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Wickramaratne AC, Wickner S, Kravats AN. Hsp90, a team player in protein quality control and the stress response in bacteria. Microbiol Mol Biol Rev 2024; 88:e0017622. [PMID: 38534118 PMCID: PMC11332350 DOI: 10.1128/mmbr.00176-22] [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: 03/28/2024] Open
Abstract
SUMMARYHeat shock protein 90 (Hsp90) participates in proteostasis by facilitating protein folding, activation, disaggregation, prevention of aggregation, degradation, and protection against degradation of various cellular proteins. It is highly conserved from bacteria to humans. In bacteria, protein remodeling by Hsp90 involves collaboration with the Hsp70 molecular chaperone and Hsp70 cochaperones. In eukaryotes, protein folding by Hsp90 is more complex and involves collaboration with many Hsp90 cochaperones as well as Hsp70 and Hsp70 cochaperones. This review focuses primarily on bacterial Hsp90 and highlights similarities and differences between bacterial and eukaryotic Hsp90. Seminal research findings that elucidate the structure and the mechanisms of protein folding, disaggregation, and reactivation promoted by Hsp90 are discussed. Understanding the mechanisms of bacterial Hsp90 will provide fundamental insight into the more complex eukaryotic chaperone systems.
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Affiliation(s)
- Anushka C. Wickramaratne
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrea N. Kravats
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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Monti M, Herman R, Mancini L, Capitanchik C, Davey K, Dawson CS, Ule J, Thomas GH, Willis AE, Lilley KS, Villanueva E. Interrogation of RNA-protein interaction dynamics in bacterial growth. Mol Syst Biol 2024; 20:573-589. [PMID: 38531971 PMCID: PMC11066096 DOI: 10.1038/s44320-024-00031-y] [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: 09/26/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them are orthologs of human mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. For the first time, the dynamics of the bacterial RBPome have been interrogated, showcasing how this approach can reveal the function of uncharacterised proteins and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.
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Affiliation(s)
- Mie Monti
- MRC Toxicology Unit, University of Cambridge, University of Cambridge, CB2 1QR, Cambridge, UK
| | - Reyme Herman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Leonardo Mancini
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Charlotte Capitanchik
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Karen Davey
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, University of Cambridge, CB2 1QR, Cambridge, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK.
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK.
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Addington E, Sandalli S, Roe AJ. Current understandings of colibactin regulation. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001427. [PMID: 38314762 PMCID: PMC10924459 DOI: 10.1099/mic.0.001427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024]
Abstract
The biosynthetic machinery for the production of colibactin is encoded by 19 genes (clbA - S) within the pks pathogenicity island harboured by many E. coli of the B2-phylogroup. Colibactin is a potent genotoxic metabolite which causes DNA-damage and which has potential roles in microbial competition and fitness of pks+ bacteria. Colibactin has also been strongly implicated in the development of colorectal cancer. Given the genotoxicity of colibactin and the metabolic cost of its synthesis, the regulatory system governing the clb cluster is accordingly highly complex, and many of the mechanisms remain to be elucidated. In this review we summarise the current understanding of regulation of colibactin biosynthesis by internal molecular components and how these factors are modulated by signals from the external environment.
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Affiliation(s)
- Emily Addington
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
| | - Sofia Sandalli
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
| | - Andrew J. Roe
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
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Lv Q, Shang Y, Bi H, Yang J, Lin L, Shi C, Wang M, Xie R, Zhu Z, Wang F, Hua L, Chen H, Wu B, Peng Z. Identification of two-component system ArcAB and the universal stress protein E in Pasteurella multocida and their effects on bacterial fitness and pathogenesis. Microbes Infect 2023:105235. [PMID: 37802468 DOI: 10.1016/j.micinf.2023.105235] [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: 08/05/2023] [Revised: 09/28/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
Two-component regulatory system (TCS) is a widespread bacterial signal transduction mechanism and plays a critical role in bacterial adaptation to environments as well as regulating bacterial virulence. However, few studies have reported the actions of TCS in Pasteurella multocida, a zoonotic bacterial pathogen. In this study, genes encoding proteins homologous to the ArcAB TCS were identified in genome sequences of P. multocida belonging to different serogroups, and the transcription of both arcA and arcB was up-regulated in anaerobic and superoxygen environment. Compared to wild type strains, P. multocida arcA-deletion mutants (ΔarcA) displayed a decrease in growing under anaerobic conditions, biofilm formation, as well as the capacities of anti-serum bactericidal effect, cell adherence and invasion, anti-phagocytosis, and virulence in different in vivo models (Galleria mellonella and mice). RNA-Seq identified 70 significantly downregulated genes in ΔarcA compared to the wild type strain, and several of them are associated with P. multocida virulence. Among them, a universal stress protein E encoding gene uspE was characterized in P. multocida for the first time. Electrophoretic mobility shift assay (EMSA) demonstrated that the ArcAB TCS could regulate uspE directly. Deletion of uspE also led to a decrease of P. multocida in growing under anaerobic conditions, biofilm formation, anti-serum bactericidal effect, cell adherence and invasion, anti-phagocytosis, and virulence in mice. The data provided from this study will help further understanding the fitness and pathogenesis of P. multocida.
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Affiliation(s)
- Qingjie Lv
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yuyao Shang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Haixin Bi
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jie Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lin Lin
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Congcong Shi
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Mixue Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Xie
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhanwei Zhu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Fei Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lin Hua
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bin Wu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Zhong Peng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China; Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Central for Sustainable Pig Production, Wuhan, China.
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Jin X, Ou Z, Zhang G, Shi R, Yang J, Liu W, Luo G, Deng J, Wang W. A CO-mediated photothermal therapy to kill drug-resistant bacteria and minimize thermal injury for infected diabetic wound healing. Biomater Sci 2023; 11:6236-6251. [PMID: 37531204 DOI: 10.1039/d3bm00774j] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
With an increasing proportion of drug-resistant bacteria, photothermal therapy (PTT) is a promising alternative to antibiotic treatment for infected diabetic skin ulcers. However, the inevitable thermal damage to the tissues restricts its clinical practice. Carbon monoxide (CO), as a bioactive gas molecule, can selectively inhibit bacterial growth and promote tissue regeneration, which may be coordinated with PTT for drug-resistant bacteria killing and tissue protection. Herein, a CO-mediated PTT agent (CO@mPDA) was engineered by loading manganese carbonyl groups into mesoporous polydopamine (mPDA) nanoparticles via coordination interactions between the metal center and a catechol group. Compared to the traditional PTT, the CO-mediated PTT increases the inhibition ratio of the drug-resistant bacteria both in vitro and in diabetic wound beds by selectively inhibiting the co-chaperone of the heat shock protein 90 kDa (Hsp90), and lowers the heat resistance of the bacteria rather than the mammalian tissues. Meanwhile, the tissue-protective proteins, such as Hsp90 and vimentin (Vim), are upregulated via the WNT and PI3K-Akt pathways to reduce thermal injury, especially with a laser with a high-power density. The CO-mediated PTT unified the bacterial killing with tissue protection, which offers a promising concept to improve PTT efficiency and minimize the side-effects of PTT when treating infected skin wounds.
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Affiliation(s)
- Xin Jin
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin, University, Tianjin 300350, China
| | - Zelin Ou
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China.
- Institute of Burn Research, State Key Lab of Trauma, Burn, and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Guowei Zhang
- Institute of Burn Research, State Key Lab of Trauma, Burn, and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Rong Shi
- Institute of Burn Research, State Key Lab of Trauma, Burn, and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Jumin Yang
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin, University, Tianjin 300350, China
| | - Wenguang Liu
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin, University, Tianjin 300350, China
| | - Gaoxing Luo
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China.
- Institute of Burn Research, State Key Lab of Trauma, Burn, and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Jun Deng
- Institute of Burn Research, State Key Lab of Trauma, Burn, and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Wei Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311215, China.
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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