1
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Padhy I, Dwibedy SK, Mohapatra SS. A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development. Microbiol Res 2024; 283:127679. [PMID: 38508087 DOI: 10.1016/j.micres.2024.127679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India.
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2
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Materon IC, Palzkill T. Structural biology of MCR-1-mediated resistance to polymyxin antibiotics. Curr Opin Struct Biol 2023; 82:102647. [PMID: 37399693 PMCID: PMC10527939 DOI: 10.1016/j.sbi.2023.102647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023]
Abstract
Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and structural analysis concerning residues important for substrate binding in MCR-1, and finally, advancements in inhibitors targeting MCR-1.
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Affiliation(s)
- Isabel Cristina Materon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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3
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Thai VC, Stubbs KA, Sarkar-Tyson M, Kahler CM. Phosphoethanolamine Transferases as Drug Discovery Targets for Therapeutic Treatment of Multi-Drug Resistant Pathogenic Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:1382. [PMID: 37760679 PMCID: PMC10525099 DOI: 10.3390/antibiotics12091382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic resistance caused by multidrug-resistant (MDR) bacteria is a major challenge to global public health. Polymyxins are increasingly being used as last-in-line antibiotics to treat MDR Gram-negative bacterial infections, but resistance development renders them ineffective for empirical therapy. The main mechanism that bacteria use to defend against polymyxins is to modify the lipid A headgroups of the outer membrane by adding phosphoethanolamine (PEA) moieties. In addition to lipid A modifying PEA transferases, Gram-negative bacteria possess PEA transferases that decorate proteins and glycans. This review provides a comprehensive overview of the function, structure, and mechanism of action of PEA transferases identified in pathogenic Gram-negative bacteria. It also summarizes the current drug development progress targeting this enzyme family, which could reverse antibiotic resistance to polymyxins to restore their utility in empiric therapy.
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Affiliation(s)
- Van C. Thai
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (V.C.T.); (M.S.-T.)
| | - Keith A. Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia;
| | - Mitali Sarkar-Tyson
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (V.C.T.); (M.S.-T.)
| | - Charlene M. Kahler
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (V.C.T.); (M.S.-T.)
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4
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Hanpaibool C, Ngamwongsatit N, Ounjai P, Yotphan S, Wolschann P, Mulholland AJ, Spencer J, Rungrotmongkol T. Pyrazolones Potentiate Colistin Activity against MCR-1-Producing Resistant Bacteria: Computational and Microbiological Study. ACS OMEGA 2023; 8:8366-8376. [PMID: 36910942 PMCID: PMC9996792 DOI: 10.1021/acsomega.2c07165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The polymyxin colistin is a last line antibiotic for extensively resistant Gram-negative bacteria. Colistin binding to lipid A disrupts the Gram-negative outer membrane, but mobile colistin resistance (mcr) gene family members confer resistance by catalyzing phosphoethanolamine (PEA) transfer onto lipid A, neutralizing its negative charge to reduce colistin interactions. Multiple mcr isoforms have been identified in clinical and environmental isolates, with mcr-1 being the most widespread and mcr-3 being common in South and East Asia. Preliminary screening revealed that treatment with pyrazolones significantly reduced mcr-1, but not mcr-3, mediated colistin resistance. Molecular dynamics (MD) simulations of the catalytic domains of MCR-1 and a homology model of MCR-3, in different protonation states of active site residues H395/H380 and H478/H463, indicate that the MCR-1 active site has greater water accessibility than MCR-3, but that this is less influenced by changes in protonation. MD-optimized structures of MCR-1 and MCR-3 were used in virtual screening of 20 pyrazolone derivatives. Docking of these into the MCR-1/MCR-3 active sites identifies common residues likely to be involved in protein-ligand interactions, specifically the catalytic threonine (MCR-1 T285, MCR-3 T277) site of PEA addition, as well as differential interactions with adjacent amino acids. Minimal inhibitory concentration assays showed that the pyrazolone with the lowest predicted binding energy (ST3f) restores colistin susceptibility of mcr-1, but not mcr-3, expressing Escherichia coli. Thus, simulations indicate differences in the active site structure between MCR-1 and MCR-3 that may give rise to differences in pyrazolone binding and so relate to differential effects upon producer E. coli. This work identifies pyrazolones as able to restore colistin susceptibility of mcr-1-producing bacteria, laying the foundation for further investigations of their activity as phosphoethanolamine transferase inhibitors as well as of their differential activity toward mcr isoforms.
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Affiliation(s)
- Chonnikan Hanpaibool
- Center
of Excellence in Biocatalyst and Sustainable Biotechnology, Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Natharin Ngamwongsatit
- Department
of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
- Laboratory
of Bacteria, Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Puey Ounjai
- Department
of Biology, Faculty of Science, Mahidol
University, Bangkok 10400, Thailand
- Center
of Excellence on Environmental Health and Toxicology, Office of Higher
Education Commission, Ministry of Education, Bangkok 10400, Thailand
| | - Sirilata Yotphan
- Center of
Excellence for Innovation in Chemistry (PERCH-CIC), Department of
Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Peter Wolschann
- Institute
of Theoretical Chemistry, University of
Vienna, Vienna 1090, Austria
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - James Spencer
- School
of Cellular and Molecular Medicine, University
of Bristol, Bristol BS8 1TD, U.K.
| | - Thanyada Rungrotmongkol
- Center
of Excellence in Biocatalyst and Sustainable Biotechnology, Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10400, Thailand
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5
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The MCR-3 inside linker appears as a facilitator of colistin resistance. Cell Rep 2021; 35:109135. [PMID: 34010644 DOI: 10.1016/j.celrep.2021.109135] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/23/2020] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
An evolving family of mobile colistin resistance (MCR) enzymes is threatening public health. However, the molecular mechanism by which the MCR enzyme as a rare member of lipid A-phosphoethanolamine (PEA) transferases gains the ability to confer phenotypic colistin resistance remains enigmatic. Here, we report an unusual example that genetic duplication and amplification produce a functional variant (Ah762) of MCR-3 in certain Aeromonas species. The lipid A-binding cavity of Ah762 is functionally defined. Intriguingly, we locate a hinge linker of Ah762 (termed Linker 59) that determines the MCR. Genetic and biochemical characterization reveals that Linker 59 behaves as a facilitator to render inactive MCR variants to regain the ability of colistin resistance. Along with molecular dynamics (MD) simulation, isothermal titration calorimetry (ITC) suggests that this facilitator guarantees the formation of substrate phosphatidylethanolamine (PE)-accessible pocket within MCR-3-like enzymes. Therefore, our finding defines an MCR-3 inside facilitator for colistin resistance.
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6
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Ullah S, Ji K, Li J, Xu Y, Jiang C, Zhang H, Huang M, Feng Y. Characterization of NMCR-2, a new non-mobile colistin resistance enzyme: implications for an MCR-8 ancestor. Environ Microbiol 2020; 23:844-860. [PMID: 32686285 DOI: 10.1111/1462-2920.15171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/07/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022]
Abstract
MCR-4 and MCR-8 are two recently identified members of an ongoing MCR family of colistin resistance. Although that aquatic reservoir for MCR-4 is proposed, the origin and mechanism of MCR-8 is poorly understood. Here we report a previously unrecognized non-mobile colistin resistance enzyme, termed NMCR-2, originating from the plant pathogen Kosakonia pseudosacchari. NMCR-2 (551aa) gives 67.3% identity to MCR-8 (565aa). NMCR-2 is placed as a progenitor/ancestor for MCR-8 in phylogeny of MCR members. Genetic study reveals that nmcr-2 is comparable to mcr-8 in the ability of producing phenotypic colistin resistance. Biochemical analyses determine that these two enzymes catalyse the transfer of PEA from the donor PE lipid substrate to the recipient lipid A molecule by a putative 'ping-pong' trade-off. Further experiment of protein engineering demonstrates that the two motifs (TM region and catalytic domain) of NMCR-2 are functionally exchangeable with that of MCR-8, rather than MCR-1. Physiological impacts of nmcr-2 and/or mcr-8 are detected in Escherichia coli, featuring with fitness cost. Evidently, the action and mechanism of NMCR-2 is analogous to that of MCR-8. Therefore, our finding underlines that NMCR-2 might be a possible progenitor of MCR-8.
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Affiliation(s)
- Saif Ullah
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China
| | - Kai Ji
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China.,Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Guangxi, China
| | - Jun Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Zhejiang, Hangzhou, China
| | - Yongchang Xu
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China.,Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, 610500, China
| | - Chengjian Jiang
- Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Guangxi, China
| | - Huimin Zhang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Man Huang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China.,Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Guangxi, China.,Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, 610500, China.,College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
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7
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Salam LB. Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil. 3 Biotech 2020; 10:238. [PMID: 32405442 PMCID: PMC7205953 DOI: 10.1007/s13205-020-02219-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
The antibiotic and heavy metal resistome of a chronically polluted soil (3S) obtained from an automobile workshop in Ilorin, Kwara State, Nigeria was deciphered via functional annotation of putative ORFs (open reading frames). Functional annotation of antibiotic and heavy metal resistance genes in 3S metagenome was conducted using the Comprehensive Antibiotic Resistance Database (CARD), Antibiotic Resistance Gene-annotation (ARG-ANNOT) and Antibacterial Biocide and Metal Resistance Gene Database (BacMet). Annotation revealed detection of resistance genes for 15 antibiotic classes with the preponderance of beta lactamases, mobilized colistin resistance determinant (mcr), glycopepetide and tetracycline resistance genes, the OqxBgb and OqxA RND-type multidrug efflux pumps, among others. The dominance of resistance genes for antibiotics effective against members of the Enterobacteriaceae indicate possible contamination with faecal materials. Annotation of heavy metal resistance genes revealed diverse resistance genes responsible for the uptake, transport, detoxification, efflux and regulation of copper, zinc, cadmium, nickel, chromium, cobalt, mercury, arsenic, iron, molybdenum and several others. Majority of the antibiotic and heavy metal resistance genes detected in this study are borne on mobile genetic elements, which facilitate their spread and dissemination in the polluted soil. The presence of the heavy metal resistance genes is strongly believed to play a major role in the proliferation of antibiotic resistance genes. This study has established that soil is a huge repertoire of antibiotic and heavy metal resistome and due to the intricate link between human, animals and the soil environment, it may be a major contributor to the proliferation of multidrug-resistant clinical pathogens.
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Affiliation(s)
- Lateef Babatunde Salam
- Microbiology Unit, Department of Biological Sciences, Summit University, Offa, Kwara Nigeria
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8
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Samantha A, Vrielink A. Lipid A Phosphoethanolamine Transferase: Regulation, Structure and Immune Response. J Mol Biol 2020; 432:5184-5196. [PMID: 32353363 DOI: 10.1016/j.jmb.2020.04.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 01/23/2023]
Abstract
A wide variety of antibiotics are targeted to the bacterial membrane due to its unique arrangement and composition relative to the host mammalian membranes. By modification of their membranes, some gram-negative pathogens resist the action of antibiotics. Lipid A phosphoethanolamine transferase (EptA) is an intramembrane enzyme that modifies the lipid A portion of lipopolysaccharide/lipooligosaccharide by the addition of phosphoethanolamine. This modification reduces the overall net-negative charge of the outer membrane of some gram-negative bacteria, conferring resistance to polymyxin. This resistance mechanism has resulted in a global public health issue due to the increased use of polymyxin as last-resort antibiotic treatments against multi-drug-resistant pathogens. Studies show that, without EptA, pathogenic bacteria become more sensitive to polymyxin and to clearance by the host immune system, suggesting the importance of this target enzyme for the development of novel therapeutic agents. In this review, EptA will be discussed comprehensively. Specifically, this review will cover the regulation of eptA expression by the two component systems PmrA/PmrB and PhoP/PhoQ, the site of modification on lipid A, the structure and catalytic mechanism of EptA in comparison to MCR-1 and Escherichia coli alkaline phosphatase, and the host immune system's response to lipid A modification by EptA. The overarching aim of this review is to provide a comprehensive overview of polymyxin resistance mediated by EptA.
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Affiliation(s)
- Ariela Samantha
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia.
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9
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Lythell E, Suardíaz R, Hinchliffe P, Hanpaibool C, Visitsatthawong S, Oliveira ASF, Lang EJM, Surawatanawong P, Lee VS, Rungrotmongkol T, Fey N, Spencer J, Mulholland AJ. Resistance to the “last resort” antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes. Chem Commun (Camb) 2020; 56:6874-6877. [DOI: 10.1039/d0cc02520h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simulations show the mono-zinc form of MCR to be stable and competent for covalent phospho(ethanolamine) intermediate formation.
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10
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Recent progress on elucidating the molecular mechanism of plasmid-mediated colistin resistance and drug design. Int Microbiol 2019; 23:355-366. [PMID: 31872322 PMCID: PMC7347692 DOI: 10.1007/s10123-019-00112-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/29/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022]
Abstract
Antibiotic resistance is a growing global challenge to public health. Polymyxin is considered to be the last-resort antibiotic against most gram-negative bacteria. Recently, discoveries of a plasmid-mediated, transferable mobilized polymyxin resistance gene (mcr-1) in many countries have heralded the increased threat of the imminent emergence of pan-drug-resistant super bacteria. MCR-1 is an inner membrane protein that enables bacteria to develop resistance to polymyxin by transferring phosphoethanolamine to lipid A. However, the mechanism associated with polymyxin resistance has yet to be elucidated, and few drugs exist to address this issue. Here, we review our current understanding regarding MCR-1 and small molecule inhibitors to provide a detailed enzymatic mechanism of MCR-1 and the associated implications for drug design.
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11
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Zhang H, Srinivas S, Xu Y, Wei W, Feng Y. Genetic and Biochemical Mechanisms for Bacterial Lipid A Modifiers Associated with Polymyxin Resistance. Trends Biochem Sci 2019; 44:973-988. [PMID: 31279652 DOI: 10.1016/j.tibs.2019.06.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/02/2019] [Accepted: 06/05/2019] [Indexed: 01/29/2023]
Abstract
Polymyxins are a group of detergent-like antimicrobial peptides that are the ultimate line of defense against carbapenem-resistant pathogens in clinical settings. Polymyxin resistance primarily originates from structural remodeling of lipid A anchored on bacterial surfaces. We integrate genetic, structural, and biochemical aspects of three major types of lipid A modifiers that have been shown to confer intrinsic colistin resistance. Namely, we highlight ArnT, a glycosyltransferase, EptA, a phosphoethanolamine transferase, and the AlmEFG tripartite system, which is restricted to EI Tor biotype of Vibrio cholerae O1. We also discuss the growing family of mobile colistin resistance (MCR) enzymes, each of which is analogous to EptA, and which pose great challenges to global public health.
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Affiliation(s)
- Huimin Zhang
- Department of Pathogen Biology and Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Swaminath Srinivas
- Department of Pathogen Biology and Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yongchang Xu
- Department of Pathogen Biology and Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Wenhui Wei
- Department of Pathogen Biology and Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Youjun Feng
- Department of Pathogen Biology and Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; College of Animal Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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12
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Zhang H, Wei W, Huang M, Umar Z, Feng Y. Definition of a Family of Nonmobile Colistin Resistance (NMCR-1) Determinants Suggests Aquatic Reservoirs for MCR-4. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900038. [PMID: 31179218 PMCID: PMC6548957 DOI: 10.1002/advs.201900038] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Polymyxins, a family of cationic antimicrobial peptides, are recognized as a last-resort clinical option used in the treatment of lethal infections with carbapenem-resistant pathogens. A growing body of mobile colistin resistance (MCR) determinants renders colistin ineffective in the clinical and human sectors, posing a challenge to human health and food security. However, the origin and reservoir of the MCR family enzymes is poorly understood. Herein, a new family of nonmobile colistin resistance (from nmcr-1 to nmcr-1.8) from the aquatic bacterium Shewanella is reported. NMCR-1 (541aa) displays 62.78% identity to MCR-4. Genetic and structural analyses reveal that NMCR-1 shares a similar catalytic mechanism and functional motifs, both of which are required for MCR action and its resultant phenotypic resistance to polymyxin. Phylogeny and domain-swapping demonstrate that NMCR-1 is a progenitor of MCR-4 rather than MCR-1/2. Additionally, the experiment of bacterial growth and viability reveals that NMCR-1 promotes fitness cost as MCR-1/4 does in the recipient Escherichia coli. In summary, the finding suggests that the aquatic bacterium Shewanella (and even its associated aquaculture) is a reservoir for MCR-4 mobile colistin resistance.
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Affiliation(s)
- Huimin Zhang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Wenhui Wei
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Man Huang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Zeeshan Umar
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
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13
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Zhang H, Hou M, Xu Y, Srinivas S, Huang M, Liu L, Feng Y. Action and mechanism of the colistin resistance enzyme MCR-4. Commun Biol 2019; 2:36. [PMID: 30701201 PMCID: PMC6347640 DOI: 10.1038/s42003-018-0278-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/17/2018] [Indexed: 12/29/2022] Open
Abstract
Colistin is the last-resort antibiotic against lethal infections with multidrug-resistant bacterial pathogens. A rainbow coalition of mobile colistin resistance (mcr) genes raises global health concerns. Here, we describe the action and mechanism of colistin resistance imparted by MCR-4, a recently-identified member from the broader MCR family. We found that MCR-4 originates from the silenced variant of Shewanella frigidimarina via progressive evolution and forms a phylogenetically-distinct group from the well-studied MCR-1/2 family. Domain-swapping experiments further confirmed that MCR-1 and MCR-4 transmembrane and catalytic domains are not functionally-interchangeable. However, structural and functional analyses demonstrated that MCR-4 possesses a similar PE lipid substrate-recognizable cavity and exploits an almost-identical ping-pong catalysis mechanism. MCR-4 also can alleviate colistin-triggered accumulation of reactive oxygen species (ROS). Taken together, this finding constitutes a functional proof that MCR-4 proceeds in a distinct evolutionary path to fulfill a consistent molecular mechanism, resulting in phenotypic colistin resistance.
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Affiliation(s)
- Huimin Zhang
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Mengyun Hou
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
| | - Yongchang Xu
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
| | - Swaminath Srinivas
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Man Huang
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
| | - Lizhang Liu
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
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Büdel T, Clément M, Bernasconi OJ, Principe L, Perreten V, Luzzaro F, Endimiani A. Evaluation of EDTA- and DPA-Based Microdilution Phenotypic Tests for the Detection of MCR-Mediated Colistin Resistance in Enterobacteriaceae. Microb Drug Resist 2018; 25:494-500. [PMID: 30431401 DOI: 10.1089/mdr.2018.0275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence of the colistin-resistant (COL-R) Enterobacteriaceae represents a worrying health issue. However, only a portion of these strains may carry the plasmid-mediated mcr colistin resistance genes. We evaluated the ability of both ethylenediaminetetraacetic acid (EDTA)-based and dipicolinic acid (DPA)-based broth microdilution (BMD) tests to detect mcr-1 to mcr-5 producers. Of 92 Enterobacteriaceae (85 COL-R), 44 mcr-positive strains (39 Escherichia coli, 3 Klebsiella pneumoniae, and 2 Salmonella spp.) were tested. EDTA (100 μg/mL) was tested in Mueller-Hinton broth (MHB), whereas the DPA (900 μg/mL) was used in cation-adjusted MHB. Results were categorized as positive if in presence of chelator strains exhibited ≥3 two fold MIC decrease compared to the COL MIC alone. The EDTA-based BMD assay detected 41 mcr-positive strains, but 22 false-positive strains (including 12 E. coli and 4 K. pneumoniae) were recorded (sensitivity [SN], 93.2%; specificity [SP], 54.2%). The DPA-based BMD assay detected 37 mcr-positive strains, with 7 false-negative (2 E. coli, 3 K. pneumoniae, 2 Salmonella spp.) strains (SN, 84.1%; SP, 100%). Overall, the EDTA-based BMD assay is not accurate to detect mcr producers, whereas the DPA-based BMD test ("colistin-MAC test") demonstrated good accuracy, but only when implemented for E. coli strains (SN, 94.9%; SP, 100%). With the aim to prevent the dissemination of mcr-possessing E. coli strains, the COL-MAC test could be implemented by clinical laboratories that are unable to perform molecular tests. Moreover, this assay could be applied to screen large collections of isolates to reveal the expression of new mcr-like genes not yet targeted by the current molecular assays.
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Affiliation(s)
- Thomas Büdel
- 1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Mathieu Clément
- 1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,2 Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Odette J Bernasconi
- 1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,2 Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Luigi Principe
- 3 Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Vincent Perreten
- 4 Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Francesco Luzzaro
- 3 Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Andrea Endimiani
- 1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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15
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Structural and functional insights into MCR-2 mediated colistin resistance. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1432-1436. [DOI: 10.1007/s11427-018-9363-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022]
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16
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Ding S, Han X, Li J, Gao W, Chen Z, Feng Y. Discovery of multi-drug resistant, MCR-1 and ESBL-coproducing ST117 Escherichia coli from diseased chickens in northeast China. Sci Bull (Beijing) 2018; 63:1059-1066. [PMID: 36755458 DOI: 10.1016/j.scib.2018.07.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/11/2018] [Accepted: 06/22/2018] [Indexed: 11/26/2022]
Abstract
An endemic multi-drug resistant ST117 E. coli isolate coproducing MCR-1 and 3 ESBL loci was, for the first time, detected from diseased chicken, Liaoning Province, in Northeast China, from 2011 to 2012. Whole-genome sequencing revealed 5 unique plasmids, namely pHXH-1, pHXH-2, pHXH-3, pHXH-4 and pHXH-5). Among them, pHXH1 and pHXH4 encode ESBL, and pHXH-5 mediates MCR-1 colistin resistance. The results indicate that the potentially-national dissemination of MCR-1-positive pathogens with pan-drug resistance proceeds via food chains.
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Affiliation(s)
- Sijia Ding
- School of Stomatology, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiaohu Han
- Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, China
| | - Jun Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Weifan Gao
- Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, China
| | - Zeliang Chen
- Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, China.
| | - Youjun Feng
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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17
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The EDTA-based disk-combination tests are unreliable for the detection of MCR-mediated colistin-resistance in Enterobacteriaceae. J Microbiol Methods 2018; 153:31-34. [PMID: 30138643 DOI: 10.1016/j.mimet.2018.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 12/28/2022]
Abstract
We evaluated several EDTA-based combined-disk tests to detect 25 mcr producers among 48 Enterobacteriaceae. Colistin disks plus EDTA (292/584 μg) on MH and CAMH agar were used. Results were positive if with chelator there was an inhibition zone increase ≥3 mm compared to colistin alone. All tests resulted unreliable (sensitivity ≤68%).
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18
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Xu Y, Zhong LL, Srinivas S, Sun J, Huang M, Paterson DL, Lei S, Lin J, Li X, Tang Z, Feng S, Shen C, Tian GB, Feng Y. Spread of MCR-3 Colistin Resistance in China: An Epidemiological, Genomic and Mechanistic Study. EBioMedicine 2018; 34:139-157. [PMID: 30061009 PMCID: PMC6116419 DOI: 10.1016/j.ebiom.2018.07.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/16/2018] [Accepted: 07/19/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mobilized resistance to colistin is evolving rapidly and its global dissemination poses a severe threat to human health and safety. Transferable colistin resistance gene, mcr-3, first identified in Shandong, China, has already been found in several countries in multidrug-resistant human infections. Here we track the spread of mcr-3 within 13 provinces in China and provide a complete characterization of its evolution, structure and function. METHODS A total of 6497 non-duplicate samples were collected from thirteen provinces in China, from 2016 to 2017 and then screened for the presence of mcr-3 gene by PCR amplification. mcr-3-positive isolates were analyzed for antibiotic resistance and by southern blot hybridization, transfer analysis and plasmid typing. We then examined the molecular evolution of MCR-3 through phylogenetic analysis. Furthermore, we also characterized the structure and function of MCR-3 through circular dichroism analyses, inductively coupled plasma mass spectrometry (ICP-MS), liquid chromatography mass spectrometry (LC/MS), confocal microscopy and chemical rescue tests. FINDINGS 49 samples (49/6497 = 0.75%) were mcr-3 positive, comprising 40 samples (40/4144 = 0.97%) from 2017 and 9 samples (9/2353 = 0.38%) from 2016. Overall, mcr-3-positive isolates were distributed in animals and humans in 8 of the 13 provinces. Three mcr-3-positive IncP-type and one mcr-1-bearing IncHI2-like plasmids were identified and characterized. MCR-3 clusters with PEA transferases from Aeromonas and other bacteria and forms a phylogenetic entity that is distinct from the MCR-1/2/P(M) family, the largest group of transferable colistin resistance determinants. Despite that the two domains of MCR-3 not being exchangeable with their counterparts in MCR-1/2, structure-guided functional mapping of MCR-3 defines a conserved PE-lipid recognizing cavity prerequisite for its enzymatic catalysis and its resultant phenotypic resistance to colistin. We therefore propose that MCR-3 uses a possible "ping-pong" mechanism to transfer the moiety of PEA from its donor PE to the 1(or 4')-phosphate of lipid A via an adduct of MCR-3-bound PEA. Additionally, the expression of MCR-3 in E. coli prevents the colistin-triggered formation of reactive oxygen species (ROS) and interferes bacterial growth and viability. INTERPRETATION Our results provide an evolutionary, structural and functional definition of MCR-3 and its epidemiology in China, paving the way for smarter policies, better surveillance and effective treatments.
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Affiliation(s)
- Yongchang Xu
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Lan-Lan Zhong
- Zhongshan School of Medicine, Key Laboratory of Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Man Huang
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - David L Paterson
- Centre for Clinical Research, Royal Brisbane and Women's Hospital, University of Queensland, Building 71/918, Brisbane QLD 4029, Australia
| | - Sheng Lei
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingxia Lin
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan 471023, China
| | - Zichen Tang
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan 471023, China
| | - Siyuan Feng
- Zhongshan School of Medicine, Key Laboratory of Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Cong Shen
- Zhongshan School of Medicine, Key Laboratory of Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Guo-Bao Tian
- Zhongshan School of Medicine, Key Laboratory of Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Youjun Feng
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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19
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Sun L, Vella P, Schnell R, Polyakova A, Bourenkov G, Li F, Cimdins A, Schneider TR, Lindqvist Y, Galperin MY, Schneider G, Römling U. Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium. J Mol Biol 2018; 430:3170-3189. [PMID: 30017920 DOI: 10.1016/j.jmb.2018.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 11/17/2022]
Abstract
Many bacteria secrete cellulose, which forms the structural basis for bacterial multicellular aggregates, termed biofilms. The cellulose synthase complex of Salmonella typhimurium consists of the catalytic subunits BcsA and BcsB and several auxiliary subunits that are encoded by two divergently transcribed operons, bcsRQABZC and bcsEFG. Expression of the bcsEFG operon is required for full-scale cellulose production, but the functions of its products are not fully understood. This work aimed to characterize the BcsG subunit of the cellulose synthase, which consists of an N-terminal transmembrane fragment and a C-terminal domain in the periplasm. Deletion of the bcsG gene substantially decreased the total amount of BcsA and cellulose production. BcsA levels were partially restored by the expression of the transmembrane segment, whereas restoration of cellulose production required the presence of the C-terminal periplasmic domain and its characteristic metal-binding residues. The high-resolution crystal structure of the periplasmic domain characterized BcsG as a member of the alkaline phosphatase/sulfatase superfamily of metalloenzymes, containing a conserved Zn2+-binding site. Sequence and structural comparisons showed that BcsG belongs to a specific family within alkaline phosphatase-like enzymes, which includes bacterial Zn2+-dependent lipopolysaccharide phosphoethanolamine transferases such as MCR-1 (colistin resistance protein), EptA, and EptC and the Mn2+-dependent lipoteichoic acid synthase (phosphoglycerol transferase) LtaS. These enzymes use the phospholipids phosphatidylethanolamine and phosphatidylglycerol, respectively, as substrates. These data are consistent with the recently discovered phosphoethanolamine modification of cellulose by BcsG and show that its membrane-bound and periplasmic parts play distinct roles in the assembly of the functional cellulose synthase and cellulose production.
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Affiliation(s)
- Lei Sun
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Peter Vella
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Anna Polyakova
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Fengyang Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Annika Cimdins
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Ylva Lindqvist
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden.
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20
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Stogios PJ, Cox G, Zubyk HL, Evdokimova E, Wawrzak Z, Wright GD, Savchenko A. Substrate Recognition by a Colistin Resistance Enzyme from Moraxella catarrhalis. ACS Chem Biol 2018; 13:1322-1332. [PMID: 29631403 DOI: 10.1021/acschembio.8b00116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipid A phosphoethanolamine (PEtN) transferases render bacteria resistant to the last resort antibiotic colistin. The recent discoveries of pathogenic bacteria harboring plasmid-borne PEtN transferase ( mcr) genes have illustrated the serious potential for wide dissemination of these resistance elements. The origin of mcr-1 is traced to Moraxella species co-occupying environmental niches with Enterobacteriaceae. Here, we describe the crystal structure of the catalytic domain of the chromosomally encoded colistin resistance PEtN transferase, ICR Mc (for intrinsic colistin resistance) of Moraxella catarrhalis. The ICR Mc structure in complex with PEtN reveals key molecular details including specific residues involved in catalysis and PEtN binding. It also demonstrates that ICR Mc catalytic domain dimerization is required for substrate binding. Our structure-guided phylogenetic analysis provides sequence signatures defining potentially colistin-active representatives in this enzyme family. Combined, these results advance the molecular and mechanistic understanding of PEtN transferases and illuminate their origins.
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Affiliation(s)
| | - Georgina Cox
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Haley L. Zubyk
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | | | - Zdzislaw Wawrzak
- LS-CAT, Synchrotron Research Center, Northwestern University, Argonne, Illinois 60439, United States
| | - Gerard D. Wright
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Alexei Savchenko
- Center for Structural
Genomics of Infectious Diseases (CSGID)
- Department of Microbiology, Immunology and Infectious Diseases, Health Research Innovation Centre, University of Calgary, 3330 Hospital Drive NW, HRIC-2C66, Calgary, Alberta T2N 4N1, Canada
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21
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Wei W, Srinivas S, Lin J, Tang Z, Wang S, Ullah S, Kota VG, Feng Y. Defining ICR-Mo, an intrinsic colistin resistance determinant from Moraxella osloensis. PLoS Genet 2018; 14:e1007389. [PMID: 29758020 PMCID: PMC5983563 DOI: 10.1371/journal.pgen.1007389] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/01/2018] [Accepted: 05/02/2018] [Indexed: 11/19/2022] Open
Abstract
Polymyxin is the last line of defense against severe infections caused by carbapenem-resistant gram-negative pathogens. The emergence of transferable MCR-1/2 polymyxin resistance greatly challenges the renewed interest in colistin (polymyxin E) for clinical treatments. Recent studies have suggested that Moraxella species are a putative reservoir for MCR-1/2 genetic determinants. Here, we report the functional definition of ICR-Mo from M. osloensis, a chromosomally encoded determinant of colistin resistance, in close relation to current MCR-1/2 family. ICR-Mo transmembrane protein was prepared and purified to homogeneity. Taken along with an in vitro enzymatic detection, MALDI-TOF mass spectrometry of bacterial lipid A pools determined that the ICR-Mo enzyme might exploit a possible "ping-pong" mechanism to accept the phosphoethanolamine (PEA) moiety from its donor phosphatidylethanolamine (PE) and then transfer it to the 1(or 4')-phosphate position of lipid A via an ICR-Mo-bound PEA adduct. Structural decoration of LPS-lipid A by ICR-Mo renders the recipient strain of E. coli resistant to polymyxin. Domain swapping assays indicate that the two domains of ICR-Mo cannot be functionally-exchanged with its counterparts in MCR-1/2 and EptA, validating its phylogenetic position in a distinct set of MCR-like genes. Structure-guided functional mapping of ICR-Mo reveals a PE lipid substrate recognizing cavity having a role in enzymatic catalysis and the resultant conference of antibiotic resistance. Expression of icr-Mo in E. coli significantly prevents the formation of reactive oxygen species (ROS) induced by colistin. Taken together, our results define a member of a group of intrinsic colistin resistance genes phylogenetically close to the MCR-1/2 family, highlighting the evolution of transferable colistin resistance.
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Affiliation(s)
- Wenhui Wei
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, United States of America
| | - Jingxia Lin
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zichen Tang
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shihua Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Saif Ullah
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Vishnu Goutham Kota
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Youjun Feng
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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22
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Abstract
Antibiotic resistance has become a global public health priority. Polymyxins, a family of cationic polypeptide antibiotics, act as a final line of refuge against severe infections by Gram-negative pathogens with pan-drug resistance. Unfortunately, this last-resort antibiotic has been challenged by the emergence and global spread of mobilized colistin resistance determinants (mcr). Given the fact that it has triggered extensive concerns worldwide, we present here an updated view of MCR-like colistin resistance. These studies provide a basic framework for understanding the molecular epidemiology and resistance mechanism of MCR-like genes. However, further large-scale epidemiology and functional studies are urgently needed to better understand the biology of this clinically important antibiotic resistance.
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Affiliation(s)
- Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; These authors contributed equally to this work
| | - Huimin Zhang
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou 310058, China; These authors contributed equally to this work
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China.
| | - Youjun Feng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou 310058, China; College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China.
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