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Evgeny Klimuk
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Subray Hedge
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - Marleen Voet
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Hanne Hendrix
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jan Paeshuyse
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Bart Landuyt
- Department of Biology, KU Leuven, 3000 Leuven, Belgium;
| | - Hua Xu
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - John Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - Konstantin Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
- Correspondence: ; Tel.: +32-16-379-524
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Rémy B, Plener L, Decloquement P, Armstrong N, Elias M, Daudé D, Chabrière É. Lactonase Specificity Is Key to Quorum Quenching in Pseudomonas aeruginosa. Front Microbiol 2020; 11:762. [PMID: 32390993 PMCID: PMC7193897 DOI: 10.3389/fmicb.2020.00762] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/30/2020] [Indexed: 12/31/2022] Open
Abstract
The human opportunistic pathogen Pseudomonas aeruginosa orchestrates the expression of many genes in a cell density-dependent manner by using quorum sensing (QS). Two acyl-homoserine lactones (AHLs) are involved in QS circuits and contribute to the regulation of virulence factors production, biofilm formation, and antimicrobial sensitivity. Disrupting QS, a strategy referred to as quorum quenching (QQ) can be achieved using exogenous AHL-degrading lactonases. However, the importance of enzyme specificity on quenching efficacy has been poorly investigated. Here, we used two lactonases both targeting the signal molecules N-(3-oxododecanoyl)-L-homoserine lactone (3-oxo-C12 HSL) and butyryl-homoserine lactone (C4 HSL) albeit with different efficacies on C4 HSL. Interestingly, both lactonases similarly decreased AHL concentrations and comparably impacted the expression of AHL-based QS genes. However, strong variations were observed in Pseudomonas Quinolone Signal (PQS) regulation depending on the lactonase used. Both lactonases were also found to decrease virulence factors production and biofilm formation in vitro, albeit with different efficiencies. Unexpectedly, only the lactonase with lower efficacy on C4 HSL was able to inhibit P. aeruginosa pathogenicity in vivo in an amoeba infection model. Similarly, proteomic analysis revealed large variations in protein levels involved in antibiotic resistance, biofilm formation, virulence and diverse cellular mechanisms depending on the chosen lactonase. This global analysis provides evidences that QQ enzyme specificity has a significant impact on the modulation of QS-associated behavior in P. aeruginosa PA14.
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Affiliation(s)
- Benjamin Rémy
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France.,Gene&GreenTK, Marseille, France
| | | | - Philippe Decloquement
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics - BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | | | - Éric Chabrière
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
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Marakasova E, Ii A, Nelson KT, van Hoek ML. Proteome Wide Profiling of N-ε-Lysine Acetylation Reveals a Novel Mechanism of Regulation of the Chitinase Activity in Francisella novicida. J Proteome Res 2020; 19:1409-1422. [PMID: 32056440 DOI: 10.1021/acs.jproteome.9b00512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Francisella tularensis is a Gram-negative bacterium that causes the zoonotic disease tularemia. The historical development of tularemia as a biological weapon has led to it being characterized by the CDC as a category A biothreat agent. Neither posttranslational modification (PTM) of proteins, in particular lysine acetylation, in Francisella nor its subsequent regulation of the protein activity has been well studied. In this work, we analyze N-ε-lysine acetylation of the F. tularensis ssp. novicida proteome by mass spectrometry for the first time. To create a comprehensive acetylation profile, we enriched protein acetylation using two approaches: (1) the addition of glucose or acetate into the culture medium and (2) direct chemical acetylation of N-ε-lysines with acetyl phosphate. We discovered 280 acetylated proteins with 1178 acetylation sites in the F. tularensis ssp. novicida strain U112. Lysine acetylation is an important PTM that regulates multiple cellular processes in bacteria, including metabolism, transcription, translation, stress response, and protein folding. We discovered that Francisella chitinases A and B are acetylated naturally and when chemically induced by acetyl phosphate. Moreover, chemical overacetylation of chitinases results in silencing of the enzymatic activity. Our findings suggest a novel mechanism of posttranslational regulation of the chitinase activity and that acetylation may play a role in Francisella's regulation of the protein activity.
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Affiliation(s)
- Ekaterina Marakasova
- School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, Virginia 20110, United States
| | - Alexandra Ii
- School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, Virginia 20110, United States
| | - Kristina T Nelson
- Chemical and Proteomic Mass Spectrometry Core Facility, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284, United States
| | - Monique L van Hoek
- School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, Virginia 20110, United States
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Li D, Ramanathan S, Wang G, Wu Y, Tang Q, Li G. Acetylation of lysine 7 of AhyI affects the biological function in Aeromonas hydrophila. Microb Pathog 2020; 140:103952. [DOI: 10.1016/j.micpath.2019.103952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/04/2019] [Accepted: 12/26/2019] [Indexed: 01/18/2023]
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46
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Mærk M, Jakobsen ØM, Sletta H, Klinkenberg G, Tøndervik A, Ellingsen TE, Valla S, Ertesvåg H. Identification of Regulatory Genes and Metabolic Processes Important for Alginate Biosynthesis in Azotobacter vinelandii by Screening of a Transposon Insertion Mutant Library. Front Bioeng Biotechnol 2020; 7:475. [PMID: 32010681 PMCID: PMC6979010 DOI: 10.3389/fbioe.2019.00475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/23/2019] [Indexed: 12/23/2022] Open
Abstract
Azotobacter vinelandii produces the biopolymer alginate, which has a wide range of industrial and pharmaceutical applications. A random transposon insertion mutant library was constructed from A. vinelandii ATCC12518Tc in order to identify genes and pathways affecting alginate biosynthesis, and about 4,000 mutant strains were screened for altered alginate production. One mutant, containing a mucA disruption, displayed an elevated alginate production level, and several mutants with decreased or abolished alginate production were identified. The regulatory proteins AlgW and AmrZ seem to be required for alginate production in A. vinelandii, similarly to Pseudomonas aeruginosa. An algB mutation did however not affect alginate yield in A. vinelandii although its P. aeruginosa homolog is needed for full alginate production. Inactivation of the fructose phosphoenolpyruvate phosphotransferase system protein FruA resulted in a mutant that did not produce alginate when cultivated in media containing various carbon sources, indicating that this system could have a role in regulation of alginate biosynthesis. Furthermore, impaired or abolished alginate production was observed for strains with disruptions of genes involved in peptidoglycan biosynthesis/recycling and biosynthesis of purines, isoprenoids, TCA cycle intermediates, and various vitamins, suggesting that sufficient access to some of these compounds is important for alginate production. This hypothesis was verified by showing that addition of thiamine, succinate or a mixture of lysine, methionine and diaminopimelate increases alginate yield in the non-mutagenized strain. These results might be used in development of optimized alginate production media or in genetic engineering of A. vinelandii strains for alginate bioproduction.
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Affiliation(s)
- Mali Mærk
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | | | | | | | - Svein Valla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
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Sun L, Yao Z, Guo Z, Zhang L, Wang Y, Mao R, Lin Y, Fu Y, Lin X. Comprehensive analysis of the lysine acetylome in Aeromonas hydrophila reveals cross-talk between lysine acetylation and succinylation in LuxS. Emerg Microbes Infect 2020; 8:1229-1239. [PMID: 31448697 PMCID: PMC6735345 DOI: 10.1080/22221751.2019.1656549] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lysine acetylation and succinylation are both prevalent protein post-translational modifications (PTMs) in bacteria species, whereas the effect of the cross-talk between both PTMs on bacterial biological function remains largely unknown. Our previously study found lysine succinylated sites on proteins play important role on metabolic pathways in fish pathogenic Aeromonas hydrophila. A total of 3189 lysine-acetylation sites were further identified on 1013 proteins of this pathogen using LC-MS/MS in this study. Functional examination of these PTMs peptides showed associations with basal biological processes, especially metabolic pathways. Additionally, when comparing the obtained lysine acetylome to a previously obtained lysine succinylome, 1198 sites in a total of 547 proteins were found to be in common and associated with various metabolic pathways. As the autoinducer-2 (AI-2) synthase involved in quorum sensing of bacteria, the site-directed mutagenesis of LuxS at the K165 site was performed and revealed that the cross-talk between lysine acetylation and succinylation exerts an inverse influence on bacterial quorum sensing and on LuxS enzymatic activity. In summary, this study provides an in-depth A. hydrophila lysine acetylome profile and for the first time reveals the role of cross-talk between lysine acetylation and succinylation, and its potential impact on bacterial physiological functions.
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Affiliation(s)
- Lina Sun
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Zujie Yao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences , Shanghai , People's Republic of China
| | - Zhuang Guo
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Yuqian Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Ranran Mao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Yuexu Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Yuying Fu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University , Fuzhou , People's Republic of China.,Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University , Fuzhou , People's Republic of China
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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.
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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
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Duport C, Alpha-Bazin B, Armengaud J. Advanced Proteomics as a Powerful Tool for Studying Toxins of Human Bacterial Pathogens. Toxins (Basel) 2019; 11:toxins11100576. [PMID: 31590258 PMCID: PMC6832400 DOI: 10.3390/toxins11100576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022] Open
Abstract
Exotoxins contribute to the infectious processes of many bacterial pathogens, mainly by causing host tissue damages. The production of exotoxins varies according to the bacterial species. Recent advances in proteomics revealed that pathogenic bacteria are capable of simultaneously producing more than a dozen exotoxins. Interestingly, these toxins may be subject to post-transcriptional modifications in response to environmental conditions. In this review, we give an outline of different bacterial exotoxins and their mechanism of action. We also report how proteomics contributed to immense progress in the study of toxinogenic potential of pathogenic bacteria over the last two decades.
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Affiliation(s)
- Catherine Duport
- SQPOV, UMR0408, Avignon Université, INRA, F-84914 Avignon, France
- Correspondence:
| | - Béatrice Alpha-Bazin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France; (B.A.-B.); (J.A.)
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France; (B.A.-B.); (J.A.)
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50
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Zhou C, Dai J, Lu H, Chen Z, Guo M, He Y, Gao K, Ge T, Jin J, Wang L, Tian B, Hua Y, Zhao Y. Succinylome Analysis Reveals the Involvement of Lysine Succinylation in the Extreme Resistance of Deinococcus radiodurans. Proteomics 2019; 19:e1900158. [PMID: 31487437 DOI: 10.1002/pmic.201900158] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/17/2019] [Indexed: 01/18/2023]
Abstract
Increasing evidence shows that the succinylation of lysine residues mainly regulates enzymes involved in the carbon metabolism pathway, in both prokaryotic and eukaryotic cells. Deinococcus radiodurans is one of the most radioresistant organisms on earth and is famous for its robust resistance. A major goal in the current study of protein succinylation is to explore its function in D. radiodurans. High-resolution LC-MS/MS is used for qualitative proteomics to perform a global succinylation analysis of D. radiodurans and 492 succinylation sites in 270 proteins are identified. These proteins are involved in a variety of biological processes and pathways. It is found that the enzymes involved in nucleic acid binding/processing are enriched in D. radiodurans compared with their previously reported levels in other bacteria. The mutagenesis studies confirm that succinylation regulates the enzymatic activities of species-specific proteins PprI and DdrB, which belong to the radiation-desiccation response regulon. Together, these results provide insight into the role of lysine succinylation in the extreme resistance of D. radiodurans.
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Affiliation(s)
- Congli Zhou
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Jingli Dai
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Huizhi Lu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Zijing Chen
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Miao Guo
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Yuan He
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Kaixuan Gao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Tong Ge
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Jiayu Jin
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Liangyan Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Bing Tian
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
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