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Bing C, Mengjuan A, Xinyu M, Chixin Z, Xinyao T, Yan S, Zhi L. Efflux pump inhibitor chlorpromazine effectively increases the susceptibility of Escherichia coli to antimicrobial peptide Brevinin-2CE. Future Microbiol 2024. [PMID: 38683168 DOI: 10.2217/fmb-2023-0272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
Aim: The response of E. coli ATCC8739 to Brevinin-2CE (B2CE) was evaluated as a strategy to prevent the development of antimicrobial peptide (AMP)-resistant bacteria. Methods: Gene expression levels were detected by transcriptome sequencing and RT-PCR. Target genes were knocked out using CRISPR-Cas9. MIC was measured to evaluate strain resistance. Results: Expression of acrZ and sugE were increased with B2CE stimulation. ATCC8739ΔacrZ and ATCC8739ΔsugE showed twofold and fourfold increased sensitivity, respectively. The survival rate of ATCC8739 was reduced in the presence of B2CE/chlorpromazine (CPZ). Combinations of other AMPs with CPZ also showed antibacterial effects. Conclusion: The results indicate that combinations of AMPs/efflux pump inhibitors (EPIs) may be a potential approach to combat resistant bacteria.
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Affiliation(s)
- Cao Bing
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
| | - An Mengjuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
| | - Ma Xinyu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
| | - Zhu Chixin
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
| | - Tan Xinyao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
| | - Sun Yan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
| | - Li Zhi
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
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2
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Lucero RM, Demirer K, Yeh TJ, Stockbridge RB. Transport of metformin metabolites by guanidinium exporters of the small multidrug resistance family. J Gen Physiol 2024; 156:e202313464. [PMID: 38294434 PMCID: PMC10829512 DOI: 10.1085/jgp.202313464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/01/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Proteins from the small multidrug resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in the metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMRGdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid-supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMRGdx homologs. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMRGdx homologs, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homolog, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMRGdx homolog Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMRGdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.
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Affiliation(s)
- Rachael M. Lucero
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Kemal Demirer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Randy B. Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
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3
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Seppälä S, Gierke T, Schauer EE, Brown JL, O'Malley MA. Identification and expression of small multidrug resistance transporters in early-branching anaerobic fungi. Protein Sci 2023; 32:e4730. [PMID: 37470750 PMCID: PMC10443351 DOI: 10.1002/pro.4730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/05/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023]
Abstract
Membrane-embedded transporters impart essential functions to cells as they mediate sensing and the uptake and extrusion of nutrients, waste products, and effector molecules. Promiscuous multidrug exporters are implicated in resistance to drugs and antibiotics and are highly relevant for microbial engineers who seek to enhance the tolerance of cell factory strains to hydrophobic bioproducts. Here, we report on the identification of small multidrug resistance (SMR) transporters in early-branching anaerobic fungi (Neocallimastigomycetes). The SMR class of transporters is commonly found in bacteria but has not previously been reported in eukaryotes. In this study, we show that SMR transporters from anaerobic fungi can be produced heterologously in the model yeast Saccharomyces cerevisiae, demonstrating the potential of these proteins as targets for further characterization. The discovery of these novel anaerobic fungal SMR transporters offers a promising path forward to enhance bioproduction from engineered microbial strains.
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Affiliation(s)
- Susanna Seppälä
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Taylor Gierke
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Elizabeth E. Schauer
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Jennifer L. Brown
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Michelle A. O'Malley
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
- Bioengineering ProgramUniversity of CaliforniaSanta BarbaraCaliforniaUSA
- Joint BioEnergy Institute (JBEI)EmeryvilleCaliforniaUSA
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4
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Lucero RM, Demirer K, Yeh TJ, Stockbridge RB. Transport of metformin metabolites by guanidinium exporters of the Small Multidrug Resistance family. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552832. [PMID: 37645731 PMCID: PMC10461911 DOI: 10.1101/2023.08.10.552832] [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
Proteins from the Small Multidrug Resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMRGdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMRGdx homologues. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMRGdx homologues, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homologue, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMRGdx homologue Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMRGdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.
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Affiliation(s)
| | - Kemal Demirer
- Department of Molecular, Cellular, and Developmental Biology
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randy B Stockbridge
- Program in Chemical Biology
- Department of Molecular, Cellular, and Developmental Biology
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
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5
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Burata OE, Yeh TJ, Macdonald CB, Stockbridge RB. Still rocking in the structural era: A molecular overview of the small multidrug resistance (SMR) transporter family. J Biol Chem 2022; 298:102482. [PMID: 36100040 PMCID: PMC9574504 DOI: 10.1016/j.jbc.2022.102482] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
The small multidrug resistance (SMR) family is composed of widespread microbial membrane proteins that fulfill different transport functions. Four functional SMR subtypes have been identified, which variously transport the small, charged metabolite guanidinium, bulky hydrophobic drugs and antiseptics, polyamines, and glycolipids across the membrane bilayer. The transporters possess a minimalist architecture, with ∼100-residue subunits that require assembly into homodimers or heterodimers for transport. In part because of their simple construction, the SMRs are a tractable system for biochemical and biophysical analysis. Studies of SMR transporters over the last 25 years have yielded deep insights for diverse fields, including membrane protein topology and evolution, mechanisms of membrane transport, and bacterial multidrug resistance. Here, we review recent advances in understanding the structures and functions of SMR transporters. New molecular structures of SMRs representing two of the four functional subtypes reveal the conserved structural features that have permitted the emergence of disparate substrate transport functions in the SMR family and illuminate structural similarities with a distantly related membrane transporter family, SLC35/DMT.
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Affiliation(s)
- Olive E Burata
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Randy B Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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6
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Gregorchuk BSJ, Reimer SL, Slipski CJ, Milner KA, Hiebert SL, Beniac DR, Booth TF, Zhanel GG, Bay DC. Applying fluorescent dye assays to discriminate Escherichia coli chlorhexidine resistance phenotypes from porin and mlaA deletions and efflux pumps. Sci Rep 2022; 12:12149. [PMID: 35840757 PMCID: PMC9287405 DOI: 10.1038/s41598-022-15775-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022] Open
Abstract
Bacterial resistance to the antiseptic chlorhexidine (CHX), is a growing problem, recently shown to be caused by deleterious mutations to the phospholipid transport system component (mlaA) as well as efflux pump overexpression. Comparisons of CHX resistance mechanisms, such as porin deletions (ompCF), and over-expressed efflux pumps (acrB, qacE, aceI), are lacking and may be distinguishable using antiseptic rapid fluorescent dye testing assays. Using E. coli K-12 CHX adapted isolates (CHXR1), gene deletion mutants, and over-expressed transformants the phenotypes of these CHX resistance genes were compared using antimicrobial susceptibility tests (AST), rapid fluorescent propidium iodide dye-based membrane integrity assays (RFDMIA), and scanning electron microscopy (SEM). AST findings showed CHXR1, ΔacrB, ΔompCF, and transformants pCA24N-aceI and pCA24N-mlaA conferred greater (two to fourfold) MIC changes when compared to matched controls. Examination of these mutants/transformants using CHX RFDMIA showed that porin dual-deletions (ΔompCF) and mlaA alterations (ΔmlaA; pCA24N-mlaA, CHXR1) were distinguishable from controls. Results for over-expressed (pMS119EH-aceI) and deleted (ΔacrB) efflux pump RFDMIA could not be distinguished with propidium iodide, only with ethidium bromide, suggesting propidium iodide is better suited for detecting porin and mlaA associated CHX resistance mechanisms. SEM of CHXR1 and unadapted E. coli cells exposed to increasing CHX concentrations revealed that CHX does not visibly damage cell envelope integrity at any tested concentration but did identify elongated CHXR1 cells. ΔmlaA confers similar levels of CHX resistance as efflux overexpression and porin deletions, however, only outer membrane-altering porin and mlaA deletions can be reliably distinguished using RFDMIA.
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Affiliation(s)
- Branden S J Gregorchuk
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Shelby L Reimer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Carmine J Slipski
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Kieran A Milner
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Shannon L Hiebert
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Daniel R Beniac
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Timothy F Booth
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Denice C Bay
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada. .,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
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7
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Characterization of proteobacterial plasmid integron-encoded qac efflux pump sequence diversity and quaternary ammonium compound antiseptic selection in E. coli grown planktonically and as biofilms. Antimicrob Agents Chemother 2021; 65:e0106921. [PMID: 34280018 PMCID: PMC8448097 DOI: 10.1128/aac.01069-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Qac efflux pumps from proteobacterial multidrug-resistant plasmids are integron encoded and confer resistance to quaternary ammonium compound (QAC) antiseptics; however, many are uncharacterized and misannotated. A survey of >2,000 plasmid-carried qac genes identified 37 unique qac sequences that correspond to one of five representative motifs: QacE, QacEΔ1, QacF/L, QacH/I, and QacG. Antimicrobial susceptibility testing of each cloned qac member in Escherichia coli highlighted distinctive antiseptic susceptibility patterns that were most prominent when cells grew as biofilms.
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Salvail H, Balaji A, Yu D, Roth A, Breaker RR. Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria. Biochemistry 2020; 59:4654-4662. [PMID: 33236895 DOI: 10.1021/acs.biochem.0c00793] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An intriguing consequence of ongoing riboswitch discovery efforts is the occasional identification of metabolic or toxicity response pathways for unusual ligands. Recently, we reported the experimental validation of three distinct bacterial riboswitch classes that regulate gene expression in response to the selective binding of a guanidinium ion. These riboswitch classes, called guanidine-I, -II, and -III, regulate numerous genes whose protein products include previously misannotated guanidine exporters and enzymes that degrade guanidine via an initial carboxylation reaction. Guanidine is now recognized as the primal substrate of many multidrug efflux pumps that are important for bacterial resistance to certain antibiotics. Guanidine carboxylase enzymes had long been annotated as urea carboxylase enzymes but are now understood to participate in guanidine degradation. Herein, we report the existence of a fourth riboswitch class for this ligand, called guanidine-IV. Members of this class use a novel aptamer to selectively bind guanidine and use an unusual expression platform arrangement that is predicted to activate gene expression when ligand is present. The wide distribution of this abundant riboswitch class, coupled with the striking diversity of other guanidine-sensing RNAs, demonstrates that many bacterial species maintain sophisticated sensory and genetic mechanisms to avoid guanidine toxicity. This finding further highlights the mystery regarding the natural source of this nitrogen-rich chemical moiety.
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Affiliation(s)
- Hubert Salvail
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Adam Roth
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, United States
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