1
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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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2
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Li W, Liu Q, Qian Y, Wang C, Kong C, Sun L, Sun L, Liu H, Zhang Y, Jiang D, Jiang C, Wang S, Xia P. Adipose triglyceride lipase suppresses noncanonical inflammasome by hydrolyzing LPS. Nat Chem Biol 2024:10.1038/s41589-024-01569-6. [PMID: 38413746 DOI: 10.1038/s41589-024-01569-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 02/04/2024] [Indexed: 02/29/2024]
Abstract
Intracellular recognition of lipopolysaccharide (LPS) by mouse caspase-11 or human caspase-4 is a vital event for the activation of the noncanonical inflammasome. Whether negative regulators are involved in intracellular LPS sensing is still elusive. Here we show that adipose triglyceride lipase (ATGL) is a negative regulator of the noncanonical inflammasome. Through screening for genes participating in the noncanonical inflammasome, ATGL is identified as a negative player for intracellular LPS signaling. ATGL binds LPS and catalyzes the removal of the acylated side chains that contain ester bonds. LPS with under-acylated side chains no longer activates the inflammatory caspases. Cells with ATGL deficiency exhibit enhanced immune responses when encountering intracellular LPS, including an elevated secretion of interleukin-1β, decreased cell viability and increased cell cytotoxicity. Moreover, ATGL-deficient mice show exacerbated responses to endotoxin challenges. Our results uncover that ATGL degrades cytosolic LPS to suppress noncanonical inflammasome activation.
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Affiliation(s)
- Weitao Li
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiannv Liu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Qian
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Chunlei Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Chun Kong
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Liangliang Sun
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jiang
- Department of Sports Medicine, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Sports Injuries, Institute of Sports Medicine of Peking University, Beijing, China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Shuo Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pengyan Xia
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China.
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China.
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3
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Sondhi P, Adeniji T, Lingden D, Stine KJ. Advances in endotoxin analysis. Adv Clin Chem 2024; 118:1-34. [PMID: 38280803 DOI: 10.1016/bs.acc.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
The outer membrane of gram-negative bacteria is primarily composed of lipopolysaccharide (LPS). In addition to protection, LPS defines the distinct serogroups used to identify bacteria specifically. Furthermore, LPS also act as highly potent stimulators of innate immune cells, a phenomenon essential to understanding pathogen invasion in the body. The complex multi-step process of LPS binding to cells involves several binding partners, including LPS binding protein (LBP), CD14 in both membrane-bound and soluble forms, membrane protein MD-2, and toll-like receptor 4 (TLR4). Once these pathways are activated, pro-inflammatory cytokines are eventually expressed. These binding events are also affected by the presence of monomeric or aggregated LPS. Traditional techniques to detect LPS include the rabbit pyrogen test, the monocyte activation test and Limulus-based tests. Modern approaches are based on protein, antibodies or aptamer binding. Recently, novel techniques including electrochemical methods, HPLC, quartz crystal microbalance (QCM), and molecular imprinting have been developed. These approaches often use nanomaterials such as gold nanoparticles, quantum dots, nanotubes, and magnetic nanoparticles. This chapter reviews current developments in endotoxin detection with a focus on modern novel techniques that use various sensing components, ranging from natural biomolecules to synthetic materials. Highly integrated and miniaturized commercial endotoxin detection devices offer a variety of options as the scientific and technologic revolution proceeds.
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Affiliation(s)
- Palak Sondhi
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, Saint Louis, MO, United States
| | - Taiwo Adeniji
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, Saint Louis, MO, United States
| | - Dhanbir Lingden
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, Saint Louis, MO, United States
| | - Keith J Stine
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, Saint Louis, MO, United States.
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4
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553697. [PMID: 37645871 PMCID: PMC10462118 DOI: 10.1101/2023.08.17.553697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
A newly constructed Yersinia pseudotuberculosis mutant (YptbS46) carrying the lpxE insertion and pmrF-J deletion exclusively synthesized an adjuvant form of lipid A, monophosphoryl lipid A (MPLA). Outer membrane vesicles (OMVs) isolated from YptbS46 harboring an lcrV expression plasmid, pSMV13, were designated OMV 46 -LcrV, which contained MPLA and high amounts of LcrV and displayed low activation of Toll-like receptor 4 (TLR4). Similar to the previous OMV 44 -LcrV, intramuscular prime-boost immunization with 30 µg of OMV 46 -LcrV exhibited substantially reduced reactogenicity and conferred complete protection to mice against a high-dose of respiratory Y. pestis challenge. OMV 46 -LcrV immunization induced robust adaptive responses in both lung mucosal and systemic compartments and orchestrated innate immunity in the lung, which were correlated with rapid bacterial clearance and unremarkable lung damage during Y. pestis challenge. Additionally, OMV 46 -LcrV immunization conferred long-term protection. Moreover, immunization with reduced doses of OMV 46 -LcrV exhibited further lower reactogenicity and still provided great protection against pneumonic plague. Our studies strongly demonstrate the feasibility of OMV 46 -LcrV as a new type of plague vaccine candidate.
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5
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Tang W, Osborne J, Dortet L, Larrouy-Maumus G. A whole cell-based Matrix-assisted laser desorption/ionization mass spectrometry lipidomic assay for the discovery of compounds that target lipid a modifications. Front Microbiol 2023; 14:1156795. [PMID: 37138618 PMCID: PMC10149749 DOI: 10.3389/fmicb.2023.1156795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a powerful analytical technique that has been applied to a wide variety of applications ranging from proteomics to clinical diagnostics. One such application is its use as a tool for discovery assays, such as monitoring the inhibition of purified proteins. With the global threat from antimicrobial-resistant (AMR) bacteria, new and innovative solutions are required to identify new molecules that could revert bacterial resistance and/or target virulence factors. Here, we used a whole cell-based MALDI-TOF lipidomic assay using a routine MALDI Biotyper Sirius system operating in linear negative ion mode combined with the MBT Lipid Xtract kit to discover molecules targeting bacteria that are resistant to polymyxins, which are considered last-resort antibiotics. Methods A library of 1200 natural compounds was tested against an E. coli strain expressing mcr-1, which is known to modify lipid A by adding phosphoethanolamine (pETN), making the strain resistant to colistin. Results and Discussion Using this approach, we identified 8 compounds that led to a decrease in this lipid A modification by MCR-1 and could potentially be employed to revert resistance. Taken together, as-proof-of-principle, the data we report here represent a new workflow based on the analysis of bacterial lipid A by routine MALDI-TOF for the discovery of inhibitors that could target bacterial viability and/or virulence.
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Affiliation(s)
- Wenhao Tang
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
| | | | - Laurent Dortet
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique–Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Gerald Larrouy-Maumus
- Faculty of Natural Sciences, Department of Life Sciences, Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
- *Correspondence: Gerald Larrouy-Maumus,
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6
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Milicaj J, Hassan BA, Cote JM, Ramirez-Mondragon CA, Jaunbocus N, Rafalowski A, Patel KR, Castro CD, Muthyala R, Sham YY, Taylor EA. Discovery of first-in-class nanomolar inhibitors of heptosyltransferase I reveals a new aminoglycoside target and potential alternative mechanism of action. Sci Rep 2022; 12:7302. [PMID: 35508636 PMCID: PMC9068772 DOI: 10.1038/s41598-022-10776-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 04/04/2022] [Indexed: 11/08/2022] Open
Abstract
A clinically relevant inhibitor for Heptosyltransferase I (HepI) has been sought after for many years because of its critical role in the biosynthesis of lipopolysaccharides on bacterial cell surfaces. While many labs have discovered or designed novel small molecule inhibitors, these compounds lacked the bioavailability and potency necessary for therapeutic use. Extensive characterization of the HepI protein has provided valuable insight into the dynamic motions necessary for catalysis that could be targeted for inhibition. Structural inspection of Kdo2-lipid A suggested aminoglycoside antibiotics as potential inhibitors for HepI. Multiple aminoglycosides have been experimentally validated to be first-in-class nanomolar inhibitors of HepI, with the best inhibitor demonstrating a Ki of 600 ± 90 nM. Detailed kinetic analyses were performed to determine the mechanism of inhibition while circular dichroism spectroscopy, intrinsic tryptophan fluorescence, docking, and molecular dynamics simulations were used to corroborate kinetic experimental findings. While aminoglycosides have long been described as potent antibiotics targeting bacterial ribosomes' protein synthesis leading to disruption of the stability of bacterial cell membranes, more recently researchers have shown that they only modestly impact protein production. Our research suggests an alternative and novel mechanism of action of aminoglycosides in the inhibition of HepI, which directly leads to modification of LPS production in vivo. This finding could change our understanding of how aminoglycoside antibiotics function, with interruption of LPS biosynthesis being an additional and important mechanism of aminoglycoside action. Further research to discern the microbiological impact of aminoglycosides on cells is warranted, as inhibition of the ribosome may not be the sole and primary mechanism of action. The inhibition of HepI by aminoglycosides may dramatically alter strategies to modify the structure of aminoglycosides to improve the efficacy in fighting bacterial infections.
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Affiliation(s)
- Jozafina Milicaj
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | - Bakar A Hassan
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | - Joy M Cote
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | | | - Nadiya Jaunbocus
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | | | - Kaelan R Patel
- Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Colleen D Castro
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | - Ramaiah Muthyala
- Department of Experimental and Clinical Pharmacology, College Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Yuk Y Sham
- Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, MN, 55455, USA.
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Erika A Taylor
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA.
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7
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Guo H, Zhao T, Huang C, Chen J. The Role of the Two-Component System PhoP/PhoQ in Intrinsic Resistance of Yersinia enterocolitica to Polymyxin. Front Microbiol 2022; 13:758571. [PMID: 35222323 PMCID: PMC8867023 DOI: 10.3389/fmicb.2022.758571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 01/06/2022] [Indexed: 12/02/2022] Open
Abstract
Polymyxin is the “last resort” of antibiotics. The self-induced resistance to polymyxin in Gram-negative bacteria could be mediated by lipopolysaccharide (LPS) modification, which is regulated by the two-component system, PhoP/PhoQ. Yersinia enterocolitica is a common foodborne pathogen. However, PhoP/PhoQ has not been thoroughly studied in Y. enterocolitica. In this study, the functions of PhoP/PhoQ in Y. enterocolitica intrinsic resistance were investigated. The resistance of Y. enterocolitica was found to decrease with the deletion of PhoP/PhoQ. Further, PhoP/PhoQ was found to play an important role in maintaining membrane permeability, intercellular metabolism, and reducing membrane depolarization. Based on subsequent studies, the binding ability of polymyxin to Y. enterocolitica was decreased by the modification of LPS with structures, such as L-Ara4N and palmitate. Analysis of the gene transcription levels revealed that the LPS modification genes, pagP and arn operon, were downregulated with the deletion of PhoP/PhoQ in Y. enterocolitica during exposure to polymyxin. In addition, pmrA, pmrB, and eptA were downregulated in the mutants compared with the wild-type strain. Such findings demonstrate that PhoP/PhoQ contributes to the intrinsic resistance of Y. enterocolitica toward polymyxins. LPS modification with L-Ara4N or palmitate is mainly responsible for the resistance of Y. enterocolitica to polymyxins. The transcription of genes related to LPS modification and PmrA/PmrB can be both affected by PhoP/PhoQ in Y. enterocolitica. This study adds to current knowledge regarding the role of PhoP/PhoQ in intrinsic resistance of Y. enterocolitica to polymyxin.
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8
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Scarbrough BA, Eade CR, Reid AJ, Williams TC, Troutman JM. Lipopolysaccharide Is a 4-Aminoarabinose Donor to Exogenous Polyisoprenyl Phosphates through the Reverse Reaction of the Enzyme ArnT. ACS OMEGA 2021; 6:25729-25741. [PMID: 34632229 PMCID: PMC8495848 DOI: 10.1021/acsomega.1c04036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Indexed: 05/11/2023]
Abstract
Modification of the lipid A portion of LPS with cationic monosaccharides provides resistance to polymyxins, which are often employed as a last resort to treat multidrug-resistant bacterial infections. Here, we describe the use of fluorescent polyisoprenoids, liquid chromatography-mass spectrometry, and bacterial genetics to probe the activity of membrane-localized proteins that utilize the 55-carbon lipid carrier bactoprenyl phosphate (BP). We have discovered that a substantial background reaction occurs when B-strain E. coli cell membrane fractions are supplemented with exogenous BP. This reaction involves proteins associated with the arn operon, which is necessary for the covalent modification of lipid A with the cationic 4-aminoarabinose (Ara4N). Using a series of arn operon gene deletion mutants, we identified that the modification was dependent on ArnC, which is responsible for forming BP-linked Ara4N, or ArnT, which transfers Ara4N to lipid A. Surprisingly, we found that the majority of the Ara4N-modified isoprenoid was due to the reverse reaction catalyzed by ArnT and demonstrate this using heat-inactivated membrane fractions, isolated lipopolysaccharide fractions, and analyses of a purified ArnT. This work provides methods that will facilitate thorough and rapid investigation of bacterial outer membrane remodeling and the evaluation of polyisoprenoid precursors required for covalent glycan modifications.
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Affiliation(s)
- Beth A. Scarbrough
- Nanoscale
Science Program, The University of North
Carolina at Charlotte, Charlotte, North Carolina 28223-0001, United States
| | - Colleen R. Eade
- Department
of Chemistry, The University of North Carolina
at Charlotte, Charlotte, North Carolina 28223-0001, United States
| | - Amanda J. Reid
- Nanoscale
Science Program, The University of North
Carolina at Charlotte, Charlotte, North Carolina 28223-0001, United States
| | - Tiffany C. Williams
- Department
of Chemistry, The University of North Carolina
at Charlotte, Charlotte, North Carolina 28223-0001, United States
| | - Jerry M. Troutman
- Department
of Chemistry, The University of North Carolina
at Charlotte, Charlotte, North Carolina 28223-0001, United States
- Nanoscale
Science Program, The University of North
Carolina at Charlotte, Charlotte, North Carolina 28223-0001, United States
- . Phone: 704-687-5180
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Extraction of ADP-Heptose and Kdo2-Lipid A from E. coli Deficient in the Heptosyltransferase I Gene. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11188314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The enzymes involved in lipopolysaccharide (LPS) biosynthesis, including Heptosyltransferase I (HepI), are critical for maintaining the integrity of the bacterial cell wall, and therefore these LPS biosynthetic enzymes are validated targets for drug discovery to treat Gram-negative bacterial infections. Enzymes involved in the biosynthesis of lipopolysaccharides (LPSs) utilize substrates that are synthetically complex, with numerous stereocenters and site-specific glycosylation patterns. Due to the relatively complex substrate structures, characterization of these enzymes has necessitated strategies to generate bacterial cells with gene disruptions to enable the extraction of these substrates from large scale bacterial growths. Like many LPS biosynthetic enzymes, Heptosyltransferase I binds two substrates: the sugar acceptor substrate, Kdo2-Lipid A, and the sugar donor substrate, ADP-l-glycero-d-manno-heptose (ADPH). HepI characterization experiments require copious amounts of Kdo2-Lipid A and ADPH, and unsuccessful extractions of these two substrates can lead to serious delays in collection of data. While there are papers and theses with protocols for extraction of these substrates, they are often missing small details essential to the success of the extraction. Herein detailed protocols are given for extraction of ADPH and Kdo2-Lipid A (KLA) from E. coli, which have had proven success in the Taylor lab. Key steps in the extraction of ADPH are clearing the extract through ultracentrifugation and keeping all water that touches anything in the extraction, including filters, at a pH of 8.0. Key steps in the extraction of KLA are properly lysing the dried down cells before starting the extraction, maximizing yield by allowing precipitate to form overnight, appropriately washing the pellet with phenol and dissolving the KLA in 1% TEA using visual cues, rather than a specific volume. These protocols led to increased yield and a higher success rate of extractions thereby enabling the characterization of HepI.
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10
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Species-Specific Endotoxin Stimulus Determines Toll-Like Receptor 4- and Caspase 11-Mediated Pathway Activation Characteristics. mSystems 2021; 6:e0030621. [PMID: 34342534 PMCID: PMC8407122 DOI: 10.1128/msystems.00306-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The innate immune system is the body’s first line of defense against pathogens and its protection against infectious diseases. On the surface of host myeloid cells, Toll-like receptor 4 (TLR4) senses lipopolysaccharide (LPS), the major outer membrane component of Gram-negative bacteria. Intracellularly, LPS is recognized by caspase 11 through the noncanonical inflammasome to induce pyroptosis—an inflammatory form of lytic cell death. While TLR4-mediated signaling perturbations result in secretion of cytokines and chemokines that help clear infection and facilitate adaptive immunity, caspase 11-mediated pyroptosis leads to the release of damage-associated molecular patterns and inflammatory mediators. Although the core signaling events and many associated proteins in the TLR4 signaling pathway are known, the complex signaling events and protein networks within the noncanonical inflammasome pathway remain obscure. Moreover, there is mounting evidence for pathogen-specific innate immune tuning. We characterized the major LPS structures from two different pathogens, modeled their binding to the surface receptors, systematically examined macrophage inflammatory responses to these LPS molecules, and surveyed the temporal differences in global protein secretion resulting from TLR4 and caspase 11 activation in macrophages using mass spectrometry (MS)-based quantitative proteomics. This integrated strategy, spanning functional activity assays, top-down structural elucidation of endotoxins, and secretome analysis of stimulated macrophages, allowed us to identify crucial differences in TLR4- and caspase 11-mediated protein secretion in response to two Gram-negative bacterial endotoxins. IMPORTANCE Macrophages and monocytes are innate immune cells playing an important role in orchestrating the initial innate immune response to bacterial infection and the tissue damage. This response is facilitated by specific receptors on the cell surface and intracellularly. One of the bacterial molecules recognized is a Gram-negative bacteria cell wall component, lipopolysaccharide (LPS). The structure of LPS differs between different species. We have characterized the innate immune responses to the LPS molecules from two bacteria, Escherichia coli and Bordetella pertussis, administered either extracellularly or intracellularly, whose structures we first determined. We observed marked differences in the temporal dynamics and amounts of proteins secreted by the innate immune cells stimulated by any of these molecules and routes. This suggests that there is specificity in the first line of response to different Gram-negative bacteria that can be explored to tailor specific therapeutic interventions.
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11
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Liu S, Fang R, Zhang Y, Chen L, Huang N, Yu K, Zhou C, Cao J, Zhou T. Characterization of resistance mechanisms of Enterobacter cloacae Complex co-resistant to carbapenem and colistin. BMC Microbiol 2021; 21:208. [PMID: 34238225 PMCID: PMC8268410 DOI: 10.1186/s12866-021-02250-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 06/04/2021] [Indexed: 11/27/2022] Open
Abstract
Background The emergence of carbapenem-resistant and colistin-resistant ECC pose a huge challenge to infection control. The purpose of this study was to clarify the mechanism of the carbapenems and colistin co-resistance in Enterobacter cloacae Complex (ECC) strains. Results This study showed that the mechanisms of carbapenem resistance in this study are: 1. Generating carbapenemase (7 of 19); 2. The production of AmpC or ESBLs combined with decreased expression of out membrane protein (12 of 19). hsp60 sequence analysis suggested 10 of 19 the strains belong to colistin hetero-resistant clusters and the mechanism of colistin resistance is increasing expression of acrA in the efflux pump AcrAB-TolC alone (18 of 19) or accompanied by a decrease of affinity between colistin and outer membrane caused by the modification of lipid A (14 of 19). Moreover, an ECC strain co-harboring plasmid-mediated mcr-4.3 and blaNDM-1 has been found. Conclusions This study suggested that there is no overlap between the resistance mechanism of co-resistant ECC strains to carbapenem and colistin. However, the emergence of strain co-harboring plasmid-mediated resistance genes indicated that ECC is a potential carrier for the horizontal spread of carbapenems and colistin resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02250-x.
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Affiliation(s)
- Shixing Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Renchi Fang
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Ying Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Na Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Kaihang Yu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Jianming Cao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China.
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12
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Buré C, Le Sénéchal C, Macias L, Tokarski C, Vilain S, Brodbelt JS. Characterization of Isomers of Lipid A from Pseudomonas aeruginosa PAO1 by Liquid Chromatography with Tandem Mass Spectrometry with Higher-Energy Collisional Dissociation and Ultraviolet Photodissociation. Anal Chem 2021; 93:4255-4262. [PMID: 33625828 PMCID: PMC8377747 DOI: 10.1021/acs.analchem.0c05069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipopolysaccharides (LPS) constitute the outermost layer of Gram-negative bacteria and consequently play an important role in bacterial infections. In order to address public health issues posed by Gram-negative bacteria, it is necessary to elucidate the structure of the molecular actors at the forefront of infections. LPS virulence and toxicity are partially modulated by lipid A, a hydrophobic saccharolipid that anchors LPS to the bacterial outer membrane. Understanding the lipid A structure is inherently intertwined with understanding its role as an endotoxin. Accordingly, several successful strategies incorporating tandem mass spectrometry have been applied toward the structural analysis of lipid A. Herein, a shotgun HCD strategy was applied toward the characterization of the lipid A profile of Pseudomonas aeruginosa PAO1. This analysis was enhanced by the development of an LC-MS/MS approach to eliminate isomeric signals in the MS/MS spectra that confounded characterization. Importantly, combining reverse phase chromatography with HCD and ultraviolet photodissociation analyses of the lipid A profile revealed the presence of previously unreported lipid A acyl chain positional isomers. Altogether, these strategies provide the most in-depth structural and molecular characterization of PAO1 lipid A to date.
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Affiliation(s)
- Corinne Buré
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, University of Bordeaux, Bordeaux INP, Bordeaux, Pessac F-33076, France
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Caroline Le Sénéchal
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, University of Bordeaux, Bordeaux INP, Bordeaux, Pessac F-33076, France
| | - Luis Macias
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Caroline Tokarski
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, University of Bordeaux, Bordeaux INP, Bordeaux, Pessac F-33076, France
| | - Sébastien Vilain
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, University of Bordeaux, Bordeaux INP, Bordeaux, Pessac F-33076, France
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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13
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Liao W, Lin J, Jia H, Zhou C, Zhang Y, Lin Y, Ye J, Cao J, Zhou T. Resistance and Heteroresistance to Colistin in Escherichia coli Isolates from Wenzhou, China. Infect Drug Resist 2020; 13:3551-3561. [PMID: 33116674 PMCID: PMC7553605 DOI: 10.2147/idr.s273784] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
Background Colistin is being administered as last-line therapy for patients that have failed to respond to other available antibiotics that are active against Escherichia coli. The underlying mechanisms of colistin resistance and heteroresistance remain largely uncharacterized. The present study investigated the mechanisms of resistance and heteroresistance to colistin in Escherichia coli isolates from Wenzhou, China. Materials and Methods Colistin resistance was detected by the broth microdilution method (BMD). Colistin heteroresistance was determined by population analysis profiles (PAPs). The polymerase chain reaction (PCR) was conducted to detect mcr-1, mcr-2, mcr-3, pmrA, pmrB, phoP, phoQ and mgrB, and quantitative real-time PCR (qRT-PCR) was used to determine the expression levels of mcr-1, pmrC, pmrA and pmrB. Lipid A characterization was conducted by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Results 0.69% (2/291) of Escherichia coli strains were resistant to colistin, whereas the heteroresistance rate reached 1.37% (4/291). mcr-1, the mobile colistin-resistance gene, was present in the two resistant isolates. The substitutions in PmrB were detected in the two heteroresistant isolates. The transcripts levels of the pmrCAB operon were upregulated in two of the heteroresistant isolates. carbonylcyanide m-chlorophenylhydrazone (CCCP) was able to reverse colistin resistance of all isolates tested and exhibited a significantly higher effect on colistin-heteroresistant isolates. MALDI-TOF MS indicated that the additional phosphoethanolamine (PEtn) moieties in lipid A profiles were present both in colistin-resistant and heteroresistant isolates. Conclusion The present study was the first to investigate the differential mechanisms between colistin resistance and heteroresistance. The development of colistin heteroresistance should be addressed in future clinical surveillance.
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Affiliation(s)
- Wenli Liao
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Jie Lin
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Huaiyu Jia
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Ying Zhang
- Department of Medical Laboratory Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Yishuai Lin
- Department of Medical Laboratory Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Jianzhong Ye
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Jianming Cao
- Department of Medical Laboratory Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
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14
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McConville TH, Annavajhala MK, Giddins MJ, Macesic N, Herrera CM, Rozenberg FD, Bhushan GL, Ahn D, Mancia F, Trent MS, Uhlemann AC. CrrB Positively Regulates High-Level Polymyxin Resistance and Virulence in Klebsiella pneumoniae. Cell Rep 2020; 33:108313. [PMID: 33113377 PMCID: PMC7656232 DOI: 10.1016/j.celrep.2020.108313] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
Polymyxin resistance (PR) threatens the treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP) infections. PR frequently arises through chemical modification of the lipid A portion of lipopolysaccharide. Various mutations are implicated in PR, including in three two-component systems—CrrA/B, PmrA/B, and PhoP/Q—and the negative regulator MgrB. Few have been functionally validated. Therefore, here we adapt a CRISPR-Cas9 system to CRKP to elucidate how mutations in clinical CRKP isolates induce PR. We demonstrate that CrrB is a positive regulator of PR, and common clinical mutations lead to the addition of both 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosophethanolamine (pEtN) to lipid A, inducing notably higher polymyxin minimum inhibitory concentrations than mgrB disruption. Additionally, crrB mutations cause a significant virulence increase at a fitness cost, partially from activation of the pentose phosphate pathway. Our data demonstrate the importance of CrrB in high-level PR and establish important differences across crrB alleles in balancing resistance with fitness and virulence. McConville et al. leverage CRISPR-Cas to demonstrate that mutations in crrB induce high-level polymyxin resistance in Klebsiella pneumoniae via the addition of L-Ara4N and pEtN to lipid A. CrrB mutations also increase virulence while conferring a fitness cost and alter carbon metabolism through activation of the pentose phosphate pathway.
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Affiliation(s)
- Thomas H McConville
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Medini K Annavajhala
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Marla J Giddins
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nenad Macesic
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, 3004 VIC, Australia
| | - Carmen M Herrera
- Departments of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Felix D Rozenberg
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gitanjali L Bhushan
- Division of Pediatric Critical Care, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Danielle Ahn
- Division of Pediatric Critical Care, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology, Columbia University, New York, NY 10032, USA
| | - M Stephen Trent
- Departments of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
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15
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Clairfeuille T, Buchholz KR, Li Q, Verschueren E, Liu P, Sangaraju D, Park S, Noland CL, Storek KM, Nickerson NN, Martin L, Dela Vega T, Miu A, Reeder J, Ruiz-Gonzalez M, Swem D, Han G, DePonte DP, Hunter MS, Gati C, Shahidi-Latham S, Xu M, Skelton N, Sellers BD, Skippington E, Sandoval W, Hanan EJ, Payandeh J, Rutherford ST. Structure of the essential inner membrane lipopolysaccharide-PbgA complex. Nature 2020; 584:479-483. [PMID: 32788728 DOI: 10.1038/s41586-020-2597-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Lipopolysaccharide (LPS) resides in the outer membrane of Gram-negative bacteria where it is responsible for barrier function1,2. LPS can cause death as a result of septic shock, and its lipid A core is the target of polymyxin antibiotics3,4. Despite the clinical importance of polymyxins and the emergence of multidrug resistant strains5, our understanding of the bacterial factors that regulate LPS biogenesis is incomplete. Here we characterize the inner membrane protein PbgA and report that its depletion attenuates the virulence of Escherichia coli by reducing levels of LPS and outer membrane integrity. In contrast to previous claims that PbgA functions as a cardiolipin transporter6-9, our structural analyses and physiological studies identify a lipid A-binding motif along the periplasmic leaflet of the inner membrane. Synthetic PbgA-derived peptides selectively bind to LPS in vitro and inhibit the growth of diverse Gram-negative bacteria, including polymyxin-resistant strains. Proteomic, genetic and pharmacological experiments uncover a model in which direct periplasmic sensing of LPS by PbgA coordinates the biosynthesis of lipid A by regulating the stability of LpxC, a key cytoplasmic biosynthetic enzyme10-12. In summary, we find that PbgA has an unexpected but essential role in the regulation of LPS biogenesis, presents a new structural basis for the selective recognition of lipids, and provides opportunities for future antibiotic discovery.
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Affiliation(s)
| | - Kerry R Buchholz
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Qingling Li
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Erik Verschueren
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Peter Liu
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Dewakar Sangaraju
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA, USA
| | - Summer Park
- Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Cameron L Noland
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | | | - Lynn Martin
- BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Trisha Dela Vega
- BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Anh Miu
- Biochemical & Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Janina Reeder
- Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Maria Ruiz-Gonzalez
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Danielle Swem
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Guanghui Han
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cornelius Gati
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Stanford University, Department of Structural Biology, Stanford, CA, USA
| | | | - Min Xu
- Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas Skelton
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin D Sellers
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Elizabeth Skippington
- Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Emily J Hanan
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA.
| | - Jian Payandeh
- Structural Biology, Genentech Inc., South San Francisco, CA, USA. .,Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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16
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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17
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Chen L, Lin J, Lu H, Zhang X, Wang C, Liu H, Zhang X, Li J, Cao J, Zhou T. Deciphering colistin heteroresistance in Acinetobacter baumannii clinical isolates from Wenzhou, China. J Antibiot (Tokyo) 2020; 73:463-470. [DOI: 10.1038/s41429-020-0289-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/01/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
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18
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Zhu L, Zhou Z, Liu Y, Lin Z, Shuai X, Xu L, Chen H. Comprehensive Understanding of the Plasmid-Mediated Colistin Resistance Gene mcr-1 in Aquatic Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1603-1613. [PMID: 31886662 DOI: 10.1021/acs.est.9b05919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The emergence of plasmid-mediated colistin resistance gene mcr-1 has attracted global attention and raised serious concerns about its possible cross-environment dissemination. However, the systematic exploration of mcr-1 both by monitoring and genetic dissection in aquatic environments has not been conducted. This study addresses the gap related to the occurrence and distribution of mcr-1 in watersheds, eastern China. The results showed an abundance of mcr-1 gene in four watersheds, and the highest level of mcr-1 reached 1.8 × 109 gene copies per liter of water. Furthermore, the transfer frequencies of the plasmids in isolated Escherichia coli were 2.76 × 10-6-6.11 × 10-4 within genera and minimal inhibitory concentrations of polymyxin resistance were 8-16 mg/L for transconjugants. Mass spectrometry data allowed visualization of the function of mcr-1 expression, rendering bacterial resistance to colistin. The genetic details of six mcr-1-harboring plasmids in E. coli isolates of aquatic origin were obtained by single-molecule real-time sequencing. These plasmids were closely associated with E. coli strains of pig and human origin, supporting the concept of mcr-1 dissemination across natural environments, livestock farms, and humans. In conclusion, this study provides the first glimpse of the profile of mcr-1-harboring plasmids and their genetic environment in aquatic ecosystems.
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Affiliation(s)
- Lin Zhu
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Yang Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Lan Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , China
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19
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Resistance and Heteroresistance to Colistin in Pseudomonas aeruginosa Isolates from Wenzhou, China. Antimicrob Agents Chemother 2019; 63:AAC.00556-19. [PMID: 31383654 DOI: 10.1128/aac.00556-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/28/2019] [Indexed: 01/26/2023] Open
Abstract
The goal was to investigate the mechanisms of colistin resistance and heteroresistance in Pseudomonas aeruginosa clinical isolates. Colistin resistance was determined by the broth microdilution method. Colistin heteroresistance was evaluated by population analysis profiling. Time-kill assays were also conducted. PCR sequencing was performed to detect the resistance genes among (hetero)resistant isolates, and quantitative real-time PCR assays were performed to determine their expression levels. Pulsed-field gel electrophoresis and multilocus sequence typing were performed. Lipid A characteristics were determined via matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS). Two resistant isolates and 9 heteroresistant isolates were selected in this study. Substitutions in PmrB were detected in 2 resistant isolates. Among heteroresistant isolates, 8 of 9 heteroresistant isolates had nonsynonymous PmrB substitutions, and 2 isolates, including 1 with a PmrB substitution, had PhoQ alterations. Correspondingly, the expression levels of pmrA or phoP were upregulated in PmrB- or PhoQ-substituted isolates. One isolate also found alterations in ParRS and CprRS. The transcript levels of the pmrH gene were observed to increase across all investigated isolates. MALDI-TOF MS showed additional 4-amino-4-deoxy-l-arabinose (l-Ara4N) moieties in lipid A profiles in (hetero)resistant isolates. In conclusion, both colistin resistance and heteroresistance in P. aeruginosa in this study mainly involved alterations of the PmrAB regulatory system. There were strong associations between mutations in specific genetic loci for lipid A synthesis and regulation of modifications to lipid A. The transition of colistin heteroresistance to resistance should be addressed in future clinical surveillance.
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20
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Powers MJ, Herrera CM, Tucker AT, Davies BW, Trent MS. Isolation of Lipid Cell Envelope Components from Acinetobacter baumannii. Methods Mol Biol 2019; 1946:233-252. [PMID: 30798560 DOI: 10.1007/978-1-4939-9118-1_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
With the increasing occurrence of antibiotic resistance among Acinetobacter sp., the race is on for researchers to not only isolate resistant isolates but also utilize basic and applied microbiological techniques to study mechanisms of resistance. For many antibiotics, the limit of efficacy against Gram-negative bacteria is dependent on its ability to permeate the outer membrane and access its target. As such, it is critical that researchers be able to isolate and analyze the lipid components of the cell envelope from any number of Acinetobacter sp. that are either resistant or sensitive to antibiotics of interest. The following chapter provides in-depth protocols to confirm the presence or absence of lipooligosaccharide (LOS) in Acinetobacter sp., isolate lipid A, and glycerophospholipids and analyze them using qualitative (mass spectrometry) and semiquantitative (thin-layer chromatography) methods.
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Affiliation(s)
- Matthew J Powers
- Department of Microbiology, University of Georgia, Athens, GA, USA.,Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Carmen M Herrera
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Ashley T Tucker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.,John Ring LaMontagne Center for Infectious Diseases, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - M Stephen Trent
- Department of Microbiology, University of Georgia, Athens, GA, USA. .,Department of Infectious Diseases, University of Georgia, Athens, GA, USA.
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21
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Tolefree JA, Garcia AJ, Farrell J, Meadows V, Kennedy L, Hargrove L, Demieville J, Francis N, Mirabel J, Francis H. Alcoholic liver disease and mast cells: What's your gut got to do with it? LIVER RESEARCH 2019. [DOI: 10.1016/j.livres.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Molecular Insights into Functional Differences between mcr-3- and mcr-1-Mediated Colistin Resistance. Antimicrob Agents Chemother 2018; 62:AAC.00366-18. [PMID: 29987148 DOI: 10.1128/aac.00366-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/27/2018] [Indexed: 11/20/2022] Open
Abstract
The global emergence of plasmid-mediated colistin resistance genes mcr-1 and mcr-3 has threatened the role of the "last-resort" drug colistin in the defense against infections caused by multidrug-resistant Gram-negative bacteria. However, functional differences between these two genes in mediating colistin resistance remain poorly understood. Protein sequence alignment of MCR-3 and MCR-1 was therefore conducted in Clustal Omega to identify sequence divergence. The molecular recognition of lipid A head group phosphatidylethanolamine and MCR-3 enzyme was studied by homology modeling and molecular docking, with the catalytic mechanism of MCR-3 also being explored. Thr277 in MCR-3 was validated as the key amino acid residue responsible for the catalytic reaction using site-directed mutagenesis and was shown to act as a nucleophile. Lipid A modification induced by the MCR-3 and MCR-1 enzymes was confirmed by electrospray ionization-time of flight mass spectrometry. Far-UV circular dichroism spectra of the MCR-3 and MCR-1 enzymes suggested that MCR-3 was more thermostable than MCR-1, with a melting temperature of 66.19°C compared with 61.14°C for MCR-1. These data provided molecular insight into the functional differences between mcr-3 and mcr-1 in conferring colistin resistance.
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23
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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24
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Crittenden CM, Herrera CM, Williams PE, Ricci DP, Swem LR, Trent MS, Brodbelt JS. Mapping phosphate modifications of substituted lipid A via a targeted MS 3 CID/UVPD strategy. Analyst 2018; 143:3091-3099. [PMID: 29881855 PMCID: PMC6019210 DOI: 10.1039/c8an00561c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Structural characterization of lipid A from Gram-negative bacteria remains a significant challenge, especially with respect to localizing modifications of the phosphate groups typically found on the reducing and non-reducing ends of the β-1',6-linked glucosamine disaccharide backbone of lipid A. As reported here, combining traditional collisional activated dissociation (CAD) and ultraviolet photodissociation (UVPD) in a hybrid MS3 approach facilitates identification and localization of substituents of the phosphate groups. The focus is on rapid identification and characterization of substituted lipid A species with specific emphasis on the modifications on the 1 and 4' phosphate moieties. Mapping these modifications, typically ones that modify the surface charges of lipopolysaccharides, is particularly important owing to the impact of these types of modifications on antibiotic resistance. The presence of phosphoethanolamine, aminoarabinose, and galactosamine moieties in hexaacylated and heptaacylated lipid A species, including ones from Enterobacter cloacae and Acinetobacter baumannii, are characterized using a targeted MS3 strategy to identify glycosidic product ions (1,5X1 and 0,4A2, typically) which allow localization of the substituents.
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Almostafa M, Fridgen TD, Banoub JH. Structural investigation by tandem mass spectrometry analysis of a heterogeneous mixture of Lipid A n isolated from the lipopolysaccharide of Aeromonas hydrophila SJ-55Ra. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:167-183. [PMID: 29065225 DOI: 10.1002/rcm.8017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/15/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE We report herein the electrospray ionization mass spectrometry (ESI-MS) negative ion mode and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS) analysis of a mixture of lipid An isolated from the lipopolysaccharide (LPS) of a rough-resistant wild strain of the Gram-negative bacteria Aeromonas hydrophila grown in the presence of phages (SJ-55Ra). This investigation indicates that the presence of a mixture of lipid A acylated disaccharides, whose molecular structures were not relatively conserved, resulted from the incomplete LPS biosynthesis caused by the phage treatment. METHODS The heterogeneous lipid An mixture from the LPS-SJ55Ra was obtained following growth of the Gram-negative bacteria Aeromonas hydrophila (SJ-55R) in the presence of phages and isolation by the aqueous phenol method. Following hydrolysis and purification of the lipopolysaccharide, ESI-MS and low-energy CID-MS/MS analyses were performed on a triple-quadrupole (QqQ) and a Fourier transform ion cyclotron resonance (FTICR) instrument. RESULTS ESI-MS analysis suggested that this lipid An mixture contained eight molecular disaccharide anions and three monosaccharide anions. This series of lipid An was asymmetrically substituted with ((R)-14:0(3-OH)) fatty acids located at O-3 and N-2 and with branched fatty acids: (Cl4:0(3-(R)-O-C14:0)) and (C12:0(3-(R)-O-(14:0)) at the O-3' and N-2' positions. CONCLUSIONS Tandem mass spectrometric analyses allowed the exact determination of the fatty acid acylation locations on the D-GlcpN disaccharide. The MS/MS results established that it was possible to selectively cleave C-O, C-N, and C-C bonds, together with glycosidic C-O and cross-ring cleavages, affording excellent structural analysis of lipid A biomolecules.
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Affiliation(s)
- Mervt Almostafa
- Chemistry Department, Memorial University of Newfoundland, St. John's, Canada
| | - Travis D Fridgen
- Chemistry Department, Memorial University of Newfoundland, St. John's, Canada
| | - Joseph H Banoub
- Chemistry Department, Memorial University of Newfoundland, St. John's, Canada
- Special Projects, Science Branch, Department of Fisheries and Oceans Canada, St. John's, Canada
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Yang Q, Li M, Spiller OB, Andrey DO, Hinchliffe P, Li H, MacLean C, Niumsup P, Powell L, Pritchard M, Papkou A, Shen Y, Portal E, Sands K, Spencer J, Tansawai U, Thomas D, Wang S, Wang Y, Shen J, Walsh T. Balancing mcr-1 expression and bacterial survival is a delicate equilibrium between essential cellular defence mechanisms. Nat Commun 2017; 8:2054. [PMID: 29233990 PMCID: PMC5727292 DOI: 10.1038/s41467-017-02149-0] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/09/2017] [Indexed: 12/20/2022] Open
Abstract
MCR-1 is a lipid A modifying enzyme that confers resistance to the antibiotic colistin. Here, we analyse the impact of MCR-1 expression on E. coli morphology, fitness, competitiveness, immune stimulation and virulence. Increased expression of mcr-1 results in decreased growth rate, cell viability, competitive ability and significant degradation in cell membrane and cytoplasmic structures, compared to expression of catalytically inactive MCR-1 (E246A) or MCR-1 soluble component. Lipopolysaccharide (LPS) extracted from mcr-1 strains induces lower production of IL-6 and TNF, when compared to control LPS. Compared to their parent strains, high-level colistin resistance mutants (HLCRMs) show reduced fitness (relative fitness is 0.41-0.78) and highly attenuated virulence in a Galleria mellonella infection model. Furthermore, HLCRMs are more susceptible to most antibiotics than their respective parent strains. Our results show that the bacterium is challenged to find a delicate equilibrium between expression of MCR-1-mediated colistin resistance and minimalizing toxicity and thus ensuring cell survival.
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Affiliation(s)
- Qiue Yang
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Mei Li
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Owen B Spiller
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Diego O Andrey
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
- Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, 1211, Geneva, Switzerland
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Hui Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, 100013, China
| | - Craig MacLean
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Pannika Niumsup
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Lydia Powell
- Advanced Therapies Group, Oral and Biomedical Sciences, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Manon Pritchard
- Advanced Therapies Group, Oral and Biomedical Sciences, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrei Papkou
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Yingbo Shen
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Edward Portal
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Kirsty Sands
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Uttapoln Tansawai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - David Thomas
- Advanced Therapies Group, Oral and Biomedical Sciences, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Shaolin Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yang Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Timothy Walsh
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK.
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Crittenden CM, Akin LD, Morrison LJ, Trent MS, Brodbelt JS. Characterization of Lipid A Variants by Energy-Resolved Mass Spectrometry: Impact of Acyl Chains. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1118-1126. [PMID: 27966172 PMCID: PMC5438766 DOI: 10.1007/s13361-016-1542-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/19/2016] [Accepted: 10/24/2016] [Indexed: 05/04/2023]
Abstract
Lipid A molecules consist of a diglucosamine sugar core with a number of appended acyl chains that vary in their length and connectivity. Because of the challenging nature of characterizing these molecules and differentiating between isomeric species, an energy-resolved MS/MS strategy was undertaken to track the fragmentation trends and map genealogies of product ions originating from consecutive cleavages of acyl chains. Generalizations were developed based on the number and locations of the primary and secondary acyl chains as well as variations in preferential cleavages arising from the location of the phosphate groups. Secondary acyl chain cleavage occurs most readily for lipid A species at the 3' position, followed by primary acyl chain fragmentation at both the 3' and 3 positions. In the instances of bisphosphorylated lipid A variants, phosphate loss occurs readily in conjunction with the most favorable primary and secondary acyl chain cleavages. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Lucas D Akin
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | | | - M Stephen Trent
- Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
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Abstract
Antibiotic resistance is a prevalent problem in public health worldwide. In general, the carbapenem β-lactam antibiotics are considered a final resort against lethal infections by multidrug-resistant bacteria. Colistin is a cationic polypeptide antibiotic and acts as the last line of defense for treatment of carbapenem-resistant bacteria. Very recently, a new plasmid-borne colistin resistance gene, mcr-2, was revealed soon after the discovery of the paradigm gene mcr-1, which has disseminated globally. However, the molecular mechanisms for MCR-2 colistin resistance are poorly understood. Here we show a unique transposon unit that facilitates the acquisition and transfer of mcr-2 Evolutionary analyses suggested that both MCR-2 and MCR-1 might be traced to their cousin phosphoethanolamine (PEA) lipid A transferase from a known polymyxin producer, Paenibacillus Transcriptional analyses showed that the level of mcr-2 transcripts is relatively higher than that of mcr-1 Genetic deletions revealed that the transmembrane regions (TM1 and TM2) of both MCR-1 and MCR-2 are critical for their location and function in bacterial periplasm, and domain swapping indicated that the TM2 is more efficient than TM1. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) confirmed that all four MCR proteins (MCR-1, MCR-2, and two chimeric versions [TM1-MCR-2 and TM2-MCR-1]) can catalyze chemical modification of lipid A moiety anchored on lipopolysaccharide (LPS) with the addition of phosphoethanolamine to the phosphate group at the 4' position of the sugar. Structure-guided site-directed mutagenesis defined an essential 6-residue-requiring zinc-binding/catalytic motif for MCR-2 colistin resistance. The results further our mechanistic understanding of transferable colistin resistance, providing clues to improve clinical therapeutics targeting severe infections by MCR-2-containing pathogens.IMPORTANCE Carbapenem and colistin are the last line of refuge in fighting multidrug-resistant Gram-negative pathogens. MCR-2 is a newly emerging variant of the mobilized colistin resistance protein MCR-1, posing a potential challenge to public health. Here we report transfer of the mcr-2 gene by a unique transposal event and its possible origin. Distribution of MCR-2 in bacterial periplasm is proposed to be a prerequisite for its role in the context of biochemistry and the colistin resistance. We also define the genetic requirement of a zinc-binding/catalytic motif for MCR-2 colistin resistance. This represents a glimpse of transferable colistin resistance by MCR-2.
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Wacker MA, Teghanemt A, Weiss JP, Barker JH. High-affinity caspase-4 binding to LPS presented as high molecular mass aggregates or in outer membrane vesicles. Innate Immun 2017; 23:336-344. [PMID: 28409545 DOI: 10.1177/1753425917695446] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Caspases of the non-canonical inflammasome (caspases -4, -5, and -11) directly bind endotoxin (LOS/LPS) and can be activated in the absence of any co-factors. Models of LPS-induced caspase activation have postulated that 1:1 binding of endotoxin monomers to caspase trigger caspase oligomerization and activation, analogous to that established for endotoxin-induced activation of MD-2/TLR4. However, using metabolically radiolabeled LOS and LPS, we now show high affinity and selective binding of caspase-4 to high molecular mass aggregates of purified endotoxin and to endotoxin-rich outer membrane vesicles without formation of 1:1 endotoxin:caspase complexes. Thus, our findings demonstrate markedly different endotoxin recognition properties of caspase-4 from that of MD-2/TLR4 and strongly suggest that activation of caspase-4 (and presumably caspase-5 and caspase-11) are mediated by interactions with activating endotoxin-rich membrane interfaces rather than by endotoxin monomers.
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Affiliation(s)
- Mark A Wacker
- 1 Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
| | - Athmane Teghanemt
- 2 Inflammation Program, University of Iowa, and Iowa City VA Health Care System, Iowa City, IA, USA.,3 Department of Internal Medicine, University of Iowa, and Iowa City VA Health Care System, Iowa City, IA, USA
| | - Jerrold P Weiss
- 2 Inflammation Program, University of Iowa, and Iowa City VA Health Care System, Iowa City, IA, USA.,3 Department of Internal Medicine, University of Iowa, and Iowa City VA Health Care System, Iowa City, IA, USA.,4 Department of Microbiology, University of Iowa, and Iowa City VA Health Care System, Iowa City, IA, USA
| | - Jason H Barker
- 2 Inflammation Program, University of Iowa, and Iowa City VA Health Care System, Iowa City, IA, USA.,3 Department of Internal Medicine, University of Iowa, and Iowa City VA Health Care System, Iowa City, IA, USA.,4 Department of Microbiology, University of Iowa, and Iowa City VA Health Care System, Iowa City, IA, USA
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30
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Morrison LJ, Parker WR, Holden DD, Henderson JC, Boll JM, Trent MS, Brodbelt JS. UVliPiD: A UVPD-Based Hierarchical Approach for De Novo Characterization of Lipid A Structures. Anal Chem 2016; 88:1812-20. [PMID: 26728944 DOI: 10.1021/acs.analchem.5b04098] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The lipid A domain of the endotoxic lipopolysaccharide layer of Gram-negative bacteria is comprised of a diglucosamine backbone to which a variable number of variable length fatty acyl chains are anchored. Traditional characterization of these tails and their linkages by nuclear magnetic resonance (NMR) or mass spectrometry is time-consuming and necessitates databases of pre-existing structures for structural assignment. Here, we introduce an automated de novo approach for characterization of lipid A structures that is completely database-independent. A hierarchical decision-tree MS(n) method is used in conjunction with a hybrid activation technique, UVPDCID, to acquire characteristic fragmentation patterns of lipid A variants from a number of Gram-negative bacteria. Structural assignments are derived from integration of key features from three to five spectra and automated interpretation is achieved in minutes without the need for pre-existing information or candidate structures. The utility of this strategy is demonstrated for a mixture of lipid A structures from an enzymatically modified E. coli lipid A variant. A total of 27 lipid A structures were discovered, many of which were isomeric, showcasing the need for a rapid de novo approach to lipid A characterization.
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Affiliation(s)
- Lindsay J Morrison
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - W Ryan Parker
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Dustin D Holden
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Jeremy C Henderson
- Department of Infectious Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - Joseph M Boll
- Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - M Stephen Trent
- Department of Infectious Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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31
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Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. PLoS Comput Biol 2015; 11:e1004400. [PMID: 26275208 PMCID: PMC4537216 DOI: 10.1371/journal.pcbi.1004400] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/11/2015] [Indexed: 12/29/2022] Open
Abstract
How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E. coli in stationary phase as a result of being starved for glucose, not on the genetic adaptation of E. coli to utilize alternative nutrients. In our analysis, we have taken advantage of the temporal correlations within and among RNA and protein abundances to identify systematic trends in gene regulation. Specifically, we have developed a general computational strategy for classifying expression-profile time courses into distinct categories in an unbiased manner. We have also developed, from dynamic models of gene expression, a framework to characterize protein degradation patterns based on the observed temporal relationships between mRNA and protein abundances. By comparing and contrasting our transcriptomic and proteomic data, we have identified several broad physiological trends in the E. coli starvation response. Strikingly, mRNAs are widely down-regulated in response to glucose starvation, presumably as a strategy for reducing new protein synthesis. By contrast, protein abundances display more varied responses. The abundances of many proteins involved in energy-intensive processes mirror the corresponding mRNA profiles while proteins involved in nutrient metabolism remain abundant even though their corresponding mRNAs are down-regulated. Bacteria frequently experience starvation conditions in their natural environments. Yet how they modify their physiology in response to these conditions remains poorly understood. Here, we performed a detailed, two-week starvation experiment in E. coli. We exhaustively monitored changes in cellular components, such as RNA and protein abundances, over time. We subsequently compared and contrasted these measurements using novel computational approaches we developed specifically for analyzing gene-expression time-course data. Using these approaches, we could identify systematic trends in the E. coli starvation response. In particular, we found that cells systematically limit mRNA and protein production, degrade proteins involved in energy-intensive processes, and maintain or increase the amount of proteins involved in energy production. Thus, the bacteria assume a cellular state in which their ongoing energy use is limited while they are poised to take advantage of any nutrients that may become available.
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Affiliation(s)
- John R. Houser
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Craig Barnhart
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Daniel R. Boutz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Sean M. Carroll
- Department of Organismic and Evolutionary Biology, Harvard University, Boston, Massachusetts, United States of America
| | - Aurko Dasgupta
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Joshua K. Michener
- Department of Organismic and Evolutionary Biology, Harvard University, Boston, Massachusetts, United States of America
| | - Brittany D. Needham
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Ophelia Papoulas
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Viswanadham Sridhara
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
| | - Dariya K. Sydykova
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Boston, Massachusetts, United States of America
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Boston, Massachusetts, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - M. Stephen Trent
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Jeffrey E. Barrick
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (JEB); (EMM); (COW)
| | - Edward M. Marcotte
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (JEB); (EMM); (COW)
| | - Claus O. Wilke
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (JEB); (EMM); (COW)
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Nowicki EM, O'Brien JP, Brodbelt JS, Trent MS. Extracellular zinc induces phosphoethanolamine addition to Pseudomonas aeruginosa lipid A via the ColRS two-component system. Mol Microbiol 2015; 97:166-78. [PMID: 25846400 DOI: 10.1111/mmi.13018] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2015] [Indexed: 01/01/2023]
Abstract
Gram-negative bacteria survive harmful environmental stressors by modifying their outer membrane. Much of this protection is afforded upon remodeling of the lipid A region of the major surface molecule lipopolysaccharide (LPS). For example, the addition of cationic substituents, such as 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoehthanolamine (pEtN) at the lipid A phosphate groups, is often induced in response to specific environmental flux stabilizing the outer membrane. The work herein represents the first report of pEtN addition to Pseudomonas aeruginosa lipid A. We have identified the key pEtN transferase which we named EptAPa and characterized its strict activity on only one position of lipid A, contrasting from previously studied EptA enzymes. We further show that transcription of eptAP a is regulated by zinc via the ColRS two-component system instead of the PmrAB system responsible for eptA regulation in E. coli and Salmonella enterica. Further, although L-Ara4N is readily added to the same position of lipid A as pEtN under certain environmental conditions, ColR specifically induces pEtN addition to lipid A in lieu of L-Ara4N when Zn2+ is present. The unique, specific regulation of eptAP a transcription and enzymatic activity described in this work demonstrates the tight yet inducible control over LPS modification in P. aeruginosa.
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Affiliation(s)
- Emily M Nowicki
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - John P O'Brien
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | | | - M Stephen Trent
- Department of Infectious Diseases, University of Georgia, College of Veterinary Medicine, Athens, GA, USA
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33
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Badmasti F, Shahcheraghi F, Siadat SD, Bouzari S, Ajdary S, Amin M, Halabian R, Imani Fooladi AA. Heterologous Expression of 3-O-Deacylase in Acinetobacter baumannii Modulates the Endotoxicity of Lipopolysaccharide. J Mol Microbiol Biotechnol 2015; 25:37-44. [DOI: 10.1159/000371815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The lipopolysaccharide (LPS) of <i>Acinetobacter baumannii</i> is a potent stimulator of proinflammatory cytokines, such as interleukin-6 (IL-6). The 3-O-deacylase (PagL)-modifying enzyme that removes the 3-O-linked acyl chain from the disaccharide backbone of lipid A provides the opportunity to develop a new therapeutic compound that could reduce detrimental inflammatory responses. The plasmid pMMB66EH-PagL obtained by recombinant DNA technology was electroporated into <i>A. baumannii</i> ATCC 19606. Compared with wild-type LPS, outer membrane vesicles and inactivated whole cells of engineered bacteria had a statistically significant decreased ability to produce IL-6. Structural analysis of lipid A by negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry revealed that the profile of lipid A fractions under PagL expression was changed. Taken together, our data showed that recombinant penta-acylated lipid A had less immunoreactivity and that the tetra-acylated version of lipid A with TLR4 antagonist activity decreased the induction of IL-6 production in the murine macrophage cell line J774 A.1.
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34
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O'Brien JP, Needham BD, Brown DB, Trent MS, Brodbelt JS. Top-Down Strategies for the Structural Elucidation of Intact Gram-negative Bacterial Endotoxins. Chem Sci 2014; 5:4291-4301. [PMID: 25386333 PMCID: PMC4224326 DOI: 10.1039/c4sc01034e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Re-modelling of lipopolysaccharides, which are the primary constituent of the outer cell membrane of Gram-negative bacteria, modulates pathogenesis and resistance to microbials. Reported herein is the characterization of intact Gram-negative bacterial lipooligosaccharides (LOS) via a new strategy utilizing online liquid chromatography (LC) coupled with ultraviolet photodissociation (UVPD) mass spectrometry. Compared to collision-based MS/MS methods, UVPD and UVPD/HCD promoted a greater array of cleavages within both the glycan and lipid moieties, including C-C, C-N, C-O cleavages in the acyl chains as well as glycosidic and cross-ring cleavages, thus providing the most far-reaching structural characterization of LOS. This LC-MS/MS strategy affords a robust analytical method to structurally characterize complex mixtures of bacterial endotoxins that maintains the integrity of the core oligosaccharide and lipid A domains of LOS, providing direct feedback about the cell envelope architectures and LOS modification strategies involved in resistance host innate immune defense.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
| | - Brittany D Needham
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - Dusty B Brown
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - M Stephen Trent
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
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35
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Nowicki EM, O'Brien JP, Brodbelt JS, Trent MS. Characterization of Pseudomonas aeruginosa LpxT reveals dual positional lipid A kinase activity and co-ordinated control of outer membrane modification. Mol Microbiol 2014; 94:728-41. [PMID: 25223756 DOI: 10.1111/mmi.12796] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2014] [Indexed: 01/01/2023]
Abstract
Gram-negative bacteria have evolved modification machinery to promote a dynamic outer membrane in response to a continually fluctuating environment. The kinase LpxT, for example, adds a phosphate group to the lipid A moiety of some Gram-negatives including Escherichia coli and Salmonella enterica. LpxT activity is inhibited under conditions that compromise membrane integrity, resulting instead in the addition of positively charged groups to lipid A that increase membrane stability and provide resistance to cationic antimicrobial peptides. We have now identified a functional lpxT orthologue in P. aeruginosa. LpxTPa has unique enzymatic characteristics, as it is able to phosphorylate P. aeruginosa lipid A at two sites of the molecule. Surprisingly, a previously uncharacterized lipid A 4'-dephospho-1-triphosphate species was detected. LpxTPa activity is inhibited by magnesium independently of lpxTPa transcription. Modulation of LpxTPa activity is influenced by transcription of the lipid A aminoarabinose transferase ArnT, known to be activated in response to limiting magnesium. These results demonstrate a divergent activity of LpxTPa , and suggest the existence of a co-ordinated regulatory mechanism that permits adaptation to a changing environment.
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Affiliation(s)
- Emily M Nowicki
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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