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Benediktsdottir A, Sooriyaarachchi S, Cao S, Ottosson NE, Lindström S, Lundgren B, Kloditz K, Lola D, Bobileva O, Loza E, Hughes D, Jones TA, Mowbray SL, Zamaratski E, Sandström A, Karlén A. Design, synthesis, and in vitro biological evaluation of meta-sulfonamidobenzamide-based antibacterial LpxH inhibitors. Eur J Med Chem 2024; 278:116790. [PMID: 39236497 DOI: 10.1016/j.ejmech.2024.116790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 09/07/2024]
Abstract
New antibacterial compounds are urgently needed, especially for infections caused by the top-priority Gram-negative bacteria that are increasingly difficult to treat. Lipid A is a key component of the Gram-negative outer membrane and the LpxH enzyme plays an important role in its biosynthesis, making it a promising antibacterial target. Inspired by previously reported ortho-N-methyl-sulfonamidobenzamide-based LpxH inhibitors, novel benzamide substitutions were explored in this work to assess their in vitro activity. Our findings reveal that maintaining wild-type antibacterial activity necessitates removal of the N-methyl group when shifting the ortho-N-methyl-sulfonamide to the meta-position. This discovery led to the synthesis of meta-sulfonamidobenzamide analogs with potent antibacterial activity and enzyme inhibition. Moreover, we demonstrate that modifying the benzamide scaffold can alter blocking of the cardiac voltage-gated potassium ion channel hERG. Furthermore, two LpxH-bound X-ray structures show how the enzyme-ligand interactions of the meta-sulfonamidobenzamide analogs differ from those of the previously reported ortho analogs. Overall, our study has identified meta-sulfonamidobenzamide derivatives as promising LpxH inhibitors with the potential for optimization in future antibacterial hit-to-lead programs.
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Affiliation(s)
- Andrea Benediktsdottir
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden.
| | | | - Sha Cao
- Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-75123, Uppsala, Sweden
| | - Nina E Ottosson
- Department of Biomedical and Clinical Sciences, BKV, Linköping University, SE-581 85, Linköping, Sweden; Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Tomtebodavägen 23a, 171 65, Solna, Sweden
| | - Stefan Lindström
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Bo Lundgren
- Department of Biochemistry and Biophysics, Stockholm University, Biochemical and Cellular Assay Unit, Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23A, SE-17165, Solna, Sweden
| | - Katharina Kloditz
- Department of Biochemistry and Biophysics, Stockholm University, Biochemical and Cellular Assay Unit, Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23A, SE-17165, Solna, Sweden
| | - Daina Lola
- Latvian Institute of Organic Synthesis, Riga, LV-1006, Latvia
| | - Olga Bobileva
- Latvian Institute of Organic Synthesis, Riga, LV-1006, Latvia
| | - Einars Loza
- Latvian Institute of Organic Synthesis, Riga, LV-1006, Latvia
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-75123, Uppsala, Sweden
| | - T Alwyn Jones
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-75123, Uppsala, Sweden
| | - Sherry L Mowbray
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-75123, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden
| | - Edouard Zamaratski
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden.
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2
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Vergoz D, Schaumann A, Schmitz I, Afonso C, Dé E, Loutelier-Bourhis C, Alexandre S. Lipidome of Acinetobacter baumannii antibiotic persister cells. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159539. [PMID: 39067686 DOI: 10.1016/j.bbalip.2024.159539] [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: 05/27/2024] [Revised: 07/02/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Persister cells constitute a bacterial subpopulation able to survive to high concentrations of antibiotics. This phenotype is temporary and reversible, and thus could be involved in the recurrence of infections and emergence of antibiotic resistance. To better understand how persister cells survive to such high antibiotic concentration, we examined changes in their lipid composition. We thus compared the lipidome of Acinetobacter baumannii ATCC 19606T persister cells formed under ciprofloxacin treatment with the lipidome of control cells grown without antibiotic. Using matrix assisted laser desorption ionisation-Fourier transform ion cyclotron resonance mass spectrometry, we observed a higher abundance of short chains and secondary chains without hydroxylation for lipid A in persister cells. Using liquid chromatography-tandem mass spectrometry, we found that persister cells produced particular phosphatidylglycerols, as LPAGPE and PAGPE, but also lipids with particular acyl chains containing additional hydroxyl group or uncommon di-unsaturation on C18 and C16 acyl chains. In order to determine the impact of these multiple lipidome modifications on membrane fluidity, fluorescence anisotropy assays were performed. They showed an increase of rigidity for the membrane of persister cells, inducing likely a decrease membrane permeability to protect cells during dormancy. Finally, we highlighted that A. baumannii persister cells also produced particular wax esters, composed of two fatty acids and a fatty diol. These uncommon storage lipids are key metabolites allowing a rapid bacterial regrow when antibiotic pressure disappears. These overall changes in persister lipidome may constitute new therapeutic targets to combat these particular dormant cells.
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Affiliation(s)
- Delphine Vergoz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., F-76000 Rouen, France; Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Annick Schaumann
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., F-76000 Rouen, France
| | - Isabelle Schmitz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., F-76000 Rouen, France; Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Carlos Afonso
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Emmanuelle Dé
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., F-76000 Rouen, France
| | - Corinne Loutelier-Bourhis
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Stéphane Alexandre
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., F-76000 Rouen, France.
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3
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Choi BJ, Choi U, Ryu DB, Lee CR. PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in Escherichia coli. mSystems 2024:e0096424. [PMID: 39345149 DOI: 10.1128/msystems.00964-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 09/08/2024] [Indexed: 10/01/2024] Open
Abstract
Tetracyclines and glycylcycline are among the important antibiotics used to combat infections caused by multidrug-resistant Gram-negative pathogens. Despite the clinical importance of these antibiotics, their mechanisms of resistance remain unclear. In this study, we elucidated a novel mechanism of resistance to tetracycline and glycylcycline antibiotics via lipopolysaccharide (LPS) modification. Disruption of the Escherichia coli PhoPQ two-component system, which regulates the transcription of various genes involved in magnesium transport and LPS modification, leads to increased susceptibility to tetracycline, minocycline, doxycycline, and tigecycline. These phenotypes are caused by enhanced expression of phosphoethanolamine transferase EptB, which catalyzes the modification of the inner core sugar of LPS. PhoPQ-mediated regulation of EptB expression appears to affect the intracellular transportation of doxycycline. Disruption of EptB increases resistance to tetracycline and glycylcycline antibiotics, whereas the other two phosphoethanolamine transferases, EptA and EptC, that participate in the modification of other LPS residues, are not associated with resistance to tetracyclines and glycylcycline. Overall, our results demonstrated that PhoPQ-mediated modification of a specific residue of LPS by phosphoethanolamine transferase EptB governs intrinsic resistance to tetracycline and glycylcycline antibiotics. IMPORTANCE Elucidating the resistance mechanisms of clinically important antibiotics helps in maintaining the clinical efficacy of antibiotics and in the prescription of adequate antibiotic therapy. Although tetracycline and glycylcycline antibiotics are clinically important in combating multidrug-resistant Gram-negative bacterial infections, their mechanisms of resistance are not fully understood. Our research demonstrates that the E. coli PhoPQ two-component system affects resistance to tetracycline and glycylcycline antibiotics by controlling the expression of phosphoethanolamine transferase EptB, which catalyzes the modification of the inner core residue of lipopolysaccharide (LPS). Therefore, our findings highlight a novel resistance mechanism to tetracycline and glycylcycline antibiotics and the physiological significance of LPS core modification in E. coli.
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Affiliation(s)
- Byoung Jun Choi
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Umji Choi
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Dae-Beom Ryu
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
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Vergoz D, Schaumann A, Schmitz I, van Agthoven M, Martí S, Vila J, Afonso C, Dé E, Loutelier-Bourhis C, Alexandre S. Direct analysis by ultra-high-resolution mass spectrometry of lipid A and phospholipids from Acinetobacter baumannii cells. Biochimie 2024:S0300-9084(24)00222-0. [PMID: 39326489 DOI: 10.1016/j.biochi.2024.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 08/13/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Acinetobacter baumannii, classified as priority number one by the World Health Organization (WHO), is an opportunistic pathogen responsible for infection and is able to develop antibiotic resistance easily. Membranes are bacteria's first line of defense against external aggression, such as antibiotics. A chemical modification of a lipid family or a change in lipid composition can lead to resistance to antibiotics. In this work, we analyzed different A. baumannii strains from various environments with different antibiotic resistance profiles, using matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR MS). This study shows that it is possible to describe the main lipidome (phospholipids and lipid A) from the simple preparation of lysed cells, and that despite the complexity of the mixture. This ultra-high resolution mass spectrometry technique enables the separation of isobaric ion, to report a new class of lipids. Given its performance, this technique can be used to quickly and reliably characterize the lipidome of clinical strains from different environments.
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Affiliation(s)
- Delphine Vergoz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., 76000, Rouen, France; Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France.
| | - Annick Schaumann
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., 76000, Rouen, France
| | - Isabelle Schmitz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., 76000, Rouen, France; Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Maria van Agthoven
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Sara Martí
- Department of Microbiology, Hospital Universitari de Bellvitge, CIBERes, IDIBELL, Barcelona, Spain
| | - Jordi Vila
- Servei de Microbiologia, Centre de Diagnòstic Biomèdic, Hospital Clínic, ISGLOBAL, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Carlos Afonso
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Emmanuelle Dé
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., 76000, Rouen, France
| | - Corinne Loutelier-Bourhis
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Stéphane Alexandre
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, Polymers, Biopolymers, Surfaces Lab., 76000, Rouen, France
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5
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Strobl S, Zucchetta D, Vašíček T, Monti A, Ruda A, Widmalm G, Heine H, Zamyatina A. Nonreducing Sugar Scaffold Enables the Development of Immunomodulatory TLR4-specific LPS Mimetics with Picomolar Potency. Angew Chem Int Ed Engl 2024; 63:e202408421. [PMID: 38870340 DOI: 10.1002/anie.202408421] [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: 05/03/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
Innate immune defense mechanisms against infection and cancer encompass the modulation of pattern recognition receptor (PRR)-mediated inflammation, including upregulation of various transcription factors and the activation of pro-inflammatory pathways important for immune surveillance. Dysfunction of PRRs-mediated signaling has been implicated in cancer and autoimmune diseases, while the overactivation of PRRs-driven responses during infection can lead to devastating consequences such as acute lung injury or sepsis. We used crystal structure-based design to develop immunomodulatory lipopolysaccharide (LPS) mimetics targeting one of the ubiquitous PRRs, Toll-like Receptor 4 (TLR4). Taking advantage of an exo-anomeric conformation and specific molecular shape of synthetic nonreducing β,β-diglucosamine, which was investigated by NMR, we developed two sets of lipid A mimicking glycolipids capable of either potently activating innate immune responses or inhibiting pro-inflammatory signaling. Stereoselective 1,1'-glycosylation towards fully orthogonally protected nonreducing GlcNβ(1↔1')βGlcN followed by stepwise assembly of differently functionalised phosphorylated glycolipids provided biologically active molecules that were evaluated for their ability to trigger or to inhibit cellular innate immune responses. Two LPS mimetics, identified as potent TLR4-specific inducers of the intracellular signaling pathways, serve as vaccine adjuvant- and immunotherapy candidates, while anionic glycolipids with TLR4-inhibitory potential hold therapeutic promise for the management of acute or chronic inflammation.
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Affiliation(s)
- Sebastian Strobl
- Department of Chemistry, BOKU University, Muthgasse 18, Vienna, A-1190, Austria
| | - Daniele Zucchetta
- Department of Chemistry, BOKU University, Muthgasse 18, Vienna, A-1190, Austria
| | - Tomáš Vašíček
- Department of Chemistry, BOKU University, Muthgasse 18, Vienna, A-1190, Austria
| | - Alessandro Monti
- Department of Chemistry, BOKU University, Muthgasse 18, Vienna, A-1190, Austria
| | - Alessandro Ruda
- Department of Organic Chemistry, Stockholm University, S-106 91, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Stockholm University, S-106 91, Stockholm, Sweden
| | - Holger Heine
- Research Group Innate Immunity, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 22, Borstel, 23845, Germany
| | - Alla Zamyatina
- Department of Chemistry, BOKU University, Muthgasse 18, Vienna, A-1190, Austria
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6
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Mielniczuk S, Hoff K, Baselious F, Li Y, Haupenthal J, Kany AM, Riedner M, Rohde H, Rox K, Hirsch AKH, Krimm I, Sippl W, Holl R. Development of Fragment-Based Inhibitors of the Bacterial Deacetylase LpxC with Low Nanomolar Activity. J Med Chem 2024. [PMID: 39303295 DOI: 10.1021/acs.jmedchem.4c01262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
In a fragment-based approach using NMR spectroscopy, benzyloxyacetohydroxamic acid-derived inhibitors of the bacterial deacetylase LpxC bearing a substituent to target the uridine diphosphate-binding site of the enzyme were developed. By appending privileged fragments via a suitable linker, potent LpxC inhibitors with promising antibacterial activities could be obtained, like the one-digit nanomolar LpxC inhibitor (S)-13j [Ki (EcLpxC C63A) = 9.5 nM; Ki (PaLpxC): 5.6 nM]. To rationalize the observed structure-activity relationships, molecular docking and molecular dynamics studies were performed. Initial in vitro absorption-distribution-metabolism-excretion-toxicity (ADMET) studies of the most potent compounds have paved the way for multiparameter optimization of our newly developed isoserine-based amides.
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Affiliation(s)
- Sebastian Mielniczuk
- Institute of Organic Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20146 Hamburg, Germany
| | - Katharina Hoff
- Institute of Organic Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20146 Hamburg, Germany
| | - Fady Baselious
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120 Halle (Saale), Germany
| | - Yunqi Li
- Team "Small Molecules for Biological Targets", Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008 Lyon, France
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences & School of Life Sciences, East China Normal University, 200241 Shanghai, China
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Andreas M Kany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Maria Riedner
- Technology Platform Mass Spectrometry, Universität Hamburg, Mittelweg 177, 20148 Hamburg, Germany
| | - Holger Rohde
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20146 Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Katharina Rox
- Department of Chemical Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-infectives, Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Isabelle Krimm
- Team "Small Molecules for Biological Targets", Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008 Lyon, France
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120 Halle (Saale), Germany
| | - Ralph Holl
- Institute of Organic Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20146 Hamburg, Germany
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7
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Fathy Mohamed Y, Fernandez RC. Programming Bordetella pertussis lipid A to promote adjuvanticity. Microb Cell Fact 2024; 23:250. [PMID: 39272136 PMCID: PMC11401268 DOI: 10.1186/s12934-024-02518-7] [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: 06/18/2024] [Accepted: 08/31/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Bordetella pertussis is the causative agent of whooping cough or pertussis. Although both acellular (aP) and whole-cell pertussis (wP) vaccines protect against disease, the wP vaccine, which is highly reactogenic, is better at preventing colonization and transmission. Reactogenicity is mainly attributed to the lipid A moiety of B. pertussis lipooligosaccharide (LOS). Within LOS, lipid A acts as a hydrophobic anchor, engaging with TLR4-MD2 on host immune cells to initiate both MyD88-dependent and TRIF-dependent pathways, thereby influencing adaptive immune responses. Lipid A variants, such as monophosphoryl lipid A (MPLA) can also act as adjuvants. Adjuvants may overcome the shortcomings of aP vaccines. RESULTS This work used lipid A modifying enzymes from other bacteria to produce an MPLA-like adjuvant strain in B. pertussis. We created B. pertussis strains with distinct lipid A modifications, which were validated using MALDI-TOF. We engineered a hexa-acylated monophosphorylated lipid A that markedly decreased human TLR4 activation and activated the TRIF pathway. The modified lipooligosaccharide (LOS) promoted IRF3 phosphorylation and type I interferon production, similar to MPLA responses. We generated three other variants with increased adjuvanticity properties and reduced endotoxicity. Pyrogenicity studies using the Monocyte Activation Test (MAT) revealed that these four lipid A variants significantly decreased the IL-6, a marker for fever, response in peripheral blood mononuclear cells (PBMCs). CONCLUSION These findings pave the way for developing wP vaccines that are possibly less reactogenic and designing adaptable adjuvants for current vaccine formulations, advancing more effective immunization strategies against pertussis.
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Affiliation(s)
- Yasmine Fathy Mohamed
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, V6T1Z3, Canada
- Department of Microbiology & Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Rachel C Fernandez
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, V6T1Z3, Canada.
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8
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Zuber J, Lopes Cascabulho P, Gemini Piperni S, Farias Corrêa do Amaral RJ, Vogt C, Carre V, Hertzog J, Kontturi E, Trubetskaya A. Fast, Easy, and Reproducible Fingerprint Methods for Endotoxin Characterization in Nanocellulose and Alginate-Based Hydrogel Scaffolds. Biomacromolecules 2024. [PMID: 39262301 DOI: 10.1021/acs.biomac.4c00989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Nanocellulose- and alginate-based hydrogels have been suggested as potential wound-healing materials, but their utilization is limited by the Food and Drug Administration (FDA) requirements regarding endotoxin levels. Cytotoxicity and the presence of endotoxin were assessed after gel sterilization using an autoclave and UV treatment. A new fingerprinting method was developed to characterize the compounds detected in cellulose nanocrystal (CNC)- and cellulose-nanofiber (CNF)-based hydrogels using both positive- and negative-ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectroscopy (ESI FT-ICR MS). These biobased hydrogels were used as scaffolds for the cultivation and growth of human dermal fibroblasts to test their biocompatibility. A resazurin-based assay was preferred over all other biocompatibility methodologies since it allowed for the evaluation of viability over time in the same sample without causing cell lysis. The CNF dispersion of 6 EU mL-1 was slightly above the limits, and it did not affect the cell viability, whereas CNC hydrogels induced a reduction of metabolic activity by the fibroblasts. The chemical structure of the detected endotoxins did not contain phosphates, but it encompassed hydrophobic sulfonate groups, requiring the development of new high-pressure sterilization methods for the use of cellulose hydrogels in medicine.
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Affiliation(s)
- Jan Zuber
- Department of Analytical Chemistry, TU Freiberg, Leipziger Street 29, 09599 Freiberg, Germany
| | - Paula Lopes Cascabulho
- Faculty of Medicine, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho 373, 21941-853 Rio de Janeiro, Brazil
- Laboratory of Cellular Proliferation and Differentiation, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho 373, 21941 Rio de Janeiro, Brazil
- Laboratory of Biomineralization, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho 373, 21941 Rio de Janeiro, Brazil
| | - Sara Gemini Piperni
- Laboratory of Biotechnology, Bioengineering and Nanostructured Biomaterials, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho 373, 21941 Rio de Janeiro, Brazil
| | - Ronaldo José Farias Corrêa do Amaral
- Faculty of Medicine, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho 373, 21941-853 Rio de Janeiro, Brazil
- Laboratory of Cellular Proliferation and Differentiation, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho 373, 21941 Rio de Janeiro, Brazil
- Laboratory of Biomineralization, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho 373, 21941 Rio de Janeiro, Brazil
| | - Carla Vogt
- Department of Analytical Chemistry, TU Freiberg, Leipziger Street 29, 09599 Freiberg, Germany
| | - Vincent Carre
- Université de Lorraine, LCP-A2MC, 1 Boulevard Arago, 57000 Metz, France
| | - Jasmine Hertzog
- Université de Lorraine, LCP-A2MC, 1 Boulevard Arago, 57000 Metz, France
| | - Eero Kontturi
- Department of Bioproducts and Biosystems, Aalto University, Vuorimiehentie 1, 02150 Espoo, Finland
| | - Anna Trubetskaya
- Department of Biosciences, Nord University, Kongensgate 42, 7713 Steinkjer, Norway
- Department of Engineering, University of Limerick, Castletroy, Co. Limerick V94T9PX, Ireland
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9
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Kim M, Kim M, Ryu S. Identification of amino acid residue in the Cronobacter sakazakii LamB responsible for the receptor compatibility of polyvalent coliphage CSP1. J Virol 2024:e0067624. [PMID: 39248490 DOI: 10.1128/jvi.00676-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/20/2024] [Indexed: 09/10/2024] Open
Abstract
Polyvalent bacteriophages show the feature of infecting bacteria across multiple species or even orders. Infectivity of a polyvalent phage is variable depending on the host bacteria, which can disclose differential inhibition of bacteria by the phage. In this study, a polyvalent phage CSP1 infecting both Cronobacter sakazakii ATCC 29544 and Escherichia coli MG1655 was isolated. CSP1 showed higher growth inhibition and adsorption rate in E. coli compared to C. sakazakii, and identification of host receptors revealed that CSP1 uses E. coli LamB (LamBE) as a receptor but that CSP1 requires both C. sakazakii LamB (LamBC) and lipopolysaccharide (LPS) core for C. sakazakii infection. The substitution of LamBC with LamBE in C. sakazakii enhanced CSP1 susceptibility and made C. sakazakii LPS core no more essential for CSP1 infection. Comparative analysis of LamBC and LamBE disclosed that the extra proline at amino acid residue 284 in LamBC made a structural distinction by forming a longer loop and that the deletion of 284P in LamBC aligns its structure and makes LamBC function like LamBE, enhancing CSP1 adsorption and growth inhibition of C. sakazakii. These results suggest that 284P of LamBC plays a critical role in determining the CSP1-host bacteria interaction. These findings could provide insight into the elucidation of molecular determinants in the interaction between polyvalent phages and host bacteria and help us to understand the phage infectivity for efficient phage application. IMPORTANCE Polyvalent phages have the advantage of a broader host range, overcoming the limitation of the narrow host range of phages. However, the limited molecular biological understanding on the host bacteria-polyvalent phage interaction hinders its effective application. Here, we revealed that the ability of the polyvalent phage CSP1 to infect Cronobacter sakazakii ATCC 29544 is disturbed by a single proline residue in the LamB protein and that lipopolysaccharide is used as an auxiliary receptor for CSP1 to support the adsorption and the subsequent infection of C. sakazakii. These results can contribute to a better understanding of the interaction between polyvalent phages and host bacteria for efficient phage application.
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Affiliation(s)
- Moosung Kim
- Department of Food and Animal Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minsik Kim
- Department of Food and Nutrition, College of Human Ecology, Yonsei University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
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10
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Weerakoon D, Marzinek JK, Pedebos C, Bond PJ, Khalid S. Polymyxin B1 in the E. coli inner membrane: a complex story of protein and lipopolysaccharide mediated insertion. J Biol Chem 2024:107754. [PMID: 39260694 DOI: 10.1016/j.jbc.2024.107754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 08/21/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024] Open
Abstract
The rise in multi-drug resistant Gram-negative bacterial infections has led to an increased need for 'last-resort' antibiotics such as polymyxins. However, the emergence of polymyxin-resistant strains threatens to bring about a post-antibiotic era. Thus, there is a need to develop new polymyxin-based antibiotics, but a lack of knowledge of the mechanism of action of polymyxins hinders such efforts. It has recently been suggested that polymyxins induce cell lysis of the Gram-negative bacterial inner membrane (IM) by targeting trace amounts of lipopolysaccharide (LPS) localized there. We use multiscale molecular dynamics (MD) including long-timescale coarse-grained (CG) and all-atom (AA) simulations to investigate the interactions of polymyxin B1 (PMB1) with bacterial IM models containing phospholipids (PLs), small quantities of LPS, and IM proteins. LPS was observed to (transiently) phase separate from PLs at multiple LPS concentrations, and associate with proteins in the IM. PMB1 spontaneously inserted into the IM and localized at the LPS-PL interface, where it cross-linked lipid headgroups via hydrogen bonds, sampling a wide range of interfacial environments. In the presence of membrane proteins, a small number of PMB1 molecules formed interactions with them, in a manner that was modulated by local LPS molecules. Electroporation-driven translocation of PMB1 via water-filled pores was favored at the protein-PL interface, supporting the 'destabilizing' role proteins may have within the IM. Overall, this in-depth characterization of PMB1 modes of interaction reveals how small amounts of mislocalized LPS may play a role in pre-lytic targeting and provides insights that may facilitate rational improvement of polymyxin-based antibiotics.
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Affiliation(s)
- Dhanushka Weerakoon
- School of Chemistry, University of Southampton, SO17 1BJ, UK; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Conrado Pedebos
- Department of Biochemistry, University of Oxford, OX1 3QU, UK; Programa de Pós-Graduação em Biociências (PPGBio), Universidade Federal de Ciências da Saudé de Porto Alegre - UFCSPA, Brazil
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, OX1 3QU, UK
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11
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Sheng Q, Wang X, Hou Z, Liu B, Jiang M, Ren M, Fu J, He M, Zhang J, Xiang Y, Zhang Q, Zhou L, Deng Y, Shen X. Novel functions of o-cymen-5-ol nanoemulsion in reversing colistin resistance in multidrug-resistant Klebsiella pneumoniae infections. Biochem Pharmacol 2024; 227:116384. [PMID: 38909787 DOI: 10.1016/j.bcp.2024.116384] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Multidrug resistance (MDR) Klebsiella pneumoniae (K. pneumoniae) is a major emerging threat to human health, and leads to very high mortality rate. The effectiveness of colistin, the last resort against MDR Gram-negative bacteria, is significantly compromised due to the widespread presence of plasmid- or chromosome-mediated resistance genes. In this study, o-cymen-5-ol has been found to greatly restore colistin sensitivity in MDR K. pneumoniae. Importantly, this compound does not impact bacterial viability, induce resistance, or cause any noticeable cell toxicity. Various routes disclosed the potential mechanism of o-cymen-5-ol potentiating colistin activity against MDR K. pneumoniae. These include inhibiting the activity of plasmid-mediated mobile colistin resistance gene (mcr-1), accelerating lipopolysaccharide (LPS) - mediated membrane damage, and promoting the ATP-binding cassette (ABC) transporter pathway. To enhance the administration and bioavailability of o-cymen-5-ol, a nanoemulsion has been designed, which significantly improves the loading efficiency and solubility of o-cymen-5-ol, resulting in antimicrobial potentiation of colistin against K. pneumoniae infection. This study has revealed a new understanding of the o-cymen-5-ol nanoemulsion as a means to enhance the effectiveness of colistin against resistant factors. The finding also suggests that o-cymen-5-ol nanoemulsion could be a promising approach in the development of potential treatments for multidrug-resistant Gram-negative bacterial infections.
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Affiliation(s)
- Qiushuang Sheng
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Xiao Wang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Zhaoyan Hou
- Changchun Center for Disease Control and Prevention, Changchun, China
| | - Bin Liu
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Mingquan Jiang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Mingyue Ren
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Jingchao Fu
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Miao He
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Jingchen Zhang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Yue Xiang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Qingbo Zhang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Lanying Zhou
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Yanhong Deng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Xue Shen
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun 130062, China; State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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12
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Yang H, O’Keefe I, Smith RD, Sumner KP, Sherman ME, Goodlett DR, Sweet CR, Ernst RK. A Multimodal System for Lipid A Structural Analysis from a Single Colony. Anal Chem 2024; 96. [PMID: 39149983 PMCID: PMC11359392 DOI: 10.1021/acs.analchem.4c01566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
Structural elucidation of Gram-negative bacterial lipid A traditionally requires chemical extraction followed by tandem MS data in the negative ion mode. Previously, we reported FLAT and FLATn as methods to rapidly determine the structure of lipid A without chromatographic techniques. In this work, we extend the capability and effectiveness of these techniques to elucidate the chemical structure in a de novo manner by including the use of positive ion mode (FLAT+ and FLATn+) spectral approaches. Advantages of positive mode analysis of lipid A include the generation of more interpretable and informative fragmentation patterns that include the identification of diagnostic fragments, including selective dissociation of a glycosidic bond between two glucosamine units and the selective dissociation at the secondary acyl chain in 2'-N, allowing for the determination of the composition of fatty acids. As a proof of principle, we present here two previously uncharacterized structures of lipid A from Roseomonas mucosa (R. mucosa) and Moraxella canis (M. canis). In R. mucosa, we determined the lipid A structure with a nonconventional backbone of-β-1,6 linked 2,3-dideoxy-2,3-diamno-d-glucopyranose further modified with galacturonic acid in the place of typical 1-phosphate, and in M. canis, we assigned a single discrete structure using the specific fragmentation patterns of terminal phosphate groups present in lipid A. Therefore, FLATn+, in combination with FLAT and FLATn, provides a multimodal structural platform for rapid structure characterization of unusual and complex lipid A structures from a single colony.
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Affiliation(s)
- Hyojik Yang
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Ian O’Keefe
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Richard D. Smith
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
- Department
of Pathology, School of Medicine, University
of Maryland, Baltimore, Maryland 21201, United
States
| | - Kylie P. Sumner
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Matthew E. Sherman
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - David R. Goodlett
- Department
of Biochemistry and Microbiology, University
of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Genome
British Columbia Proteomics Centre, University
of Victoria, Victoria, British Columbia V8Z 7Z8, Canada
| | - Charles R. Sweet
- Chemistry
Department, United States Naval Academy, Annapolis, Maryland 21402, United States
| | - Robert K. Ernst
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
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13
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Nemchinova M, Schuurman-Wolters GK, Whittaker JJ, Arkhipova V, Marrink SJ, Poolman B, Guskov A. Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ. J Phys Chem B 2024; 128:7822-7832. [PMID: 39090964 PMCID: PMC11331510 DOI: 10.1021/acs.jpcb.4c02662] [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: 04/23/2024] [Revised: 07/21/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
The adenosine triphosphate (ATP)-binding cassette (ABC) importer GlnPQ from Lactococcus lactis has two sequential covalently linked substrate-binding domains (SBDs), which capture the substrates and deliver them to the translocon. The two SBDs differ in their ligand specificities, binding affinities and the distance to the transmembrane domain; interestingly, both SBDs can bind their ligands simultaneously without affecting each other. In this work, we studied the binding of ligands to both SBDs using X-ray crystallography and molecular dynamics simulations. We report three high-resolution structures of SBD1, namely, the wild-type SBD1 with bound asparagine or arginine, and E184D SBD1 with glutamine bound. Molecular dynamics (MD) simulations provide a detailed insight into the dynamics associated with open-closed transitions of the SBDs.
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Affiliation(s)
- Mariia Nemchinova
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Gea K. Schuurman-Wolters
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Jacob J. Whittaker
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Valentina Arkhipova
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Bert Poolman
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Albert Guskov
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
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14
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Li Z, Gu J, Huang X, Lu Z, Feng Y, Xu X, Yang J. Transcriptome-based network analysis reveals hub immune genes and pathways of hepatopancreas against LPS in Amphioctopus fangsiao. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109696. [PMID: 38871144 DOI: 10.1016/j.fsi.2024.109696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/13/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
The hepatopancreas is the biggest digestive organ in Amphioctopus fangsiao (A. fangsiao), but also undertakes critical functions like detoxification and immune defense. Generally, pathogenic bacteria or endotoxin from the gut microbiota would be arrested and detoxified in the hepatopancreas, which could be accompanied by the inevitable immune responses. In recent years, studies related to cephalopods immune have been increasing, but the molecular mechanisms associated with the hepatopancreatic immunity are still unclear. In this study, lipopolysaccharide (LPS), a major component of the cell wall of Gram-negative bacteria, was used for imitating bacteria infection to stimulate the hepatopancreas of A. fangsiao. To investigate the immune process happened in A. fangsiao hepatopancreas, we performed transcriptome analysis of hepatopancreas tissue after LPS injection, and identified 2615 and 1943 differentially expressed genes (DEGs) at 6 and 24 h post-injection, respectively. GO and KEGG enrichment analysis showed that these DEGs were mainly involved in immune-related biological processes and signaling pathways, including ECM-receptor interaction signaling pathway, Phagosome signaling pathway, Lysosome signaling pathway, and JAK-STAT signaling pathways. The function relationships between these DEGs were further analyzed through protein-protein interaction (PPI) networks. It was found that Mtor, Mapk14 and Atm were the three top interacting DEGs under LPS stimulation. Finally, 15 hub genes involving multiple KEGG signaling pathways and PPI relationships were selected for qRT-PCR validation. In this study, for the first time we explored the molecular mechanisms associated with hepatopancreatic immunity in A. fangsiao using a PPI networks approach, and provided new insights for understanding hepatopancreatic immunity in A. fangsiao.
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Affiliation(s)
- Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Jingjing Gu
- Binzhou Testing Center, Binzhou 256600, China
| | - Xiaolan Huang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Zhengcai Lu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China
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15
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Hofstaedter CE, O’Keefe IP, Met CM, Wu L, Vanderwoude J, Shin S, Diggle SP, Riquelme SA, Rasko DA, Doi Y, Harro JM, Kopp BT, Ernst RK. Pseudomonas aeruginosa Lipid A Structural Variants Induce Altered Immune Responses. Am J Respir Cell Mol Biol 2024; 71:207-218. [PMID: 38656811 PMCID: PMC11299085 DOI: 10.1165/rcmb.2024-0059oc] [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: 02/09/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024] Open
Abstract
Pseudomonas aeruginosa causes chronic lung infection in cystic fibrosis (CF), resulting in structural lung damage and progressive pulmonary decline. P. aeruginosa in the CF lung undergoes numerous changes, adapting to host-specific airway pressures while establishing chronic infection. P. aeruginosa undergoes lipid A structural modification during CF chronic infection that is not seen in any other disease state. Lipid A, the membrane anchor of LPS (i.e., endotoxin), comprises the majority of the outer membrane of Gram-negative bacteria and is a potent Toll-like receptor 4 (TLR4) agonist. The structure of P. aeruginosa lipid A is intimately linked with its recognition by TLR4 and subsequent immune response. Prior work has identified P. aeruginosa strains with altered lipid A structures that arise during chronic CF lung infection; however, the impact of the P. aeruginosa lipid A structure on airway disease has not been investigated. Here, we show that P. aeruginosa lipid A lacks PagL-mediated deacylation during human airway infection using a direct-from-sample mass spectrometry approach on human BAL fluid. This structure triggers increased proinflammatory cytokine production by primary human macrophages. Furthermore, alterations in lipid A 2-hydroxylation impact cytokine response in a site-specific manner, independent of CF transmembrane conductance regulator function. It is interesting that there is a CF-specific reduction in IL-8 secretion within the epithelial-cell compartment that only occurs in CF bronchial epithelial cells when infected with CF-adapted P. aeruginosa that lacks PagL-mediated lipid A deacylation. Taken together, we show that P. aeruginosa alters its lipid A structure during acute lung infection and that this lipid A structure induces stronger signaling through TLR4.
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Affiliation(s)
| | | | | | - Ling Wu
- Department of Microbiology and
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jelly Vanderwoude
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | - Stephen P. Diggle
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | - David A. Rasko
- Institute for Genome Sciences
- Department of Microbiology and Immunology, and
- Center for Pathogen Research, University of Maryland, Baltimore, Baltimore, Maryland
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and
| | | | - Benjamin T. Kopp
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia
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16
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Chang T, Gavelis GS, Brown JM, Stepanauskas R. Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton. MICROBIOME 2024; 12:126. [PMID: 39010229 PMCID: PMC11247762 DOI: 10.1186/s40168-024-01848-3] [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: 02/09/2024] [Accepted: 05/28/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are the predominant sources of information about the coding potential of uncultured microbial lineages, but their strengths and limitations remain poorly understood. Here, we performed a direct comparison of two previously published collections of thousands of SAGs and MAGs obtained from the same, global environment. RESULTS We found that SAGs were less prone to chimerism and more accurately reflected the relative abundance and the pangenome content of microbial lineages inhabiting the epipelagic of the tropical and subtropical ocean, as compared to MAGs. SAGs were also better suited to link genome information with taxa discovered through 16S rRNA amplicon analyses. Meanwhile, MAGs had the advantage of more readily recovering genomes of rare lineages. CONCLUSIONS Our analyses revealed the relative strengths and weaknesses of the two most commonly used genome recovery approaches in environmental microbiology. These considerations, as well as the need for better tools for genome quality assessment, should be taken into account when designing studies and interpreting data that involve SAGs or MAGs. Video Abstract.
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Affiliation(s)
- Tianyi Chang
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Gregory S Gavelis
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
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17
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Penkov S, Fedorova M. Membrane Epilipidome-Lipid Modifications, Their Dynamics, and Functional Significance. Cold Spring Harb Perspect Biol 2024; 16:a041417. [PMID: 38253416 PMCID: PMC11216179 DOI: 10.1101/cshperspect.a041417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Lipids are characterized by extremely high structural diversity translated into a wide range of physicochemical properties. As such, lipids are vital for many different functions including organization of cellular and organelle membranes, control of cellular and organismal energy metabolism, as well as mediating multiple signaling pathways. To maintain the lipid chemical diversity and to achieve rapid lipid remodeling required for the responsiveness and adaptability of cellular membranes, living systems make use of a network of chemical modifications of already existing lipids that complement the rather slow biosynthetic pathways. Similarly to biopolymers, which can be modified epigenetically and posttranscriptionally (for nucleic acids) or posttranslationally (for proteins), lipids can also undergo chemical alterations through oxygenation, nitration, phosphorylation, glycosylation, etc. In this way, an expanded collective of modified lipids that we term the "epilipidome," provides the ultimate level of complexity to biological membranes and delivers a battery of active small-molecule compounds for numerous regulatory processes. As many lipid modifications are tightly controlled and often occur in response to extra- and intracellular stimuli at defined locations, the emergence of the epilipidome greatly contributes to the spatial and temporal compartmentalization of diverse cellular processes. Accordingly, epilipid modifications are observed in all living organisms and are among the most consistent prerequisites for complex life.
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Affiliation(s)
- Sider Penkov
- Lipid Metabolism: Analysis and Integration, Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden 01307, Germany
| | - Maria Fedorova
- Lipid Metabolism: Analysis and Integration, Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden 01307, Germany
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18
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Yates CR, Nguyen A, Liao J, Cheng RA. What's on a prophage: analysis of Salmonella spp. prophages identifies a diverse range of cargo with multiple virulence- and metabolism-associated functions. mSphere 2024; 9:e0003124. [PMID: 38775467 PMCID: PMC11332146 DOI: 10.1128/msphere.00031-24] [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: 01/13/2024] [Accepted: 04/22/2024] [Indexed: 06/26/2024] Open
Abstract
The gain of mobile elements, such as prophages, can introduce cargo to the recipient bacterium that could facilitate its persistence in or expansion to a new environment, such as a host. While previous studies have focused on identifying and characterizing the genetic diversity of prophages, analyses characterizing the cargo that prophages carry have not been extensively explored. We characterized prophage regions from 303 Salmonella spp. genomes (representing 254 unique serovars) to assess the distribution of prophages in diverse Salmonella. On average, prophages accounted for 3.7% (0.1%-8.8%) of the total genomic content of each isolate. Prophage regions annotated as Gifsy 1 and Salmon Fels 1 were the most commonly identified intact prophages, suggesting that they are common throughout the Salmonella genus. Among 21,687 total coding sequences (CDSs) from intact prophage regions in subsp. enterica genomes, 7.5% (median; range: 1.1%-47.6%) were categorized as having a function not related to prophage integration or phage structure, some of which could potentially provide a functional attribute to the host Salmonella cell. These predicted functions could be broadly categorized into CDSs involved in: (i) modification of cell surface structures (i.e., glycosyltransferases); (ii) modulation of host responses (e.g., SodC/SodA, SopE, ArtAB, and typhoid toxin); (iii) conferring resistance to heavy metals and antimicrobials; (iv) metabolism of carbohydrates, amino acids, and nucleotides; and (v) DNA replication, repair, and regulation. Overall, our systematic analysis of prophage cargo highlights a broader role for prophage cargo in influencing the metabolic, virulence, and resistance characteristics of Salmonella. IMPORTANCE Lysogenic bacteriophages (phages) can integrate their genome into a bacterial host's genome, potentially introducing genetic elements that can affect the fitness of the host bacterium. The functions of prophage-encoded genes are important to understand as these genes could be mobilized and transferred to a new host. Using a large genomic dataset representing >300 isolates from all known subspecies and species of Salmonella, our study contributes important new findings on the distribution of prophages and the types of cargo that diverse Salmonella prophages carry. We identified a number of coding sequences (CDSs) annotated as having cell surface-modifying attributes, suggesting that prophages may have played an important role in shaping Salmonella's diverse surface antigen repertoire. Furthermore, our characterization of prophages suggests that they play a broader role in facilitating the acquisition and transfer of CDSs associated with metabolism, DNA replication and repair, virulence factors, and to a lesser extent, antimicrobial resistance.
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Affiliation(s)
- Caroline R. Yates
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Anthony Nguyen
- Computational Modeling and Data Analytics Program, Virginia Tech, Blacksburg, Virginia, USA
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Rachel A. Cheng
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
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Tajer L, Paillart JC, Dib H, Sabatier JM, Fajloun Z, Abi Khattar Z. Molecular Mechanisms of Bacterial Resistance to Antimicrobial Peptides in the Modern Era: An Updated Review. Microorganisms 2024; 12:1259. [PMID: 39065030 PMCID: PMC11279074 DOI: 10.3390/microorganisms12071259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a serious global health concern, resulting in a significant number of deaths annually due to infections that are resistant to treatment. Amidst this crisis, antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics (ATBs). These cationic peptides, naturally produced by all kingdoms of life, play a crucial role in the innate immune system of multicellular organisms and in bacterial interspecies competition by exhibiting broad-spectrum activity against bacteria, fungi, viruses, and parasites. AMPs target bacterial pathogens through multiple mechanisms, most importantly by disrupting their membranes, leading to cell lysis. However, bacterial resistance to host AMPs has emerged due to a slow co-evolutionary process between microorganisms and their hosts. Alarmingly, the development of resistance to last-resort AMPs in the treatment of MDR infections, such as colistin, is attributed to the misuse of this peptide and the high rate of horizontal genetic transfer of the corresponding resistance genes. AMP-resistant bacteria employ diverse mechanisms, including but not limited to proteolytic degradation, extracellular trapping and inactivation, active efflux, as well as complex modifications in bacterial cell wall and membrane structures. This review comprehensively examines all constitutive and inducible molecular resistance mechanisms to AMPs supported by experimental evidence described to date in bacterial pathogens. We also explore the specificity of these mechanisms toward structurally diverse AMPs to broaden and enhance their potential in developing and applying them as therapeutics for MDR bacteria. Additionally, we provide insights into the significance of AMP resistance within the context of host-pathogen interactions.
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Affiliation(s)
- Layla Tajer
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, Department of Cell Culture, EDST, Lebanese University, Tripoli 1300, Lebanon; (L.T.); (Z.F.)
| | - Jean-Christophe Paillart
- CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg, 2 Allée Konrad Roentgen, F-67000 Strasbourg, France;
| | - Hanna Dib
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait;
| | - Jean-Marc Sabatier
- CNRS, INP, Inst Neurophysiopathol, Aix-Marseille Université, 13385 Marseille, France
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, Department of Cell Culture, EDST, Lebanese University, Tripoli 1300, Lebanon; (L.T.); (Z.F.)
- Department of Biology, Faculty of Sciences 3, Lebanese University, Campus Michel Slayman Ras Maska, Tripoli 1352, Lebanon
| | - Ziad Abi Khattar
- Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat, P.O. Box 100, Tripoli, Lebanon
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20
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Zhang H, Yang Z, Liu J. Genetic Analysis of the Plasmid-Based Temperature-Lethal Mutant pa1792|lpxH(Ts) in Pseudomonas aeruginosa. Genes (Basel) 2024; 15:784. [PMID: 38927720 PMCID: PMC11202943 DOI: 10.3390/genes15060784] [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: 05/23/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Many enzymes in the Raetz pathway for lipid A biosynthesis in Escherichia coli are essential. A homologous protein Pa1792|LpxH in Pseudomonas aeruginosa is known to complement the loss of LpxH in E. coli. Genome-wide transposon-insertion sequencing analysis indicates that lpxH is essential in P. aeruginosa. However, genetic analysis of lpxH in P. aeruginosa has not been carried out, partly because the conditional alleles of essential genes are not readily constructed. In this study, we first constructed a plasmid-based temperature-sensitive mutant ΔlpxH/pTS-lpxH or lpxH(Ts) in P. aeruginosa PAO1. Spot-plating assay indicated that lpxH(Ts) was lethal at a restrictive temperature, confirming its essentiality for growth. Microscopic analysis revealed that lpxH(Ts) exhibited an oval-shaped morphology, suggesting that lpxH was required for rod-shape formation. SDS-PAGE and Western blotting analysis showed that lpxH(Ts) failed to synthesize lipid A, consistent with its function in lipid A biosynthesis. Strong expression of lpxH but not the non-homologous isoenzyme lpxI or lpxG impeded growth and caused cell lysis, implying that lpxH-specific cofactors were required for this toxic effect in P. aeruginosa. Together, our results demonstrate that lpxH is essential for lipid A biosynthesis, rod-shaped growth, and viability in P. aeruginosa. We propose that this plasmid-based conditional allele is a useful tool for the genetic study of essential genes in P. aeruginosa.
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Affiliation(s)
| | | | - Jianhua Liu
- Systems Biology, School for Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (H.Z.); (Z.Y.)
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21
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Sherman ME, Michalski J, Das S, Yang H, Chandrasekaran L, O’Meara TR, Dowling DJ, Levy O, Barnoy S, Venkatesan M, Ernst RK. BECC-engineered live-attenuated Shigella vaccine candidates display reduced endotoxicity with robust immunogenicity in mice. RESEARCH SQUARE 2024:rs.3.rs-4448907. [PMID: 38946947 PMCID: PMC11213197 DOI: 10.21203/rs.3.rs-4448907/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Shigella spp. infection contributes significantly to the global disease burden, primarily affecting young children in developing countries. Currently, there are no FDA-approved vaccines against Shigella, and the prevalence of antibiotic resistance is increasing, making therapeutic options limited. Live-attenuated vaccine strains WRSs2 (S. sonnei) and WRSf2G12 (S. flexneri 2a) are highly immunogenic, making them promising vaccine candidates, but possess an inflammatory lipid A structure on their lipopolysaccharide (LPS; also known as endotoxin). Here, we utilized bacterial enzymatic combinatorial chemistry (BECC) to ectopically express lipid A modifying enzymes in WRSs2 and WRSf2G12, as well as their respective wild-type strains, generating targeted lipid A modifications across the Shigella backgrounds. Dephosphorylation of lipid A, rather than deacylation, reduced LPS-induced TLR4 signaling in vitro and dampened endotoxic effects in vivo. These BECC-modified vaccine strains retained the phenotypic traits of their parental strains, such as invasion of epithelial cells and immunogenicity in mice without adverse endotoxicity. Overall, our observations suggest that BECC-engineered live attenuated vaccines are a promising approach to safe and effective Shigella vaccines.
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Affiliation(s)
- Matthew E Sherman
- University of Maryland-Baltimore, Department of Microbial Pathogenesis, Baltimore, MD 21201 USA
| | - Jane Michalski
- University of Maryland-Baltimore, Department of Microbial Pathogenesis, Baltimore, MD 21201 USA
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD 21201 USA
| | - Sayan Das
- University of Maryland-Baltimore, Department of Microbial Pathogenesis, Baltimore, MD 21201 USA
| | - Hyojik Yang
- University of Maryland-Baltimore, Department of Microbial Pathogenesis, Baltimore, MD 21201 USA
| | - Lakshmi Chandrasekaran
- Walter Reed Army Institute of Research, Department of Diarrheal Disease Research, Bacterial Disease Branch, Silver Spring, MD 20910 USA
| | - Timothy R O’Meara
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA 02115 USA
| | - David J Dowling
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of MIT & Harvard, Cambridge, MA 02142 USA
| | - Shoshana Barnoy
- Walter Reed Army Institute of Research, Department of Diarrheal Disease Research, Bacterial Disease Branch, Silver Spring, MD 20910 USA
| | - Malabi Venkatesan
- Walter Reed Army Institute of Research, Department of Diarrheal Disease Research, Bacterial Disease Branch, Silver Spring, MD 20910 USA
| | - Robert K Ernst
- University of Maryland-Baltimore, Department of Microbial Pathogenesis, Baltimore, MD 21201 USA
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22
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Grumov D, Kostarnoy A, Gancheva P, Kondratev A. A Simple and Rapid Microscale Method for Isolating Bacterial Lipopolysaccharides. Int J Mol Sci 2024; 25:6345. [PMID: 38928052 PMCID: PMC11203638 DOI: 10.3390/ijms25126345] [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: 04/19/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Bacterial endotoxins (lipopolysaccharides (LPSs)) are important mediators of inflammatory processes induced by Gram-negative microorganisms. LPSs are the key inducers of septic shock due to a Gram-negative bacterial infection; thus, the structure and functions of LPSs are of specific interest. Often, highly purified bacterial endotoxins must be isolated from small amounts of biological material. Each of the currently available methods for LPS extraction has certain limitations. Herein, we describe a rapid and simple microscale method for extracting LPSs. The method consists of the following steps: ultrasonic destruction of the bacterial material, LPS extraction via heating, LPS purification with organic solvents, and treatment with proteinase K. LPSs that were extracted by using this method contained less than 2-3% protein and 1% total nucleic acid. We also demonstrated the structural integrity of the O-antigen and lipid A via the sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) methods, respectively. We demonstrated the ability of the extracted LPSs to induce typical secretion of cytokines and chemokines by primary macrophages. Overall, this method may be used to isolate purified LPSs with preserved structures of both the O-antigen and lipid A and unchanged functional activity from small amounts of bacterial biomass.
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Affiliation(s)
- Daniil Grumov
- Laboratory of Rickettsial Ecology, N. F. Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Alexey Kostarnoy
- Laboratory of Rickettsial Ecology, N. F. Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
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23
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Keener JE, Goh B, Yoo JS, Oh SF, Brodbelt JS. Top-Down Characterization of Bacterial Lipopolysaccharides and Lipooligosaccharides Using Activated-Electron Photodetachment Mass Spectrometry. Anal Chem 2024; 96:9151-9158. [PMID: 38758019 PMCID: PMC11384421 DOI: 10.1021/acs.analchem.4c00952] [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] [Indexed: 05/18/2024]
Abstract
Lipopolysaccharides (LPS) and lipooligosaccharides (LOS) are located in the outer membrane of Gram-negative bacteria and are comprised of three distinctive parts: lipid A, core oligosaccharide (OS), and O-antigen. The structure of each region influences bacterial stability, toxicity, and pathogenesis. Here, we highlight the use of targeted activated-electron photodetachment (a-EPD) tandem mass spectrometry to characterize LPS and LOS from two crucial players in the human gut microbiota, Escherichia coli Nissle and Bacteroides fragilis. a-EPD is a hybrid activation method that uses ultraviolet photoirradiation to generate charge-reduced radical ions followed by collisional activation to produce informative fragmentation patterns. We benchmark the a-EPD method for top-down characterization of triacyl LOS from E. coli R2, then focus on characterization of LPS from E. coli Nissle and B. fragilis. Notably, a-EPD affords extensive fragmentation throughout the backbone of the core OS and O-antigen regions of LPS from E. coli Nissle. This hybrid approach facilitated the elucidation of structural details for LPS from B. fragilis, revealing a putative hexuronic acid (HexA) conjugated to lipid A.
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Affiliation(s)
- James E Keener
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Byoungsook Goh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
| | - Ji-Sun Yoo
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
| | - Sungwhan F Oh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Program in Immunology, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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24
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Steyaert S, Peeters C, Wieme AD, Muyldermans A, Vandoorslaer K, Spilker T, Wybo I, Piérard D, LiPuma JJ, Vandamme P. Novel Ralstonia species from human infections: improved matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification and analysis of antimicrobial resistance patterns. Microbiol Spectr 2024; 12:e0402123. [PMID: 38661349 PMCID: PMC11237764 DOI: 10.1128/spectrum.04021-23] [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: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
A collection of 161 Ralstonia isolates, including 90 isolates from persons with cystic fibrosis, 27 isolates from other human clinical samples, 8 isolates from the hospital environment, 7 isolates from industrial samples, and 19 environmental isolates, was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification and yielded confident species level identification scores for only 62 (39%) of the isolates, including four that proved misidentified subsequently. Whole-genome sequence analysis of 32 representative isolates for which no confident MALDI-TOF MS species level identification was obtained revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively, and provided the basis for updating an in-house MALDI-TOF MS database. A reanalysis of all mass spectra with the updated MALDI-TOF MS database increased the percentage of isolates with confident species level identification up to 77%. The antimicrobial susceptibility of 30 isolates mainly representing novel human clinical and environmental Ralstonia species was tested toward 17 antimicrobial agents and demonstrated that the novel Ralstonia species were generally multi-resistant, yet susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline. An analysis of genomic antimicrobial resistance genes in 32 novel and publicly available genome sequences revealed broadly distributed beta-lactam resistance determinants.IMPORTANCEThe present study demonstrated that a commercial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification database can be tailored to improve the identification of Ralstonia species. It also revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively. An analysis of minimum inhibitory concentration values demonstrated that the novel Ralstonia species were generally multi-resistant but susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline.
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Affiliation(s)
- Stephanie Steyaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
| | - Anneleen D. Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Astrid Muyldermans
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ingrid Wybo
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Denis Piérard
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - John J. LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
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25
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Huang D, Chen L, Wang Y, Wang Z, Wang J, Wang X. Characterization of a secondary hydroxy-acyltransferase for lipid A in Vibrio parahaemolyticus. Microbiol Res 2024; 283:127712. [PMID: 38593580 DOI: 10.1016/j.micres.2024.127712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Lipid A plays a crucial role in Vibrio parahaemolyticus. Previously we have reported the diversity of secondary acylation of lipid A in V. parahaemolyticus and four V. parahaemolyticus genes VP_RS08405, VP_RS01045, VP_RS12170, and VP_RS00880 exhibiting homology to the secondary acyltransferases in Escherichia coli. In this study, the gene VP_RS12170 was identified as a specific lipid A secondary hydroxy-acyltransferase responsible for transferring a 3-hydroxymyristate to the 2'-position of lipid A. Four E. coli mutant strains WHL00, WHM00, WH300, and WH001 were constructed, and they would synthesize lipid A with different structures due to the absence of genes encoding lipid A secondary acyltransferases or Kdo transferase. Then V. parahaemolyticus VP_RS12170 was overexpressed in W3110, WHL00, WHM00, WH300, and WH001, and lipid A was isolated from these strains and analyzed by using thin-layer chromatography and high-performance liquid chromatography-tandem mass spectrometry. The detailed structural changes of lipid A in these mutant strains with and without VP_RS12170 overexpression were compared and conclude that VP_RS12170 can specifically transfer a 3-hydroxymyristate to the 2'-position of lipid A. This study also demonstrated that the function of VP_RS12170 is Kdo-dependent and its favorite substrate is Kdo-lipid IVA. These findings give us better understanding the biosynthetic pathway and the structural diversity of V. parahaemolyticus lipid A.
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Affiliation(s)
- Danyang Huang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Lingyan Chen
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yang Wang
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhe Wang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianli Wang
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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26
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Robinson KS, Boucher D. Inflammasomes in epithelial innate immunity: front line warriors. FEBS Lett 2024; 598:1335-1353. [PMID: 38485451 DOI: 10.1002/1873-3468.14848] [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: 11/23/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 06/12/2024]
Abstract
Our epithelium represents a battle ground against a variety of insults including pathogens and danger signals. It encodes multiple sensors that detect and respond to such insults, playing an essential role in maintaining and defending tissue homeostasis. One key set of defense mechanisms is our inflammasomes which drive innate immune responses including, sensing and responding to pathogen attack, through the secretion of pro-inflammatory cytokines and cell death. Identification of physiologically relevant triggers for inflammasomes has greatly influenced our ability to decipher the mechanisms behind inflammasome activation. Furthermore, identification of patient mutations within inflammasome components implicates their involvement in a range of epithelial diseases. This review will focus on exploring the roles of inflammasomes in epithelial immunity and cover: the diversity and differential expression of inflammasome sensors amongst our epithelial barriers, their ability to sense local infection and damage and the contribution of the inflammasomes to epithelial homeostasis and disease.
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Affiliation(s)
- Kim Samirah Robinson
- The Skin Innate Immunity and Inflammatory Disease Lab, Skin Research Centre, Department of Hull York Medical School, University of York, UK
- York Biomedical Research Institute, University of York, UK
| | - Dave Boucher
- York Biomedical Research Institute, University of York, UK
- Department of Biology, University of York, UK
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27
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Padhy I, Dwibedy SK, Mohapatra SS. A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development. Microbiol Res 2024; 283:127679. [PMID: 38508087 DOI: 10.1016/j.micres.2024.127679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India.
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28
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Chen L, Deng M, Wang J, Wu T, Zhou S, Yang R, Zhang D, Zou M. Antibiotic resistance and epidemiological characteristics of polymyxin-resistant Klebsiella pneumoniae. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2024; 49:737-747. [PMID: 39174888 PMCID: PMC11341233 DOI: 10.11817/j.issn.1672-7347.2024.230567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Indexed: 08/24/2024]
Abstract
OBJECTIVES The emergence of polymyxin-resistant Klebsiella pneumoniae (KPN) in clinical settings necessitates an analysis of its antibiotic resistance characteristics, epidemiological features, and risk factors for its development. This study aims to provide insights for the prevention and control of polymyxin-resistant KPN infections. METHODS Thirty clinical isolates of polymyxin-resistant KPN were collected from the Third Xiangya Hospital of Central South University. Their antibiotic resistance profiles were analyzed. The presence of carbapenemase KPC, OXA-48, VIM, IMP, and NDM was detected using colloidal gold immunochromatography. Hypervirulent KPN was initially screened using the string test. Biofilm formation capacity was assessed using crystal violet staining. Combination drug susceptibility tests (polymyxin B with meropenem, tigecycline, cefoperazone/sulbactam) were conducted using the checkerboard method. Polymyxin-related resistance genes were detected by PCR. Multi-locus sequence typing (MLST) was performed for genotyping and phylogenetic tree construction. The study also involved collecting data from carbapenem-resistant (CR)-KPN polymyxin-resistant strains (23 strains, experimental group) and CR-KPN polymyxin-sensitive strains (57 strains, control group) to analyze potential risk factors for polymyxin-resistant KPN infection through univariate analysis and multivariate Logistic regression. The induction of resistance by continuous exposure to polymyxin B and colistin E was also tested. RESULTS Among the 30 polymyxin-resistant KPN isolates, 28 were CR-KPN, all producing KPC enzyme. Four isolates were positive in the string test. Most isolates showed strong biofilm formation capabilities. Combination therapy showed additive or synergistic effects. All isolates carried the pmrA and phoP genes, while no mcr-1 or mcr-2 genes were detected. MLST results indicated that ST11 was the predominant type. The phylogenetic tree suggested that polymyxin-resistant KPN had not caused a hospital outbreak in the institution. The use of two or more different classes of antibiotics and the use of polymyxin were identified as independent risk factors for the development of polymyxin-resistant strains. Continuous use of polymyxin induced drug resistance. CONCLUSIONS Polymyxin-resistant KPN is resistant to nearly all commonly used antibiotics, making polymyxin-based combination therapy a viable option. No plasmid-mediated polymyxin-resistant KPN has been isolated in the hospital. Polymyxin can induce resistance in KPN, highlighting the need for rational antibiotic use in clinical settings to delay the emergence of resistance.
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Affiliation(s)
- Lihua Chen
- Department of Laboratory Medicine, Third Xiangya Hospital, Central South University, Changsha 410013.
| | - Mengqian Deng
- Department of Laboratory Medicine, Third Xiangya Hospital, Central South University, Changsha 410013
| | - Jiali Wang
- Xiangya School of Medicine, Central South University, Changsha 410013
| | - Tianrui Wu
- Xiangya School of Medicine, Central South University, Changsha 410013
| | - Shenghong Zhou
- Xiangya School of Medicine, Central South University, Changsha 410013
| | - Ruyin Yang
- Xiangya School of Medicine, Central South University, Changsha 410013
| | - Di Zhang
- Department of Laboratory Medicine, Third Xiangya Hospital, Central South University, Changsha 410013.
| | - Mingxiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China.
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29
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Li H, Xu H. Mechanisms of bacterial resistance to environmental silver and antimicrobial strategies for silver: A review. ENVIRONMENTAL RESEARCH 2024; 248:118313. [PMID: 38280527 DOI: 10.1016/j.envres.2024.118313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
The good antimicrobial properties of silver make it widely used in food, medicine, and environmental applications. However, the release and accumulation of silver-based antimicrobial agents in the environment is increasing with the extensive use of silver-based antimicrobials, and the prevalence of silver-resistant bacteria is increasing. To prevent the emergence of superbugs, it is necessary to exercise rational and strict control over drug use. The mechanism of bacterial resistance to silver has not been fully elucidated, and this article provides a review of the progress of research on the mechanism of bacterial resistance to silver. The results indicate that bacterial resistance to silver can occur through inducing silver particles aggregation and Ag+ reduction, inhibiting silver contact with and entry into cells, efflux of silver particles and Ag+ in cells, and activation of damage repair mechanisms. We propose that the bacterial mechanism of silver resistance involves a combination of interrelated systems. Finally, we discuss how this information can be used to develop the next generation of silver-based antimicrobials and antimicrobial therapies. And some antimicrobial strategies are proposed such as the "Trojan Horse" - camouflage, using efflux pump inhibitors to reduce silver efflux, working with "minesweeper", immobilization of silver particles.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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Man L, Soh PXY, McEnearney TE, Cain JA, Dale AL, Cordwell SJ. Multi-Omics of Campylobacter jejuni Growth in Chicken Exudate Reveals Molecular Remodelling Associated with Altered Virulence and Survival Phenotypes. Microorganisms 2024; 12:860. [PMID: 38792690 PMCID: PMC11123243 DOI: 10.3390/microorganisms12050860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Campylobacter jejuni is the leading cause of foodborne human gastroenteritis in the developed world. Infections are largely acquired from poultry produced for human consumption and poor food handling is thus a major risk factor. Chicken exudate (CE) is a liquid produced from defrosted commercial chicken products that facilitates C. jejuni growth. We examined the response of C. jejuni to growth in CE using a multi-omics approach. Changes in the C. jejuni proteome were assessed by label-based liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We quantified 1328 and 1304 proteins, respectively, in experiments comparing 5% CE in Mueller-Hinton (MH) medium and 100% CE with MH-only controls. These proteins represent 81.8% and 80.3% of the predicted C. jejuni NCTC11168 proteome. Growth in CE induced profound remodelling of the proteome. These changes were typically conserved between 5% and 100% CE, with a greater magnitude of change observed in 100% CE. We confirmed that CE induced C. jejuni biofilm formation, as well as increasing motility and resistance against oxidative stress, consistent with changes to proteins representing those functions. Assessment of the C. jejuni metabolome showed CE also led to increased intracellular abundances of serine, proline, and lactate that were correlated with the elevated abundances of their respective transporters. Analysis of carbon source uptake showed prolonged culture supernatant retention of proline and succinate in CE-supplemented medium. Metabolomics data provided preliminary evidence for the uptake of chicken-meat-associated dipeptides. C. jejuni exposed to CE showed increased resistance to several antibiotics, including polymyxin B, consistent with changes to tripartite efflux system proteins and those involved in the synthesis of lipid A. The C. jejuni CE proteome was also characterised by very large increases in proteins associated with iron acquisition, while a decrease in proteins containing iron-sulphur clusters was also observed. Our data suggest CE is both oxygen- and iron-limiting and provide evidence of factors required for phenotypic remodelling to enable C. jejuni survival on poultry products.
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Affiliation(s)
- Lok Man
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Pamela X. Y. Soh
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Tess E. McEnearney
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joel A. Cain
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ashleigh L. Dale
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Stuart J. Cordwell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW 2006, Australia
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Kong FS, Huang P, Chen JH, Ma Y. The Novel Insight of Gut Microbiota from Mouse Model to Clinical Patients and the Role of NF-κB Pathway in Polycystic Ovary Syndrome. Reprod Sci 2024:10.1007/s43032-024-01562-3. [PMID: 38653859 DOI: 10.1007/s43032-024-01562-3] [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: 12/21/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Polycystic Ovary Syndrome (PCOS) is a metabolic disorder characterized by hyperandrogenism and related symptoms in women of reproductive age. Emerging evidence suggests that chronic low-grade inflammation plays a significant role in the development of PCOS. The gut microbiota, a complex bacterial ecosystem, has been extensively studied for various diseases, including PCOS, while the underlying mechanisms are not fully understood. This review comprehensively summarizes the changes in gut microbiota and metabolites observed in PCOS and their potential association with the condition. Additionally, we discuss the role of abnormal nuclear factor κB signaling in the pathogenesis of PCOS. These findings offer valuable insights into the mechanisms of PCOS and may pave the way for the development of control and therapeutic strategies for this condition in clinical practice. By bridging the gap between mouse models and clinical patients, this review contributes to a better understanding of the interplay between gut microbiota and inflammation in PCOS, thus paving new ways for future investigations and interventions.
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Affiliation(s)
- Fan-Sheng Kong
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Panwang Huang
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China.
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China.
| | - Yaping Ma
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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Boreak N, Alrajab EA, Nahari RA, Najmi LE, Masmali MA, Ghawi AA, Al Moaleem MM, Alhazmi MY, Maqbul AA. Unveiling Therapeutic Potential: Targeting Fusobacterium nucleatum's Lipopolysaccharide Biosynthesis for Endodontic Infections-An In Silico Screening Study. Int J Mol Sci 2024; 25:4239. [PMID: 38673822 PMCID: PMC11049844 DOI: 10.3390/ijms25084239] [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: 03/04/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Complex microbial communities have been reported to be involved in endodontic infections. The microorganisms invade the dental pulp leading to pulpitis and initiating pulp inflammation. Fusobacterium nucleatum is a dominant bacterium implicated in both primary and secondary endodontic infections. Drugs targeting the molecular machinery of F. nucleatum will minimize pulp infection. LpxA and LpxD are early acyltransferases involved in the formation of lipid A, a major component of bacterial membranes. The identification of leads which exhibit preference towards successive enzymes in a single pathway can also prevent the development of bacterial resistance. A stringent screening strategy utilizing physicochemical and pharmacokinetic parameters along with a virtual screening approach identified two compounds, Lomefloxacin and Enoxacin, with good binding affinity towards the early acyltransferases LpxA and LpxD. Lomefloxacin and Enoxacin, members of the fluoroquinolone antibiotic class, exhibit wide-ranging activity against diverse bacterial strains. Nevertheless, their effectiveness in the context of endodontic treatment requires further investigation. This study explored the potential of Lomefloxacin and Enoxacin to manage endodontic infections via computational analysis. Moreover, the compounds identified herein serve as a foundation for devising novel combinatorial libraries with enhanced efficacy for endodontic therapeutic strategies.
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Affiliation(s)
- Nezar Boreak
- College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia; (E.A.A.); (R.A.N.); (L.E.N.); (M.A.M.); (A.A.G.); (M.M.A.M.); (M.Y.A.); (A.A.M.)
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Huseby DL, Cao S, Zamaratski E, Sooriyaarachchi S, Ahmad S, Bergfors T, Krasnova L, Pelss J, Ikaunieks M, Loza E, Katkevics M, Bobileva O, Cirule H, Gukalova B, Grinberga S, Backlund M, Simoff I, Leber AT, Berruga-Fernández T, Antonov D, Konda VR, Lindström S, Olanders G, Brandt P, Baranczewski P, Vingsbo Lundberg C, Liepinsh E, Suna E, Jones TA, Mowbray SL, Hughes D, Karlén A. Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria. Proc Natl Acad Sci U S A 2024; 121:e2317274121. [PMID: 38579010 PMCID: PMC11009625 DOI: 10.1073/pnas.2317274121] [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: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 04/07/2024] Open
Abstract
Here, we describe the identification of an antibiotic class acting via LpxH, a clinically unexploited target in lipopolysaccharide synthesis. The lipopolysaccharide synthesis pathway is essential in most Gram-negative bacteria and there is no analogous pathway in humans. Based on a series of phenotypic screens, we identified a hit targeting this pathway that had activity on efflux-defective strains of Escherichia coli. We recognized common structural elements between this hit and a previously published inhibitor, also with activity against efflux-deficient bacteria. With the help of X-ray structures, this information was used to design inhibitors with activity on efflux-proficient, wild-type strains. Optimization of properties such as solubility, metabolic stability and serum protein binding resulted in compounds having potent in vivo efficacy against bloodstream infections caused by the critical Gram-negative pathogens E. coli and Klebsiella pneumoniae. Other favorable properties of the series include a lack of pre-existing resistance in clinical isolates, and no loss of activity against strains expressing extended-spectrum-β-lactamase, metallo-β-lactamase, or carbapenemase-resistance genes. Further development of this class of antibiotics could make an important contribution to the ongoing struggle against antibiotic resistance.
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Affiliation(s)
- Douglas L. Huseby
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Edouard Zamaratski
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | | | - Shabbir Ahmad
- Department of Cell and Molecular Biology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Terese Bergfors
- Department of Cell and Molecular Biology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Laura Krasnova
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | - Juris Pelss
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | | | - Einars Loza
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | | | - Olga Bobileva
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | - Helena Cirule
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | - Baiba Gukalova
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | | | - Maria Backlund
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling, Uppsala University, UppsalaSE-75123, Sweden
| | - Ivailo Simoff
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling, Uppsala University, UppsalaSE-75123, Sweden
| | - Anna T. Leber
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Talía Berruga-Fernández
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Dmitry Antonov
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Vivekananda R. Konda
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Stefan Lindström
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Gustav Olanders
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Pawel Baranczewski
- Department of Pharmacy, SciLifeLab Drug Discovery and Development Platform, Uppsala University, UppsalaSE-75123, Sweden
| | | | | | - Edgars Suna
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | - T. Alwyn Jones
- Department of Cell and Molecular Biology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Sherry L. Mowbray
- Department of Cell and Molecular Biology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
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Yadav M, Sathe J, Teronpi V, Kumar A. Navigating the signaling landscape of Ralstonia solanacearum: a study of bacterial two-component systems. World J Microbiol Biotechnol 2024; 40:153. [PMID: 38564115 DOI: 10.1007/s11274-024-03950-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024]
Abstract
Ralstonia solanacearum, the bacterium that causes bacterial wilt, is a destructive phytopathogen that can infect over 450 different plant species. Several agriculturally significant crop plants, including eggplant, tomato, pepper, potato, and ginger, are highly susceptible to this plant disease, which has a global impact on crop quality and yield. There is currently no known preventive method that works well for bacterial wilt. Bacteria use two-component systems (TCSs) to sense their environment constantly and react appropriately. This is achieved by an extracellular sensor kinase (SK) capable of sensing a suitable signal and a cytoplasmic response regulator (RR) which gives a downstream response. Moreover, our investigation revealed that R. solanacearum GMI1000 possesses a substantial count of TCSs, specifically comprising 36 RRs and 27 SKs. While TCSs are known targets for various human pathogenic bacteria, such as Salmonella, the role of TCSs in R. solanacearum remains largely unexplored in this context. Notably, numerous inhibitors targeting TCSs have been identified, including GHL (Gyrase, Hsp, and MutL) compounds, Walk inhibitors, and anti-TCS medications like Radicicol. Consequently, the investigation into the involvement of TCSs in virulence and pathogenesis has gained traction; however, further research is imperative to ascertain whether TCSs could potentially supplant conventional anti-wilt therapies. This review delves into the prospective utilization of TCSs as an alternative anti-wilt therapy, focusing on the lethal phytopathogen R. solanacearum.
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Affiliation(s)
- Mohit Yadav
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Janhavi Sathe
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, 560065, India
| | - Valentina Teronpi
- Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, Assam, 784184, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
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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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Majumder S, Das S, Li P, Yang N, Dellario H, Sui H, Guan Z, Sun W. Pneumonic Plague Protection Induced by a Monophosphoryl Lipid A Decorated Yersinia Outer-Membrane-Vesicle Vaccine. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307066. [PMID: 38009518 PMCID: PMC11009084 DOI: 10.1002/smll.202307066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/19/2023] [Indexed: 11/29/2023]
Abstract
A new Yersinia pseudotuberculosis mutant strain, YptbS46, carrying the lpxE insertion and pmrF-J deletion is constructed and shown to exclusively produce monophosphoryl lipid A (MPLA) having adjuvant properties. Outer membrane vesicles (OMVs) isolated from YptbS46 harboring an lcrV expression plasmid, pSMV13, are designated OMV46-LcrV, which contained MPLA and high amounts of LcrV (Low Calcium response V) and displayed low activation of Toll-like receptor 4 (TLR4). Intramuscular prime-boost immunization with 30 µg of of OMV46-LcrV exhibited substantially reduced reactogenicity than the parent OMV44-LcrV and conferred complete protection to mice against a high-dose of respiratory Y. pestis challenge. OMV46-LcrV immunization induced robust adaptive responses in both lung mucosal and systemic compartments and orchestrated innate immunity in the lung, which are correlated with rapid bacterial clearance and unremarkable lung damage during Y. pestis challenge. Additionally, OMV46-LcrV immunization conferred long-term protection. Moreover, immunization with reduced doses of OMV46-LcrV exhibited further lower reactogenicity and still provided great protection against pneumonic plague. The studies strongly demonstrate the feasibility of OMV46-LcrV as a new type of plague vaccine candidate.
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Affiliation(s)
- Saugata Majumder
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Shreya Das
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Peng Li
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Nicole Yang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Hazel Dellario
- Wadsworth Center, New York State Department of Health, Albany, NY, 12237, USA
| | - Haixin Sui
- Wadsworth Center, New York State Department of Health, Albany, NY, 12237, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Wei Sun
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
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37
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Cho J, Song H, Yoon HC, Yoon H. Rapid Dot-Blot Immunoassay for Detecting Multiple Salmonella enterica Serotypes. J Microbiol Biotechnol 2024; 34:340-348. [PMID: 37986605 PMCID: PMC10940738 DOI: 10.4014/jmb.2308.08006] [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: 08/08/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023]
Abstract
Salmonella, a major contributor to foodborne infections, typically causes self-limiting gastroenteritis. However, it is frequently invasive and disseminates across the intestinal epithelium, leading to deadly bacteremia. Although the genus is subdivided into >2,600 serotypes based on their antigenic determinants, only few serotypes are responsible for most human infections. In this study, a rapid dot-blot immunoassay was developed to diagnose multiple Salmonella enterica serotypes with high incidence rates in humans. The feasibility of 10 commercial antibodies (four polyclonal and six monoclonal antibodies) was tested using the 18 serotypes associated with 67.5% Salmonella infection cases in the United States of America (U.S.A) in 2016. Ab 3 (polyclonal; eight of 18 serotypes), Ab 8 (monoclonal; 13 of 18 serotypes), and Ab 9 (monoclonal; 10 of 18 serotypes) antibodies exhibited high detection rates in western blotting and combinations of two antibodies (Ab 3+8, Ab 3+9, and Ab 8+9) were applied to dot-blot assays. The combination of Ab 3+8 identified 15 of the tested 18 serotypes in 3 h, i.e., S. Enteritidis, S. Typhimurium, S. Javiana, S. I 4,[5],12:i:-, S. Infantis, S. Montevideo, S. Braenderup, S. Thompson, S. Saintpaul, S. Heidelberg, S. Oranienburg, S. Bareilly, S. Berta, S. Agona, and S. Anatum, which were responsible for 53.7% Salmonella infections in the U.S. in 2016. This cost-effective and rapid method can be utilized as an on-site colorimetric method for Salmonella detection.
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Affiliation(s)
- Jeongik Cho
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Heymin Song
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Hyun C. Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
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Shvets Y, Khranovska N, Senchylo N, Ostapchenko D, Tymoshenko I, Onysenko S, Kobyliak N, Falalyeyeva T. Microbiota substances modulate dendritic cells activity: A critical view. Heliyon 2024; 10:e27125. [PMID: 38444507 PMCID: PMC10912702 DOI: 10.1016/j.heliyon.2024.e27125] [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: 11/21/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024] Open
Abstract
Contemporary research in the field of microbiota shows that commensal bacteria influence physiological activity of different organs and systems of a human organism, such as brain, lungs, immune and metabolic systems. This influence is realized by various processes. One of them is trough modulation of immune mechanisms. Interactions between microbiota and the human immune system are known to be complex and ambiguous. Dendritic cells (DCs) are unique cells, which initiate the development and polarization of adaptive immune response. These cells also interconnect native and specific immune reactivity. A large set of biochemical signals from microbiota in the form of different microbiota associated molecular patterns (MAMPs) and bacterial metabolites that act locally and distantly in the human organism. As a result, commensal bacteria influence the maturity and activity of dendritic cells and affect the overall immune reactivity of the human organism. It then determines the response to pathogenic microorganisms, inflammation, associated with different pathological conditions and even affects the effectiveness of vaccination.
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Affiliation(s)
- Yuliia Shvets
- Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska Str., Kyiv, Ukraine
| | - Natalia Khranovska
- National Cancer Institute of Ukraine, 33/43 Yuliia Zdanovska Str., Kyiv, Ukraine
| | - Natalia Senchylo
- Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska Str., Kyiv, Ukraine
| | - Danylo Ostapchenko
- Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska Str., Kyiv, Ukraine
| | - Iryna Tymoshenko
- Bogomolets National Medical University, 13 Shevchenka Blvd., Kyiv, Ukraine
| | - Svitlana Onysenko
- Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska Str., Kyiv, Ukraine
| | - Nazarii Kobyliak
- Bogomolets National Medical University, 13 Shevchenka Blvd., Kyiv, Ukraine
- Medical Laboratory CSD, 22b Zhmerynska Str., Kyiv, Ukraine
| | - Tetyana Falalyeyeva
- Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska Str., Kyiv, Ukraine
- Medical Laboratory CSD, 22b Zhmerynska Str., Kyiv, Ukraine
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Janet-Maitre M, Job V, Bour M, Robert-Genthon M, Brugière S, Triponney P, Cobessi D, Couté Y, Jeannot K, Attrée I. Pseudomonas aeruginosa MipA-MipB envelope proteins act as new sensors of polymyxins. mBio 2024; 15:e0221123. [PMID: 38345374 PMCID: PMC10936184 DOI: 10.1128/mbio.02211-23] [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: 08/16/2023] [Accepted: 01/09/2024] [Indexed: 03/14/2024] Open
Abstract
Due to the rising incidence of antibiotic-resistant infections, the last-line antibiotics, polymyxins, have resurged in the clinics in parallel with new bacterial strategies of escape. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa develops resistance to colistin/polymyxin B by distinct molecular mechanisms, mostly through modification of the lipid A component of the LPS by proteins encoded within the arnBCDATEF-ugd (arn) operon. In this work, we characterized a polymyxin-induced operon named mipBA, present in P. aeruginosa strains devoid of the arn operon. We showed that mipBA is activated by the ParR/ParS two-component regulatory system in response to polymyxins. Structural modeling revealed that MipA folds as an outer-membrane β-barrel, harboring an internal negatively charged channel, able to host a polymyxin molecule, while the lipoprotein MipB adopts a β-lactamase fold with two additional C-terminal domains. Experimental work confirmed that MipA and MipB localize to the bacterial envelope, and they co-purify in vitro. Nano differential scanning fluorimetry showed that polymyxins stabilized MipA in a specific and dose-dependent manner. Mass spectrometry-based quantitative proteomics on P. aeruginosa membranes demonstrated that ∆mipBA synthesized fourfold less MexXY-OprA proteins in response to polymyxin B compared to the wild-type strain. The decrease was a direct consequence of impaired transcriptional activation of the mex operon operated by ParR/ParS. We propose MipA/MipB to act as membrane (co)sensors working in concert to activate ParS histidine kinase and help the bacterium to cope with polymyxin-mediated envelope stress through synthesis of the efflux pump, MexXY-OprA.IMPORTANCEDue to the emergence of multidrug-resistant isolates, antibiotic options may be limited to polymyxins to eradicate Gram-negative infections. Pseudomonas aeruginosa, a leading opportunistic pathogen, has the ability to develop resistance to these cationic lipopeptides by modifying its lipopolysaccharide through proteins encoded within the arn operon. Herein, we describe a sub-group of P. aeruginosa strains lacking the arn operon yet exhibiting adaptability to polymyxins. Exposition to sub-lethal polymyxin concentrations induced the expression and production of two envelope-associated proteins. Among those, MipA, an outer-membrane barrel, is able to specifically bind polymyxins with an affinity in the 10-µM range. Using membrane proteomics and phenotypic assays, we showed that MipA and MipB participate in the adaptive response to polymyxins via ParR/ParS regulatory signaling. We propose a new model wherein the MipA-MipB module functions as a novel polymyxin sensing mechanism.
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Affiliation(s)
- Manon Janet-Maitre
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Viviana Job
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Maxime Bour
- UMR6249 Chrono-Environnement, UFR Santé, University of Franche-Comté, Besançon, France
- French National Reference Center for Antibiotic Resistance, Besançon, France
| | - Mylène Robert-Genthon
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Sabine Brugière
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, FranceGrenoble
| | - Pauline Triponney
- French National Reference Center for Antibiotic Resistance, Besançon, France
| | - David Cobessi
- University Grenoble Alpes, IBS, UMR5075, Team Synchrotron, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, FranceGrenoble
| | - Katy Jeannot
- UMR6249 Chrono-Environnement, UFR Santé, University of Franche-Comté, Besançon, France
- French National Reference Center for Antibiotic Resistance, Besançon, France
- Department of Bacteriology, Teaching Hospital of Besançon, Besançon, France
| | - Ina Attrée
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
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Amudala S, Sumit, Aidhen IS. LpxC inhibition: Potential and opportunities with carbohydrate scaffolds. Carbohydr Res 2024; 537:109057. [PMID: 38402732 DOI: 10.1016/j.carres.2024.109057] [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: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024]
Abstract
Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a key enzyme involved in the biosynthesis of lipid A, an essential building block, for the construction and assembly of the outer membrane (OM) of Gram-negative bacteria. The enzyme is highly conserved in almost all Gram-negative bacteria and hence has emerged as a promising target for drug discovery in the fight against multi-drug resistant Gram-negative infections. Since the first nanomolar LpxC inhibitor, L-161,240, an oxazoline-based hydroxamate, the two-decade-long ongoing search has provided valuable information regarding essential features necessary for inhibition. Although the design and structure optimization for arriving at the most efficacious inhibitor of this enzyme has made good use of different heterocyclic moieties, the use of carbohydrate scaffold is scant. This review briefly covers the advancement and progress made in LpxC inhibition. The field awaits the use of potential associated with carbohydrate-based scaffolds for LpxC inhibition and the discovery of anti-bacterial agents against Gram-negative infections.
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Affiliation(s)
- Subramanyam Amudala
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Sumit
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Indrapal Singh Aidhen
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India.
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Baijal K, Abramchuk I, Herrera CM, Mah TF, Trent MS, Lavallée-Adam M, Downey M. Polyphosphate kinase regulates LPS structure and polymyxin resistance during starvation in E. coli. PLoS Biol 2024; 22:e3002558. [PMID: 38478588 PMCID: PMC10962826 DOI: 10.1371/journal.pbio.3002558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 03/25/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1,000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work, we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (Δppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and Δppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of the required building blocks. From our data set, we were particularly interested in Arn and EptA proteins, which were down-regulated in Δppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins in K-12 strains and a uropathogenic isolate, and provide evidence that this mis-regulation in Δppk cells stems from a failure to induce the BasRS two-component system during starvation. We also show that Δppk mutants unable to up-regulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
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Affiliation(s)
- Kanchi Baijal
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Iryna Abramchuk
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carmen M. Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Thien-Fah Mah
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Lobertti CA, Gizzi FO, Magni C, Rial A, Chabalgoity JA, Yim L, Blancato VS, Asquith CRM, García Véscovi E. Enhancing colistin efficacy against Salmonella infections with a quinazoline-based dual therapeutic strategy. Sci Rep 2024; 14:5148. [PMID: 38429351 PMCID: PMC10907601 DOI: 10.1038/s41598-024-55793-0] [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: 10/23/2023] [Accepted: 02/27/2024] [Indexed: 03/03/2024] Open
Abstract
Colistin remains one of the last-resort therapies for combating infections caused by multidrug-resistant (MDR) Enterobacterales, despite its adverse nephro- and neuro-toxic effects. This study elucidates the mechanism of action of a non-antibiotic 4-anilinoquinazoline-based compound that synergistically enhances the effectiveness of colistin against Salmonella enterica. The quinazoline sensitizes Salmonella by deactivating intrinsic, mutational, and transferable resistance mechanisms that enable Salmonella to counteract the antibiotic impact colistin, together with an induced disruption to the electrochemical balance of the bacterial membrane. The attenuation of colistin resistance via the combined treatment approach also proves efficacious against E. coli, Klebsiella, and Acinetobacter strains. The dual therapy reduces the mortality of Galleria mellonella larvae undergoing a systemic Salmonella infection when compared to individual drug treatments. Overall, our findings unveil the potential of the quinazoline-colistin combined therapy as an innovative strategy against MDR bacteria.
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Affiliation(s)
- Carlos A Lobertti
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Nacional de Rosario, Predio CCT-CONICET Rosario, S2000, Santa Fe, Rosario, Argentina
| | - Fernán O Gizzi
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Nacional de Rosario, Predio CCT-CONICET Rosario, S2000, Santa Fe, Rosario, Argentina
| | - Christian Magni
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Nacional de Rosario, Predio CCT-CONICET Rosario, S2000, Santa Fe, Rosario, Argentina
| | - Analía Rial
- Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Universidad de La República, Avda. Alfredo Navarro 3051, 11600, Montevideo, Uruguay
| | - José A Chabalgoity
- Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Universidad de La República, Avda. Alfredo Navarro 3051, 11600, Montevideo, Uruguay
| | - Lucía Yim
- Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Universidad de La República, Avda. Alfredo Navarro 3051, 11600, Montevideo, Uruguay
| | - Víctor S Blancato
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Nacional de Rosario, Predio CCT-CONICET Rosario, S2000, Santa Fe, Rosario, Argentina
| | - Christopher R M Asquith
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Eleonora García Véscovi
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Nacional de Rosario, Predio CCT-CONICET Rosario, S2000, Santa Fe, Rosario, Argentina.
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Gasanov V, Vorotelyak E, Vasiliev A. Expression of the Antimicrobial Peptide SE-33-A2P, a Modified Analog of Cathelicidin, and an Analysis of Its Properties. Antibiotics (Basel) 2024; 13:190. [PMID: 38391576 PMCID: PMC10886013 DOI: 10.3390/antibiotics13020190] [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: 10/30/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
In this study, we developed a method for the expression of the antimicrobial peptide SE-33-A2P in E. coli bacterial cells. The SE-33-A2P peptide consists of A2P and SE-33 peptides and is a retro analog of cathelicidin possessing antimicrobial activity against both Gram-positive and Gram-negative bacteria. Furthermore, the A2P peptide is a self-cleaving peptide. For an efficient expression of the SE-33-A2P peptide, a gene encoding several repetitive sequences of the SE-33 peptide separated by A2P sequences was created. The gene was cloned into a plasmid, with which E. coli cells were transformed. An induction of the product expression was carried out by IPTG after the cell culture gained high density. The inducible expression product, due to the properties of the A2P peptide, was cleaved in the cell into SE-33-A2P peptides. As the next step, the SE-33-A2P peptide was purified using filtration and chromatography. Its activity against both Gram-positive and Gram-negative bacteria, including antibiotic-resistant bacteria, was proved. The developed approach for obtaining a prokaryotic system for the expression of a highly active antimicrobial peptide expands the opportunities for producing antimicrobial peptides via industrial methods.
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Affiliation(s)
- Vagif Gasanov
- Laboratory of Cell Biology, N.K. Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Vavilov Str. 26, 119334 Moscow, Russia
| | - Ekaterina Vorotelyak
- Laboratory of Cell Biology, N.K. Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Vavilov Str. 26, 119334 Moscow, Russia
| | - Andrey Vasiliev
- Laboratory of Cell Biology, N.K. Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Vavilov Str. 26, 119334 Moscow, Russia
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Hofstaedter CE, Chandler CE, Met CM, Gillespie JJ, Harro JM, Goodlett DR, Rasko DA, Ernst RK. Divergent Pseudomonas aeruginosa LpxO enzymes perform site-specific lipid A 2-hydroxylation. mBio 2024; 15:e0282323. [PMID: 38131669 PMCID: PMC10865791 DOI: 10.1128/mbio.02823-23] [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: 10/18/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Pseudomonas aeruginosa can survive in a myriad of environments, partially due to modifications of its lipid A, the membrane anchor of lipopolysaccharide. We previously demonstrated that divergent late acyltransferase paralogs, HtrB1 and HtrB2, add acyloxyacyl laurate to lipid A 2- and 2'-acyl chains, respectively. The genome of P. aeruginosa also has genes which encode two dioxygenase enzymes, LpxO1 and LpxO2, that individually hydroxylate a specific secondary laurate. LpxO1 acts on the 2'-acyloxyacyl laurate (added by HtrB2), whereas LpxO2 acts on the 2-acyloxyacyl laurate (added by HtrB1) in a site-specific manner. Furthermore, while both enzyme pairs are evolutionarily linked, phylogenomic analysis suggests the LpxO1/HtrB2 enzyme pair as being of ancestral origin, present throughout the Pseudomonas lineage, whereas the LpxO2/HtrB1 enzyme pair likely arose via horizontal gene transfer and has been retained in P. aeruginosa over time. Using a murine pulmonary infection model, we showed that both LpxO1 and LpxO2 enzymes are functional in vivo, as direct analysis of in vivo lipid A structure from bronchoalveolar lavage fluid revealed 2-hydroxylated lipid A. Gene expression analysis reveals increased lpxO2 but unchanged lpxO1 expression in vivo, suggesting differential regulation of these enzymes during infection. We also demonstrate that loss-of-function mutations arise in lpxO1 and lpxO2 during chronic lung infection in people with cystic fibrosis (CF), indicating a potential role for pathogenesis and airway adaptation. Collectively, our study characterizes lipid A 2-hydroxylation during P. aeruginosa airway infection that is regulated by two distinct lipid A dioxygenase enzymes.IMPORTANCEPseudomonas aeruginosa is an opportunistic pathogen that causes severe infection in hospitalized and chronically ill individuals. During infection, P. aeruginosa undergoes adaptive changes to evade host defenses and therapeutic interventions, increasing mortality and morbidity. Lipid A structural alteration is one such change that P. aeruginosa isolates undergo during chronic lung infection in CF. Investigating genetic drivers of this lipid A structural variation is crucial in understanding P. aeruginosa adaptation during infection. Here, we describe two lipid A dioxygenases with acyl-chain site specificity, each with different evolutionary origins. Further, we show that loss of function in these enzymes occurs in CF clinical isolates, suggesting a potential pathoadaptive phenotype. Studying these bacterial adaptations provides insight into selection pressures of the CF airway on P. aeruginosa phenotypes that persist during chronic infection. Understanding these adaptive changes may ultimately provide clinicians better control over bacterial populations during chronic infection.
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Affiliation(s)
- Casey E. Hofstaedter
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, Maryland, USA
- Medical Scientist Training Program, University of Maryland, Baltimore, Baltimore, Maryland, USA
| | - Courtney E. Chandler
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, Maryland, USA
| | - Charles M. Met
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, Maryland, USA
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA
| | - Janette M. Harro
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, Maryland, USA
| | - David R. Goodlett
- Departments of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - David A. Rasko
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute for Genome Sciences, University of Maryland, Baltimore, Baltimore, Maryland, USA
- Center for Pathogen Research, University of Maryland, Baltimore, Baltimore, Maryland, USA
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA
- Center for Pathogen Research, University of Maryland, Baltimore, Baltimore, Maryland, USA
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Lyu J, Zhang T, Marty MT, Clemmer D, Russell DH, Laganowsky A. Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions. eLife 2024; 12:RP91094. [PMID: 38252560 PMCID: PMC10945598 DOI: 10.7554/elife.91094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298 K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, The University of ArizonaTucsonUnited States
| | - David Clemmer
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - David H Russell
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
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Fleitas O, Fontes W, De Souza CM, Da Costa MC, Cardoso MH, Castro MS, Sousa MV, Ricart CAO, Ramada MHS, Duque HM, Porto WF, Silva ON, Franco OL. A proteomic perspective on the resistance response of Klebsiella pneumoniae to antimicrobial peptide PaDBS1R1. J Antimicrob Chemother 2024; 79:112-122. [PMID: 37966053 DOI: 10.1093/jac/dkad354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/31/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND The synthetic antimicrobial peptide, PaDBS1R1, has been reported as a powerful anti-Klebsiella pneumoniae antimicrobial. However, there is only scarce knowledge about whether K. pneumoniae could develop resistance against PaDBS1R1 and which resistance mechanisms could be involved. OBJECTIVES Identify via label-free shotgun proteomics the K. pneumoniae resistance mechanisms developed against PaDBS1R1. METHODS An adaptive laboratory evolution experiment was performed to obtain a PaDBS1R1-resistant K. pneumoniae lineage. Antimicrobial susceptibility was determined through microdilution assay. Modifications in protein abundances between the resistant and sensitive lineages were measured via label-free quantitative shotgun proteomics. Enriched Gene Ontology terms and KEGG pathways were identified through over-representation analysis. Data are available via ProteomeXchange with identifier PXD033020. RESULTS K. pneumoniae ATCC 13883 parental strain challenged with increased subinhibitory PaDBS1R1 concentrations allowed the PaDBS1R1-resistant K. pneumoniae lineage to emerge. Proteome comparisons between PaDBS1R1-resistant K. pneumoniae and PaDBS1R1-sensitive K. pneumoniae under PaDBS1R1-induced stress conditions enabled the identification and quantification of 1702 proteins, out of which 201 were differentially abundant proteins (DAPs). The profiled DAPs comprised 103 up-regulated proteins (adjusted P value < 0.05, fold change ≥ 2) and 98 down-regulated proteins (adjusted P value < 0.05, fold change ≤ 0.5). The enrichment analysis suggests that PhoPQ-guided LPS modifications and CpxRA-dependent folding machinery could be relevant resistance mechanisms against PaDBS1R1. CONCLUSIONS Based on experimental evolution and a label-free quantitative shotgun proteomic approach, we showed that K. pneumoniae developed resistance against PaDBS1R1, whereas PhoPQ-guided LPS modifications and CpxRA-dependent folding machinery appear to be relevant resistance mechanisms against PaDBS1R1.
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Affiliation(s)
- Osmel Fleitas
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Wagner Fontes
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Laboratório de Bioquímica e Química de Proteínas, Universidade de Brasília, Brasília, Brazil
| | - Camila M De Souza
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Mylena C Da Costa
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Marlon H Cardoso
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Instituto de Biociências (INBIO), Universidade Federal de Mato Grosso do Sul, Cidade Universitária, 79070900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Mariana S Castro
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Laboratório de Bioquímica e Química de Proteínas, Universidade de Brasília, Brasília, Brazil
| | - Marcelo V Sousa
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Laboratório de Bioquímica e Química de Proteínas, Universidade de Brasília, Brasília, Brazil
| | - Carlos A O Ricart
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Laboratório de Bioquímica e Química de Proteínas, Universidade de Brasília, Brasília, Brazil
| | - Marcelo H S Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Harry M Duque
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - William F Porto
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Osmar N Silva
- Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Evangélica de Anapólis, University City, 75083-515 Anápolis-GO, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
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Jouan R, Lextrait G, Lachat J, Yokota A, Cossard R, Naquin D, Timchenko T, Kikuchi Y, Ohbayashi T, Mergaert P. Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont Caballeronia insecticola. ISME COMMUNICATIONS 2024; 4:ycad001. [PMID: 38282642 PMCID: PMC10809759 DOI: 10.1093/ismeco/ycad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/30/2024]
Abstract
Caballeronia insecticola is a bacterium belonging to the Burkholderia genus sensu lato, which is able to colonize multiple environments like soils and the gut of the bean bug Riptortus pedestris. We constructed a saturated Himar1 mariner transposon library and revealed by transposon-sequencing that 498 protein-coding genes constitute the essential genome of Caballeronia insecticola for growth in free-living conditions. By comparing essential gene sets of Caballeronia insecticola and seven related Burkholderia s.l. strains, only 120 common genes were identified, indicating that a large part of the essential genome is strain-specific. In order to reproduce specific nutritional conditions that are present in the gut of Riptortus pedestris, we grew the mutant library in minimal media supplemented with candidate gut nutrients and identified several condition-dependent fitness-defect genes by transposon-sequencing. To validate the robustness of the approach, insertion mutants in six fitness genes were constructed and their growth deficiency in media supplemented with the corresponding nutrient was confirmed. The mutants were further tested for their efficiency in Riptortus pedestris gut colonization, confirming that gluconeogenic carbon sources, taurine and inositol, are nutrients consumed by the symbiont in the gut. Thus, our study provides insights about specific contributions provided by the insect host to the bacterial symbiont.
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Grants
- JSPS Research Fellowship for Young Scientists, Japan
- Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan
- Ministry of Higher Education, Research, and Innovation, France
- CNRS International Research Project, France
- JSPS-CNRS Bilateral Open Partnership Joint Research Project, France-Japan
- Agence Nationale de la Recherche, France
- Saclay Plant Sciences-SPS
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Affiliation(s)
- Romain Jouan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Gaëlle Lextrait
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Joy Lachat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Aya Yokota
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Raynald Cossard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Tatiana Timchenko
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, Sapporo 062-8517, Japan
| | - Tsubasa Ohbayashi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8604, Japan
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
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48
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Zhang W, Hu W, Zhu Q, Niu M, An N, Feng Y, Kawamura K, Fu P. Hydroxy fatty acids in the surface Earth system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167358. [PMID: 37793460 DOI: 10.1016/j.scitotenv.2023.167358] [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: 08/01/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/06/2023]
Abstract
Lipids are ubiquitous and highly abundant in a wide range of organisms and have been found in various types of environmental media. These molecules play a crucial role as organic tracers by providing a chemical perspective on viewing the material world, as well as offering a wealth of information on metabolic activities. Among the diverse lipid compounds, hydroxy fatty acids (HFAs) with one to multiple hydroxyl groups attached to the carbon chain stand out as important biomarkers for different sources of organic matter. HFAs are widespread in nature and are involved in biotransformation and oxidation processes in living organisms. The unique chemical and physical properties attributed to the hydroxyl group make HFAs ideal biomarkers in biomedicine and environmental toxicology, as well as organic geochemistry. The molecular distribution patterns of HFAs can be unique and diagnostic for a given class of organisms, including animals, plants, and microorganisms. Thus, HFAs can act as a valuable proxy for understanding the ecological relationships between different organisms and their environment. Furthermore, HFAs have numerous industrial applications due to their higher reactivity, viscosity, and solvent miscibility. This review paper integrates the latest research on the sources and chemical analyses of HFAs, as well as their applications in industrial/medicinal production and as biomarkers in environmental studies. This review article also provides insights into the biogeochemical cycles of HFAs in the surface Earth system, highlighting the importance of these compounds in understanding the complex interactions between living organisms and the environment.
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Affiliation(s)
- Wenxin Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Wei Hu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin University, Tianjin 300072, China.
| | - Quanfei Zhu
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Mutong Niu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Na An
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yuqi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Kimitaka Kawamura
- Chubu Institute for Advanced Studies, Chubu University, Kasugai 487-8501, Japan
| | - Pingqing Fu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China.
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49
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Salas E, Gorfer M, Bandian D, Eichorst SA, Schmidt H, Horak J, Rittmann SKMR, Schleper C, Reischl B, Pribasnig T, Jansa J, Kaiser C, Wanek W. Reevaluation and novel insights into amino sugar and neutral sugar necromass biomarkers in archaea, bacteria, fungi, and plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167463. [PMID: 37793447 DOI: 10.1016/j.scitotenv.2023.167463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
Abstract
Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42-91% to total AS content, while glucose was the most common NS found, contributing 56-79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively.
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Affiliation(s)
- Erika Salas
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Markus Gorfer
- AIT Austrian Institute of Technology GmbH, Bioresources, Tulln, Austria
| | - Dragana Bandian
- AIT Austrian Institute of Technology GmbH, Bioresources, Tulln, Austria
| | - Stephanie A Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Julia Horak
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Barbara Reischl
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thomas Pribasnig
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Jan Jansa
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Christina Kaiser
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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50
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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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