1
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Zhang LL, Zhong CB, Huang TJ, Zhang LM, Yan F, Ying YL. High-throughput single biomarker identification using droplet nanopore. Chem Sci 2024; 15:8355-8362. [PMID: 38846401 PMCID: PMC11151865 DOI: 10.1039/d3sc06795e] [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: 12/18/2023] [Accepted: 03/28/2024] [Indexed: 06/09/2024] Open
Abstract
Biomarkers are present in various metabolism processes, demanding precise and meticulous analysis at the single-molecule level for accurate clinical diagnosis. Given the need for high sensitivity, biological nanopore have been applied for single biomarker sensing. However, the detection of low-volume biomarkers poses challenges due to their low concentrations in dilute buffer solutions, as well as difficulty in parallel detection. Here, a droplet nanopore technique is developed for low-volume and high-throughput single biomarker detection at the sub-microliter scale, which shows a 2000-fold volume reduction compared to conventional setups. To prove the concept, this nanopore sensing platform not only enables multichannel recording but also significantly lowers the detection limit for various types of biomarkers such as angiotensin II, to 42 pg. This advancement enables direct biomarker detection at the picogram level. Such a leap forward in detection capability positions this nanopore sensing platform as a promising candidate for point-of-care testing of biomarker at single-molecule level, while substantially minimizing the need for sample dilution.
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Affiliation(s)
- Lin-Lin Zhang
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Cheng-Bing Zhong
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Ting-Jing Huang
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Li-Min Zhang
- School of Electronic Science and Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Yi-Lun Ying
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 P. R. China
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2
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Dash R, Holsinger KA, Chordia MD, Gh. MS, Pires MM. Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli. ACS Infect Dis 2024; 10:1602-1611. [PMID: 38592927 PMCID: PMC11091882 DOI: 10.1021/acsinfecdis.3c00684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Antibiotic resistance is an alarming public health concern that affects millions of individuals across the globe each year. A major challenge in the development of effective antibiotics lies in their limited ability to permeate cells, noting that numerous susceptible antibiotic targets reside within the bacterial cytosol. Consequently, improving the cellular permeability is often a key consideration during antibiotic development, underscoring the need for reliable methods to assess the permeability of molecules across cellular membranes. Currently, methods used to measure permeability often fail to discriminate between the arrival within the cytoplasm and the overall association of molecules with the cell. Additionally, these techniques typically possess throughput limitations. In this work, we describe a luciferase-based assay designed for assessing the permeability of molecules in the cytosolic compartment of Gram-negative bacteria. Our findings demonstrate a robust system that can elucidate the kinetics of intracellular antibiotic accumulation in live bacterial cells in real time.
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Affiliation(s)
- Rachita Dash
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kadie A. Holsinger
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mahendra D. Chordia
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mohammad Sharifian Gh.
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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3
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Ma X, Kaw HY, Yu J, Yang Q, Zhu L, Wang W. The intracellular concentrations of fluoroquinolones determined the antibiotic resistance response of Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134057. [PMID: 38508108 DOI: 10.1016/j.jhazmat.2024.134057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
The extensive consumption of antibiotics has been reported to significantly promote the generation of antibiotic resistance (ABR), however, a quantitative causal relationship between antibiotic exposure and ABR response is absent. This study aimed to pinpoint the accurate regulatory concentration of fluoroquinolones (FQs) and to understand the biochemical mechanism of the mutual action between FQ exposure and FQ resistance response. Highly sensitive analytical methods were developed by using UPLC-MS/MS to determine the total residual, extracellular residual, total intracellular, intracellular residual and intracellular degraded concentration of three representative FQs, including ciprofloxacin (CIP), ofloxacin (OFL) and norfloxacin (NOR), with detection limits in the range of 0.002-0.057 μg/L, and recoveries in the range of 80-93%. The MICs of Escherichia coli (E. coli) were 7.0-31.4-fold of the respective MIC0 after 40-day FQ exposure, and significant negative associations were discovered between the intracellular (residual, degraded or the sum) FQ concentrations and FQ resistance. Transcriptional expression and whole-genome sequencing results indicated that reduced membrane permeability and enhanced multi-drug efflux pumps contributed to the decreasing intracellular concentration. These results unveiled the pivotal role of intracellular concentration in triggering FQ resistance, providing important information to understand the dose-response relationship between FQ exposure and FQ resistance response, and ascertain the target dose metric of FQs for eliminating FQ resistance crisis.
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Affiliation(s)
- Xuejing Ma
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Han Yeong Kaw
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Jing Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Qi Yang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Wei Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
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4
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Squire S, Sebghati S, Hammond MC. Cytoplasmic Accumulation and Permeability of Antibiotics in Gram Positive and Gram Negative Bacteria Visualized in Real-Time via a Fluorogenic Tagging Strategy. ACS Chem Biol 2024; 19:3-8. [PMID: 38096425 PMCID: PMC10805102 DOI: 10.1021/acschembio.3c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024]
Abstract
In this study, we describe the first real-time live cell assay for compound accumulation and permeability in both Gram positive and Gram negative bacteria. The assay utilizes a novel fluorogenic tagging strategy that permits direct visualization of compound accumulation dynamics in the cytoplasm of live cells, unobscured by washing or other processing steps. Quantitative differences could be reproducibly measured by flow cytometry at compound concentrations below the limit of detection for MS-based approaches. We establish the fluorogenic assay in E. coli and B. subtilis and compare the intracellular accumulation of two antibiotics, ciprofloxacin and ampicillin, with related pharmacophores in these bacteria.
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Affiliation(s)
- Scott
O. Squire
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Sepehr Sebghati
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Ming C. Hammond
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
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5
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Dash R, Holsinger KA, Chordia MD, Sharifian Gh M, Pires MM. Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570448. [PMID: 38106213 PMCID: PMC10723488 DOI: 10.1101/2023.12.06.570448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Antibiotic resistance is an alarming public health concern that affects millions of individuals across the globe each year. A major challenge in the development of effective antibiotics lies in their limited ability to permeate into cells, noting that numerous susceptible antibiotic targets reside within the bacterial cytosol. Consequently, improving cellular permeability is often a key consideration during antibiotic development, underscoring the need for reliable methods to assess the permeability of molecules across cellular membranes. Currently, methods used to measure permeability often fail to discriminate between arrival within the cytoplasm and the overall association of molecules with the cell. Additionally, these techniques typically possess throughput limitations. In this work, we describe a luciferase-based assay designed for assessing the permeability of molecules into the cytosolic compartment of Gram-negative bacteria. Our findings demonstrate a robust system that can elucidate the kinetics of intracellular antibiotics accumulation in live bacterial cells in real time.
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6
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Radhakrishnan S, Nair KS, Nandi S, Bajaj H. Engineering semi-permeable giant liposomes. Chem Commun (Camb) 2023; 59:13863-13866. [PMID: 37930322 DOI: 10.1039/d3cc04039a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Giant unilamellar vesicles (GUVs) with a semi-permeable nature are prerequisites for constructing synthetic cells. Here we engineer semi-permeable GUVs by the inclusion of DOTAP lipid in vesicles. Diffusion of molecules of different charge and size across GUVs are reported. Control over size-selective permeability is demonstrated by modulating the DOTAP lipid composition in different lipid systems without reconstituting membrane proteins. Such semi-permeable GUVs have immense applications for constructing synthetic cells.
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Affiliation(s)
- Sreelakshmi Radhakrishnan
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India.
| | - Karthika S Nair
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India
| | - Samir Nandi
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India.
| | - Harsha Bajaj
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India
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7
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Nair KS, Bajaj H. Advances in giant unilamellar vesicle preparation techniques and applications. Adv Colloid Interface Sci 2023; 318:102935. [PMID: 37320960 DOI: 10.1016/j.cis.2023.102935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Giant unilamellar vesicles (GUVs) are versatile and promising cell-sized bio-membrane mimetic platforms. Their applications range from understanding and quantifying membrane biophysical processes to acting as elementary blocks in the bottom-up assembly of synthetic cells. Definite properties and requisite goals in GUVs are dictated by the preparation techniques critical to the success of their applications. Here, we review key advances in giant unilamellar vesicle preparation techniques and discuss their formation mechanisms. Developments in lipid hydration and emulsion techniques for GUV preparation are described. Novel microfluidic-based techniques involving lipid or surfactant-stabilized emulsions are outlined. GUV immobilization strategies are summarized, including gravity-based settling, covalent linking, and immobilization by microfluidic, electric, and magnetic barriers. Moreover, some of the key applications of GUVs as biomimetic and synthetic cell platforms during the last decade have been identified. Membrane interface processes like phase separation, membrane protein reconstitution, and membrane bending have been deciphered using GUVs. In addition, vesicles are also employed as building blocks to construct synthetic cells with defined cell-like functions comprising compartments, metabolic reactors, and abilities to grow and divide. We critically discuss the pros and cons of preparation technologies and the properties they confer to the GUVs and identify potential techniques for dedicated applications.
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Affiliation(s)
- Karthika S Nair
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India
| | - Harsha Bajaj
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India.
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8
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Nandi S, Nair KS, Bajaj H. Bacterial Outer-Membrane-Mimicking Giant Unilamellar Vesicle Model for Detecting Antimicrobial Permeability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5891-5900. [PMID: 37036429 DOI: 10.1021/acs.langmuir.3c00378] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The construction of bacterial outer membrane models with native lipids like lipopolysaccharide (LPS) is a barrier to understanding antimicrobial permeability at the membrane interface. Here, we engineer bacterial outer membrane (OM)-mimicking giant unilamellar vesicles (GUVs) by constituting LPS under different pH conditions and assembled GUVs with controlled dimensions. We quantify the LPS reconstituted in GUV membranes and reveal their arrangement in the leaflets of the vesicles. Importantly, we demonstrate the applications of OM vesicles by exploring antimicrobial permeability activity across membranes. Model peptides, melittin and magainin-2, are examined where both peptides exhibit lower membrane activity in OM vesicles than vesicles devoid of LPS. Our findings reveal the mode of action of antimicrobial peptides in bacterial-membrane-mimicking models. Notably, the critical peptide concentration required to elicit activity on model membranes correlates with the cell inhibitory concentrations that revalidate our models closely mimic bacterial membranes. In conclusion, we provide an OM-mimicking model capable of quantifying antimicrobial permeability across membranes.
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Affiliation(s)
- Samir Nandi
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
| | - Karthika S Nair
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India
| | - Harsha Bajaj
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India
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9
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Fletcher M, Zhu J, Rubio-Sánchez R, Sandler SE, Nahas KA, Michele LD, Keyser UF, Tivony R. DNA-Based Optical Quantification of Ion Transport across Giant Vesicles. ACS NANO 2022; 16:17128-17138. [PMID: 36222833 PMCID: PMC9620405 DOI: 10.1021/acsnano.2c07496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Accurate measurements of ion permeability through cellular membranes remains challenging due to the lack of suitable ion-selective probes. Here we use giant unilamellar vesicles (GUVs) as membrane models for the direct visualization of mass translocation at the single-vesicle level. Ion transport is indicated with a fluorescently adjustable DNA-based sensor that accurately detects sub-millimolar variations in K+ concentration. In combination with microfluidics, we employed our DNA-based K+ sensor for extraction of the permeation coefficient of potassium ions. We measured K+ permeability coefficients at least 1 order of magnitude larger than previously reported values from bulk experiments and show that permeation rates across the lipid bilayer increase in the presence of octanol. In addition, an analysis of the K+ flux in different concentration gradients allows us to estimate the complementary H+ flux that dissipates the charge imbalance across the GUV membrane. Subsequently, we show that our sensor can quantify the K+ transport across prototypical cation-selective ion channels, gramicidin A and OmpF, revealing their relative H+/K+ selectivity. Our results show that gramicidin A is much more selective to protons than OmpF with a H+/K+ permeability ratio of ∼104.
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Affiliation(s)
- Marcus Fletcher
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Jinbo Zhu
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Roger Rubio-Sánchez
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Sarah E Sandler
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Kareem Al Nahas
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Lorenzo Di Michele
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Ulrich F Keyser
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Ran Tivony
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
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10
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Moniruzzaman M, Cooper CJ, Uddin MR, Walker JK, Parks JM, Zgurskaya HI. Analysis of Orthogonal Efflux and Permeation Properties of Compounds Leads to the Discovery of New Efflux Pump Inhibitors. ACS Infect Dis 2022; 8:2149-2160. [PMID: 36070489 PMCID: PMC9942517 DOI: 10.1021/acsinfecdis.2c00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Optimization of compound permeation into Gram-negative bacteria is one of the most challenging tasks in the development of antibacterial agents. Two permeability barriers─the passive diffusion barrier of the outer membrane (OM) and active drug efflux─act synergistically to protect cells from the antibacterial action of compounds. In Escherichia coli (E. coli) and relatives, these two barriers sieve compounds based on different physicochemical properties that are defined by their interactions with OM porins and efflux pumps, respectively. In this study, we critically tested the hypothesis that the best substrates and inhibitors of efflux pumps are compounds that can effectively permeate the OM and are available at relatively high concentrations in the periplasm. For this purpose, we filtered a large subset of the ZINC15 database of commercially available compounds for compounds containing a primary amine, a chemical feature known to facilitate the uptake through E. coli general porins. The assembled library was screened by ensemble docking to AcrA, the periplasmic component of the AcrAB-TolC efflux pump, followed by experimental testing of the top predicted binders for antibacterial activities, efflux recognition, and inhibition. We found that the filtered primary amine library is a rich source of compounds with efflux-inhibiting activities and identified efflux pump inhibitors with novel chemical scaffolds effective against E. coli AcrAB-TolC and efflux pumps of multidrug-resistant clinical isolates of Acinetobacter baumannii. However, primary amines are not required for the recognition of compounds by efflux pumps and their efflux-inhibitory activities.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Muhammad R Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
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11
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Krishnan R S, Jana K, Shaji AH, Nair KS, Das AD, Vikraman D, Bajaj H, Kleinekathöfer U, Mahendran KR. Assembly of transmembrane pores from mirror-image peptides. Nat Commun 2022; 13:5377. [PMID: 36104348 PMCID: PMC9474448 DOI: 10.1038/s41467-022-33155-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Tailored transmembrane alpha-helical pores with desired structural and functional versatility have promising applications in nanobiotechnology. Herein, we present a transmembrane pore DpPorA, based on the natural pore PorACj, built from D-amino acid α-helical peptides. Using single-channel current recordings, we show that DpPorA peptides self-assemble into uniform cation-selective pores in lipid membranes and exhibit properties distinct from their L-amino acid counterparts. DpPorA shows resistance to protease and acts as a functional nanopore sensor to detect cyclic sugars, polypeptides, and polymers. Fluorescence imaging reveals that DpPorA forms well-defined pores in giant unilamellar vesicles facilitating the transport of hydrophilic molecules. A second D-amino acid peptide based on the polysaccharide transporter Wza forms transient pores confirming sequence specificity in stable, functional pore formation. Finally, molecular dynamics simulations reveal the specific alpha-helical packing and surface charge conformation of the D-pores consistent with experimental observations. Our findings will aid the design of sophisticated pores for single-molecule sensing related technologies. Alpha-helix nanopores have a range of potential applications and the inclusion of non-natural amino acids allows for modification. Here, the authors report on the creation of alpha-helix pores using D-amino acids and show the pores formed, have different properties to the L-counterparts and were resistant to proteases.
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12
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Al Nahas K, Fletcher M, Hammond K, Nehls C, Cama J, Ryadnov MG, Keyser UF. Measuring Thousands of Single-Vesicle Leakage Events Reveals the Mode of Action of Antimicrobial Peptides. Anal Chem 2022; 94:9530-9539. [PMID: 35760038 PMCID: PMC9280716 DOI: 10.1021/acs.analchem.1c03564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Host defense or antimicrobial
peptides hold promise for providing
new pipelines of effective antimicrobial agents. Their activity quantified
against model phospholipid membranes is fundamental to a detailed
understanding of their structure–activity relationships. However,
classical characterization assays often lack the ability to achieve
this insight. Leveraging a highly parallelized microfluidic platform
for trapping and studying thousands of giant unilamellar vesicles,
we conducted quantitative long-term microscopy studies to monitor
the membrane-disruptive activity of archetypal antimicrobial peptides
with a high spatiotemporal resolution. We described the modes of action
of these peptides via measurements of the disruption of the vesicle
population under the conditions of continuous peptide dosing using
a range of concentrations and related the observed modes to the molecular
activity mechanisms of these peptides. The study offers an effective
approach for characterizing membrane-targeting antimicrobial agents
in a standardized manner and for assigning specific modes of action
to the corresponding antimicrobial mechanisms.
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Affiliation(s)
- Kareem Al Nahas
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Marcus Fletcher
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K.,London Centre for Nanotechnology, University College London, London WC1H 0AH, U.K
| | - Christian Nehls
- Research Center Borstel, Leibniz Lung Center, Parkallee 10, Borstel 23845, Germany
| | - Jehangir Cama
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K.,Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, North Park Road, Exeter EX4 4QF, U.K
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K.,Department of Physics, King's College London, Strand Lane, London WC2R 2LS, U.K
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K
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13
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Popella L, Jung J, Do PT, Hayward RJ, Barquist L, Vogel J. Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli. Nucleic Acids Res 2022; 50:6435-6452. [PMID: 35687096 PMCID: PMC9226493 DOI: 10.1093/nar/gkac362] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) that target mRNAs of essential bacterial genes exhibit specific bactericidal effects in several microbial species, but our mechanistic understanding of PNA activity and their target gene spectrum is limited. Here, we present a systematic analysis of PNAs targeting 11 essential genes with varying expression levels in uropathogenic Escherichia coli (UPEC). We demonstrate that UPEC is susceptible to killing by peptide-conjugated PNAs, especially when targeting the widely-used essential gene acpP. Our evaluation yields three additional promising target mRNAs for effective growth inhibition, i.e.dnaB, ftsZ and rpsH. The analysis also shows that transcript abundance does not predict target vulnerability and that PNA-mediated growth inhibition is not universally associated with target mRNA depletion. Global transcriptomic analyses further reveal PNA sequence-dependent but also -independent responses, including the induction of envelope stress response pathways. Importantly, we show that 9mer PNAs are generally as effective in inhibiting bacterial growth as their 10mer counterparts. Overall, our systematic comparison of a range of PNAs targeting mRNAs of different essential genes in UPEC suggests important features for PNA design, reveals a general bacterial response to PNA conjugates and establishes the feasibility of using PNA antibacterials to combat UPEC.
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Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
| | - Phuong Thao Do
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
| | - Regan J Hayward
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080, Würzburg, Germany
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14
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Vikraman D, Satheesan R, Rajendran M, Kumar NA, Johnson JB, R SK, Mahendran KR. Selective Translocation of Cyclic Sugars through Dynamic Bacterial Transporter. ACS Sens 2022; 7:1766-1776. [PMID: 35671512 DOI: 10.1021/acssensors.2c00943] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The selective translocation of molecules through membrane pores is an integral process in cells. We present a bacterial sugar transporter, CymA of unusual structural conformation due to a dynamic N terminus segment in the pore, reducing its diameter. We quantified the translocation kinetics of various cyclic sugars of different charge, size, and symmetry across native and truncated CymA devoid of the N terminus using single-channel recordings. The chemically divergent cyclic hexasaccharides bind to the native and truncated pore with high affinity and translocate effectively. Specifically, these sugars bind and translocate rapidly through truncated CymA compared to native CymA. In contrast, larger cyclic heptasaccharides and octasaccharides do not translocate but bind to native and truncated CymA with distinct binding kinetics highlighting the importance of molecular charge, size and symmetry in translocation consistent with liposome assays. Based on the sugar-binding kinetics, we suggest that the N terminus most likely resides inside the native CymA barrel, regulating the transport rate of cyclic sugars. Finally, we present native CymA as a large nanopore sensor for the simultaneous single-molecule detection of various sugars at high resolution, establishing its functional versatility. This natural pore is expected to have several applications in nanobiotechnology and will help further our understanding of the fundamental mechanism of molecular transport.
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Affiliation(s)
- Devika Vikraman
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Remya Satheesan
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Mangaiyarkarasi Rajendran
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Nisha Asok Kumar
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.,Pathogen Biology, Virology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - John Bernet Johnson
- Pathogen Biology, Virology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Smrithi Krishnan R
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
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15
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Biswas A, Maitra U. Ratiometric rapid distinction of two structurally similar fluoroquinolone antibiotics by a Tb/Eu hydrogel. RSC Adv 2022; 12:26106-26110. [PMID: 36275113 PMCID: PMC9477015 DOI: 10.1039/d2ra03668a] [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: 06/14/2022] [Accepted: 09/03/2022] [Indexed: 11/21/2022] Open
Abstract
Rapid distinction of structurally similar fluoroquinolone antibiotics norfloxacin and ofloxacin, and their quantification in a mixture, were achieved using a supramolecular Tb/Eu gel cocktail.
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Affiliation(s)
- Ananya Biswas
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Uday Maitra
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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16
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Application of antibiotic-derived fluorescent probes to bacterial studies. Methods Enzymol 2022; 665:1-28. [DOI: 10.1016/bs.mie.2021.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Shetty S, Yandrapalli N, Pinkwart K, Krafft D, Vidakovic-Koch T, Ivanov I, Robinson T. Directed Signaling Cascades in Monodisperse Artificial Eukaryotic Cells. ACS NANO 2021; 15:15656-15666. [PMID: 34570489 PMCID: PMC8552445 DOI: 10.1021/acsnano.1c04219] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Indexed: 05/28/2023]
Abstract
The bottom-up assembly of multicompartment artificial cells that are able to direct biochemical reactions along a specific spatial pathway remains a considerable engineering challenge. In this work, we address this with a microfluidic platform that is able to produce monodisperse multivesicular vesicles (MVVs) to serve as synthetic eukaryotic cells. Using a two-inlet polydimethylsiloxane channel design to co-encapsulate different populations of liposomes we are able to produce lipid-based MVVs in a high-throughput manner and with three separate inner compartments, each containing a different enzyme: α-glucosidase, glucose oxidase, and horseradish peroxidase. We demonstrate the ability of these MVVs to carry out directed chemical communication between the compartments via the reconstitution of size-selective membrane pores. Therefore, the signal transduction, which is triggered externally, follows a specific spatial pathway between the compartments. We use this platform to study the effects of enzyme cascade compartmentalization by direct analytical comparison between bulk, one-, two-, and three-compartment systems. This microfluidic strategy to construct complex hierarchical structures is not only suitable to study compartmentalization effects on biochemical reactions but is also applicable for developing advanced drug delivery systems as well as minimal cells in the field of bottom-up synthetic biology.
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Affiliation(s)
- Sunidhi
C. Shetty
- Theory
and Bio-Systems, Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Naresh Yandrapalli
- Theory
and Bio-Systems, Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Kerstin Pinkwart
- Theory
and Bio-Systems, Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Dorothee Krafft
- Max
Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Tanja Vidakovic-Koch
- Max
Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Ivan Ivanov
- Max
Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Tom Robinson
- Theory
and Bio-Systems, Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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18
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Moreira J, Vale AC, Alves NM. Spin-coated freestanding films for biomedical applications. J Mater Chem B 2021; 9:3778-3799. [PMID: 33876170 DOI: 10.1039/d1tb00233c] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Spin-coating is a widely employed technique for the fabrication of thin-film coatings over large areas with smooth and homogeneous surfaces. In recent years, research has extended the scope of spin-coating by developing methods involving the interface of the substrate and the deposited solution to obtain self-supported films, also called freestanding films. Thereby, such structures have been developed for a wide range of areas. Biomedical applications of spin-coated freestanding films include wound dressings, drug delivery, and biosensing. This review will discuss the fundamental physical and chemical processes governing the conventional spin-coating as well as the techniques to obtain freestanding films. Furthermore, developments within this field with a primary focus on tissue engineering applications will be reviewed.
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Affiliation(s)
- Joana Moreira
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal. and ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - A Catarina Vale
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal. and ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Natália M Alves
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal. and ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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19
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Golubchik A, Lopes LC, Singh V, Kuss S. Pharma‐molecule Transport across Bacterial Membranes: Detection and Quantification Approaches by Electrochemistry and Bioanalytical Methods. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alon Golubchik
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
| | | | - Vikram Singh
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
| | - Sabine Kuss
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
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20
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Alegun O, Pandeya A, Cui J, Ojo I, Wei Y. Donnan Potential across the Outer Membrane of Gram-Negative Bacteria and Its Effect on the Permeability of Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10060701. [PMID: 34208097 PMCID: PMC8230823 DOI: 10.3390/antibiotics10060701] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
The cell envelope structure of Gram-negative bacteria is unique, composed of two lipid bilayer membranes and an aqueous periplasmic space sandwiched in between. The outer membrane constitutes an extra barrier to limit the exchange of molecules between the cells and the exterior environment. Donnan potential is a membrane potential across the outer membrane, resulted from the selective permeability of the membrane, which plays a pivotal role in the permeability of many antibiotics. In this review, we discussed factors that affect the intensity of the Donnan potential, including the osmotic strength and pH of the external media, the osmoregulated periplasmic glucans trapped in the periplasmic space, and the displacement of cell surface charges. The focus of our discussion is the impact of Donnan potential on the cellular permeability of selected antibiotics including fluoroquinolones, tetracyclines, β-lactams, and trimethoprim.
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Affiliation(s)
| | | | | | | | - Yinan Wei
- Correspondence: ; Tel.: +1-8592577085
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21
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Golubchik A, Lopes LC, Singh V, Kuss S. Pharma-molecule Transport across Bacterial Membranes: Detection and Quantification Approaches by Electrochemistry and Bioanalytical Methods. Angew Chem Int Ed Engl 2021; 60:22112-22124. [PMID: 33979000 DOI: 10.1002/anie.202101055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 11/07/2022]
Abstract
Antibiotic resistance is a significant challenge encountered by healthcare systems on a global scale. Knowledge about membrane transport of antibiotics and other pharmacologically relevant molecules in bacteria is crucial towards understanding and overcoming antibiotic resistance, as drug resistance often depends on drug transport. This comprehensive literature review discusses the detection and quantification of membrane transport of pharma-molecules in bacteria and highlights the importance of molecule transport to antibiotic resistance. This review emphasizes electrochemical and electrophysiological methods of detection and quantification. The results of this literature review reveal a substantial diversity in methods and types of quantitative information collected.
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Affiliation(s)
- Alon Golubchik
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | | | - Vikram Singh
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Sabine Kuss
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
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22
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Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev 2021; 121:5597-5631. [PMID: 33596653 DOI: 10.1021/acs.chemrev.0c01137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhen Zhang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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23
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Vignoli Muniz GS, Souza MC, Duarte EL, Lamy MT. Comparing the interaction of the antibiotic levofloxacin with zwitterionic and anionic membranes: Calorimetry, fluorescence, and spin label studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183622. [PMID: 33865809 DOI: 10.1016/j.bbamem.2021.183622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
The present work compares the interaction of the antibiotic levofloxacin (LVX) with zwitterionic and anionic liposomes composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG), respectively. By using differential scanning calorimetry (DSC), and with spin labels incorporated into liposomes at two different depths of the bilayers, we investigated the changes induced on the membrane by increasing concentrations of LVX. Further information was obtained using intrinsic LVX fluorescence. Under the conditions used here, all techniques evinced that LVX has little affinity for DPPC zwitterionic membrane. Opposite to that, LVX exhibits a considerable affinity for anionic bilayers, with membrane partition constants Kp = (3.3 ± 0.5) × 102 and (4.5 ± 0.3) × 102, for gel and fluid DPPG membranes, respectively. On binding to DPPG, LVX seems to give rise to the coexistence of LVX -rich and -poor domains on DPPG membranes, as detected by DSC. At the highest LVX concentration used (20 mol%), DSC trace shows an increase in the cooperativity of DPPG gel-fluid transition, also detected by spin labels as an increase in the bilayer packing. Moreover, LVX does not induce pore formation in either DPPG or POPG vesicles. Considering the possible relevance of LVX-membrane interaction for the biological and toxicological action of the antibiotic, the findings discussed here certainly contribute to a better understanding of its action, and the planning of new drugs.
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Affiliation(s)
| | - Mariana C Souza
- Instituto de Física, Universidade de São Paulo, São Paulo, SP CEP 05508-090, Brazil
| | - Evandro L Duarte
- Instituto de Física, Universidade de São Paulo, São Paulo, SP CEP 05508-090, Brazil
| | - M Teresa Lamy
- Instituto de Física, Universidade de São Paulo, São Paulo, SP CEP 05508-090, Brazil.
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24
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Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
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25
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Kaur J, Ghorbanpoor H, Öztürk Y, Kaygusuz Ö, Avcı H, Darcan C, Trabzon L, Güzel FD. On‐chip label‐free impedance‐based detection of antibiotic permeation. IET Nanobiotechnol 2021; 15:100-106. [PMID: 34694729 PMCID: PMC8675796 DOI: 10.1049/nbt2.12019] [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] [Received: 07/15/2020] [Revised: 10/14/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022] Open
Abstract
Biosensors are analytical tools used for the analysis of biomaterial samples and provide an understanding about the biocomposition, structure, and function of biomolecules and/or biomechanisms by converting the biological response into an electrical and/or optical signal. In particular, with the rise in antibiotic resistance amongst pathogenic bacteria, the study of antibiotic activity and transport across cell membranes in the field of biosensors has been gaining widespread importance. Herein, for the rapid and label‐free detection of antibiotic permeation across a membrane, a microelectrode integrated microfluidic device is presented. The integrated chip consists of polydimethylsiloxane based microfluidic channels bonded onto microelectrodes on‐glass and enables us to recognize the antibiotic permeation across a membrane into the model membranes based on electrical impedance measurement, while also allowing optical monitoring. Impedance testing is label free and therefore allows the detection of both fluorescent and non‐fluorescent antibiotics. As a model membrane, Giant Unilamellar Vesicles (GUVs) are used and impedance measurements were performed by a precision inductance, capacitance, and resistance metre. The measured signal recorded from the device was used to determine the change in concentration inside and outside of the GUVs. We have found that permeation of antibiotic molecules can be easily monitored over time using the proposed integrated device. The results also show a clear difference between bilayer permeation that occurs through the lipidic bilayer and porin‐mediated permeation through the porin channels inserted in the lipid bilayer.
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Affiliation(s)
- Jaspreet Kaur
- Department of Electrical and Electronic Engineering Yıldırım Beyazıt University Ankara Turkey
| | - Hamed Ghorbanpoor
- Department of Biomedical Engineering Yıldırım Beyazıt University Ankara Turkey
| | - Yasin Öztürk
- Department of Material Engineering Yıldırım Beyazıt University Ankara Turkey
| | - Özge Kaygusuz
- Biotechnology Application and Research Center Bilecik Şeyh Edebali University Bilecik Turkey
| | - Hüseyin Avcı
- Metallurgical and Materials Engineering Department Eskisehir Osmangazi University Eskisehir Turkey
- Cellular Therapy and Stem Cell Research Center (ESTEM) Eskisehir Osmangazi University Eskisehir Turkey
- AvciBio Research Group Eskisehir Osmangazi University Eskisehir Turkey
| | - Cihan Darcan
- Biotechnology Application and Research Center Bilecik Şeyh Edebali University Bilecik Turkey
- Department of Molecular Biology and Genetics Bilecik Seyh Edebali University Bilecik Turkey
| | - Levent Trabzon
- Department of Mechanical Engineering Istanbul Technical University Istanbul Turkey
- Nanotechnology Research and Application Center – ITUnano Istanbul Technical University Istanbul Turkey
| | - Fatma D. Güzel
- Department of Biomedical Engineering Yıldırım Beyazıt University Ankara Turkey
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26
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Carbon Source Influence on Extracellular pH Changes along Bacterial Cell-Growth. Genes (Basel) 2020; 11:genes11111292. [PMID: 33142974 PMCID: PMC7693008 DOI: 10.3390/genes11111292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/24/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
The effect of initial pH on bacterial cell-growth and its change over time was studied under aerobic heterotrophic conditions by using three bacterial strains: Escherichia coli ATCC 25922, Pseudomonas putida KT2440, and Pseudomonas pseudoalcaligenes CECT 5344. In Luria-Bertani (LB) media, pH evolved by converging to a certain value that is specific for each bacterium. By contrast, in the buffered Minimal Medium (MM), pH was generally more stable along the growth curve. In MM with glucose as carbon source, a slight acidification of the medium was observed for all strains. In the case of E. coli, a sudden drop in pH was observed during exponential cell growth that was later recovered at initial pH 7 or 8, but was irreversible below pH 6, thus arresting further cell-growth. When using other carbon sources in MM at a fixed initial pH, pH changes depended mainly on the carbon source itself. While glucose, glycerol, or octanoate slightly decreased extracellular pH, more oxidized carbon sources, such as citrate, 2-furoate, 2-oxoglutarate, and fumarate, ended up with the alkalinization of the medium. These observations are in accordance with pH change predictions using genome-scale metabolic models for the three strains, thus revealing the metabolic reasons behind pH change. Therefore, we conclude that the composition of the medium, specifically the carbon source, determines pH change during bacterial growth to a great extent and unravel the main molecular mechanism behind this phenotype. These findings pave the way for predicting pH changes in a given bacterial culture and may anticipate the interspecies interactions and fitness of bacteria in their environment.
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27
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Wang J, Prajapati JD, Kleinekathöfer U, Winterhalter M. Dynamic interaction of fluoroquinolones with magnesium ions monitored using bacterial outer membrane nanopores. Chem Sci 2020; 11:10344-10353. [PMID: 34094296 PMCID: PMC8162440 DOI: 10.1039/d0sc03486j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/30/2020] [Indexed: 01/05/2023] Open
Abstract
Divalent ions are known to have a severe effect on the translocation of several antibiotic molecules into (pathogenic) bacteria. In the present study we have investigated the effect of divalent ions on the permeability of norfloxacin across the major outer membrane channels from E. coli (OmpF and OmpC) and E. aerogenes (Omp35 and Omp36) at the single channel level. To understand the rate limiting steps in permeation, we reconstituted single porins into planar lipid bilayers and analyzed the ion current fluctuations caused in the presence of norfloxacin. Moreover, to obtain an atomistic view, we complemented the experiments with millisecond-long free energy calculations based on temperature-accelerated Brownian dynamics simulations to identify the most probable permeation pathways of the antibiotics through the respective pores. Both, the experimental analysis and the computational modelling, suggest that norfloxacin is able to permeate through the larger porins, i.e., OmpF, OmpC, and Omp35, whereas it only binds to the slightly narrower porin Omp36. Moreover, divalent ions can bind to negatively charged residues inside the porin, reversing the ion selectivity of the pore. In addition, the divalent ions can chelate with the fluoroquinolone molecules and alter their physicochemical properties. The results suggest that the conjugation with either pores or molecules must break when the antibiotic molecules pass the lumen of the porin, with the conjugation to the antibiotic being more stable than that to the respective pore. In general, the permeation or binding process of fluoroquinolones in porins occurs irrespective of the presence of divalent ions, but the presence of divalent ions can vary the kinetics significantly. Thus, a detailed investigation of the interplay of divalent ions with antibiotics and pores is of key importance in developing new antimicrobial drugs.
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Affiliation(s)
- Jiajun Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | | | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen 28759 Bremen Germany
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28
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Cama J, Voliotis M, Metz J, Smith A, Iannucci J, Keyser UF, Tsaneva-Atanasova K, Pagliara S. Single-cell microfluidics facilitates the rapid quantification of antibiotic accumulation in Gram-negative bacteria. LAB ON A CHIP 2020; 20:2765-2775. [PMID: 32613221 PMCID: PMC7953842 DOI: 10.1039/d0lc00242a] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/15/2020] [Indexed: 06/01/2023]
Abstract
The double-membrane cell envelope of Gram-negative bacteria is a formidable barrier to intracellular antibiotic accumulation. A quantitative understanding of antibiotic transport in these cells is crucial for drug development, but this has proved elusive due to a dearth of suitable investigative techniques. Here we combine microfluidics and time-lapse auto-fluorescence microscopy to rapidly quantify antibiotic accumulation in hundreds of individual Escherichia coli cells. By serially manipulating the microfluidic environment, we demonstrated that stationary phase Escherichia coli, traditionally more refractory to antibiotics than growing cells, display reduced accumulation of the antibiotic ofloxacin compared to actively growing cells. Our novel microfluidic method facilitates the quantitative comparison of the role of the microenvironment versus that of the absence of key membrane transport pathways in cellular drug accumulation. Unlike traditional techniques, our assay is rapid, studying accumulation as the cells are dosed with the drug. This platform provides a powerful new tool for studying antibiotic accumulation in bacteria, which will be critical for the rational development of the next generation of antibiotics.
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Affiliation(s)
- Jehangir Cama
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
- Cavendish Laboratory
, Department of Physics
, University of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
| | - Margaritis Voliotis
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
| | - Jeremy Metz
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Ashley Smith
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Jari Iannucci
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Ulrich F. Keyser
- Cavendish Laboratory
, Department of Physics
, University of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
| | - Stefano Pagliara
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
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29
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Reuter A, Virolle C, Goldlust K, Berne-Dedieu A, Nolivos S, Lesterlin C. Direct visualisation of drug-efflux in liveEscherichia colicells. FEMS Microbiol Rev 2020; 44:782-792. [DOI: 10.1093/femsre/fuaa031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACTDrug-efflux by pump proteins is one of the major mechanisms of antibiotic resistance in bacteria. Here, we use quantitative fluorescence microscopy to investigate the real-time dynamics of drug accumulation and efflux in live E. coli cells. We visualize simultaneously the intrinsically fluorescent protein-synthesis inhibitor tetracycline (Tc) and the fluorescently labelled Tc-specific efflux pump, TetA. We show that Tc penetrates the cells within minutes and accumulates to stable intracellular concentration after ∼20 min. The final level of drug accumulation reflects the balance between Tc-uptake by the cells and Tc-efflux by pump proteins. In wild-type Tc-sensitive cells, drug accumulation is significantly limited by the activity of the multidrug efflux pump, AcrAB-TolC. Tc-resistance wild-type cells carrying a plasmid-borne Tn10 transposon contain variable amounts of TetA protein, produced under steady-state repression by the TetR repressor. TetA content heterogeneity determines the cells’ initial ability to efflux Tc. Yet, efflux remains partial until the synthesis of additional TetA pumps allows for Tc-efflux activity to surpass Tc-uptake. Cells overproducing TetA no longer accumulate Tc and become resistant to high concentrations of the drug. This work uncovers the dynamic balance between drug entry, protein-synthesis inhibition, efflux-pump production, drug-efflux activity and drug-resistance levels.
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Affiliation(s)
- Audrey Reuter
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Chloé Virolle
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Kelly Goldlust
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Annick Berne-Dedieu
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Sophie Nolivos
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Christian Lesterlin
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
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30
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Li MF, Jia BB, Sun YY, Sun L. The Translocation and Assembly Module (TAM) of Edwardsiella tarda Is Essential for Stress Resistance and Host Infection. Front Microbiol 2020; 11:1743. [PMID: 32793174 PMCID: PMC7393178 DOI: 10.3389/fmicb.2020.01743] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/03/2020] [Indexed: 11/28/2022] Open
Abstract
Translocation and assembly module (TAM) is a protein channel known to mediate the secretion of virulence factors during pathogen infection. Edwardsiella tarda is a Gram-negative bacterium that is pathogenic to a wide range of farmed fish and other hosts including humans. In this study, we examined the function of the two components of the TAM, TamA and TamB, of E. tarda (named tamAEt and tamBEt, respectively). TamAEt was found to localize on the surface of E. tarda and be recognizable by TamAEt antibody. Compared to the wild type, the tamA and tamB knockouts, TX01ΔtamA and TX01ΔtamB, respectively, were significantly reduced in motility, flagella formation, invasion into host cells, intracellular replication, dissemination in host tissues, and inducing host mortality. The lost virulence capacities of TX01ΔtamA and TX01ΔtamB were restored by complementation with the tamAEt and tamBEt genes, respectively. Furthermore, TX01ΔtamA and TX01ΔtamB were significantly impaired in the ability to survive under low pH and oxidizing conditions, and were unable to maintain their internal pH balance and cellular structures in acidic environments, which led to increased susceptibility to lysozyme destruction. Taken together, these results indicate that TamAEt and TamBEt are essential for the virulence of E. tarda and required for E. tarda to survive under stress conditions.
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Affiliation(s)
- Mo-Fei Li
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bei-Bei Jia
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan-Yuan Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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31
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Schaich M, Sobota D, Sleath H, Cama J, Keyser UF. Characterization of lipid composition and diffusivity in OLA generated vesicles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183359. [PMID: 32416194 PMCID: PMC7322398 DOI: 10.1016/j.bbamem.2020.183359] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/15/2020] [Accepted: 05/11/2020] [Indexed: 11/19/2022]
Abstract
Giant Unilamellar Vesicles (GUVs) are a versatile tool in many branches of science, including biophysics and synthetic biology. Octanol-Assisted Liposome Assembly (OLA), a recently developed microfluidic technique enables the production and testing of GUVs within a single device under highly controlled experimental conditions. It is therefore gaining significant interest as a platform for use in drug discovery, the production of artificial cells and more generally for controlled studies of the properties of lipid membranes. In this work, we expand the capabilities of the OLA technique by forming GUVs of tunable binary lipid mixtures of DOPC, DOPG and DOPE. Using fluorescence recovery after photobleaching we investigated the lateral diffusion coefficients of lipids in OLA liposomes and found the expected values in the range of 1 μm2/s for the lipid systems tested. We studied the OLA derived GUVs under a range of conditions and compared the results with electroformed vesicles. Overall, we found the lateral diffusion coefficients of lipids in vesicles obtained with OLA to be quantitatively similar to those in vesicles obtained via traditional electroformation. Our results provide a quantitative biophysical validation of the quality of OLA derived GUVs, which will facilitate the wider use of this versatile platform.
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Affiliation(s)
- Michael Schaich
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Diana Sobota
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Hannah Sleath
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jehangir Cama
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom; Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom; College of Engineering, Mathematics and Physical Sciences, University of Exeter, Harrison Building, Streatham Campus, North Park Road, Exeter EX4 4QF, United Kingdom.
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom.
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32
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Mohanan G, Nair KS, Nampoothiri KM, Bajaj H. Engineering bio-mimicking functional vesicles with multiple compartments for quantifying molecular transport. Chem Sci 2020; 11:4669-4679. [PMID: 34122921 PMCID: PMC8159255 DOI: 10.1039/d0sc00084a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Controlled design of giant unilamellar vesicles under defined conditions has vast applications in the field of membrane and synthetic biology. Here, we bio-engineer bacterial-membrane mimicking models of controlled size under defined salt conditions over a range of pH. A complex bacterial lipid extract is used for construction of physiologically relevant Gram-negative membrane mimicking vesicles whereas a ternary mixture of charged lipids (DOPG, cardiolipin and lysyl-PG) is used for building Gram-positive bacterial-membrane vesicles. Furthermore, we construct stable multi-compartment biomimicking vesicles using the gel-assisted swelling method. Importantly, we validate the bio-application of the bacterial vesicle models by quantifying diffusion of chemically synthetic amphoteric antibiotics. The transport rate is pH-responsive and depends on the lipid composition, based on which a permeation model is proposed. The permeability properties of antimicrobial peptides reveal pH dependent pore-forming activity in the model vesicles. Finally, we demonstrate the functionality of the vesicles by quantifying the uptake of membrane-impermeable molecules facilitated by embedded pore-forming proteins. We suggest that the bacterial vesicle models developed here can be used to understand fundamental biological processes like the peptide assembly mechanism or bacterial cell division and will have a multitude of applications in the bottom-up assembly of a protocell. Giant vesicle functional models mimicking a bacterial membrane under physiological conditions are constructed.![]()
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Affiliation(s)
- Gayathri Mohanan
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST) Trivandrum 695019 Kerala India
| | - Karthika S Nair
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST) Trivandrum 695019 Kerala India
| | - K Madhavan Nampoothiri
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST) Trivandrum 695019 Kerala India
| | - Harsha Bajaj
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST) Trivandrum 695019 Kerala India
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33
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Breaching the Barrier: Quantifying Antibiotic Permeability across Gram-negative Bacterial Membranes. J Mol Biol 2019; 431:3531-3546. [DOI: 10.1016/j.jmb.2019.03.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/29/2019] [Accepted: 03/28/2019] [Indexed: 11/22/2022]
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34
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Schaich M, Cama J, Al Nahas K, Sobota D, Sleath H, Jahnke K, Deshpande S, Dekker C, Keyser UF. An Integrated Microfluidic Platform for Quantifying Drug Permeation across Biomimetic Vesicle Membranes. Mol Pharm 2019; 16:2494-2501. [PMID: 30994358 DOI: 10.1021/acs.molpharmaceut.9b00086] [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] [Indexed: 01/08/2023]
Abstract
The low membrane permeability of candidate drug molecules is a major challenge in drug development, and insufficient permeability is one reason for the failure of antibiotic treatment against bacteria. Quantifying drug transport across specific pathways in living systems is challenging because one typically lacks knowledge of the exact lipidome and proteome of the individual cells under investigation. Here, we quantify drug permeability across biomimetic liposome membranes, with comprehensive control over membrane composition. We integrate the microfluidic octanol-assisted liposome assembly platform with an optofluidic transport assay to create a complete microfluidic total analysis system for quantifying drug permeability. Our system enables us to form liposomes with charged lipids mimicking the negative charge of bacterial membranes at physiological pH and salt concentrations, which proved difficult with previous liposome formation techniques. Furthermore, the microfluidic technique yields an order of magnitude more liposomes per experiment than previous assays. We demonstrate the feasibility of the assay by determining the permeability coefficient of norfloxacin and ciprofloxacin across biomimetic liposomes.
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Affiliation(s)
- Michael Schaich
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Jehangir Cama
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K.,Living Systems Institute , University of Exeter , Stocker Road , Exeter EX4 4QD , U.K
| | - Kareem Al Nahas
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Diana Sobota
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Hannah Sleath
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Kevin Jahnke
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K.,Department of Biophysical Chemistry , University of Heidelberg , Im Neuenheimer Feld 253 , D-69120 Heidelberg , Germany.,Department of Cellular Biophysics , Max Planck Institute for Medical Research , Jahnstraße 29 , D-69120 Heidelberg , Germany
| | - Siddharth Deshpande
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , Van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , Van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Ulrich F Keyser
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
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35
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Gayen A, Kumar D, Matheshwaran S, Chandra M. Unveiling the Modulating Role of Extracellular pH in Permeation and Accumulation of Small Molecules in Subcellular Compartments of Gram-negative Escherichia coli using Nonlinear Spectroscopy. Anal Chem 2019; 91:7662-7671. [PMID: 30986344 DOI: 10.1021/acs.analchem.9b00574] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Quantitative evaluation of small molecule permeation and accumulation in Gram-negative bacteria is important for drug development against these bacteria. While these measurements are commonly performed at physiological pH, Escherichia coli and many other Enterobacteriaceae infect human gastrointestinal and urinary tracts, where they encounter different pH conditions. To understand how external pH affects permeation and accumulation of small molecules in E. coli cells, we apply second harmonic generation (SHG) spectroscopy using SHG-active antimicrobial compound malachite green as the probe molecule. Using SHG, we quantify periplasmic and cytoplasmic accumulations separately in live E. coli cells, which was never done before. Compartment-wise measurements reveal accumulation of the probe molecule in cytoplasm at physiological and alkaline pH, while entrapment in periplasm at weakly acidic pH and retention in external solution at highly acidic pH. Behind such disparity in localizations, up to 2 orders of magnitude reduction in permeability across the inner membrane at weakly acidic pH and outer membrane at highly acidic pH are found to play key roles. Our results unequivocally demonstrate the control of external pH over entry and compartment-wise distribution of small molecules in E. coli cells, which is a vital information and should be taken into account in antibiotic screening against E. coli and other Enterobacteriaceae members. In addition, our results demonstrate the ability of malachite green as an excellent SHG-indicator of changes of individual cell membrane and periplasm properties of live E. coli cells in response to external pH change from acidic to alkaline. This finding, too, has great importance, as there is barely any other molecular probe that can provide similar information.
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36
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Gumz H, Boye S, Iyisan B, Krönert V, Formanek P, Voit B, Lederer A, Appelhans D. Toward Functional Synthetic Cells: In-Depth Study of Nanoparticle and Enzyme Diffusion through a Cross-Linked Polymersome Membrane. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1801299. [PMID: 30989019 PMCID: PMC6446602 DOI: 10.1002/advs.201801299] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/04/2018] [Indexed: 05/19/2023]
Abstract
Understanding the diffusion of nanoparticles through permeable membranes in cell mimics paves the way for the construction of more sophisticated synthetic protocells with control over the exchange of nanoparticles or biomacromolecules between different compartments. Nanoparticles postloading by swollen pH switchable polymersomes is investigated and nanoparticles locations at or within polymersome membrane and polymersome lumen are precisely determined. Validation of transmembrane diffusion properties is performed based on nanoparticles of different origin-gold, glycopolymer protein mimics, and the enzymes myoglobin and esterase-with dimensions between 5 and 15 nm. This process is compared with the in situ loading of nanoparticles during polymersome formation and analyzed by advanced multiple-detector asymmetrical flow field-flow fractionation (AF4). These experiments are supported by complementary i) release studies of protein mimics from polymersomes, ii) stability and cyclic pH switches test for in polymersome encapsulated myoglobin, and iii) cryogenic transmission electron microscopy studies on nanoparticles loaded polymersomes. Different locations (e.g., membrane and/or lumen) are identified for the uptake of each protein. The protein locations are extracted from the increasing scaling parameters and the decreasing apparent density of enzyme-containing polymersomes as determined by AF4. Postloading demonstrates to be a valuable tool for the implementation of cell-like functions in polymersomes.
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Affiliation(s)
- Hannes Gumz
- Leibniz‐Institut für Polymerforschung Dresden e.V.Hohe Straße 601069DresdenGermany
- School of ScienceFaculty of Chemistry and Food ChemistryTechnische Universität Dresden01062DresdenGermany
- Cluster of Excellence “Center for Advancing Electronics Dresden”Technische Universität Dresden01062DresdenGermany
| | - Susanne Boye
- Leibniz‐Institut für Polymerforschung Dresden e.V.Hohe Straße 601069DresdenGermany
| | - Banu Iyisan
- Max‐Planck‐Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Vera Krönert
- Leibniz‐Institut für Polymerforschung Dresden e.V.Hohe Straße 601069DresdenGermany
| | - Petr Formanek
- Leibniz‐Institut für Polymerforschung Dresden e.V.Hohe Straße 601069DresdenGermany
| | - Brigitte Voit
- Leibniz‐Institut für Polymerforschung Dresden e.V.Hohe Straße 601069DresdenGermany
- School of ScienceFaculty of Chemistry and Food ChemistryTechnische Universität Dresden01062DresdenGermany
- Cluster of Excellence “Center for Advancing Electronics Dresden”Technische Universität Dresden01062DresdenGermany
| | - Albena Lederer
- Leibniz‐Institut für Polymerforschung Dresden e.V.Hohe Straße 601069DresdenGermany
- School of ScienceFaculty of Chemistry and Food ChemistryTechnische Universität Dresden01062DresdenGermany
| | - Dietmar Appelhans
- Leibniz‐Institut für Polymerforschung Dresden e.V.Hohe Straße 601069DresdenGermany
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37
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Scorciapino MA, Malloci G, Serra I, Milenkovic S, Moynié L, Naismith JH, Desarbre E, Page MGP, Ceccarelli M. Complexes formed by the siderophore-based monosulfactam antibiotic BAL30072 and their interaction with the outer membrane receptor PiuA of P. aeruginosa. Biometals 2019; 32:155-170. [DOI: 10.1007/s10534-018-00166-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/20/2018] [Indexed: 10/27/2022]
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38
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Puri SR, Kim J. Kinetics of Antimicrobial Drug Ion Transfer at a Water/Oil Interface Studied by Nanopipet Voltammetry. Anal Chem 2019; 91:1873-1879. [DOI: 10.1021/acs.analchem.8b03593] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Surendra Raj Puri
- Department of Chemistry, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Jiyeon Kim
- Department of Chemistry, The University of Rhode Island, Kingston, Rhode Island 02881, United States
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39
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Terrasse R, Winterhalter M. Translocation of small molecules through engineered outer-membrane channels from Gram-negative bacteria. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:111. [PMID: 30238205 DOI: 10.1140/epje/i2018-11721-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/28/2018] [Indexed: 06/08/2023]
Abstract
Selective permeability is a key feature of biological membranes. It is controlled by the physico-chemical properties of the lipid bilayer and by channel-forming membrane proteins. Here we focus on the permeation of small molecules across channel-forming proteins in Gram-negative bacteria called porins and present a new approach based on artificial amino acids. We introduced Hco, a fluorescent amino acid with characteristic excitation and emission wavelengths, into OmpF and measured FRET from Hco to dissolved Bocillin FL using solubilized OmpF porins. We examined four variants of OmpF and by doing so, we were able to show that small molecules, like Bocillin FL, are remaining long enough in the porin in order to undergo FRET and produce a reproducible fluorescence signal. This finding opens the way to quantify translocation in the future by the simultaneous detection of resistive pulses and differential fluorescence with FRET as an example.
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Affiliation(s)
- Rémi Terrasse
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719, Bremen, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719, Bremen, Germany.
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40
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Smith A, Kaczmar A, Bamford RA, Smith C, Frustaci S, Kovacs-Simon A, O'Neill P, Moore K, Paszkiewicz K, Titball RW, Pagliara S. The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli. Front Microbiol 2018; 9:1739. [PMID: 30158905 PMCID: PMC6104134 DOI: 10.3389/fmicb.2018.01739] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/11/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms shape the composition of the medium they are growing in, which in turn has profound consequences on the reprogramming of the population gene-expression profile. In this paper, we investigate the progressive changes in pH and sugar availability in the medium of a growing Escherichia coli (E. coli) culture. We show how these changes have an effect on both the cellular heterogeneity within the microbial community and the gene-expression profile of the microbial population. We measure the changes in gene-expression as E. coli moves from lag, to exponential, and finally into stationary phase. We found that pathways linked to the changes in the medium composition such as ribosomal, tricarboxylic acid cycle (TCA), transport, and metabolism pathways are strongly regulated during the different growth phases. In order to quantify the corresponding temporal changes in the population heterogeneity, we measure the fraction of E. coli persisters surviving different antibiotic treatments during the various phases of growth. We show that the composition of the medium in which β-lactams or quinolones, but not aminoglycosides, are dissolved strongly affects the measured phenotypic heterogeneity within the culture. Our findings contribute to a better understanding on how the composition of the culture medium influences both the reprogramming in the population gene-expression and the emergence of phenotypic variants.
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Affiliation(s)
- Ashley Smith
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | - Agnieszka Kaczmar
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rosemary A Bamford
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Simona Frustaci
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - Paul O'Neill
- Biosciences, University of Exeter, Exeter, United Kingdom
| | - Karen Moore
- Biosciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
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41
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Sanders S, Bartee D, Harrison MJ, Phillips PD, Koppisch AT, Freel Meyers CL. Growth medium-dependent antimicrobial activity of early stage MEP pathway inhibitors. PLoS One 2018; 13:e0197638. [PMID: 29771999 PMCID: PMC5957436 DOI: 10.1371/journal.pone.0197638] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/04/2018] [Indexed: 01/01/2023] Open
Abstract
The in vivo microenvironment of bacterial pathogens is often characterized by nutrient limitation. Consequently, conventional rich in vitro culture conditions used widely to evaluate antibacterial agents are often poorly predictive of in vivo activity, especially for agents targeting metabolic pathways. In one such pathway, the methylerythritol phosphate (MEP) pathway, which is essential for production of isoprenoids in bacterial pathogens, relatively little is known about the influence of growth environment on antibacterial properties of inhibitors targeting enzymes in this pathway. The early steps of the MEP pathway are catalyzed by 1-deoxy-d-xylulose 5-phosphate (DXP) synthase and reductoisomerase (IspC). The in vitro antibacterial efficacy of the DXP synthase inhibitor butylacetylphosphonate (BAP) was recently reported to be strongly dependent upon growth medium, with high potency observed under nutrient limitation and exceedingly weak activity in nutrient-rich conditions. In contrast, the well-known IspC inhibitor fosmidomycin has potent antibacterial activity in nutrient-rich conditions, but to date, its efficacy had not been explored under more relevant nutrient-limited conditions. The goal of this work was to thoroughly characterize the effects of BAP and fosmidomycin on bacterial cells under varied growth conditions. In this work, we show that activities of both inhibitors, alone and in combination, are strongly dependent upon growth medium, with differences in cellular uptake contributing to variance in potency of both agents. Fosmidomycin is dissimilar to BAP in that it displays relatively weaker activity in nutrient-limited compared to nutrient-rich conditions. Interestingly, while it has been generally accepted that fosmidomycin activity depends upon expression of the GlpT transporter, our results indicate for the first time that fosmidomycin can enter cells by an alternative mechanism under nutrient limitation. Finally, we show that the potency and relationship of the BAP-fosmidomycin combination also depends upon the growth medium, revealing a striking loss of BAP-fosmidomycin synergy under nutrient limitation. This change in BAP-fosmidomycin relationship suggests a shift in the metabolic and/or regulatory networks surrounding DXP accompanying the change in growth medium, the understanding of which could significantly impact targeting strategies against this pathway. More generally, our findings emphasize the importance of considering physiologically relevant growth conditions for predicting the antibacterial potential MEP pathway inhibitors and for studies of their intracellular targets.
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Affiliation(s)
- Sara Sanders
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Mackenzie J. Harrison
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Paul D. Phillips
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Andrew T. Koppisch
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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Giacalone G, Matoori S, Agostoni V, Forster V, Kabbaj M, Eggenschwiler S, Lussi M, De Gottardi A, Zamboni N, Leroux JC. Liposome-supported peritoneal dialysis in the treatment of severe hyperammonemia: An investigation on potential interactions. J Control Release 2018; 278:57-65. [DOI: 10.1016/j.jconrel.2018.03.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/24/2018] [Accepted: 03/26/2018] [Indexed: 12/27/2022]
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43
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Dogan Guzel F, Citak F. Development of an On-Chip Antibiotic Permeability Assay With Single Molecule Detection Capability. IEEE Trans Nanobioscience 2018; 17:155-160. [DOI: 10.1109/tnb.2018.2809592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Zhang CZ, Chang MX, Yang L, Liu YY, Chen PX, Jiang HX. Upregulation of AcrEF in Quinolone Resistance Development inEscherichia coliWhen AcrAB-TolC Function Is Impaired. Microb Drug Resist 2018; 24:18-23. [DOI: 10.1089/mdr.2016.0207] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Chuan-Zhen Zhang
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University (SCAU), Guangzhou, China
| | - Man-Xia Chang
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University (SCAU), Guangzhou, China
| | - Lei Yang
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University (SCAU), Guangzhou, China
| | - Yan-Yan Liu
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University (SCAU), Guangzhou, China
| | - Pin-Xian Chen
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University (SCAU), Guangzhou, China
| | - Hong-Xia Jiang
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University (SCAU), Guangzhou, China
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Hernández S, Porter C, Zhang X, Wei Y, Bhattacharyya D. Layer-by-layer Assembled Membranes with Immobilized Porins. RSC Adv 2017; 7:56123-56136. [PMID: 29391943 PMCID: PMC5788187 DOI: 10.1039/c7ra08737c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
With the synthesis and functionalization of membranes for selective separations, reactivity, and stimuli responsive behavior arises new and advanced opportunities. The integration of bio-based channels is one of these advancements in membrane technologies. By a layer-by-layer (LbL) assembly of polyelectrolytes, outer membrane protein F trimers (OmpF) or "porins" from Escherichia coli with a central pore of ~2 nm diameter at its opening and ~0.7 × 1.1 nm at its constricted region are immobilized within the pores of poly(vinylidene fluoride) microfiltration membranes, as opposed to traditional ruptured lipid bilayer or vesicles processes. These OmpF-membranes demonstrate selective rejections of non-charged organics over ionic solutes, allowing the passage of salts up to 2 times higher than traditional nanofiltration membranes starting with rejections of 84% for 0.4-1.0 kDa organics. The presence of charged groups in OmpF membranes also leads to pH-dependent salt rejection through Donnan exclusion. These OmpF-membranes also show exceptional durability and stability, delivering consistent and constant permeability and recovery for over 160 h of operation. Characterization of solutions containing OmpF, and membranes were conducted during each stage of the process, including detection by fluorescence labelling (FITC), zeta potential, pH responsiveness, flux changes, and rejections of organic-inorganic solutions.
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Affiliation(s)
- Sebastián Hernández
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY
| | - Cassandra Porter
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY
| | - Xinyi Zhang
- Department of Chemistry, University of Kentucky, Lexington, KY
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, KY
| | - Dibakar Bhattacharyya
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY
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Abstract
One of the main fundamental mechanisms of antibiotic resistance in Gram-negative bacteria comprises an effective change in the membrane permeability to antibiotics. The Gram-negative bacterial complex cell envelope comprises an outer membrane that delimits the periplasm from the exterior environment. The outer membrane contains numerous protein channels, termed as porins or nanopores, which are mainly involved in the influx of hydrophilic compounds, including antibiotics. Bacterial adaptation to reduce influx through these outer membrane proteins (Omps) is one of the crucial mechanisms behind antibiotic resistance. Thus to interpret the molecular basis of the outer membrane permeability is the current challenge. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in antibiotic influx. Further, it aims to study the bacterial response to antibiotic membrane permeability and hopefully provoke a discussion toward understanding and further exploration of prospects to improve our knowledge on physicochemical parameters that direct the translocation of antibiotics through the bacterial membrane protein channels.
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Affiliation(s)
- Ishan Ghai
- School of Engineering and Life Sciences, Jacobs University, Bremen
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Zhu Z, Zhou X, Li B, Wang S, Cheng F, Zhang J. Genomic Analysis and Resistance Mechanisms in Shigella flexneri 2a Strain 301. Microb Drug Resist 2017; 24:323-336. [PMID: 28853989 DOI: 10.1089/mdr.2016.0173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Shigella flexneri is one of the most prominent pathogenic bacteria in developing countries. In the battle against shigellosis and other bacterial diseases, antibiotic resistance has become an increasing global public health threat. Although the serious phenomenon of multidrug resistance (MDR) has been identified as one of the top three burdens on human health, resistance mechanisms are still poorly understood at the molecular level. In this study, we analyzed genomic data and the evolution of resistance in Shigella flexneri under sequential selection stress from three separate antibiotics: ciprofloxacin (CIP), ceftriaxone (CRO), and tetracycline. Through whole-genome sequencing, 82 chromosomal antibiotic resistance genes were identified. Re-sequencing of the evolved populations identified single nucleotide polymorphisms (SNPs) that contributed to MDR and SNPs that were specific to a single drug. A total of 40 SNPs in 8 genes and 3 intergenic regions, including mutations in metG (L582R) and 1538924, 1538924, and 1538924, appeared under each antibiotic. Several nonsynonymous mutations in gyrB (S464Y), ydgA (E378A), rob (R156H), and narX (K75E) were observed under selective pressure from CIP or CRO. Based on a bioinformatic analysis and previous reports, we discuss the contribution of these mutated genes to resistance. Therefore, more circumspect selection and use of antimicrobial drugs for treating shigellosis is necessary.
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Affiliation(s)
- Zhen Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences , CAAS, Lanzhou, People's Republic of China
| | - Xuzheng Zhou
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences , CAAS, Lanzhou, People's Republic of China
| | - Bing Li
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences , CAAS, Lanzhou, People's Republic of China
| | - Sihan Wang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences , CAAS, Lanzhou, People's Republic of China
| | - Fusheng Cheng
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences , CAAS, Lanzhou, People's Republic of China
| | - Jiyu Zhang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences , CAAS, Lanzhou, People's Republic of China
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Bajaj H, Acosta Gutierrez S, Bodrenko I, Malloci G, Scorciapino MA, Winterhalter M, Ceccarelli M. Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules. ACS NANO 2017; 11:5465-5473. [PMID: 28485920 DOI: 10.1021/acsnano.6b08613] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Transport of molecules through biological membranes is a fundamental process in biology, facilitated by selective channels and general pores. The architecture of some outer membrane pores in Gram-negative bacteria, common to other eukaryotic pores, suggests them as prototypes of electrostatically regulated nanosieve devices. In this study, we sensed the internal electrostatics of the two most abundant outer membrane channels of Escherichia coli, using norfloxacin as a dipolar probe in single molecule electrophysiology. The voltage dependence of the association rate constant of norfloxacin interacting with these nanochannels follows an exponential trend, unexpected for neutral molecules. We combined electrophysiology, channel mutagenesis, and enhanced sampling molecular dynamics simulations to explain this molecular mechanism. Voltage and temperature dependent ion current measurements allowed us to quantify the transversal electric field inside the channel as well as the distance where the applied potential drops. Finally, we proposed a general model for transport of polar molecules through these electrostatic nanosieves. Our model helps to further understand the basis for permeability in Gram-negative pathogens, contributing to fill in the innovation gap that has limited the discovery of effective antibiotics in the last 20 years.
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Affiliation(s)
- Harsha Bajaj
- Jacobs University Bremen , Campus Ring 1, D-28759 Bremen, Germany
| | | | - Igor Bodrenko
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
| | | | | | - Matteo Ceccarelli
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
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Scorciapino MA, Acosta-Gutierrez S, Benkerrou D, D'Agostino T, Malloci G, Samanta S, Bodrenko I, Ceccarelli M. Rationalizing the permeation of polar antibiotics into Gram-negative bacteria. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:113001. [PMID: 28155846 DOI: 10.1088/1361-648x/aa543b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.
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Affiliation(s)
- Mariano Andrea Scorciapino
- Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700-09042 Monserrato (CA), Italy
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50
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Acosta Gutiérrez S, Bodrenko I, Scorciapino MA, Ceccarelli M. Macroscopic electric field inside water-filled biological nanopores. Phys Chem Chem Phys 2017; 18:8855-64. [PMID: 26931352 DOI: 10.1039/c5cp07902k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Multi-drug resistance bacteria are a challenging problem of contemporary medicine. This is particularly critical for Gram-negative bacteria, where antibiotics are hindered by the outer membrane to reach internal targets. Here more polar antibiotics make use of nanometric water-filled channels to permeate inside. We present in this work a computational all-atom approach, using water as a probe, for the calculation of the macroscopic electric field inside water-filled channels. The method allows one to compare not only different systems but also the same system under different conditions, such as pH and ion concentration. This provides a detailed picture of electrostatics in biological nanopores shedding more light on how the charged residues of proteins determine the electric field inside, and also how medium can tune it. These details are central to unveil the filtering mechanism behind the permeation of small polar molecules through nanometric water-filled channels.
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Affiliation(s)
- Silvia Acosta Gutiérrez
- Department of Physics, University of Cagliari, Cittadella universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy.
| | - Igor Bodrenko
- Department of Physics, University of Cagliari, Cittadella universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy.
| | - Mariano Andrea Scorciapino
- Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Cittadella universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy.
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