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Huang Q, Duan C, Ma H, Nong C, Zheng Q, Zhou J, Zhao N, Mou X, Liu T, Zou S, Yang N, Tong A, Qin W, Bao R. Structural and functional characterization of itaconyl-CoA hydratase and citramalyl-CoA lyase involved in itaconate metabolism of Pseudomonas aeruginosa. Structure 2024:S0969-2126(24)00130-8. [PMID: 38677288 DOI: 10.1016/j.str.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/23/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024]
Abstract
Itaconate is a key anti-inflammatory/antibacterial metabolite in pathogen-macrophage interactions that induces adaptive changes in Pseudomonas aeruginosa-exposed airways. However, the impact and mechanisms underlying itaconate metabolism remain unclear. Our study reveals that itaconate significantly upregulates the expression of pyoverdine in P. aeruginosa and enhances its tolerance to tobramycin. Notably, the enzymes responsible for efficient itaconate metabolism, PaIch and PaCcl, play crucial roles in both utilizing itaconate and clearing its toxic metabolic intermediates. By using protein crystallography and molecular dynamics simulations analyses, we have elucidated the unique catalytic center and substrate-binding pocket of PaIch, which contribute to its highly efficient catalysis. Meanwhile, analysis of PaCcl has revealed how interactions between domains regulate the conformational changes of the active sites and binding pockets, influencing the catalytic process. Overall, our research uncovers the significance and mechanisms of PaIch and PaCcl in the efficient metabolism of itaconate by P. aeruginosa.
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Affiliation(s)
- Qin Huang
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chenxi Duan
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Haichuan Ma
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Cheng Nong
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qianqian Zheng
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jun Zhou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ninglin Zhao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingyu Mou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Tonggen Liu
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shuang Zou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ningchuan Yang
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Aiping Tong
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, CAS, Shanghai, China.
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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He Y, Jin Z, Cui Y, Song K, Chen B, Zhou L. RsaL is a self-regulatory switch that controls alternative biosynthesis of two AHL-type quorum sensing signals in Pseudomonas aeruginosa PA1201. MLIFE 2024; 3:74-86. [PMID: 38827515 PMCID: PMC11139201 DOI: 10.1002/mlf2.12113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 06/04/2024]
Abstract
Pseudomonas aeruginosa is a ubiquitous and metabolically versatile microorganism naturally found in soil and water. It is also an opportunistic pathogen in plants, insects, animals, and humans. In response to increasing cell density, P. aeruginosa uses two acyl-homoserine lactone (AHL) quorum-sensing (QS) signals (i.e., N-3-oxo-dodecanoyl homoserine lactone [3-oxo-C12-HSL] and N-butanoyl-homoserine lactone [C4-HSL]), which regulate the expression of hundreds of genes. However, how the biosynthesis of these two QS signals is coordinated remains unknown. We studied the regulation of these two QS signals in the rhizosphere strain PA1201. PA1201 sequentially produced 3-oxo-C12-HSL and C4-HSL at the early and late growth stages, respectively. The highest 3-oxo-C12-HSL-dependent elastase activity was observed at the early stage, while the highest C4-HSL-dependent rhamnolipid production was observed at the late stage. The atypical regulator RsaL played a pivotal role in coordinating 3-oxo-C12-HSL and C4-HSL biosynthesis and QS-associated virulence. RsaL repressed lasI transcription by binding the -10 and -35 boxes of the lasI promoter. In contrast, RsaL activated rhlI transcription by binding the region encoding the 5'-untranslated region of the rhlI mRNA. Further, RsaL repressed its own expression by binding a nucleotide motif located in the -35 box of the rsaL promoter. Thus, RsaL acts as a molecular switch that coordinates the sequential biosynthesis of AHL QS signals and differential virulence in PA1201. Finally, C4-HSL activation by RsaL was independent of the Las and Pseudomonas quinolone signal (PQS) QS signaling systems. Therefore, we propose a new model of the QS regulatory network in PA1201, in which RsaL represents a superior player acting at the top of the hierarchy.
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Affiliation(s)
- Ya‐Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, SJTU‐NLBP Joint R&D Centre for Biopesticides and Biofertilizers, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zi‐Jing Jin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, SJTU‐NLBP Joint R&D Centre for Biopesticides and Biofertilizers, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ying Cui
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, SJTU‐NLBP Joint R&D Centre for Biopesticides and Biofertilizers, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Kai Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, SJTU‐NLBP Joint R&D Centre for Biopesticides and Biofertilizers, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Bo Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, SJTU‐NLBP Joint R&D Centre for Biopesticides and Biofertilizers, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Lian Zhou
- Zhiyuan Innovative Research Centre, Student Innovation Centre, Zhiyuan CollegeShanghai Jiao Tong UniversityShanghaiChina
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Liu Y, Zhou M, Bu Y, Qin L, Zhang Y, Shao S, Wang Q. Lysine acetylation regulates the AT-rich DNA possession ability of H-NS. Nucleic Acids Res 2024; 52:1645-1660. [PMID: 38059366 PMCID: PMC10899749 DOI: 10.1093/nar/gkad1172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/01/2023] [Accepted: 11/23/2023] [Indexed: 12/08/2023] Open
Abstract
H-NS, the histone-like nucleoid-structuring protein in bacteria, regulates the stability of the bacterial genome by inhibiting the transcription of horizontally transferred genes, such as the type III and type VI secretion systems (T3/T6SS). While eukaryotic histone posttranslational modifications (PTMs) have been extensively studied, little is known about prokaryotic H-NS PTMs. Here, we report that the acetylation of H-NS attenuates its ability to silence horizontally transferred genes in response to amino acid nutrition and immune metabolites. Moreover, LC-MS/MS profiling showed that the acetyllysine sites of H-NS and K120 are indispensable for its DNA-binding ability. Acetylation of K120 leads to a low binding affinity for DNA and enhances T3/T6SS expression. Furthermore, acetylation of K120 impairs the AT-rich DNA recognition ability of H-NS. In addition, lysine acetylation in H-NS modulates in vivo bacterial virulence. These findings reveal the mechanism underlying H-NS PTMs and propose a novel mechanism by which bacteria counteract the xenogeneic silencing of H-NS.
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Affiliation(s)
- Yabo Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Mengqing Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yifan Bu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Liang Qin
- New Product R&D, GenScript Biotech Corporation, Nanjing 211100, China
| | - Yuanxing Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
- Laboratory of Aquatic Animal Diseases of MOA, Shanghai 200237, China
| | - Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
- Laboratory of Aquatic Animal Diseases of MOA, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
- Laboratory of Aquatic Animal Diseases of MOA, Shanghai 200237, China
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