1
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Nava M, Rowe SJ, Taylor RJ, Kahne D, Nocera DG. Determination of Initial Rates of Lipopolysaccharide Transport. Biochemistry 2024; 63:2440-2448. [PMID: 39264328 PMCID: PMC11447908 DOI: 10.1021/acs.biochem.4c00379] [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: 06/28/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/13/2024]
Abstract
Nonvesicular lipid trafficking pathways are an important process in every domain of life. The mechanisms of these processes are poorly understood in part due to the difficulty in kinetic characterization. One important class of glycolipids, lipopolysaccharides (LPS), are the primary lipidic component of the outer membrane of Gram-negative bacteria. LPS are synthesized in the inner membrane and then trafficked to the cell surface by the lipopolysaccharide transport proteins, LptB2FGCADE. By characterizing the interaction of a fluorescent probe and LPS, we establish a quantitative assay to monitor the flux of LPS between proteoliposomes on the time scale of seconds. We then incorporate photocaged ATP into this system, which allows for light-based control of the initiation of LPS transport. This control allows us to measure the initial rate of LPS transport (3.0 min-1 per LptDE). We also find that the rate of LPS transport by the Lpt complex is independent of the structure of LPS. In contrast, we find the rate of LPS transport is dependent on the proper function of the LptDE complex. Mutants of the outer membrane Lpt components, LptDE, that cause defective LPS assembly in live cells display attenuated transport rates and slower ATP hydrolysis compared to wild type proteins. Analysis of these mutants reveals that the rates of ATP hydrolysis and LPS transport are correlated such that 1.2 ± 0.2 ATP are hydrolyzed for each LPS transported. This correlation suggests a model where the outer membrane components ensure the coupling of ATP hydrolysis and LPS transport by stabilizing a transport-active state of the Lpt bridge.
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Affiliation(s)
| | | | - Rebecca J. Taylor
- Department of Chemistry and Chemical
Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical
Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel G. Nocera
- Department of Chemistry and Chemical
Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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2
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Kumari K, Dey J, Mahapatra SR, Ma Y, Sharma PK, Misra N, Singh RP. Protein profiling and immunoinformatic analysis of the secretome of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8. Folia Microbiol (Praha) 2024; 69:1095-1122. [PMID: 38457114 DOI: 10.1007/s12223-024-01152-5] [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: 06/14/2023] [Accepted: 02/03/2024] [Indexed: 03/09/2024]
Abstract
The bacterial secretome represents a comprehensive catalog of proteins released extracellularly that have multiple important roles in virulence and intercellular communication. This study aimed to characterize the secretome of an environmental isolate Pseudomonas aeruginosa S-8 by analyzing trypsin-digested culture supernatant proteins using nano-LC-MS/MS tool. Using a combined approach of bioinformatics and mass spectrometry, 1088 proteins in the secretome were analyzed by PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb tool for their subcellular localization and further categorization of secretome proteins according to signal peptides. Using the gene ontology tool, secretome proteins were categorized into different functional categories. KEGG pathway analysis identified the secreted proteins into different metabolic functional pathways. Moreover, our LC-MS/MS data revealed the secretion of various CAZymes into the extracellular milieu, which suggests its strong biotechnological applications to breakdown complex carbohydrate polymers. The identified immunodominant epitopes from the secretome of P. aeruginosa showed the characteristic of being non-allergenic, highly antigenic, nontoxic, and having a low risk of triggering autoimmune responses, which highlights their potential as successful vaccine targets. Overall, the identification of secreted proteins of P. aeruginosa could be important for both diagnostic purposes and the development of an effective candidate vaccine.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, 835215, India
| | - Jyotirmayee Dey
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Soumya Ranjan Mahapatra
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Namrata Misra
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, 201309, India.
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3
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Kijewski ACR, Witsø IL, Sundaram AYM, Brynildsrud OB, Pettersen K, Anonsen EB, Anonsen JH, Aspholm ME. Transcriptomic and proteomic analysis of the virulence inducing effect of ciprofloxacin on enterohemorrhagic Escherichia coli. PLoS One 2024; 19:e0298746. [PMID: 38787890 PMCID: PMC11125564 DOI: 10.1371/journal.pone.0298746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/29/2024] [Indexed: 05/26/2024] Open
Abstract
Enterohemorrhagic E. coli (EHEC) is considered to be the most dangerous pathotype of E. coli, as it causes severe conditions such as hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Antibiotic treatment of EHEC infections is generally not recommended since it may promote the production of the Shiga toxin (Stx) and lead to worsened symptoms. This study explores how exposure to the fluoroquinolone ciprofloxacin reorganizes the transcriptome and proteome of EHEC O157:H7 strain EDL933, with special emphasis on virulence-associated factors. As expected, exposure to ciprofloxacin caused an extensive upregulation of SOS-response- and Stx-phage proteins, including Stx. A range of other virulence-associated factors were also upregulated, including many genes encoded by the LEE-pathogenicity island, the enterohemolysin gene (ehxA), as well as several genes and proteins involved in LPS production. However, a large proportion of the genes and proteins (17 and 8%, respectively) whose expression was upregulated upon ciprofloxacin exposure (17 and 8%, respectively) are not functionally assigned. This indicates a knowledge gap in our understanding of mechanisms involved in EHECs response to antibiotic-induced stress. Altogether, the results contribute to better understanding of how exposure to ciprofloxacin influences the virulome of EHEC and generates a knowledge base for further studies on how EHEC responds to antibiotic-induced stress. A deeper understanding on how EHEC responds to antibiotics will facilitate development of novel and safer treatments for EHEC infections.
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Affiliation(s)
| | - Ingun Lund Witsø
- Faculty of Veterinary Medicine, Unit for Food Safety, Norwegian University of Life Sciences, Oslo, Norway
| | - Arvind Y. M. Sundaram
- Department of Medical Genetics, Norwegian Sequencing Centre, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Jan Haug Anonsen
- Department of Biosciences IBV, Mass Spectrometry and Proteomics Unit, University of Oslo, Oslo, Norway
- Norwegian Research Centre AS, Stavanger, Norway
| | - Marina Elisabeth Aspholm
- Faculty of Veterinary Medicine, Unit for Food Safety, Norwegian University of Life Sciences, Oslo, Norway
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4
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Kumar S, Davis RM, Ruiz N. YdbH and YnbE form an intermembrane bridge to maintain lipid homeostasis in the outer membrane of Escherichia coli. Proc Natl Acad Sci U S A 2024; 121:e2321512121. [PMID: 38748582 PMCID: PMC11126948 DOI: 10.1073/pnas.2321512121] [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: 12/06/2023] [Accepted: 04/09/2024] [Indexed: 05/27/2024] Open
Abstract
The outer membrane (OM) of didermic gram-negative bacteria is essential for growth, maintenance of cellular integrity, and innate resistance to many antimicrobials. Its asymmetric lipid distribution, with phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet, is required for these functions. Lpt proteins form a transenvelope bridge that transports newly synthesized LPS from the inner membrane (IM) to OM, but how the bulk of phospholipids are transported between these membranes is poorly understood. Recently, three members of the AsmA-like protein family, TamB, YhdP, and YdbH, were shown to be functionally redundant and were proposed to transport phospholipids between IM and OM in Escherichia coli. These proteins belong to the repeating β-groove superfamily, which includes eukaryotic lipid-transfer proteins that mediate phospholipid transport between organelles at contact sites. Here, we show that the IM-anchored YdbH protein interacts with the OM lipoprotein YnbE to form a functional protein bridge between the IM and OM in E. coli. Based on AlphaFold-Multimer predictions, genetic data, and in vivo site-directed cross-linking, we propose that YnbE interacts with YdbH through β-strand augmentation to extend the continuous hydrophobic β-groove of YdbH that is thought to shield acyl chains of phospholipids as they travel through the aqueous intermembrane periplasmic compartment. Our data also suggest that the periplasmic protein YdbL prevents extensive amyloid-like multimerization of YnbE in cells. We, therefore, propose that YdbL has a chaperone-like function that prevents uncontrolled runaway multimerization of YnbE to ensure the proper formation of the YdbH-YnbE intermembrane bridge.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, OH43210
| | - Rebecca M. Davis
- Department of Microbiology, The Ohio State University, Columbus, OH43210
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH43210
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5
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Zhu S, Alexander MK, Paiva TO, Rachwalski K, Miu A, Xu Y, Verma V, Reichelt M, Dufrêne YF, Brown ED, Cox G. The inactivation of tolC sensitizes Escherichia coli to perturbations in lipopolysaccharide transport. iScience 2024; 27:109592. [PMID: 38628966 PMCID: PMC11019271 DOI: 10.1016/j.isci.2024.109592] [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: 12/01/2023] [Revised: 02/02/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
The Escherichia coli outer membrane channel TolC complexes with several inner membrane efflux pumps to export compounds across the cell envelope. All components of these complexes are essential for robust efflux activity, yet E. coli is more sensitive to antimicrobial compounds when tolC is inactivated compared to the inactivation of genes encoding the inner membrane drug efflux pumps. While investigating these susceptibility differences, we identified a distinct class of inhibitors targeting the core-lipopolysaccharide translocase, MsbA. We show that tolC null mutants are sensitized to structurally unrelated MsbA inhibitors and msbA knockdown, highlighting a synthetic-sick interaction. Phenotypic profiling revealed that tolC inactivation induced cell envelope softening and increased outer membrane permeability. Overall, this work identified a chemical probe of MsbA, revealed that tolC is associated with cell envelope mechanics and integrity, and highlighted that these findings should be considered when using tolC null mutants to study efflux deficiency.
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Affiliation(s)
- Shawna Zhu
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
| | | | - Telmo O. Paiva
- Institute of Life Sciences, UCLouvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
| | - Kenneth Rachwalski
- Biochemistry and Biomedical Sciences and Degroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Anh Miu
- Genentech Inc, Biochemical and Cellular Pharmacology, South San Francisco, CA, USA
| | - Yiming Xu
- Genentech Inc, Infectious Diseases, South San Francisco, CA, USA
| | - Vishal Verma
- Genentech Inc, Discovery Chemistry, South San Francisco, CA, USA
| | - Mike Reichelt
- Genentech Inc, Pathology, South San Francisco, CA, USA
| | - Yves F. Dufrêne
- Institute of Life Sciences, UCLouvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
| | - Eric D. Brown
- Biochemistry and Biomedical Sciences and Degroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
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6
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Xu Y, Pang Y, Luo L, Sharma A, Yang J, Li C, Liu S, Zhan J, Sun Y. De Novo Designed Ru(II) Metallacycle as a Microenvironment-Adaptive Sonosensitizer and Sonocatalyst for Multidrug-Resistant Biofilms Eradication. Angew Chem Int Ed Engl 2024; 63:e202319966. [PMID: 38327168 DOI: 10.1002/anie.202319966] [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: 12/24/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
Albeit sonodynamic therapy (SDT) has achieved encouraging progress in microbial sterilization, the scarcity of guidelines for designing highly effective sonosensitizers and the intricate biofilm microenvironment (BME), substantially hamper the therapeutic efficacy against biofilm infections. To address the bottlenecks, we innovatively design a Ru(II) metallacycle-based sonosensitizer/sonocatalyst (named Ru-A3-TTD) to enhance the potency of sonotherapy by employing molecular engineering strategies tailored to BME. Our approach involves augmenting Ru-A3-TTD's production of ultrasonic-triggered reactive oxygen species (ROS), surpassing the performance of commercial sonosensitizers, through a straightforward but potent π-expansion approach. Within the BME, Ru-A3-TTD synergistically amplifies sonotherapeutic efficacy via triple-modulated approaches: (i) effective alleviation of hypoxia, leading to increased ROS generation, (ii) disruption of the antioxidant defense system, which shields ROS from glutathione consumption, and (iii) enhanced biofilm penetration, enabling ROS production in deep sites. Notably, Ru-A3-TTD sono-catalytically oxidizes NADPH, a critical coenzyme involved in antioxidant defenses. Consequently, Ru-A3-TTD demonstrates superior biofilm eradication potency against multidrug-resistant Escherichia coli compared to conventional clinical antibiotics, both in vitro and in vivo. To our knowledge, this study represents the pioneering instance of a supramolecular sonosensitizer/sonocatalyst. It provides valuable insights into the structure-activity relationship of sonosensitizers and paves a promising pathway for the treatment of biofilm infections.
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Affiliation(s)
- Yuling Xu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Yida Pang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Lishi Luo
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Amit Sharma
- Amity School of Chemical Sciences, Amity University Punjab, Mohali, 140 306, India
| | - Jingfang Yang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Chonglu Li
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Shuang Liu
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, China
| | - Jianbo Zhan
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430070, China
| | - Yao Sun
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
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7
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Chong H, Liu X, Fang S, Yang X, Zhang Y, Wang T, Liu L, Kan Y, Zhao Y, Fan H, Zhang J, Wang X, Yao H, Yang Y, Gao Y, Zhao Q, Li S, Plymoth M, Xi J, Zhang Y, Wang C, Pang H. Organo-Pt ii Complexes for Potent Photodynamic Inactivation of Multi-Drug Resistant Bacteria and the Influence of Configuration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306936. [PMID: 38298088 PMCID: PMC11005693 DOI: 10.1002/advs.202306936] [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: 09/21/2023] [Indexed: 02/02/2024]
Abstract
PtII based organometallic photosensitizers (PSs) have emerged as novel potent photodynamic inactivation (PDI) reagents through their enhanced intersystem crossing (ISC) processes. Currently, few PtII PSs have been investigated as antibacterial materials, with relatively poor performances reported and with structure-activity relationships not well described. Herein, a pair of configurational isomers are reported of Bis-BODIPY (4,4-difluoro-boradizaindacene) embedded PtII PSs. The cis-isomer (cis-BBP) displayed enhanced 1O2 generation and better bacterial membrane anchoring capability as compared to the trans-isomer (trans-BBP). The effective PDI concentrations (efficiency > 99.9%) for cis-BBP in Acinetobacter baumannii (multi-drug resistant (MDR)) and Staphylococcus aureus are 400 nM (12 J cm-2) and 100 nM (18 J cm-2), respectively; corresponding concentrations and light doses for trans-BBP in the two bacteria are 2.50 µM (30 J cm-2) and 1.50 µM (18 J cm-2), respectively. The 50% and 90% minimum inhibitory concentration (MIC50 and MIC90) ratio of trans-BBP to cis-BBP is 22.22 and 24.02 in A. baumannii (MDR); 21.29 and 22.36 in methicillin resistant S. aureus (MRSA), respectively. Furthermore, cis-BBP displays superior in vivo antibacterial performance, with acceptable dark and photoinduced cytotoxicity. These results demonstrate cis-BBP is a robust light-assisted antibacterial reagent at sub-micromolecular concentrations. More importantly, configuration of PtII PSs should be an important issue to be considered in further PDI reagents design.
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Affiliation(s)
- Hui Chong
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Xuanwei Liu
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Siyu Fang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Xiaofei Yang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Yuefei Zhang
- Department of EmergencyAffiliated Hospital of Yangzhou UniversityYangzhouJiangsu225000China
| | - Tianyi Wang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Lin Liu
- School of NursingYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesNo. 88 South University Rd.Yangzhou225009P. R. China
| | - Yinshi Kan
- School of NursingYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesNo. 88 South University Rd.Yangzhou225009P. R. China
| | - Yueqi Zhao
- School of NursingYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesNo. 88 South University Rd.Yangzhou225009P. R. China
| | - Hongying Fan
- Testing Center of Yangzhou UniversityNo. 48 Wenhui East Rd.Yangzhou225009P. R. China
| | - Jingqi Zhang
- School of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing100083P. R. China
| | - Xiaoyu Wang
- School of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing100083P. R. China
| | - Hang Yao
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Yi Yang
- Center LaboratoryAffiliated Hospital of Yangzhou UniversityYangzhou225009P. R. China
| | - Yijian Gao
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123P. R. China
| | - Qi Zhao
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123P. R. China
| | - Shengliang Li
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123P. R. China
| | - Martin Plymoth
- Westmead hospitalSydneyNSW 2145Australia
- Department of Clinical MicrobiologyUmeå UniversityUmeå90187Sweden
| | - Juqun Xi
- Department of PharmacologyInstitute of Translational MedicineSchool of MedicineYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesYangzhou225009P. R. China
| | - Yu Zhang
- School of NursingYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesNo. 88 South University Rd.Yangzhou225009P. R. China
| | - Chengyin Wang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Huan Pang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
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8
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Yoon Y, Song S. Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target. J Microbiol 2024; 62:261-275. [PMID: 38816673 DOI: 10.1007/s12275-024-00137-w] [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: 03/19/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024]
Abstract
Lipopolysaccharide (LPS) is a critical component of the extracellular leaflet within the bacterial outer membrane, forming an effective physical barrier against environmental threats in Gram-negative bacteria. After LPS is synthesized and matured in the bacterial cytoplasm and the inner membrane (IM), LPS is inserted into the outer membrane (OM) through the ATP-driven LPS transport (Lpt) pathway, which is an energy-intensive process. A trans-envelope complex that contains seven Lpt proteins (LptA-LptG) is crucial for extracting LPS from the IM and transporting it across the periplasm to the OM. The last step in LPS transport involves the mediation of the LptDE complex, facilitating the insertion of LPS into the outer leaflet of the OM. As the Lpt system plays an essential role in maintaining the impermeability of the OM via LPS decoration, the interactions between these interconnected subunits, which are meticulously regulated, may be potential targets for the development of new antibiotics to combat multidrug-resistant Gram-negative bacteria. In this review, we aimed to provide an overview of current research concerning the structural interactions within the Lpt system and their implications to clarify the function and regulation of LPS transport in the overall process of OM biogenesis. Additionally, we explored studies on the development of therapeutic inhibitors of LPS transport, the factors that limit success, and future prospects.
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Affiliation(s)
- Yurim Yoon
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Saemee Song
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.
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9
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Tao K, Narita SI, Okada U, Murakami S, Tokuda H. Dissection of an ABC transporter LolCDE function analyzed by photo-crosslinking. J Biochem 2024; 175:427-437. [PMID: 38156779 PMCID: PMC11005994 DOI: 10.1093/jb/mvad118] [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: 09/07/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024] Open
Abstract
The envelope of Escherichia coli contains approximately 100 different species of lipoproteins, most of which are localized to the inner leaflet of the outer membrane. The localization of lipoprotein (Lol) system, consisting of five Lol proteins, is responsible for the trafficking of lipoproteins to the outer membrane. LolCDE binds to lipoproteins destined for the outer membrane and transfers them to the periplasmic chaperone LolA. Although the cryo-EM structures of E. coli LolCDE have been reported, the mechanisms by which outer membrane lipoproteins are transferred to LolA remain elusive. In this study, we investigated the interaction between LolCDE and lipoproteins using site-specific photo-crosslinking. We introduced a photo-crosslinkable amino acid into different locations across the four helices which form the central lipoprotein-binding cavity, and identified domains that crosslink with peptidoglycan-associated lipoprotein (Pal) in vivo. Using one of the derivatives containing the photo-crosslinkable amino acid, we developed an in vitro system to analyze the binding of lipoproteins to LolCDE. Our results indicate that compound 2, a LolCDE inhibitor, does not inhibit the binding of lipoproteins to LolCDE, but rather promotes the dissociation of bound lipoproteins from LolCDE.
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Affiliation(s)
- Kazuyuki Tao
- Isotope Science Center, University of Tokyo, 2-11-16 Yayoi, Bunky-ku, Tokyo 113-0032, Japan
| | - Shin-ichiro Narita
- Faculty of Health and Nutrition, Yamagata Prefectural Yonezawa University of Nutrition Sciences, Yonezawa, Yamagata 992-0025, Japan
| | - Ui Okada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Hajime Tokuda
- Faculty of Nutritional Sciences, University of Morioka, Takizawa, Iwate 020-0694, Japan
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10
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Cina NP, Klug CS. Conformational investigation of the asymmetric periplasmic domains of E. coli LptB 2FGC using SDSL CW EPR spectroscopy. APPLIED MAGNETIC RESONANCE 2024; 55:141-158. [PMID: 38645307 PMCID: PMC11025719 DOI: 10.1007/s00723-023-01590-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 04/23/2024]
Abstract
The majority of pathogenic Gram-negative bacteria benefit from intrinsic antibiotic resistance, attributed primarily to the lipopolysaccharide (LPS) coating of the bacterial envelope. To effectively coat the bacterial cell envelope, LPS is transported from the inner membrane by the LPS transport (Lpt) system, which comprises seven distinct Lpt proteins, LptA-G, that form a stable protein bridge spanning the periplasm to connect the inner and outer membranes. The driving force of this process, LptB2FG, is an asymmetric ATP binding cassette (ABC) transporter with a novel architecture and function that ejects LPS from the inner membrane and facilitates transfer to the periplasmic bridge. Here, we utilize site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy to probe conformational differences between the periplasmic domains of LptF and LptG. We show that LptC solely interacts with the edge β-strand of LptF and does not directly interact with LptG. We also quantify the interaction of periplasmic LptC with LptF. Additionally, we show that LPS cannot enter the protein complex externally, supporting the unidirectional LPS transport model. Furthermore, we present our findings that the presence of LPS within the LptB2FGC binding cavity and the membrane reconstitution environment affect the structural orientation of the periplasmic domains of LptF and LptG, but overall are relatively fixed with respect to one another. This study will provide insight into the structural asymmetry associated with the newly defined type VI ABC transporter class.
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Affiliation(s)
- Nicholas P. Cina
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Candice S. Klug
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226 USA
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11
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Lehman KM, May KL, Marotta J, Grabowicz M. Genetic analysis reveals a robust and hierarchical recruitment of the LolA chaperone to the LolCDE lipoprotein transporter. mBio 2024; 15:e0303923. [PMID: 38193657 PMCID: PMC10865981 DOI: 10.1128/mbio.03039-23] [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: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024] Open
Abstract
The outer membrane (OM) is an essential organelle of Gram-negative bacteria. Lipoproteins are key to building the OM, performing essential functions in several OM assembly machines. Lipoproteins mature in the inner membrane (IM) and are then trafficked to the OM. In Escherichia coli, the LolCDE transporter is needed to extract lipoproteins from the IM to begin trafficking. Lipoproteins are then transferred from LolCDE to the periplasmic chaperone LolA which ferries them to the OM for insertion by LolB. LolA recruitment by LolC is an essential trafficking step. Structural and biochemical studies suggested that two regions (termed Hook and Pad) within a periplasmic loop of LolC worked in tandem to recruit LolA, leading to a bipartite model for recruitment. Here, we genetically examine the LolC periplasmic loop in vivo using E. coli. Our findings challenge the bipartite interaction model. We show that while the Hook is essential for lipoprotein trafficking in vivo, lipoproteins are still efficiently trafficked when the Pad residues are inactivated. We show with AlphaFold2 multimer modeling that Hook:LolA interactions are likely universal among diverse Gram-negative bacteria. Conversely, Pad:LolA interactions vary across phyla. Our in vivo data redefine LolC:LolA recruitment into a hierarchical interaction model. We propose that the Hook is the major player in LolA recruitment, while the Pad plays an ancillary role that is important for efficiency but is ultimately dispensable. Our findings expand the understanding of a fundamental step in essential lipoprotein trafficking and have implications for efforts to develop new antibacterials that target LolCDE.IMPORTANCEResistance to current antibiotics is increasingly common. New antibiotics that target essential processes are needed to expand clinical options. For Gram-negative bacteria, their cell surface-the outer membrane (OM)-is an essential organelle and antibiotic barrier that is an attractive target for new antibacterials. Lipoproteins are key to building the OM. The LolCDE transporter is needed to supply the OM with lipoproteins and has been a focus of recent antibiotic discovery. In vitro evidence recently proposed a two-part interaction of LolC with LolA lipoprotein chaperone (which traffics lipoproteins to the OM) via "Hook" and "Pad" regions. We show that this model does not reflect lipoprotein trafficking in vivo. Only the Hook is essential for lipoprotein trafficking and is remarkably robust to mutational changes. The Pad is non-essential for lipoprotein trafficking but plays an ancillary role, contributing to trafficking efficiency. These insights inform ongoing efforts to drug LolCDE.
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Affiliation(s)
- Kelly M. Lehman
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kerrie L. May
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Julianna Marotta
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Marcin Grabowicz
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
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12
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Volynkina IA, Bychkova EN, Karakchieva AO, Tikhomirov AS, Zatonsky GV, Solovieva SE, Martynov MM, Grammatikova NE, Tereshchenkov AG, Paleskava A, Konevega AL, Sergiev PV, Dontsova OA, Osterman IA, Shchekotikhin AE, Tevyashova AN. Hybrid Molecules of Azithromycin with Chloramphenicol and Metronidazole: Synthesis and Study of Antibacterial Properties. Pharmaceuticals (Basel) 2024; 17:187. [PMID: 38399402 PMCID: PMC10892836 DOI: 10.3390/ph17020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
The sustained rise of antimicrobial resistance (AMR) causes a strong need to develop new antibacterial agents. One of the methods for addressing the problem of antibiotic resistance is through the design of hybrid antibiotics. In this work, we proposed a synthetic route for the conjugation of an azithromycin derivative with chloramphenicol and metronidazole hemisuccinates and synthesized two series of new hybrid molecules 4a-g and 5a-g. While a conjugation did not result in tangible synergy for wild-type bacterial strains, new compounds were able to overcome AMR associated with the inducible expression of the ermC gene on a model E. coli strain resistant to macrolide antibiotics. The newly developed hybrids demonstrated a tendency to induce premature ribosome stalling, which might be crucial since they will not induce a macrolide-resistant phenotype in a number of pathogenic bacterial strains. In summary, the designed structures are considered as a promising direction for the further development of hybrid molecules that can effectively circumvent AMR mechanisms to macrolide antibiotics.
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Affiliation(s)
- Inna A. Volynkina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
| | - Elena N. Bychkova
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Anastasiia O. Karakchieva
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
| | - Alexander S. Tikhomirov
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - George V. Zatonsky
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Svetlana E. Solovieva
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Maksim M. Martynov
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Natalia E. Grammatikova
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Andrey G. Tereshchenkov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia
| | - Alena Paleskava
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantiniv of NRC “Kurchatov Institute”, Mkr. Orlova Roshcha 1, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Khlopina 11, 195251 Saint Petersburg, Russia
| | - Andrey L. Konevega
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantiniv of NRC “Kurchatov Institute”, Mkr. Orlova Roshcha 1, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Khlopina 11, 195251 Saint Petersburg, Russia
- NBICS Center, NRC “Kurchatov Institute”, Kurchatov Square 1, 123182 Moscow, Russia
| | - Petr V. Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia
| | - Olga A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
| | - Andrey E. Shchekotikhin
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Anna N. Tevyashova
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
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13
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Storek KM, Sun D, Rutherford ST. Inhibitors targeting BamA in gram-negative bacteria. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119609. [PMID: 37852326 DOI: 10.1016/j.bbamcr.2023.119609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/08/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023]
Abstract
Antibiotic resistance has led to an increase in the number of patient hospitalizations and deaths. The situation for gram-negative bacteria is especially dire as the last new class of antibiotics active against these bacteria was introduced to the clinic over 60 years ago, thus there is an immediate unmet need for new antibiotic classes able to overcome resistance. The outer membrane, a unique and essential structure in gram-negative bacteria, contains multiple potential antibacterial targets including BamA, an outer membrane protein that folds and inserts transmembrane β-barrel proteins. BamA is essential and conserved, and its outer membrane location eliminates a barrier that molecules must overcome to access this target. Recently, antibacterial small molecules, natural products, peptides, and antibodies that inhibit BamA activity have been reported, validating the druggability of this target and generating potential leads for antibiotic development. This review will describe these BamA inhibitors, highlight their key attributes, and identify challenges with this potential target.
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Affiliation(s)
- Kelly M Storek
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Dawei Sun
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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14
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Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D. A new antibiotic traps lipopolysaccharide in its intermembrane transporter. Nature 2024; 625:572-577. [PMID: 38172635 PMCID: PMC10794137 DOI: 10.1038/s41586-023-06799-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
Gram-negative bacteria are extraordinarily difficult to kill because their cytoplasmic membrane is surrounded by an outer membrane that blocks the entry of most antibiotics. The impenetrable nature of the outer membrane is due to the presence of a large, amphipathic glycolipid called lipopolysaccharide (LPS) in its outer leaflet1. Assembly of the outer membrane requires transport of LPS across a protein bridge that spans from the cytoplasmic membrane to the cell surface. Maintaining outer membrane integrity is essential for bacterial cell viability, and its disruption can increase susceptibility to other antibiotics2-6. Thus, inhibitors of the seven lipopolysaccharide transport (Lpt) proteins that form this transenvelope transporter have long been sought. A new class of antibiotics that targets the LPS transport machine in Acinetobacter was recently identified. Here, using structural, biochemical and genetic approaches, we show that these antibiotics trap a substrate-bound conformation of the LPS transporter that stalls this machine. The inhibitors accomplish this by recognizing a composite binding site made up of both the Lpt transporter and its LPS substrate. Collectively, our findings identify an unusual mechanism of lipid transport inhibition, reveal a druggable conformation of the Lpt transporter and provide the foundation for extending this class of antibiotics to other Gram-negative pathogens.
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Affiliation(s)
- Karanbir S Pahil
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Vadim Baidin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Thomas Clairfeuille
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Patrizio Mattei
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Christoph Bieniossek
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Fabian Dey
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Dieter Muri
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Remo Baettig
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Michael Lobritz
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Kenneth Bradley
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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15
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Mirbagheri VS, Alishahi A, Ahmadian G, Petroudi SHH, Ojagh SM, Romanazzi G. Recent findings in molecular reactions of E. coli as exposed to alkylated, nano- and ordinary chitosans. Int J Biol Macromol 2023; 253:127006. [PMID: 37734522 DOI: 10.1016/j.ijbiomac.2023.127006] [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: 11/19/2022] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
The antibacterial effects of chitosan have been widely studied, but the underlying molecular mechanisms are not fully understood. We investigated the molecular responses of Escherichia coli MG1655 cell, a model gram-negative bacterium, upon exposure to chitosan (Cs), alkylated Cs (AlkCs), and chitosan nanoparticles (CsNPs). Nine target genes involved in relevant signaling pathways (ompF, ompC, ompA, mrcA, mrcB, mgtA, glnA, kdpA, lptA) were selected for analysis. A significant reduction in the expression of mrcA, mgtA, glnA, and lptA genes was observed in the cells treated with Cs. Those treated with Cs, AlkCs, and CsNPs revealed an increase in ompF gene expression, but the expression level was lower in the cells treated with AlkCs and CsNPs compared to Cs. This increase in porin expression suggests compromised membrane integrity and disrupted nutrient transport. In addition, the changes in the expression of mgtA, kdpA, and glnA are related to different effects on membrane permeability. The higher expression in the genes mrcA and mrcB is associated with morphological changes of cells treated with AlkCs and CsNPs. These findings contribute to our understanding of the molecular mechanisms underlying chitosan-induced stress responses and provide insights for the development of safer antimicrobial compounds in the future.
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Affiliation(s)
- Vasighe Sadat Mirbagheri
- Faculty of Fisheries and Environment Science, Gorgan University of Agriculture Science and Natural Resources, Gorgan, Iran
| | - Alireza Alishahi
- Faculty of Fisheries and Environment Science, Gorgan University of Agriculture Science and Natural Resources, Gorgan, Iran.
| | - Gholamreza Ahmadian
- Department of Industrial Environmental and Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Seyyed Hamidreza Hashemi Petroudi
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, PO Box 578, Sari, Iran
| | - Seyed Mahdi Ojagh
- Faculty of Fisheries and Environment Science, Gorgan University of Agriculture Science and Natural Resources, Gorgan, Iran
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16
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Irshad IU, Sharma AK. Decoding stoichiometric protein synthesis in E. coli through translation rate parameters. BIOPHYSICAL REPORTS 2023; 3:100131. [PMID: 37789867 PMCID: PMC10542608 DOI: 10.1016/j.bpr.2023.100131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
E. coli is one of the most widely used organisms for understanding the principles of cellular and molecular genetics. However, we are yet to understand the origin of several experimental observations related to the regulation of gene expression in E. coli. One of the prominent examples in this context is the proportional synthesis in multiprotein complexes where all of their obligate subunits are produced in proportion to their stoichiometry. In this work, by combining the next-generation sequencing data with the stochastic simulations of protein synthesis, we explain the origin of proportional protein synthesis in multicomponent complexes. We find that the estimated initiation rates for the translation of all subunits in those complexes are proportional to their stoichiometry. This constraint on protein synthesis kinetics enforces proportional protein synthesis without requiring any feedback mechanism. We also find that the translation initiation rates in E. coli are influenced by the coding sequence length and the enrichment of A and C nucleotides near the start codon. Thus, this study rationalizes the role of conserved and nonrandom features of genes in regulating the translation kinetics and unravels a key principle of the regulation of protein synthesis.
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Affiliation(s)
| | - Ajeet K. Sharma
- Department of Physics, Indian Institute of Technology Jammu, Jammu, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu, India
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17
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Lehman KM, May KL, Marotta J, Grabowicz M. Genetic analysis reveals a robust and hierarchical recruitment of the LolA chaperone to the LolCDE lipoprotein transporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566237. [PMID: 37986794 PMCID: PMC10659402 DOI: 10.1101/2023.11.08.566237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The outer membrane (OM) is an essential organelle of Gram-negative bacteria. Lipoproteins are key to building the OM, performing essential functions in several OM assembly machines. Lipoproteins mature in the inner membrane (IM) and are then trafficked to the OM. In Escherichia coli, the LolCDE transporter is needed to extract lipoproteins from the IM to begin trafficking. Lipoproteins are then transferred from LolCDE to the periplasmic chaperone LolA which ferries them to the OM for insertion by LolB. LolA recruitment by LolC is an essential trafficking step. Structural and biochemical studies suggested that two regions (termed Hook and Pad) within a periplasmic loop of LolC worked in tandem to recruit LolA, leading to a bipartite model for recruitment. Here, we genetically examine the LolC periplasmic loop in vivo using E. coli. Our findings challenge the bipartite interaction model. We show that while the Hook is essential for lipoprotein trafficking in vivo, lipoproteins are still efficiently trafficked when the Pad residues are inactivated. We show with AlphaFold2 multimer modeling that Hook:LolA interactions are likely universal among diverse Gram-negative bacteria. Conversely, Pad:LolA interactions vary across phyla. Our in vivo data redefine LolC:LolA recruitment into a hierarchical interaction model. We propose that the Hook is the major player in LolA recruitment, while the Pad plays an ancillary role that is important for efficiency but is ultimately dispensable. Our findings expand the understanding of a fundamental step in essential lipoprotein trafficking and have implications for efforts to develop new antibacterials that target LolCDE.
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Affiliation(s)
- Kelly M. Lehman
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
- Kelly M. Lehman and Kerrie L. May contributed equally to this work. Author order was determined alphabetically
| | - Kerrie L. May
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
- Kelly M. Lehman and Kerrie L. May contributed equally to this work. Author order was determined alphabetically
| | - Julianna Marotta
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Marcin Grabowicz
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
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18
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Törk L, Moffatt CB, Bernhardt TG, Garner EC, Kahne D. Single-molecule dynamics show a transient lipopolysaccharide transport bridge. Nature 2023; 623:814-819. [PMID: 37938784 PMCID: PMC10842706 DOI: 10.1038/s41586-023-06709-x] [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: 07/25/2022] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
Gram-negative bacteria are surrounded by two membranes. A special feature of the outer membrane is its asymmetry. It contains lipopolysaccharide (LPS) in the outer leaflet and phospholipids in the inner leaflet1-3. The proper assembly of LPS in the outer membrane is required for cell viability and provides Gram-negative bacteria intrinsic resistance to many classes of antibiotics. LPS biosynthesis is completed in the inner membrane, so the LPS must be extracted, moved across the aqueous periplasm that separates the two membranes and translocated through the outer membrane where it assembles on the cell surface4. LPS transport and assembly requires seven conserved and essential LPS transport components5 (LptA-G). This system has been proposed to form a continuous protein bridge that provides a path for LPS to reach the cell surface6,7, but this model has not been validated in living cells. Here, using single-molecule tracking, we show that Lpt protein dynamics are consistent with the bridge model. Half of the inner membrane Lpt proteins exist in a bridge state, and bridges persist for 5-10 s, showing that their organization is highly dynamic. LPS facilitates Lpt bridge formation, suggesting a mechanism by which the production of LPS can be directly coupled to its transport. Finally, the bridge decay kinetics suggest that there may be two different types of bridges, whose stability differs according to the presence (long-lived) or absence (short-lived) of LPS. Together, our data support a model in which LPS is both a substrate and a structural component of dynamic Lpt bridges that promote outer membrane assembly.
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Affiliation(s)
- Lisa Törk
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Caitlin B Moffatt
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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19
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Sabnis A, Edwards AM. Lipopolysaccharide as an antibiotic target. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119507. [PMID: 37268022 DOI: 10.1016/j.bbamcr.2023.119507] [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: 04/04/2022] [Revised: 04/18/2023] [Accepted: 05/14/2023] [Indexed: 06/04/2023]
Abstract
Gram-negative bacteria, including Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii are amongst the highest priority drug-resistant pathogens, for which new antibiotics are urgently needed. Whilst antibiotic drug development is inherently challenging, this is particularly true for Gram-negative bacteria due to the presence of the outer membrane, a highly selective permeability barrier that prevents the ingress of several classes of antibiotic. This selectivity is largely due to an outer leaflet composed of the glycolipid lipopolysaccharide (LPS), which is essential for the viability of almost all Gram-negative bacteria. This essentiality, coupled with the conservation of the synthetic pathway across species and recent breakthroughs in our understanding of transport and membrane homeostasis has made LPS an attractive target for novel antibiotic drug development. Several different targets have been explored and small molecules developed that show promising activity in vitro. However, these endeavours have met limited success in clinical testing and the polymyxins, discovered more than 70 years ago, remain the only LPS-targeting drugs to enter the clinic thus far. In this review, we will discuss efforts to develop therapeutic inhibitors of LPS synthesis and transport and the reasons for limited success, and explore new developments in understanding polymyxin mode of action and the identification of new analogues with reduced toxicity and enhanced activity.
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Affiliation(s)
- Akshay Sabnis
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London SW7 2AZ, UK
| | - Andrew M Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London SW7 2AZ, UK.
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20
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Schultz KM, Schneider JR, Fischer MA, Cina NP, Riegert MO, Frank DW, Klug CS. Binding and transport of LPS occurs through the coordinated combination of an array of sites across the entire Escherichia coli LPS transport protein LptA. Protein Sci 2023; 32:e4724. [PMID: 37417889 PMCID: PMC10360375 DOI: 10.1002/pro.4724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023]
Abstract
The outer leaflet of the outer membrane (OM) of bacteria such as Escherichia coli, Pseudomonas aeruginosa, and other important pathogens is largely composed of lipopolysaccharide (LPS), which is essential to nearly all Gram-negative bacteria. LPS is transported to the outer leaflet of the OM through a yet unknown mechanism by seven proteins that comprise the LPS transport system. LptA, the only entirely periplasmic Lpt protein, bridges the periplasmic space between the IM LptB2 FGC and the OM LptDE complexes. LptA is postulated to protect the hydrophobic acyl chains of LPS as it crosses the hydrophilic periplasm, is essential to cell viability, and contains many conserved residues distributed across the protein. To identify which side chains are required for function of E. coli LptA in vivo, we performed a systematic, unbiased, high-throughput screen of the effect of 172 single alanine substitutions on cell viability utilizing an engineered BL21 derivative with a chromosomal knockout of the lptA gene. Remarkably, LptA is highly tolerant to amino acid substitution with alanine. Only four alanine mutants could not complement the chromosomal knockout; CD spectroscopy showed that these substitutions resulted in proteins with significantly altered secondary structure. In addition, 29 partial loss-of-function mutants were identified that led to OM permeability defects; interestingly, these sites were solely located within β-strands of the central core of the protein and each resulted in misfolding of the protein. Therefore, no single residue within LptA is responsible for LPS binding, supporting previous EPR spectroscopy data indicating that sites across the entire protein work in concert to bind and transport LPS.
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Affiliation(s)
- Kathryn M. Schultz
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - John R. Schneider
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Matthew A. Fischer
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Nicholas P. Cina
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Molly O. Riegert
- Department of Microbiology & ImmunologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Dara W. Frank
- Department of Microbiology & ImmunologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Candice S. Klug
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
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21
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He H, Pramanik AS, Swanson SK, Johnson DK, Florens L, Zückert WR. A Borrelia burgdorferi LptD homolog is required for flipping of surface lipoproteins through the spirochetal outer membrane. Mol Microbiol 2023; 119:752-767. [PMID: 37170643 PMCID: PMC10330739 DOI: 10.1111/mmi.15072] [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: 12/21/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/13/2023]
Abstract
Borrelia spirochetes are unique among diderm bacteria in their lack of lipopolysaccharide (LPS) in the outer membrane (OM) and their abundance of surface-exposed lipoproteins with major roles in transmission, virulence, and pathogenesis. Despite their importance, little is known about how surface lipoproteins are translocated through the periplasm and the OM. Here, we characterized Borrelia burgdorferi BB0838, a distant homolog of the OM LPS assembly protein LptD. Using a CRISPR interference approach, we showed that BB0838 is required for cell growth and envelope stability. Upon BB0838 knockdown, surface lipoprotein OspA was retained in the inner leaflet of the OM, as determined by its inaccessibility to in situ proteolysis but its presence in OM vesicles. The topology of the OM porin/adhesin P66 remained unaffected. Quantitative mass spectrometry of the B. burgdorferi membrane-associated proteome confirmed the selective periplasmic retention of surface lipoproteins under BB0838 knockdown conditions. Additional analysis identified a single in situ protease-accessible BB0838 peptide that mapped to a predicted β-barrel surface loop. Alphafold Multimer modeled a B. burgdorferi LptB2 FGCAD complex spanning the periplasm. Together, this suggests that BB0838/LptDBb facilitates the essential terminal step in spirochetal surface lipoprotein secretion, using an orthologous OM component of a pathway that secretes LPS in proteobacteria.
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Affiliation(s)
- Huan He
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics and Immunology, Kansas City, Kansas, USA
| | - Ankita S. Pramanik
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics and Immunology, Kansas City, Kansas, USA
| | | | - David K. Johnson
- University of Kansas, Computational Chemical Biology Core, Lawrence, Kansas, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Wolfram R. Zückert
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics and Immunology, Kansas City, Kansas, USA
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22
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Lucena ACR, Ferrarini MG, de Oliveira WK, Marcon BH, Morello LG, Alves LR, Faoro H. Modulation of Klebsiella pneumoniae Outer Membrane Vesicle Protein Cargo under Antibiotic Treatment. Biomedicines 2023; 11:1515. [PMID: 37371610 PMCID: PMC10294825 DOI: 10.3390/biomedicines11061515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/14/2023] [Accepted: 05/14/2023] [Indexed: 06/29/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen and an important propagator of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Like other Gram-negative bacteria, they secrete outer membrane vesicles (OMVs) that distribute virulence and resistance factors. Here, we subjected a K. pneumoniae-XDR to subinhibitory concentrations of meropenem, amikacin, polymyxin B, and a combination of these agents to evaluate changes in the protein cargo of OMVs through liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genome sequencing of the clinical isolate K. pneumoniae strain HCD1 (KpHCD1) revealed the presence of 41 resistance genes and 159 virulence factors. We identified 64 proteins in KpHCD1-OMVs modulated with different antibiotic treatments involved in processing genetic information, environmental information, cell envelope formation, energy metabolism, and drug resistance. The OMV proteome expression profile suggests that OMVs may be associated with pathogenicity, survival, stress response, and resistance dissemination.
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Affiliation(s)
- Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, 69622 Villeurbanne, France
| | - Willian Klassen de Oliveira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Bruna Hilzendeger Marcon
- Laboratory for Basic Biology of Stem Cells, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Luis Gustavo Morello
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Lysangela Ronalte Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
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23
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Bilsing FL, Anlauf MT, Hachani E, Khosa S, Schmitt L. ABC Transporters in Bacterial Nanomachineries. Int J Mol Sci 2023; 24:ijms24076227. [PMID: 37047196 PMCID: PMC10094684 DOI: 10.3390/ijms24076227] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Members of the superfamily of ABC transporters are found in all domains of life. Most of these primary active transporters act as isolated entities and export or import their substrates in an ATP-dependent manner across biological membranes. However, some ABC transporters are also part of larger protein complexes, so-called nanomachineries that catalyze the vectorial transport of their substrates. Here, we will focus on four bacterial examples of such nanomachineries: the Mac system providing drug resistance, the Lpt system catalyzing vectorial LPS transport, the Mla system responsible for phospholipid transport, and the Lol system, which is required for lipoprotein transport to the outer membrane of Gram-negative bacteria. For all four systems, we tried to summarize the existing data and provide a structure-function analysis highlighting the mechanistical aspect of the coupling of ATP hydrolysis to substrate translocation.
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24
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[4+2]-Cycloaddition to 5-Methylidene-Hydantoins and 5-Methylidene-2-Thiohydantoins in the Synthesis of Spiro-2-Chalcogenimidazolones. Int J Mol Sci 2023; 24:ijms24055037. [PMID: 36902468 PMCID: PMC10002963 DOI: 10.3390/ijms24055037] [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: 02/18/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Novel hydantion and thiohydantoin-based spiro-compounds were prepared via theDiels-Alder reactions between 5-methylidene-hydantoins or 5-methylidene-2-thiohydantoins and 1,3-dienes (cyclopentadiene, cyclohexadiene, 2,3-dimethylbutadiene, isoprene). It was shown that the cycloaddition reactions proceed regioselectively and stereoselectively with the formation of exo-isomers in the reactions with cyclic dienes andthe less sterically hindered products in the reactions with isoprene. Reactions of methylideneimidazolones with cyclopentadiene proceed viaco-heating the reactants; reactions with cyclohexadiene, 2,3-dimethylbutadiene, and isoprene require catalysis by Lewis acids. It was demonstrated that ZnI2 is an effective catalyst in the Diels-Alder reactions of methylidenethiohydantoins with non-activated dienes. The possibility of alkylation and acylation of the obtained spiro-hydantoinsat the N(1)nitrogen atoms with PhCH2Cl or Boc2O and the alkylation of the spiro-thiohydantoinsat the S atoms with MeI or PhCH2Cl in high yields have been demonstrated. The preparativetransformation of spiro-thiohydantoins into corresponding spiro-hydantoinsin mild conditions by treating with 35% aqueous H2O2 or nitrile oxide has been carried out. The obtained compounds show moderate cytotoxicity in the MTT test on MCF7, A549, HEK293T, and VA13 cell lines. Some of the tested compounds demonstrated some antibacterial effect against Escherichia coli (E. coli) BW25113 DTC-pDualrep2 but were almost inactive against E. coli BW25113 LPTD-pDualrep2.
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25
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Servais C, Vassen V, Verhaeghe A, Küster N, Carlier E, Phégnon L, Mayard A, Auberger N, Vincent S, De Bolle X. Lipopolysaccharide biosynthesis and traffic in the envelope of the pathogen Brucella abortus. Nat Commun 2023; 14:911. [PMID: 36806059 PMCID: PMC9938171 DOI: 10.1038/s41467-023-36442-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 01/31/2023] [Indexed: 02/19/2023] Open
Abstract
Lipopolysaccharide is essential for most Gram-negative bacteria as it is a main component of the outer membrane. In the pathogen Brucella abortus, smooth lipopolysaccharide containing the O-antigen is required for virulence. Being part of the Rhizobiales, Brucella spp. display unipolar growth and lipopolysaccharide was shown to be incorporated at the active growth sites, i.e. the new pole and the division site. By localizing proteins involved in the lipopolysaccharide transport across the cell envelope, from the inner to the outer membrane, we show that the lipopolysaccharide incorporation sites are determined by the inner membrane complex of the lipopolysaccharide transport system. Moreover, we identify the main O-antigen ligase of Brucella spp. involved in smooth lipopolysaccharide synthesis. Altogether, our data highlight a layer of spatiotemporal organization of the lipopolysaccharide biosynthesis pathway and identify an original class of bifunctional O-antigen ligases.
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Affiliation(s)
- Caroline Servais
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Victoria Vassen
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Audrey Verhaeghe
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Nina Küster
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Elodie Carlier
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Léa Phégnon
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Aurélie Mayard
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Nicolas Auberger
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "OrgaSynth", Groupe Glycochimie, 4 rue Michel Brunet, 86073, Poitiers, France
| | - Stéphane Vincent
- Bio-organic Chemistry Unit (CBO), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Xavier De Bolle
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000, Namur, Belgium.
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26
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Guest RL, Silhavy TJ. Cracking outer membrane biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119405. [PMID: 36455781 PMCID: PMC9878550 DOI: 10.1016/j.bbamcr.2022.119405] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022]
Abstract
The outer membrane is a distinguishing feature of the Gram-negative envelope. It lies on the external face of the peptidoglycan sacculus and forms a robust permeability barrier that protects extracytoplasmic structures from environmental insults. Overcoming the barrier imposed by the outer membrane presents a significant hurdle towards developing novel antibiotics that are effective against Gram-negative bacteria. As the outer membrane is an essential component of the cell, proteins involved in its biogenesis are themselves promising antibiotic targets. Here, we summarize key findings that have built our understanding of the outer membrane. Foundational studies describing the discovery and composition of the outer membrane as well as the pathways involved in its construction are discussed.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, United States of America
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, United States of America.
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27
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Lai L, Yang J, Sun W, Su X, Chen J, Chen X, Pei S. Design, synthesis and antibacterial evaluation of a novel class of tetrahydrobenzothiophene derivatives. RSC Med Chem 2023; 14:166-172. [PMID: 36760738 PMCID: PMC9890943 DOI: 10.1039/d2md00373b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 12/11/2022] Open
Abstract
In this study, a new series of tetrahydrobenzothiophene derivatives have been designed. Newly designed molecules have been synthesized through a medicinal chemistry route, and their characterization was done by using NMR and HR-MS techniques. Biological evaluation of the synthesized compounds has been done on Gram-negative and Gram-positive bacteria. The marketed antibiotics such as ciprofloxacin and gentamicin were used as controls. The in vitro evaluation results have shown that most of the targeted compounds exhibit good potency in inhibiting the growth of bacteria, including E. coli (MIC: 0.64-19.92 μM), P. aeruginosa (MIC: 0.72-45.30 μM), Salmonella (MIC: 0.54-90.58 μM) and S. aureus (MIC: 1.11-99.92 μM). In particular, compound 3b showed excellent activity with an MIC value of 1.11 μM against E. coli, 1.00 μM against P. aeruginosa, 0.54 μM against Salmonella, and 1.11 μM against S. aureus. From the results, a promising lead compound was identified for future development.
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Affiliation(s)
- Lin Lai
- Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology Chongqing 401331 China
| | - Jinhua Yang
- Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology Chongqing 401331 China
| | - Wanlin Sun
- Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology Chongqing 401331 China
| | - Xiaoyan Su
- Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology Chongqing 401331 China
| | - Jun Chen
- Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology Chongqing 401331 China
| | - Xinan Chen
- German Institute of Engineering, Chongqing College of Mobile Communtion Chongqing 401520 China
| | - Shuchen Pei
- Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology Chongqing 401331 China
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28
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Bowen HG, Kenedy MR, Johnson DK, MacKerell AD, Akins DR. Identification of a novel transport system in Borrelia burgdorferi that links the inner and outer membranes. Pathog Dis 2023; 81:ftad014. [PMID: 37385817 PMCID: PMC10353723 DOI: 10.1093/femspd/ftad014] [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: 04/20/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023] Open
Abstract
Borrelia burgdorferi, the spirochete that causes Lyme disease, is a diderm organism that is similar to Gram-negative organisms in that it contains both an inner and outer membrane. Unlike typical Gram-negative organisms, however, B. burgdorferi lacks lipopolysaccharide (LPS). Using computational genome analyses and structural modeling, we identified a transport system containing six proteins in B. burgdorferi that are all orthologs to proteins found in the lipopolysaccharide transport (LPT) system that links the inner and outer membranes of Gram-negative organisms and is responsible for placing LPS on the surface of these organisms. While B. burgdorferi does not contain LPS, it does encode over 100 different surface-exposed lipoproteins and several major glycolipids, which like LPS are also highly amphiphilic molecules, though no system to transport these molecules to the borrelial surface is known. Accordingly, experiments supplemented by molecular modeling were undertaken to determine whether the orthologous LPT system identified in B. burgdorferi could transport lipoproteins and/or glycolipids to the borrelial outer membrane. Our combined observations strongly suggest that the LPT transport system does not transport lipoproteins to the surface. Molecular dynamic modeling, however, suggests that the borrelial LPT system could transport borrelial glycolipids to the outer membrane.
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Affiliation(s)
- Hannah G Bowen
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., BMSB 1053 Oklahoma City, OK 73104, United States
| | - Melisha R Kenedy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., BMSB 1053 Oklahoma City, OK 73104, United States
| | - David K Johnson
- Shenkel Structural Biology Center, Molecular Graphics and Modeling Laboratory and the Computational Biology Core, University of Kansas, 2034 Becker Drive Lawrence, Kansas 66047, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore 20 North Pine Street Baltimore, Maryland 21201, United States
| | - Darrin R Akins
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., BMSB 1053 Oklahoma City, OK 73104, United States
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29
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SurA-like and Skp-like Proteins as Important Virulence Determinants of the Gram Negative Bacterial Pathogens. Int J Mol Sci 2022; 24:ijms24010295. [PMID: 36613738 PMCID: PMC9820271 DOI: 10.3390/ijms24010295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
In the Gram-negative bacteria, many important virulence factors reach their destination via two-step export systems, and they must traverse the periplasmic space before reaching the outer membrane. Since these proteins must be maintained in a structure competent for transport into or across the membrane, they frequently require the assistance of chaperones. Based on the results obtained for the model bacterium Escherichia coli and related species, it is assumed that in the biogenesis of the outer membrane proteins and the periplasmic transit of secretory proteins, the SurA peptidyl-prolyl isomerase/chaperone plays a leading role, while the Skp chaperone is rather of secondary importance. However, detailed studies carried out on several other Gram-negative pathogens indicate that the importance of individual chaperones in the folding and transport processes depends on the properties of client proteins and is species-specific. Taking into account the importance of SurA functions in bacterial virulence and severity of phenotypes due to surA mutations, this folding factor is considered as a putative therapeutic target to combat microbial infections. In this review, we present recent findings regarding SurA and Skp proteins: their mechanisms of action, involvement in processes related to virulence, and perspectives to use them as therapeutic targets.
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30
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Construction of a 980 nm laser-activated Pt(II) metallacycle nanosystem for efficient and safe photo-induced bacteria sterilization. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1440-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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31
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Zeczycki TN, Milton ME, Jung D, Thompson RJ, Jaimes FE, Hondros AD, Palethorpe S, Melander C, Cavanagh J. 2-Aminoimidazole Analogs Target PhoP Altering DNA Binding Activity and Affect Outer Membrane Stability in Gram-Negative Bacteria. Biochemistry 2022; 61:2948-2960. [DOI: 10.1021/acs.biochem.2c00560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Tonya N. Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina27834, United States
| | - Morgan E. Milton
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina27834, United States
| | - David Jung
- Agile Sciences Inc., 617 Hutton Street, Raleigh, North Carolina27606, United States
| | - Richele J. Thompson
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina27834, United States
| | - Felicia E. Jaimes
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina27834, United States
| | - Alexander D. Hondros
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina27834, United States
| | - Samantha Palethorpe
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina27834, United States
| | - Christian Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556, United States
| | - John Cavanagh
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina27834, United States
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32
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Webby MN, Oluwole AO, Pedebos C, Inns PG, Olerinyova A, Prakaash D, Housden NG, Benn G, Sun D, Hoogenboom BW, Kukura P, Mohammed S, Robinson CV, Khalid S, Kleanthous C. Lipids mediate supramolecular outer membrane protein assembly in bacteria. SCIENCE ADVANCES 2022; 8:eadc9566. [PMID: 36322653 PMCID: PMC9629720 DOI: 10.1126/sciadv.adc9566] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
β Barrel outer membrane proteins (OMPs) cluster into supramolecular assemblies that give function to the outer membrane (OM) of Gram-negative bacteria. How such assemblies form is unknown. Here, through photoactivatable cross-linking into the Escherichia coli OM, coupled with simulations, and biochemical and biophysical analysis, we uncover the basis for OMP clustering in vivo. OMPs are typically surrounded by an annular shell of asymmetric lipids that mediate higher-order complexes with neighboring OMPs. OMP assemblies center on the abundant porins OmpF and OmpC, against which low-abundance monomeric β barrels, such as TonB-dependent transporters, are packed. Our study reveals OMP-lipid-OMP complexes to be the basic unit of supramolecular OMP assembly that, by extending across the entire cell surface, couples the requisite multifunctionality of the OM to its stability and impermeability.
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Affiliation(s)
- Melissa N. Webby
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Abraham O. Oluwole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QZ, UK
| | - Conrado Pedebos
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Patrick G. Inns
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Dheeraj Prakaash
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Nicholas G. Housden
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Georgina Benn
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Dawei Sun
- Structural Biology, Genentech Inc., South San Francisco, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
- Department of Physics and Astronomy, University College London, WC1E 6BT London, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Shabaz Mohammed
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3QZ, UK
- Mechanistic Proteomics, Rosalind Franklin Institute, Harwell Campus, Didcot OX11 OFA, UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QZ, UK
| | - Syma Khalid
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
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Bei W, Luo Q, Shi H, Zhou H, Zhou M, Zhang X, Huang Y. Cryo-EM structures of LolCDE reveal the molecular mechanism of bacterial lipoprotein sorting in Escherichia coli. PLoS Biol 2022; 20:e3001823. [PMID: 36228045 PMCID: PMC9595528 DOI: 10.1371/journal.pbio.3001823] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 10/25/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022] Open
Abstract
Bacterial lipoproteins perform a diverse array of functions including bacterial envelope biogenesis and microbe–host interactions. Lipoproteins in gram-negative bacteria are sorted to the outer membrane (OM) via the localization of lipoproteins (Lol) export pathway. The ATP-binding cassette (ABC) transporter LolCDE initiates the Lol pathway by selectively extracting and transporting lipoproteins for trafficking. Here, we report cryo-EM structures of LolCDE in apo, lipoprotein-bound, and AMPPNP-bound states at a resolution of 3.5 to 4.2 Å. Structure-based disulfide crosslinking, photo-crosslinking, and functional complementation assay verify the apo-state structure and reveal the molecular details regarding substrate selectivity and substrate entry route. Our studies snapshot 3 functional states of LolCDE in a transport cycle, providing deep insights into the mechanisms that underlie LolCDE-mediated lipoprotein sorting in E. coli. Lipoproteins in Gram-negative bacteria are sorted to the outer membrane via the Lol export pathway. The ABC transporter LolCDE initiates this pathway by selectively extracting and transporting lipoproteins for trafficking; this study provides a structural basis for the LolCDE-mediated bacterial lipoprotein sorting, with implications for novel antibiotic design against Gram-negative bacterial pathogens.
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Affiliation(s)
- Weiwei Bei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingshan Luo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huigang Shi
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haizhen Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No.200 Xiao Ling Wei Street, Nanjing, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (XZ); (YH)
| | - Yihua Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (XZ); (YH)
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An Unprecedented Tolerance to Deletion of the Periplasmic Chaperones SurA, Skp, and DegP in the Nosocomial Pathogen Acinetobacter baumannii. J Bacteriol 2022; 204:e0005422. [PMID: 36106853 PMCID: PMC9578438 DOI: 10.1128/jb.00054-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria efficiently protects from harmful environmental stresses such as antibiotics, disinfectants, or dryness. The main constituents of the OM are integral OM β-barrel proteins (OMPs). In Gram-negative bacteria such as Escherichia coli, Yersinia enterocolitica, and Pseudomonas aeruginosa, the insertion of OMPs depends on a sophisticated biogenesis pathway. This comprises the SecYEG translocon, which enables inner membrane (IM) passage; the chaperones SurA, Skp, and DegP, which facilitate the passage of β-barrel OMPs through the periplasm; and the β-barrel assembly machinery (BAM), which facilitates insertion into the OM. In E. coli, Y. enterocolitica, and P. aeruginosa, the deletion of SurA is particularly detrimental and leads to a loss of OM integrity, sensitization to antibiotic treatment, and reduced virulence. In search of targets that could be exploited to develop compounds that interfere with OM integrity in Acinetobacter baumannii, we employed the multidrug-resistant strain AB5075 to generate single gene knockout strains lacking individual periplasmic chaperones. In contrast to E. coli, Y. enterocolitica, and P. aeruginosa, AB5075 tolerates the lack of SurA, Skp, or DegP with only weak mutant phenotypes. While the double knockout strains ΔsurAΔskp and ΔsurAΔdegP are conditionally lethal in E. coli, all double deletions were well tolerated by AB5075. Strikingly, even a triple-knockout strain of AB5075, lacking surA, skp, and degP, was viable. IMPORTANCEAcinetobacter baumannii is a major threat to human health due to its ability to persist in the hospital environment, resistance to antibiotic treatment, and ability to deploy multiple and redundant virulence factors. In a rising number of cases, infections with multidrug-resistant A. baumannii end up fatally, because all antibiotic treatment options fail. Thus, novel targets have to be identified and alternative therapeutics have to be developed. The knockout of periplasmic chaperones has previously proven to significantly reduce virulence and even break antibiotic resistance in other Gram-negative pathogens. Our study in A. baumannii demonstrates how variable the importance of the periplasmic chaperones SurA, Skp, and DegP can be and suggests the existence of mechanisms allowing A. baumannii to cope with the lack of the three periplasmic chaperones.
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Long wavelength-emissive Ru(II) metallacycle-based photosensitizer assisting in vivo bacterial diagnosis and antibacterial treatment. Proc Natl Acad Sci U S A 2022; 119:e2209904119. [PMID: 35914164 PMCID: PMC9371697 DOI: 10.1073/pnas.2209904119] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Ruthenium (Ru) complexes are developed as latent emissive photosensitizers for cancer and pathogen photodiagnosis and therapy. Nevertheless, most existing Ru complexes are limited as photosensitizers in terms of short excitation and emission wavelengths. Herein, we present an emissive Ru(II) metallacycle (herein referred to as 1) that is excited by 808-nm laser and emits at a wavelength of ∼1,000 nm via coordination-driven self-assembly. Metallacycle 1 exhibits good optical penetration (∼7 mm) and satisfactory reactive oxygen species production properties. Furthermore, 1 shows broad-spectrum antibacterial activity (including against drug-resistant Escherichia coli) as well as low cytotoxicity to normal mammalian cells. In vivo studies reveal that 1 is employed in precise, second near-infrared biomedical window fluorescent imaging-guided, photo-triggered treatments in Staphylococcus aureus-infected mice models, with negligible side effects. This work thus broads the applications of supramolecular photosensitizers through the strategy of lengthening their wavelengths.
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A Defect in Lipoprotein Modification by Lgt Leads to Abnormal Morphology and Cell Death in Escherichia coli That Is Independent of Major Lipoprotein Lpp. J Bacteriol 2022; 204:e0016422. [PMID: 35938851 PMCID: PMC9487459 DOI: 10.1128/jb.00164-22] [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] [Indexed: 12/01/2022] Open
Abstract
Lgt is an essential enzyme in proteobacteria and therefore a potential target for novel antibiotics. The effect of Lgt depletion on growth, morphology, and viability was studied in Escherichia coli to assess whether absence of Lgt leads to cell death. Two Lgt depletion strains were used in which lgt was under the control of an arabinose-inducible promoter that allowed regulation of Lgt protein levels. Reduced levels of Lgt led to severe growth and morphological defects that could be restored by expressing lgt in trans, demonstrating that only Lgt is responsible for the distorted phenotypes. In the absence of major lipoprotein Lpp, growth defects were partially restored when low levels of Lgt were still present; however, lgt could not be deleted in the absence of Lpp. Our results demonstrate that Lpp is not the main cause of cell death under conditions of Lgt depletion and that other lipoproteins are important in cell envelope biogenesis and cell viability. Specific inhibitors of Lgt are thus promising for the development of novel antibiotics. IMPORTANCE Incomplete maturation and envelope mislocalization of lipoproteins, through inhibition or mutations in lipoprotein modification enzymes or transport to the outer membrane, are lethal in proteobacteria. Resistance to small-molecule inhibition or the appearance of suppressor mutations is often directly correlated with the presence of abundant outer membrane lipoprotein Lpp. Our results show that Lgt, the first enzyme of the lipoprotein modification pathway, is still required for growth and viability in the absence of Lpp and thus is necessary for the function of other essential lipoproteins in the cell envelope. This adds credence to the hypothesis that Lgt is essential in proteobacteria and an attractive target for the development of novel antibiotics.
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Filatov VE, Iuzabchuk DA, Tafeenko VA, Grishin YK, Roznyatovsky VA, Lukianov DA, Fedotova YA, Sukonnikov MA, Skvortsov DA, Zyk NV, Beloglazkina EK. Dispirooxindole-β-Lactams: Synthesis via Staudinger Ketene-Imine Cycloaddition and Biological Evaluation. Int J Mol Sci 2022; 23:6666. [PMID: 35743110 PMCID: PMC9223813 DOI: 10.3390/ijms23126666] [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: 05/17/2022] [Revised: 06/05/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
In this work, we present the first synthesis of dispirooxindole-β-lactams employing optimized methodology of one-pot Staudinger ketene-imine cycloaddition with N-aryl-2-oxo-pyrrolidine-3-carboxylic acids as the ketene source. Spiroconjugation of indoline-2-one with β-lactams ring is considered to be able to provide stabilization and wide scope of functionalization to resulting scaffolds. The dispipooxindoles obtained demonstrated medium cytotoxicity in the MTT test on A549, MCF7, HEK293, and VA13 cell lines, and one of the compounds demonstrated antibacterial activity against E. coli strain LPTD.
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Affiliation(s)
- Vadim E. Filatov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Dmitrii A. Iuzabchuk
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Viktor A. Tafeenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Yuri K. Grishin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Vitaly A. Roznyatovsky
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Dmitrii A. Lukianov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia
| | - Yulia A. Fedotova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Maxim A. Sukonnikov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Dmitry A. Skvortsov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Nikolai V. Zyk
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
| | - Elena K. Beloglazkina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119234 Moscow, Russia; (V.E.F.); (D.A.I.); (V.A.T.); (Y.K.G.); (V.A.R.); (D.A.L.); (Y.A.F.); (M.A.S.); (D.A.S.); (N.V.Z.)
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Prasad NK, Seiple IB, Cirz RT, Rosenberg OS. Leaks in the Pipeline: a Failure Analysis of Gram-Negative Antibiotic Development from 2010 to 2020. Antimicrob Agents Chemother 2022; 66:e0005422. [PMID: 35471042 PMCID: PMC9112940 DOI: 10.1128/aac.00054-22] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The World Health Organization (WHO) has warned that our current arsenal of antibiotics is not innovative enough to face impending infectious diseases, especially those caused by multidrug-resistant Gram-negative pathogens. Although the current preclinical pipeline is well stocked with novel candidates, the last U.S. Food and Drug Administration (FDA)-approved antibiotic with a novel mechanism of action against Gram-negative bacteria was discovered nearly 60 years ago. Of all the antibiotic candidates that initiated investigational new drug (IND) applications in the 2000s, 17% earned FDA approval within 12 years, while an overwhelming 62% were discontinued in that time frame. These "leaks" in the clinical pipeline, where compounds with clinical potential are abandoned during clinical development, indicate that scientific innovations are not reaching the clinic and providing benefits to patients. This is true for not only novel candidates but also candidates from existing antibiotic classes with clinically validated targets. By identifying the sources of the leaks in the clinical pipeline, future developmental efforts can be directed toward strategies that are more likely to flow into clinical use. In this review, we conduct a detailed failure analysis of clinical candidates with Gram-negative activity that have fallen out of the clinical pipeline over the past decade. Although limited by incomplete data disclosure from companies engaging in antibiotic development, we attempt to distill the developmental challenges faced by each discontinued candidate. It is our hope that this insight can help de-risk antibiotic development and bring new, effective antibiotics to the clinic.
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Affiliation(s)
- Neha K. Prasad
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Ian B. Seiple
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | | | - Oren S. Rosenberg
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Department of Biochemistry, University of California, San Francisco, San Francisco, California, USA
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Botte M, Ni D, Schenck S, Zimmermann I, Chami M, Bocquet N, Egloff P, Bucher D, Trabuco M, Cheng RKY, Brunner JD, Seeger MA, Stahlberg H, Hennig M. Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation. Nat Commun 2022; 13:1826. [PMID: 35383177 PMCID: PMC8983717 DOI: 10.1038/s41467-022-29459-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram-negative bacteria. The last step of LPS insertion via the Lpt pathway is mediated by the LptD/E protein complex. Detailed insights into the architecture of LptDE transporter complexes have been derived from X-ray crystallography. However, no structure of a laterally open LptD transporter, a transient state that occurs during LPS release, is available to date. Here, we report a cryo-EM structure of a partially opened LptDE transporter in complex with rigid chaperones derived from nanobodies, at 3.4 Å resolution. In addition, a subset of particles allows to model a structure of a laterally fully opened LptDE complex. Our work offers insights into the mechanism of LPS insertion, provides a structural framework for the development of antibiotics targeting LptD and describes a highly rigid chaperone scaffold to enable structural biology of challenging protein targets.
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Affiliation(s)
- Mathieu Botte
- leadXpro AG, Park Innovaare, 5234, Villigen, Switzerland
| | - Dongchun Ni
- C-CINA, Biozentrum, University of Basel, Mattenstr. 24, 4058, Basel, Switzerland
| | - Stephan Schenck
- leadXpro AG, Park Innovaare, 5234, Villigen, Switzerland
- VIB-VUB Center for Structural Biology, VIB, 1050, Brussels, Belgium
| | - Iwan Zimmermann
- Institute of Medical Microbiology, University of Zürich, Gloriastasse 28/30, 8006, Zürich, Switzerland
- Linkster Therapeutics AG, 8006, Zürich, Switzerland
| | - Mohamed Chami
- C-CINA, Biozentrum, University of Basel, Mattenstr. 24, 4058, Basel, Switzerland
| | | | - Pascal Egloff
- Institute of Medical Microbiology, University of Zürich, Gloriastasse 28/30, 8006, Zürich, Switzerland
- Linkster Therapeutics AG, 8006, Zürich, Switzerland
| | - Denis Bucher
- leadXpro AG, Park Innovaare, 5234, Villigen, Switzerland
| | | | | | - Janine D Brunner
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute (PSI), 5232, Villigen, Switzerland
- VIB-VUB Center for Structural Biology, VIB, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zürich, Gloriastasse 28/30, 8006, Zürich, Switzerland
| | - Henning Stahlberg
- C-CINA, Biozentrum, University of Basel, Mattenstr. 24, 4058, Basel, Switzerland
| | - Michael Hennig
- leadXpro AG, Park Innovaare, 5234, Villigen, Switzerland.
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Xu Y, Tuo W, Yang L, Sun Y, Li C, Chen X, Yang W, Yang G, Stang PJ, Sun Y. Design of a Metallacycle-Based Supramolecular Photosensitizer for In Vivo Image-Guided Photodynamic Inactivation of Bacteria. Angew Chem Int Ed Engl 2022; 61:e202110048. [PMID: 34806264 DOI: 10.1002/anie.202110048] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 12/22/2022]
Abstract
Bacterial infection is one of the greatest threats to public health. In vivo real-time monitoring and effective treatment of infected sites through non-invasive techniques, remain a challenge. Herein, we designed a PtII metallacycle-based supramolecular photosensitizer through the host-guest interaction between a pillar[5]arene-modified metallacycle and 1-butyl-4-[4-(diphenylamino)styryl]pyridinium. Leveraging the aggregation-induced emission supramolecular photosensitizer, we improved fluorescence performance and antimicrobial photodynamic inactivation. In vivo studies revealed that it displayed precise fluorescence tracking of S. aureus-infected sites, and in situ performed image-guided efficient PDI of S. aureus without noticeable side effects. These results demonstrated that metallacycle combined with host-guest chemistry could provide a paradigm for the development of powerful photosensitizers for biomedicine.
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Affiliation(s)
- Yuling Xu
- Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Wei Tuo
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, UT, 84112, USA
| | - Liang Yang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yan Sun
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, UT, 84112, USA
| | - Chonglu Li
- Guangxi Key laboratory of High-Incidence-Tumor Prevention & Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Xiaoqiang Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing, 210009, China
| | - Wenchao Yang
- Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Guangfu Yang
- Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Peter J Stang
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, UT, 84112, USA
| | - Yao Sun
- Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
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41
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Xu Y, Tuo W, Yang L, Sun Y, Li C, Chen X, Yang W, Yang G, Stang PJ, Sun Y. Design of a Metallacycle‐Based Supramolecular Photosensitizer for In Vivo Image‐Guided Photodynamic Inactivation of Bacteria. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yuling Xu
- Key Laboratory of Pesticides and Chemical Biology Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health College of Chemistry Central China Normal University Wuhan 430079 China
| | - Wei Tuo
- Department of Chemistry University of Utah 315 South 1400 East, Room 2020 Salt Lake City UT 84112 USA
| | - Liang Yang
- Department of Radiology Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan 430022 China
| | - Yan Sun
- Department of Chemistry University of Utah 315 South 1400 East, Room 2020 Salt Lake City UT 84112 USA
| | - Chonglu Li
- Guangxi Key laboratory of High-Incidence-Tumor Prevention & Treatment Guangxi Medical University Nanning 530021 China
| | - Xiaoqiang Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering Nanjing University of Technology Nanjing 210009 China
| | - Wenchao Yang
- Key Laboratory of Pesticides and Chemical Biology Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health College of Chemistry Central China Normal University Wuhan 430079 China
| | - Guangfu Yang
- Key Laboratory of Pesticides and Chemical Biology Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health College of Chemistry Central China Normal University Wuhan 430079 China
| | - Peter J. Stang
- Department of Chemistry University of Utah 315 South 1400 East, Room 2020 Salt Lake City UT 84112 USA
| | - Yao Sun
- Key Laboratory of Pesticides and Chemical Biology Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health College of Chemistry Central China Normal University Wuhan 430079 China
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Martorana AM, Moura ECCM, Sperandeo P, Di Vincenzo F, Liang X, Toone E, Zhou P, Polissi A. Degradation of Components of the Lpt Transenvelope Machinery Reveals LPS-Dependent Lpt Complex Stability in Escherichia coli. Front Mol Biosci 2022; 8:758228. [PMID: 35004843 PMCID: PMC8727689 DOI: 10.3389/fmolb.2021.758228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Lipopolysaccharide (LPS) is a peculiar component of the outer membrane (OM) of many Gram-negative bacteria that renders these bacteria highly impermeable to many toxic molecules, including antibiotics. LPS is assembled at the OM by a dedicated intermembrane transport system, the Lpt (LPS transport) machinery, composed of seven essential proteins located in the inner membrane (IM) (LptB2CFG), periplasm (LptA), and OM (LptDE). Defects in LPS transport compromise LPS insertion and assembly at the OM and result in an overall modification of the cell envelope and its permeability barrier properties. LptA is a key component of the Lpt machine. It connects the IM and OM sub-complexes by interacting with the IM protein LptC and the OM protein LptD, thus enabling the LPS transport across the periplasm. Defects in Lpt system assembly result in LptA degradation whose stability can be considered a marker of an improperly assembled Lpt system. Indeed, LptA recruitment by its IM and OM docking sites requires correct maturation of the LptB2CFG and LptDE sub-complexes, respectively. These quality control checkpoints are crucial to avoid LPS mistargeting. To further dissect the requirements for the complete Lpt transenvelope bridge assembly, we explored the importance of LPS presence by blocking its synthesis using an inhibitor compound. Here, we found that the interruption of LPS synthesis results in the degradation of both LptA and LptD, suggesting that, in the absence of the LPS substrate, the stability of the Lpt complex is compromised. Under these conditions, DegP, a major chaperone–protease in Escherichia coli, is responsible for LptD but not LptA degradation. Importantly, LptD and LptA stability is not affected by stressors disturbing the integrity of LPS or peptidoglycan layers, further supporting the notion that the LPS substrate is fundamental to keeping the Lpt transenvelope complex assembled and that LptA and LptD play a major role in the stability of the Lpt system.
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Affiliation(s)
- Alessandra M Martorana
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
| | - Elisabete C C M Moura
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
| | - Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
| | - Flavia Di Vincenzo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
| | - Xiaofei Liang
- Department of Chemistry, Duke University, Durham, NC, United States
| | - Eric Toone
- Department of Chemistry, Duke University, Durham, NC, United States
| | - Pei Zhou
- Department of Chemistry, Duke University, Durham, NC, United States.,Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università Degli Studi di Milano, Milan, Italy
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The sacrificial adaptor protein Skp functions to remove stalled substrates from the β-barrel assembly machine. Proc Natl Acad Sci U S A 2022; 119:2114997119. [PMID: 34969846 PMCID: PMC8740687 DOI: 10.1073/pnas.2114997119] [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] [Accepted: 11/22/2021] [Indexed: 01/25/2023] Open
Abstract
The outer membrane (OM) of gram-negative bacteria acts as a robust permeability barrier to enable cell survival in a wide variety of harsh environments. Crucial to OM integrity are β-barrel outer membrane proteins (OMPs) that are assembled into the membrane by the broadly conserved β-barrel assembly machine (Bam) complex. Here, we identify specific roles for the periplasmic chaperone Skp in functioning as a sacrificial adaptor protein to remove stalled substrates from the Bam complex, imposing an active quality control mechanism that ensures efficient assembly of nascent OMPs into the OM. This work identifies the molecular mechanism of the Skp/DegP functional relationship and clarifies the long-standing paradox of how substrate release from the high-affinity, long-lived Skp–OMP complex is achieved in vivo. The biogenesis of integral β-barrel outer membrane proteins (OMPs) in gram-negative bacteria requires transport by molecular chaperones across the aqueous periplasmic space. Owing in part to the extensive functional redundancy within the periplasmic chaperone network, specific roles for molecular chaperones in OMP quality control and assembly have remained largely elusive. Here, by deliberately perturbing the OMP assembly process through use of multiple folding-defective substrates, we have identified a role for the periplasmic chaperone Skp in ensuring efficient folding of OMPs by the β-barrel assembly machine (Bam) complex. We find that β-barrel substrates that fail to integrate into the membrane in a timely manner are removed from the Bam complex by Skp, thereby allowing for clearance of stalled Bam–OMP complexes. Following the displacement of OMPs from the assembly machinery, Skp subsequently serves as a sacrificial adaptor protein to directly facilitate the degradation of defective OMP substrates by the periplasmic protease DegP. We conclude that Skp acts to ensure efficient β-barrel folding by directly mediating the displacement and degradation of assembly-compromised OMP substrates from the Bam complex.
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Martorana AM, Santambrogio C, Polissi A. Affinity Purification and Coimmunoprecipitation of Transenvelope Protein Complexes in Gram-Negative Bacteria. Methods Mol Biol 2022; 2548:129-144. [PMID: 36151496 DOI: 10.1007/978-1-0716-2581-1_9] [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: 06/16/2023]
Abstract
Multiprotein complexes are important machineries that organize a large number of different proteins into functional units. Studying protein-protein interactions in the complexes, rather than individual proteins, is a fundamental step to gaining functional insights into a biological process. Here, we present the sequential affinity purification and coimmunoprecipitation system that was applied to enable the efficient purification of all the proteins that compose the Lpt system complex in Escherichia coli and their identification by western blotting and mass spectrometry (MS).
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Affiliation(s)
- Alessandra M Martorana
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy.
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, Università di Milano Bicocca, Milan, Italy
| | - Alessandra Polissi
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
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45
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Falchi FA. Analyzing the Function of Essential Genes by Plasmid Shuffling. Methods Mol Biol 2022; 2548:37-49. [PMID: 36151490 DOI: 10.1007/978-1-0716-2581-1_3] [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: 06/16/2023]
Abstract
Investigations on gene essentiality have important implications in several fields of basic and applied research. A variety of strategies have been developed over the years to identify essential genes. Here, we describe an implemented plasmid shuffling method useful to assess the essentiality of overlapped genes under very stringent conditions. A host strain harboring the chromosomal deletion of the genes of interest is complemented by a thermosensitive plasmid carrying the copy of gene 1, gene 2, and rpsL allele, conferring streptomycin sensitivity to an otherwise resistant strain. A compatible plasmid harboring a different selectable marker and the copy of gene 2 only is transformed into the host strain, resulting in the coexistence of two plasmids. These cells are grown at high temperatures in a medium containing streptomycin. Under such conditions, viable cells are expected to contain only the incoming plasmid and to carry suppressor mutation(s) that bypass the loss of the essential gene 1. The system may thus represent a valuable tool to identify interactions between essential proteins and cell pathways.
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Bautista DE, Carr JF, Mitchell AM. Suppressor Mutants: History and Today's Applications. EcoSal Plus 2021; 9:eESP00372020. [PMID: 34910591 PMCID: PMC9008745 DOI: 10.1128/ecosalplus.esp-0037-2020] [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: 05/25/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022]
Abstract
For decades, biologist have exploited the near boundless advantages that molecular and genetic tools and analysis provide for our ability to understand biological systems. One of these genetic tools, suppressor analysis, has proven invaluable in furthering our understanding of biological processes and pathways and in discovering unknown interactions between genes and gene products. The power of suppressor analysis lies in its ability to discover genetic interactions in an unbiased manner, often leading to surprising discoveries. With advancements in technology, high-throughput approaches have aided in large-scale identification of suppressors and have helped provide insight into the core functional mechanisms through which suppressors act. In this review, we examine some of the fundamental discoveries that have been made possible through analysis of suppressor mutations. In addition, we cover the different types of suppressor mutants that can be isolated and the biological insights afforded by each type. Moreover, we provide considerations for the design of experiments to isolate suppressor mutants and for strategies to identify intergenic suppressor mutations. Finally, we provide guidance and example protocols for the isolation and mapping of suppressor mutants.
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Affiliation(s)
- David E. Bautista
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Joseph F. Carr
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Angela M. Mitchell
- Department of Biology, Texas A&M University, College Station, Texas, USA
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Smithers L, Olatunji S, Caffrey M. Bacterial Lipoprotein Posttranslational Modifications. New Insights and Opportunities for Antibiotic and Vaccine Development. Front Microbiol 2021; 12:788445. [PMID: 34950121 PMCID: PMC8689077 DOI: 10.3389/fmicb.2021.788445] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
Lipoproteins are some of the most abundant proteins in bacteria. With a lipid anchor to the cell membrane, they function as enzymes, inhibitors, transporters, structural proteins, and as virulence factors. Lipoproteins activate the innate immune system and have biotechnological applications. The first lipoprotein was described by Braun and Rehn in 1969. Up until recently, however, work on lipoproteins has been sluggish, in part due to the challenges of handling proteins that are anchored to membranes by covalently linked lipids or are membrane integral. Activity in the area has quickened of late. In the past 5 years, high-resolution structures of the membrane enzymes of the canonical lipoprotein synthesis pathway have been determined, new lipoprotein types have been discovered and the enzymes responsible for their synthesis have been characterized biochemically. This has led to a flurry of activity aimed at developing novel antibiotics targeting these enzymes. In addition, surface exposed bacterial lipoproteins have been utilized as candidate vaccine antigens, and their potential to act as self-adjuvanting antigens is increasingly recognized. A summary of the latest developments in lipoproteins and their synthesis, as well as how this information is being exploited for therapeutic purposes is presented here.
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Affiliation(s)
- Luke Smithers
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Samir Olatunji
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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Lipopolysaccharide Transport System Links Physiological Roles of σ E and ArcA in the Cell Envelope Biogenesis in Shewanella oneidensis. Microbiol Spectr 2021; 9:e0069021. [PMID: 34406804 PMCID: PMC8552667 DOI: 10.1128/spectrum.00690-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The bacterial cell envelope is not only a protective structure that surrounds the cytoplasm but also the place where a myriad of biological processes take place. This multilayered complex is particularly important for electroactive bacteria such as Shewanella oneidensis, as it generally hosts branched electron transport chains and numerous reductases for extracellular respiration. However, little is known about how the integrity of the cell envelope is established and maintained in these bacteria. By tracing the synthetic lethal effect of Arc two-component system and σE in S. oneidensis, in this study, we identified the lipopolysaccharide transport (Lpt) system as the determining factor. Both Arc and σE, by regulating transcription of lptFG and lptD, respectively, are required for the Lpt system to function properly. The ArcA loss results in an LptFG shortage that triggers activation of σE and leads to LptD overproduction. LptFG and LptD at abnormal levels cause a defect in the lipopolysaccharide (LPS) transport, leading to cell death unless σE-dependent envelope stress response is in place. Overall, our report reveals for the first time that Arc works together with σE to maintain the integrity of the S. oneidensis cell envelope by participating in the regulation of the LPS transport system. IMPORTANCE Arc is a well-characterized global regulatory system that modulates cellular respiration by responding to changes in the redox status in bacterial cells. In addition to regulating expression of respiratory enzymes, Shewanella oneidensis Arc also plays a critical role in cell envelope integrity. The absence of Arc and master envelope stress response (ESR) regulator σE causes a synthetic lethal phenotype. Our research shows that the Arc loss downregulates lptFG expression, leading to cell envelope defects that require σE-mediated ESR for viability. The complex mechanisms revealed here underscore the importance of the interplay between global regulators in bacterial adaption to their natural inhabits.
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Miyazaki R, Watanabe T, Yoshitani K, Akiyama Y. Edge-strand of BepA interacts with immature LptD on the β-barrel assembly machine to direct it to on- and off-pathways. eLife 2021; 10:70541. [PMID: 34463613 PMCID: PMC8423444 DOI: 10.7554/elife.70541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/26/2021] [Indexed: 01/06/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria functions as a selective permeability barrier. Escherichia coli periplasmic Zn-metallopeptidase BepA contributes to the maintenance of OM integrity through its involvement in the biogenesis and degradation of LptD, a β-barrel protein component of the lipopolysaccharide translocon. BepA either promotes the maturation of LptD when it is on the normal assembly pathway (on-pathway) or degrades it when its assembly is compromised (off-pathway). BepA performs these functions probably on the β‐barrel assembly machinery (BAM) complex. However, how BepA recognizes and directs an immature LptD to different pathways remains unclear. Here, we explored the interactions among BepA, LptD, and the BAM complex. We found that the interaction of the BepA edge-strand located adjacent to the active site with LptD was crucial not only for proteolysis but also, unexpectedly, for assembly promotion of LptD. Site-directed crosslinking analyses indicated that the unstructured N-terminal half of the β-barrel-forming domain of an immature LptD contacts with the BepA edge-strand. Furthermore, the C-terminal region of the β-barrel-forming domain of the BepA-bound LptD intermediate interacted with a ‘seam’ strand of BamA, suggesting that BepA recognized LptD assembling on the BAM complex. Our findings provide important insights into the functional mechanism of BepA.
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Affiliation(s)
- Ryoji Miyazaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tetsuro Watanabe
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kohei Yoshitani
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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50
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Bachert BA, Richardson JB, Mlynek KD, Klimko CP, Toothman RG, Fetterer DP, Luquette AE, Chase K, Storrs JL, Rogers AK, Cote CK, Rozak DA, Bozue JA. Development, Phenotypic Characterization and Genomic Analysis of a Francisella tularensis Panel for Tularemia Vaccine Testing. Front Microbiol 2021; 12:725776. [PMID: 34456897 PMCID: PMC8386241 DOI: 10.3389/fmicb.2021.725776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/21/2021] [Indexed: 11/23/2022] Open
Abstract
Francisella tularensis is one of several biothreat agents for which a licensed vaccine is needed to protect against this pathogen. To aid in the development of a vaccine protective against pneumonic tularemia, we generated and characterized a panel of F. tularensis isolates that can be used as challenge strains to assess vaccine efficacy. Our panel consists of both historical and contemporary isolates derived from clinical and environmental sources, including human, tick, and rabbit isolates. Whole genome sequencing was performed to assess the genetic diversity in comparison to the reference genome F. tularensis Schu S4. Average nucleotide identity analysis showed >99% genomic similarity across the strains in our panel, and pan-genome analysis revealed a core genome of 1,707 genes, and an accessory genome of 233 genes. Three of the strains in our panel, FRAN254 (tick-derived), FRAN255 (a type B strain), and FRAN256 (a human isolate) exhibited variation from the other strains. Moreover, we identified several unique mutations within the Francisella Pathogenicity Island across multiple strains in our panel, revealing unexpected diversity in this region. Notably, FRAN031 (Scherm) completely lacked the second pathogenicity island but retained virulence in mice. In contrast, FRAN037 (Coll) was attenuated in a murine pneumonic tularemia model and had mutations in pdpB and iglA which likely led to attenuation. All of the strains, except FRAN037, retained full virulence, indicating their effectiveness as challenge strains for future vaccine testing. Overall, we provide a well-characterized panel of virulent F. tularensis strains that can be utilized in ongoing efforts to develop an effective vaccine against pneumonic tularemia to ensure protection is achieved across a range F. tularensis strains.
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Affiliation(s)
- Beth A. Bachert
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Joshua B. Richardson
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Kevin D. Mlynek
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Christopher P. Klimko
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Ronald G. Toothman
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - David P. Fetterer
- Division of Biostatistics, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Andrea E. Luquette
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Kitty Chase
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Jessica L. Storrs
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Ashley K. Rogers
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Christopher K. Cote
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - David A. Rozak
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Joel A. Bozue
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
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