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Hoffmann A, Steffens U, Maček B, Franz-Wachtel M, Nieselt K, Harbig TA, Scherlach K, Hertweck C, Sahl HG, Bierbaum G. The unusual mode of action of the polyketide glycoside antibiotic cervimycin C. mSphere 2024; 9:e0076423. [PMID: 38722162 DOI: 10.1128/msphere.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
Cervimycins A-D are bis-glycosylated polyketide antibiotics produced by Streptomyces tendae HKI 0179 with bactericidal activity against Gram-positive bacteria. In this study, cervimycin C (CmC) treatment caused a spaghetti-like phenotype in Bacillus subtilis 168, with elongated curved cells, which stayed joined after cell division, and exhibited a chromosome segregation defect, resulting in ghost cells without DNA. Electron microscopy of CmC-treated Staphylococcus aureus (3 × MIC) revealed swollen cells, misshapen septa, cell wall thickening, and a rough cell wall surface. Incorporation tests in B. subtilis indicated an effect on DNA biosynthesis at high cervimycin concentrations. Indeed, artificial downregulation of the DNA gyrase subunit B gene (gyrB) increased the activity of cervimycin in agar diffusion tests, and, in high concentrations (starting at 62.5 × MIC), the antibiotic inhibited S. aureus DNA gyrase supercoiling activity in vitro. To obtain a more global view on the mode of action of CmC, transcriptomics and proteomics of cervimycin treated versus untreated S. aureus cells were performed. Interestingly, 3 × MIC of cervimycin did not induce characteristic responses, which would indicate disturbance of the DNA gyrase activity in vivo. Instead, cervimycin induced the expression of the CtsR/HrcA heat shock operon and the expression of autolysins, exhibiting similarity to the ribosome-targeting antibiotic gentamicin. In summary, we identified the DNA gyrase as a target, but at low concentrations, electron microscopy and omics data revealed a more complex mode of action of cervimycin, which comprised induction of the heat shock response, indicating protein stress in the cell.IMPORTANCEAntibiotic resistance of Gram-positive bacteria is an emerging problem in modern medicine, and new antibiotics with novel modes of action are urgently needed. Secondary metabolites from Streptomyces species are an important source of antibiotics, like the cervimycin complex produced by Streptomyces tendae HKI 0179. The phenotypic response of Bacillus subtilis and Staphylococcus aureus toward cervimycin C indicated a chromosome segregation and septum formation defect. This effect was at first attributed to an interaction between cervimycin C and the DNA gyrase. However, omics data of cervimycin treated versus untreated S. aureus cells indicated a different mode of action, because the stress response did not include the SOS response but resembled the response toward antibiotics that induce mistranslation or premature chain termination and cause protein stress. In summary, these results point toward a possibly novel mechanism that generates protein stress in the cells and subsequently leads to defects in cell and chromosome segregation.
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Affiliation(s)
- Alina Hoffmann
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Ursula Steffens
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Boris Maček
- University of Tübingen, Proteome Center Tübingen, Tübingen, Germany
| | | | - Kay Nieselt
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Theresa Anisja Harbig
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
- Friedrich Schiller University Jena, Institute of Microbiology, Faculty of Biological Sciences, Jena, Germany
| | - Hans-Georg Sahl
- University of Bonn, Institute for Pharmaceutical Microbiology, Bonn, Germany
| | - Gabriele Bierbaum
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
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2
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Peerzade IJ, Mutturi S, Halami PM. Improved production of RNA-inhibiting antimicrobial peptide by Bacillus licheniformis MCC 2514 facilitated by a genetic algorithm optimized medium. Bioprocess Biosyst Eng 2024; 47:683-695. [PMID: 38521865 DOI: 10.1007/s00449-024-02998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
One of the significant challenges during the purification and characterization of antimicrobial peptides (AMPs) from Bacillus sp. is the interference of unutilized peptides from complex medium components during analytical procedures. In this study, a semi-synthetic medium was devised to overcome this challenge. Using a genetic algorithm, the production medium of AMP is optimized. The parent organism, Bacillus licheniformis MCC2514, produces AMP in very small quantities. This AMP is known to inhibit RNA biosynthesis. The findings revealed that lactose, NH4Cl and NaNO3 were crucial medium constituents for enhanced AMP synthesis. The potency of the AMP produced was studied using bacterium, Kocuria rhizophila ATCC 9341. The AMP produced from the optimized medium was eightfold higher than that produced from the unoptimized medium. Furthermore, activity was increased by 1.5-fold when cultivation conditions were standardized using the optimized medium. Later, AMP was produced in a 5 L bioreactor under controlled conditions, which led to similar results as those of shake-flask production. The mode of action of optimally produced AMP was confirmed to be inhibition of RNA biosynthesis. Here, we demonstrate that improved production of AMP is possible with the developed semi-synthetic medium recipe and could help further AMP production in an industrial setup.
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Affiliation(s)
- Ishrat Jahan Peerzade
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Sarma Mutturi
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Prakash M Halami
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India.
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3
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Shideler S, Bookout T, Qasim A, Bowron L, Wu Q, Duan K, Treu R, Reckseidler-Zenteno S, Lewenza S. Biosensor-guided detection of outer membrane-specific antimicrobial activity against Pseudomonas aeruginosa from fungal cultures and medicinal plant extracts. Microbiol Spectr 2023; 11:e0153623. [PMID: 37882578 PMCID: PMC10714926 DOI: 10.1128/spectrum.01536-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE New approaches are needed to discover novel antimicrobials, particularly antibiotics that target the Gram-negative outer membrane. By exploiting bacterial sensing and responses to outer membrane (OM) damage, we used a biosensor approach consisting of polymyxin resistance gene transcriptional reporters to screen natural products and a small drug library for biosensor activity that indicates damage to the OM. The diverse antimicrobial compounds that cause induction of the polymyxin resistance genes, which correlates with outer membrane damage, suggest that these LPS and surface modifications also function in short-term repair to sublethal exposure and are required against broad membrane stress conditions.
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Affiliation(s)
- Steve Shideler
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Tyson Bookout
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Azka Qasim
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Lauren Bowron
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Qiaolian Wu
- College of Life Sciences, Northwest University, Xian, China
| | - Kangmin Duan
- Department of Oral Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Roland Treu
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
| | - Shauna Reckseidler-Zenteno
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
| | - Shawn Lewenza
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
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4
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Sudzinová P, Šanderová H, Koval' T, Skálová T, Borah N, Hnilicová J, Kouba T, Dohnálek J, Krásný L. What the Hel: recent advances in understanding rifampicin resistance in bacteria. FEMS Microbiol Rev 2023; 47:fuac051. [PMID: 36549665 PMCID: PMC10719064 DOI: 10.1093/femsre/fuac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
Rifampicin is a clinically important antibiotic that binds to, and blocks the DNA/RNA channel of bacterial RNA polymerase (RNAP). Stalled, nonfunctional RNAPs can be removed from DNA by HelD proteins; this is important for maintenance of genome integrity. Recently, it was reported that HelD proteins from high G+C Actinobacteria, called HelR, are able to dissociate rifampicin-stalled RNAPs from DNA and provide rifampicin resistance. This is achieved by the ability of HelR proteins to dissociate rifampicin from RNAP. The HelR-mediated mechanism of rifampicin resistance is discussed here, and the roles of HelD/HelR in the transcriptional cycle are outlined. Moreover, the possibility that the structurally similar HelD proteins from low G+C Firmicutes may be also involved in rifampicin resistance is explored. Finally, the discovery of the involvement of HelR in rifampicin resistance provides a blueprint for analogous studies to reveal novel mechanisms of bacterial antibiotic resistance.
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Affiliation(s)
- Petra Sudzinová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Tomáš Koval'
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Tereza Skálová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Nabajyoti Borah
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Tomáš Kouba
- Cryogenic Electron Microscopy Research-Service Group, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16000 Prague, Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
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5
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Szekat C, Josten M, Rickmeyer J, Crüsemann M, Bierbaum G. A Staphylococcus capitis strain with unusual bacteriocin production. Microb Biotechnol 2023; 16:2181-2193. [PMID: 37850940 PMCID: PMC10616647 DOI: 10.1111/1751-7915.14356] [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: 07/21/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Staphylococcus capitis is a member of the human and mammal skin microbiomes and is considered less harmful than Staphylococcus aureus. S. capitis subsp. urealyticus BN2 was isolated from a cat and expressed strong antibacterial activity against a range of Gram-positive species, most notably including S. aureus strains with resistance to methicillin (MRSA) and strains with intermediate resistance to vancomycin (VISA). These latter strains are normally relatively resistant to bacteriocins, due to cell wall and cell membrane modifications. Genomic sequencing showed that the strain harboured at least two complete gene clusters for biosynthesis of antagonistic substances. The complete biosynthetic gene cluster of the well-known lantibiotic gallidermin was encoded on a large plasmid and the mature peptide was present in isopropanol cell extracts. In addition, a chromosomal island contained a novel non-ribosomal peptide synthetase (NRPS) gene cluster. Accidental deletion of two NRPS modules and partial purification of the anti-VISA activity showed that this novel bacteriocin represents a complex of differently decorated, non-ribosomal peptides. Additionally, a number of phenol-soluble modulins (PSMs) was detected by mass spectrometry of whole cells. Producing these compounds, the strain was able to outcompete several S. aureus strains, including MRSA and VISA, in tube cultures.
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Affiliation(s)
- Christiane Szekat
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Michaele Josten
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Jasmin Rickmeyer
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Max Crüsemann
- Institute of Pharmaceutical BiologyUniversity of BonnBonnGermany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
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6
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Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
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Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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7
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Galarion LH, Mitchell JK, Randall CP, O’Neill AJ. An extensively validated whole-cell biosensor for specific, sensitive and high-throughput detection of antibacterial inhibitors targeting cell-wall biosynthesis. J Antimicrob Chemother 2023; 78:646-655. [PMID: 36626387 PMCID: PMC9978594 DOI: 10.1093/jac/dkac429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/02/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Whole-cell biosensor strains are powerful tools for antibacterial drug discovery, in principle allowing the identification of inhibitors acting on specific, high-value target pathways. Whilst a variety of biosensors have been described for detecting cell-wall biosynthesis inhibitors (CWBIs), these strains typically lack specificity and/or sensitivity, and have for the most part not been rigorously evaluated as primary screening tools. Here, we describe several Staphylococcus aureus CWBI biosensors and show that specific and sensitive biosensor-based discovery of CWBIs is achievable. METHODS Biosensors comprised lacZ reporter fusions with S. aureus promoters (PgltB, PilvD, PmurZ, PoppB, PORF2768, PsgtB) that are subject to up-regulation following inhibition of cell-wall biosynthesis. Induction of biosensors was detected by measuring expression of β-galactosidase using fluorogenic or luminogenic substrates. RESULTS Three of the six biosensors tested (those based on PgltB, PmurZ, PsgtB) exhibited apparently specific induction of β-galactosidase expression in the presence of CWBIs. Further validation of one of these (PmurZ) using an extensive array of positive and negative control compounds and conditional mutants established that it responded appropriately and uniquely to inhibition of cell-wall biosynthesis. Using this biosensor, we established, validated and deployed a high-throughput assay that identified a potentially novel CWBI from a screen of >9000 natural product extracts. CONCLUSIONS Our extensively validated PmurZ biosensor strain offers specific and sensitive detection of CWBIs, and is well-suited for high-throughput screening; it therefore represents a valuable tool for antibacterial drug discovery.
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Affiliation(s)
- Luiza H Galarion
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Jennifer K Mitchell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Christopher P Randall
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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8
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Novikov A, Sayfutdinova A, Botchkova E, Kopitsyn D, Fakhrullin R. Antibiotic Susceptibility Testing with Raman Biosensing. Antibiotics (Basel) 2022; 11:antibiotics11121812. [PMID: 36551469 PMCID: PMC9774239 DOI: 10.3390/antibiotics11121812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotics guard us against bacterial infections and are among the most commonly used medicines. The immediate consequence of their large-scale production and prescription is the development of antibiotic resistance. Therefore, rapid detection of antibiotic susceptibility is required for efficient antimicrobial therapy. One of the promising methods for rapid antibiotic susceptibility testing is Raman spectroscopy. Raman spectroscopy combines fast and contactless acquisition of spectra with good selectivity towards bacterial cells. The antibiotic-induced changes in bacterial cell physiology are detected as distinct features in Raman spectra and can be associated with antibiotic susceptibility. Therefore, the Raman-based approach may be beneficial in designing therapy against multidrug-resistant infections. The surface-enhanced Raman spectroscopy (SERS) and resonance Raman spectroscopy (RRS) additionally provide excellent sensitivity. In this review, we present an analysis of the Raman spectroscopy-based optical biosensing approaches aimed at antibiotic susceptibility testing.
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Affiliation(s)
- Andrei Novikov
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
- Correspondence: (A.N.); (R.F.)
| | - Adeliya Sayfutdinova
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Ekaterina Botchkova
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Dmitry Kopitsyn
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Rawil Fakhrullin
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Republic of Tatarstan, Russia
- Correspondence: (A.N.); (R.F.)
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9
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VanArsdale E, Pitzer J, Wang S, Stephens K, Chen CY, Payne GF, Bentley WE. Enhanced electrochemical measurement of β-galactosidase activity in whole cells by coexpression of lactose permease, LacY. Biotechniques 2022; 73:233-237. [DOI: 10.2144/btn-2022-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Whole-cell biosensing links the sensing and computing capabilities of microbes to the generation of a detectable reporter. Whole cells enable dynamic biological computation (filtered noise, amplified signals, logic gating etc.). Enzymatic reporters enable in situ signal amplification. Electrochemical measurements are easily quantified and work in turbid environments. In this work we show how the coexpression of the lactose permease, LacY, dramatically improves electrochemical sensing of β-galactosidase (LacZ) expressed as a reporter in whole cells. The permease facilitates transport of the LacZ substrate, 4-aminophenyl β-d-galactopyranoside, which is converted to redox active p-aminophenol, which, in turn, is detected via cyclic voltammetry or chronocoulometry. We show a greater than fourfold improvement enabled by lacY coexpression in cells engineered to respond to bacterial signal molecules, pyocyanin and quorum-sensing autoinducer-2.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Chen-yu Chen
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Gregory F Payne
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
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10
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Cervimycin-Resistant Staphylococcus aureus Strains Display Vancomycin-Intermediate Resistant Phenotypes. Microbiol Spectr 2022; 10:e0256722. [PMID: 36173303 PMCID: PMC9603734 DOI: 10.1128/spectrum.02567-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Resistance to antibiotics is an increasing problem and necessitates novel antibacterial therapies. The polyketide antibiotics cervimycin A to D are natural products of Streptomyces tendae HKI 0179 with promising activity against multidrug-resistant staphylococci and vancomycin-resistant enterococci. To initiate mode of action studies, we selected cervimycin C- and D-resistant (CmR) Staphylococcus aureus strains. Genome sequencing of CmR mutants revealed amino acid exchanges in the essential histidine kinase WalK, the Clp protease proteolytic subunit ClpP or the Clp ATPase ClpC, and the heat shock protein DnaK. Interestingly, all characterized CmR mutants harbored a combination of mutations in walK and clpP or clpC. In vitro and in vivo analyses showed that the mutations in the Clp proteins abolished ClpP or ClpC activity, and the deletion of clpP rendered S. aureus but not all Bacillus subtilis strains cervimycin-resistant. The essential gene walK was the second mutational hotspot in the CmR S. aureus strains, which decreased WalK activity in vitro and generated a vancomycin-intermediate resistant phenotype, with a thickened cell wall, a lower growth rate, and reduced cell lysis. Transcriptomic and proteomic analyses revealed massive alterations in the CmR strains compared to the parent strain S. aureus SG511, with major shifts in the heat shock regulon, the metal ion homeostasis, and the carbohydrate metabolism. Taken together, mutations in the heat shock genes clpP, clpC, and dnaK, and the walK kinase gene in CmR mutants induced a vancomycin-intermediate resistant phenotype in S. aureus, suggesting cell wall metabolism or the Clp protease system as primary target of cervimycin. IMPORTANCE Staphylococcus aureus is a frequent cause of infections in both the community and hospital setting. Resistance development of S. aureus to various antibiotics is a severe problem for the treatment of this pathogen worldwide. New powerful antimicrobial agents against Gram-positives are needed, since antibiotics like vancomycin fail to cure vancomycin-intermediate resistant S. aureus (VISA) and vancomycin-resistant enterococci (VRE) infections. One candidate substance with promising activity against these organisms is cervimycin, which is an antibiotic complex with a yet unknown mode of action. In our study, we provide first insights into the mode of action of cervimycins. By characterizing cervimycin-resistant S. aureus strains, we revealed the Clp system and the essential kinase WalK as mutational hotspots for cervimycin resistance in S. aureus. It further emerged that cervimycin-resistant S. aureus strains show a VISA phenotype, indicating a role of cervimycin in perturbing the bacterial cell envelope.
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11
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Rütten A, Kirchner T, Musiol-Kroll EM. Overview on Strategies and Assays for Antibiotic Discovery. Pharmaceuticals (Basel) 2022; 15:1302. [PMID: 36297414 PMCID: PMC9607151 DOI: 10.3390/ph15101302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
The increase in antibiotic resistance poses a major threat to global health. Actinomycetes, the Gram-positive bacteria of the order Actinomycetales, are fertile producers of bioactive secondary metabolites, including antibiotics. Nearly two-thirds of antibiotics that are used for the treatment of bacterial infections were originally isolated from actinomycetes strains belonging to the genus Streptomyces. This emphasizes the importance of actinomycetes in antibiotic discovery. However, the identification of a new antimicrobial compound and the exploration of its mode of action are very challenging tasks. Therefore, different approaches that enable the "detection" of an antibiotic and the characterization of the mechanisms leading to the biological activity are indispensable. Beyond bioinformatics tools facilitating the identification of biosynthetic gene clusters (BGCs), whole cell-screenings-in which cells are exposed to actinomycete-derived compounds-are a common strategy applied at the very early stage in antibiotic drug development. More recently, target-based approaches have been established. In this case, the drug candidates were tested for interactions with usually validated targets. This review focuses on the bioactivity-based screening methods and provides the readers with an overview on the most relevant assays for the identification of antibiotic activity and investigation of mechanisms of action. Moreover, the article includes examples of the successful application of these methods and suggestions for improvement.
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Affiliation(s)
- Anika Rütten
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Teresa Kirchner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ewa Maria Musiol-Kroll
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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12
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Development of Whole-Cell Biosensors for Screening of Peptidoglycan-Targeting Antibiotics in a Gram-Negative Bacterium. Appl Environ Microbiol 2022; 88:e0084622. [PMID: 36040151 PMCID: PMC9499016 DOI: 10.1128/aem.00846-22] [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: 11/20/2022] Open
Abstract
There is an urgent need to develop novel antibiotics since antibiotic resistance is an increasingly serious threat to global public health. Whole-cell biosensors are one of the promising strategies for new antibiotic discovery. The peptidoglycan (PG) of the bacterial cell wall is one of the most important targets for antibiotics. However, the biosensors for the detection of PG-targeting antibiotics in Gram-negative bacteria have not been developed, mainly because of the lack of the regulatory systems that sense and respond to PG stress. Recently, we identified a novel two-component signal transduction system (PghKR) that is responsible for sensing and responding to PG damage in the Gram-negative bacterium Shewanella oneidensis. Based on this system, we developed biosensors for the detection of PG-targeting antibiotics. Using ampicillin as an inducer for PG stress and the bacterial luciferase LuxCDABE as the reporter, we found that the PghKR biosensors are specific to antibiotics targeting PG synthesis, including β-lactams, vancomycin, and d-cycloserine. Deletion of genes encoding PG permease AmpG and β-lactamase BlaA improves the sensitivity of the biosensors substantially. The PghKR biosensor in the background of ΔblaA is also functional on agar plates, providing a simple method for screening bacteria that produce PG-targeting antibiotics. IMPORTANCE The growing problem of antibiotic resistance in Gram-negative bacteria urgently needs new strategies so that researchers can develop novel antibiotics. Microbial whole-cell biosensors are capable of sensing various stimuli with a quantifiable output and show tremendous potential for the discovery of novel antibiotics. As the Achilles' heel of bacteria, the synthesis of the peptidoglycan (PG) is targeted by many antibiotics. However, the regulatory systems that sense and respond to PG-targeting stress in Gram-negative bacteria are reported rarely, restricting the development of biosensors for the detection of PG-targeting antibiotics. In this study, we developed a highly sensitive and specific biosensor based on a novel two-component system in the Gram-negative bacterium Shewanella oneidensis that is responsible for the sensing and responding to PG stress. Our biosensors have great potential for discovering novel antibiotics and determining the mode of action of antibiotics.
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13
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Kepplinger B, Mardiana L, Cowell J, Morton-Laing S, Dashti Y, Wills C, Marrs ECL, Perry JD, Gray J, Goodfellow M, Errington J, Probert MR, Clegg W, Bogaerts J, Herrebout W, Allenby NEE, Hall MJ. Discovery, isolation, heterologous expression and mode-of-action studies of the antibiotic polyketide tatiomicin from Amycolatopsis sp. DEM30355. Sci Rep 2022; 12:15579. [PMID: 36114335 PMCID: PMC9481585 DOI: 10.1038/s41598-022-18726-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
A genomic and bioactivity informed analysis of the metabolome of the extremophile Amycolatopsis sp. DEM30355 has allowed for the discovery and isolation of the polyketide antibiotic tatiomicin. Identification of the biosynthetic gene cluster was confirmed by heterologous expression in Streptomyces coelicolor M1152. Structural elucidation, including absolute stereochemical assignment, was performed using complementary crystallographic, spectroscopic and computational methods. Tatiomicin shows antibiotic activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Cytological profiling experiments suggest a putative antibiotic mode-of-action, involving membrane depolarisation and chromosomal decondensation of the target bacteria.
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Affiliation(s)
- Bernhard Kepplinger
- Biopharmaceutical Bioprocessing Technology Centre, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK.
- Demuris Limited, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK.
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, 50-383, Wrocław, Poland.
| | - Lina Mardiana
- Chemistry, School of Environmental and Natural Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Joseph Cowell
- Chemistry, School of Environmental and Natural Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Stephanie Morton-Laing
- Chemistry, School of Environmental and Natural Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Yousef Dashti
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Corinne Wills
- Chemistry, School of Environmental and Natural Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Emma C L Marrs
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - John D Perry
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - Joe Gray
- Pinnacle Laboratory, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Michael Goodfellow
- Biology, School of Environmental and Natural Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
- Demuris Limited, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Michael R Probert
- Chemistry, School of Environmental and Natural Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - William Clegg
- Chemistry, School of Environmental and Natural Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jonathan Bogaerts
- Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Wouter Herrebout
- Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Nick E E Allenby
- Demuris Limited, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK.
| | - Michael J Hall
- Chemistry, School of Environmental and Natural Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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14
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Revilla-Guarinos A, Popp PF, Dürr F, Lozano-Cruz T, Hartig J, de la Mata FJ, Gómez R, Mascher T. Synthesis and mechanism-of-action of a novel synthetic antibiotic based on a dendritic system with bow-tie topology. Front Microbiol 2022; 13:912536. [PMID: 36090105 PMCID: PMC9459136 DOI: 10.3389/fmicb.2022.912536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/26/2022] [Indexed: 12/05/2022] Open
Abstract
Over the course of the last decades, the continuous exposure of bacteria to antibiotics-at least in parts due to misprescription, misuse, and misdosing-has led to the widespread development of antimicrobial resistances. This development poses a threat to the available medication in losing their effectiveness in treating bacterial infections. On the drug development side, only minor advances have been made to bring forward novel therapeutics. In addition to increasing the efforts and approaches of tapping the natural sources of new antibiotics, synthetic approaches to developing novel antimicrobials are being pursued. In this study, BDTL049 was rationally designed using knowledge based on the properties of natural antibiotics. BDTL049 is a carbosilane dendritic system with bow-tie type topology, which has antimicrobial activity at concentrations comparable to clinically established natural antibiotics. In this report, we describe its mechanism of action on the Gram-positive model organism Bacillus subtilis. Exposure to BDTL049 resulted in a complex transcriptional response, which pointed toward disturbance of the cell envelope homeostasis accompanied by disruption of other central cellular processes of bacterial metabolism as the primary targets of BDTL049 treatment. By applying a combination of whole-cell biosensors, molecular staining, and voltage sensitive dyes, we demonstrate that the mode of action of BDTL049 comprises membrane depolarization concomitant with pore formation. As a result, this new molecule kills Gram-positive bacteria within minutes. Since BDTL049 attacks bacterial cells at different targets simultaneously, this might decrease the chances for the development of bacterial resistances, thereby making it a promising candidate for a future antimicrobial agent.
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Affiliation(s)
- Ainhoa Revilla-Guarinos
- Department of General Microbiology, Institut Für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Philipp F. Popp
- Department of General Microbiology, Institut Für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Franziska Dürr
- Department of General Microbiology, Institut Für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Tania Lozano-Cruz
- Department of Organic and Inorganic Chemistry, Research Institute in Chemistry “Andrés M. Del Río” (IQAR), University de Alcalá, Madrid, Spain
- Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Johanna Hartig
- Department of General Microbiology, Institut Für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Francisco Javier de la Mata
- Department of Organic and Inorganic Chemistry, Research Institute in Chemistry “Andrés M. Del Río” (IQAR), University de Alcalá, Madrid, Spain
- Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Rafael Gómez
- Department of Organic and Inorganic Chemistry, Research Institute in Chemistry “Andrés M. Del Río” (IQAR), University de Alcalá, Madrid, Spain
- Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Thorsten Mascher
- Department of General Microbiology, Institut Für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
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15
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Mendes SS, Marques J, Mesterházy E, Straetener J, Arts M, Pissarro T, Reginold J, Berscheid A, Bornikoel J, Kluj RM, Mayer C, Oesterhelt F, Friães S, Royo B, Schneider T, Brötz-Oesterhelt H, Romão CC, Saraiva LM. Synergetic Antimicrobial Activity and Mechanism of Clotrimazole-Linked CO-Releasing Molecules. ACS BIO & MED CHEM AU 2022; 2:419-436. [PMID: 35996473 PMCID: PMC9389576 DOI: 10.1021/acsbiomedchemau.2c00007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Several metal-based
carbon monoxide-releasing molecules (CORMs)
are active CO donors with established antibacterial activity. Among
them, CORM conjugates with azole antibiotics of type [Mn(CO)3(2,2′-bipyridyl)(azole)]+ display important synergies
against several microbes. We carried out a structure–activity
relationship study based upon the lead structure of [Mn(CO)3(Bpy)(Ctz)]+ by producing clotrimazole (Ctz) conjugates
with varying metal and ligands. We concluded that the nature of the
bidentate ligand strongly influences the bactericidal activity, with
the substitution of bipyridyl by small bicyclic ligands leading to
highly active clotrimazole conjugates. On the contrary, the metal
did not influence the activity. We found that conjugate [Re(CO)3(Bpy)(Ctz)]+ is more than the sum of its parts:
while precursor [Re(CO)3(Bpy)Br] has no antibacterial activity
and clotrimazole shows only moderate minimal inhibitory concentrations,
the potency of [Re(CO)3(Bpy)(Ctz)]+ is one order
of magnitude higher than that of clotrimazole, and the spectrum of
bacterial target species includes Gram-positive and Gram-negative
bacteria. The addition of [Re(CO)3(Bpy)(Ctz)]+ to Staphylococcus aureus causes a
general impact on the membrane topology, has inhibitory effects on
peptidoglycan biosynthesis, and affects energy functions. The mechanism
of action of this kind of CORM conjugates involves a sequence of events
initiated by membrane insertion, followed by membrane disorganization,
inhibition of peptidoglycan synthesis, CO release, and break down
of the membrane potential. These results suggest that conjugation
of CORMs to known antibiotics may produce useful structures with synergistic
effects that increase the conjugate’s activity relative to
that of the antibiotic alone.
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Affiliation(s)
- Sofia S Mendes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Joana Marques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Edit Mesterházy
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Jan Straetener
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Microbial Bioactive Compounds, Cluster of Excellence Controlling Microbes to Fight Infection. University of Tuebingen, Auf der Morgenstelle 28, 72070 Tuebingen, Germany
| | - Melina Arts
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Teresa Pissarro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Jorgina Reginold
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Anne Berscheid
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Microbial Bioactive Compounds, Cluster of Excellence Controlling Microbes to Fight Infection. University of Tuebingen, Auf der Morgenstelle 28, 72070 Tuebingen, Germany
| | - Jan Bornikoel
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Microbial Bioactive Compounds, Cluster of Excellence Controlling Microbes to Fight Infection. University of Tuebingen, Auf der Morgenstelle 28, 72070 Tuebingen, Germany
| | - Robert M Kluj
- Institute of Microbiology and Infection Medicine, Dept. of Organismic Interactions, University of Tuebingen, Auf der Morgenstelle 28, 72070 Tuebingen, Germany
| | - Christoph Mayer
- Institute of Microbiology and Infection Medicine, Dept. of Organismic Interactions, University of Tuebingen, Auf der Morgenstelle 28, 72070 Tuebingen, Germany
| | - Filipp Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Microbial Bioactive Compounds, Cluster of Excellence Controlling Microbes to Fight Infection. University of Tuebingen, Auf der Morgenstelle 28, 72070 Tuebingen, Germany
| | - Sofia Friães
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Beatriz Royo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Microbial Bioactive Compounds, Cluster of Excellence Controlling Microbes to Fight Infection. University of Tuebingen, Auf der Morgenstelle 28, 72070 Tuebingen, Germany
| | - Carlos C Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
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16
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Transcription Factor-Based Biosensors for Detecting Pathogens. BIOSENSORS 2022; 12:bios12070470. [PMID: 35884273 PMCID: PMC9312912 DOI: 10.3390/bios12070470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 12/23/2022]
Abstract
Microorganisms are omnipresent and inseparable from our life. Many of them are beneficial to humans, while some are not. Importantly, foods and beverages are susceptible to microbial contamination, with their toxins causing illnesses and even death in some cases. Therefore, monitoring and detecting harmful microorganisms are critical to ensuring human health and safety. For several decades, many methods have been developed to detect and monitor microorganisms and their toxicants. Conventionally, nucleic acid analysis and antibody-based analysis were used to detect pathogens. Additionally, diverse chromatographic methods were employed to detect toxins based on their chemical and structural properties. However, conventional techniques have several disadvantages concerning analysis time, sensitivity, and expense. With the advances in biotechnology, new approaches to detect pathogens and toxins have been reported to compensate for the disadvantages of conventional analysis from different research fields, including electrochemistry, nanotechnology, and molecular biology. Among them, we focused on the recent studies of transcription factor (TF)-based biosensors to detect microorganisms and discuss their perspectives and applications. Additionally, the other biosensors for detecting microorganisms reported in recent studies were also introduced in this review.
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17
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Juskewitz E, Mishchenko E, Dubey VK, Jenssen M, Jakubec M, Rainsford P, Isaksson J, Andersen JH, Ericson JU. Lulworthinone: In Vitro Mode of Action Investigation of an Antibacterial Dimeric Naphthopyrone Isolated from a Marine Fungus. Mar Drugs 2022; 20:md20050277. [PMID: 35621928 PMCID: PMC9147123 DOI: 10.3390/md20050277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 01/27/2023] Open
Abstract
Treatment options for infections caused by antimicrobial-resistant bacteria are rendered ineffective, and drug alternatives are needed—either from new chemical classes or drugs with new modes of action. Historically, natural products have been important contributors to drug discovery. In a recent study, the dimeric naphthopyrone lulworthinone produced by an obligate marine fungus in the family Lulworthiaceae was discovered. The observed potent antibacterial activity against Gram-positive bacteria, including several clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates, prompted this follow-up mode of action investigation. This paper aimed to characterize the antibacterial mode of action (MOA) of lulworthinone by combining in vitro assays, NMR experiments and microscopy. The results point to a MOA targeting the bacterial membrane, leading to improper cell division. Treatment with lulworthinone induced an upregulation of genes responding to cell envelope stress in Bacillus subtilis. Analysis of the membrane integrity and membrane potential indicated that lulworthinone targets the bacterial membrane without destroying it. This was supported by NMR experiments using artificial lipid bilayers. Fluorescence microscopy revealed that lulworthinone affects cell morphology and impedes the localization of the cell division protein FtsZ. Surface plasmon resonance and dynamic light scattering assays showed that this activity is linked with the compound‘s ability to form colloidal aggregates. Antibacterial agents acting at cell membranes are of special interest, as the development of bacterial resistance to such compounds is deemed more difficult to occur.
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Affiliation(s)
- Eric Juskewitz
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (E.M.); (V.K.D.)
- Correspondence: (E.J.); (J.U.E.)
| | - Ekaterina Mishchenko
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (E.M.); (V.K.D.)
| | - Vishesh K. Dubey
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (E.M.); (V.K.D.)
| | - Marte Jenssen
- Marbio, The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (M.J.); (J.H.A.)
| | - Martin Jakubec
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (M.J.); (P.R.); (J.I.)
| | - Philip Rainsford
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (M.J.); (P.R.); (J.I.)
| | - Johan Isaksson
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (M.J.); (P.R.); (J.I.)
| | - Jeanette H. Andersen
- Marbio, The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (M.J.); (J.H.A.)
| | - Johanna U. Ericson
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (E.M.); (V.K.D.)
- Correspondence: (E.J.); (J.U.E.)
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18
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Shinjyo Y, Midorikawa N, Matsumoto T, Sugaya Y, Ozawa Y, Oana A, Horie C, Yoshikawa H, Takahashi Y, Hasegawa T, Asai K. Analysis of cell death in Bacillus subtilis caused by sesquiterpenes from Chrysopogon zizanioides (L.) Roberty. J GEN APPL MICROBIOL 2022; 68:62-70. [PMID: 35418537 DOI: 10.2323/jgam.2021.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recently, the antibacterial effects of essential oils have been investigated in addition to their therapeutic purposes. Owing to their hydrophobic nature, they are thought to perturb the integrity of the bacterial cell membrane, leading to cell death. Against such antibiotic challenges, bacteria develop mechanisms for cell envelope stress responses (CESR). In Bacillus subtilis, a gram-positive sporulating soil bacterium, the extracytoplasmic function (ECF) sigma factor-mediated response system plays a pivotal role in CESR. Among them, σM is strongly involved in response to cell envelope stress, including a shortage of available bactoprenol. Vetiver essential oil, a product of Chrysopogon zizanioides (L.) Roberty root, is also known to possess bactericidal activity. σM was exclusively and strongly induced when the cells were exposed to Vetiver extract, and depletion of multi-ECF sigma factors (ΔsigM, ΔsigW, ΔsigX, and ΔsigV) enhanced sensitivity to it. From this quadruple mutant strain, the suppressor strains, which restored resistance to the bactericidal activity of Vetiver extract, emerged, although attempts to obtain resistant strains from the wild type did not succeed. Whole-genome resequencing of the suppressor strains and genetic analysis revealed inactivation of xseB or pnpA, which code for exodeoxyribonuclease or polynucleotide phosphorylase, respectively. This allowed the quadruple mutant strain to escape from cell death caused by Vetiver extract. Composition analysis suggested that the sesquiterpene, khusimol, might contribute to the bactericidal activity of the Vetiver extract.
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Affiliation(s)
- Yu Shinjyo
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Naoya Midorikawa
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University
| | - Takashi Matsumoto
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture
| | - Yuki Sugaya
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Yoshiki Ozawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Ayumi Oana
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Chiaki Horie
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture.,Department of Bioscience, Tokyo University of Agriculture
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Toshio Hasegawa
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University
| | - Kei Asai
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University.,Department of Bioscience, Tokyo University of Agriculture
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19
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Jiang B, Shen Y, Lu X, Du Y, Jin N, Li G, Zhang D, Xing Y. Toxicity assessment and microbial response to soil antibiotic exposure: differences between individual and mixed antibiotics. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:460-473. [PMID: 35166274 DOI: 10.1039/d1em00405k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Increasing amounts of antibiotics are introduced into soils, raising great concerns on their ecotoxicological impacts on the soil environment. This work investigated the individual and joint toxicity of three antibiotics, tetracycline (TC), sulfonamide (SD) and erythromycin (EM) via a whole-cell bioreporter assay. TC, SD and EM in aqueous solution demonstrated cytotoxicity, whilst soil exposure showed genotoxicity, indicating that soil particles possibly affected the bioavailability of antibiotics. Toxicity of soils exposed to TC, SD and EM changed over time, demonstrating cytotoxic effects within 14-d exposure and genotoxic effects after 30 days. Joint toxicity of TC, SD and EM in soils instead showed cytotoxicity, suggesting a synergetic effect. High-throughput sequencing suggested that the soil microbial response to individual antibiotics and their mixtures showed a different pattern. Soil microbial community composition was more sensitive to TC, in which the abundance of Pseudomonas, Pirellula, Subdivision3_genera_incertae_sedis and Gemmata varied significantly. Microbial community functions were significantly shifted by EM amendments, including signal transduction mechanisms, cytoskeleton, cell wall/membrane/envelope biogenesis, transcription, chromatin structure and dynamics, and carbohydrate transport and metabolism. This work contributes to a better understanding of the ecological effects and potential risks of individual and joint antibiotics on the soil environment.
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Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Yaoxin Shen
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Xin Lu
- Petrochina North China Gas Marketing Company, Beijing, 100029, PR China
| | - Yufan Du
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Naifu Jin
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
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20
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Yin J, Cheng D, Zhu Y, Liang Y, Yu Z. Development of a whole-cell biosensor for detection of antibiotics targeting bacterial cell envelope in Bacillus subtilis. Appl Microbiol Biotechnol 2022; 106:789-798. [DOI: 10.1007/s00253-022-11762-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/15/2021] [Accepted: 01/05/2022] [Indexed: 12/29/2022]
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21
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THCz: Small molecules with antimicrobial activity that block cell wall lipid intermediates. Proc Natl Acad Sci U S A 2021; 118:2108244118. [PMID: 34785593 PMCID: PMC8617507 DOI: 10.1073/pnas.2108244118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Considering the alarming emergence of resistance to most antibiotics and the need for new antibiotics, the finding here of a small-molecule class, THCz, that displayed bactericidal activity against gram-positive and selected gram-negative bacteria, is of the greatest importance. We found that THCz target the cell envelope synthesis and can easily be synthesized and modified, and resistance did not readily develop in vitro. Thus, THCz are promising scaffolds for development of bacterial cell wall inhibitors. Emerging antibiotic resistance demands identification of novel antibacterial compound classes. A bacterial whole-cell screen based on pneumococcal autolysin-mediated lysis induction was developed to identify potential bacterial cell wall synthesis inhibitors. A hit class comprising a 1-amino substituted tetrahydrocarbazole (THCz) scaffold, containing two essential amine groups, displayed bactericidal activity against a broad range of gram-positive and selected gram-negative pathogens in the low micromolar range. Mode of action studies revealed that THCz inhibit cell envelope synthesis by targeting undecaprenyl pyrophosphate–containing lipid intermediates and thus simultaneously inhibit peptidoglycan, teichoic acid, and polysaccharide capsule biosynthesis. Resistance did not readily develop in vitro, and the ease of synthesizing and modifying these small molecules, as compared to natural lipid II–binding antibiotics, makes THCz promising scaffolds for development of cell wall–targeting antimicrobials.
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22
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Terra L, Ratcliffe N, Castro HC, Vicente ACP, Dyson P. Biotechnological Potential of Streptomyces Siderophores as New Antibiotics. Curr Med Chem 2021; 28:1407-1421. [PMID: 32389112 DOI: 10.2174/0929867327666200510235512] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/29/2020] [Accepted: 03/23/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Siderophores are small-molecule iron-chelators produced by microorganisms and plants growing mostly under low iron conditions. Siderophores allow iron capture and transport through cell membranes into the cytoplasm, where iron is released for use in biological processes. These bacterial iron uptake systems can be used for antibiotic conjugation or as targets for killing pathogenic bacteria. Siderophores have been explored recently because of their potential applications in environmental and therapeutic research. They are present in Streptomyces, Grampositive bacteria that are an important source for discovering new siderophores. OBJECTIVE This review summarizes siderophore molecules produced by the genus Streptomyces emphasizing their potential as biotechnological producers and also illustrating genomic tools for discovering siderophores useful for treating bacterial infections. METHODS The literature search was performed using PUBMED and MEDLINE databases with keywords siderophore, secondary metabolites, Trojan horse strategy, sideromycin and Streptomyces. The literature research focused on bibliographic databases including all siderophores identified in the genus Streptomyces. In addition, reference genomes of Streptomyces from GenBank were used to identify siderophore biosynthetic gene clusters by using the antiSMASH platform. RESULTS This review has highlighted some of the many siderophore molecules produced by Streptomyces, illustrating the diversity of their chemical structures and a wide spectrum of bioactivities against pathogenic bacteria. Furthermore, the possibility of using siderophores conjugated with antibiotics could be an alternative to overcome bacterial resistance to drugs and could improve their therapeutic efficacy. CONCLUSION This review confirms the importance of Streptomyces as a rich source of siderophores, and underlines their potential as antibacterial agents.
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Affiliation(s)
- Luciana Terra
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | - Norman Ratcliffe
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | - Helena Carla Castro
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | | | - Paul Dyson
- Institute of Life Science, Swansea University Medical School, Singleton Park, Swansea SA2 8PP, United Kingdom
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23
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Wex KW, Saur JS, Handel F, Ortlieb N, Mokeev V, Kulik A, Niedermeyer THJ, Mast Y, Grond S, Berscheid A, Brötz-Oesterhelt H. Bioreporters for direct mode of action-informed screening of antibiotic producer strains. Cell Chem Biol 2021; 28:1242-1252.e4. [PMID: 33761329 DOI: 10.1016/j.chembiol.2021.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/27/2021] [Accepted: 02/23/2021] [Indexed: 01/17/2023]
Abstract
A big challenge in natural product research of today is rapid dereplication of already known substances, to free capacities for the exploration of new agents. Prompt information on bioactivities and mode of action (MOA) speeds up the lead discovery process and is required for rational compound optimization. Here, we present a bioreporter approach as a versatile strategy for combined bioactivity- and MOA-informed primary screening for antimicrobials. The approach is suitable for directly probing producer strains grown on agar, without need for initial compound enrichment or purification, and works along the entire purification pipeline with culture supernatants, extracts, fractions, and pure substances. The technology allows for MOA-informed purification to selectively prioritize activities of interest. In combination with high-resolution mass spectrometry, the biosensor panel is an efficient and sensitive tool for compound deconvolution. Concomitant information on the affected metabolic pathway enables the selection of appropriate follow-up assays to elucidate the molecular target.
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Affiliation(s)
- Katharina W Wex
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Julian S Saur
- Biomolecular Chemistry, Institute of Organic Chemistry, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Franziska Handel
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Nico Ortlieb
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Vladislav Mokeev
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Andreas Kulik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Timo H J Niedermeyer
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department of Pharmaceutical Biology/Pharmacognosy Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Sachsen-Anhalt 06120, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Yvonne Mast
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Niedersachsen 38124, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Stephanie Grond
- Biomolecular Chemistry, Institute of Organic Chemistry, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany.
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24
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Hansen KØ, Hansen IKØ, Richard CS, Jenssen M, Andersen JH, Hansen EH. Antimicrobial Activity of Securamines From the Bryozoan Securiflustra securifrons. Nat Prod Commun 2021. [DOI: 10.1177/1934578x21996180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Natural products and their derivatives have served as powerful therapeutics against pathogenic microorganisms and are the mainstay of our currently available treatment options to combat infections. As part of our ongoing search for antimicrobial natural products from marine organisms, one fraction prepared from the Arctic marine bryozoan Securiflustra securifrons was found to be active against the human pathogenic bacterium Streptococcus agalactiae (gr. B). Chemical investigation of the fraction revealed that it contained several variants of the highly modified secondary metabolites known as securamines. The securamines are alkaloids sharing a common isoprene-histamine-tryptamine backbone. In this study, we describe the antimicrobial activities of securamine C, E, and H – J (4, 5, and 1-3) and the attempt to deconvolute the mode of action of 1.
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Affiliation(s)
- Kine Ø. Hansen
- Marbio, UiT–The Arctic University of Norway, Breivika, Tromsø, Norway
| | - Ida K. Ø. Hansen
- Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Breivika, Norway
| | - Céline S. Richard
- Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Breivika, Norway
| | - Marte Jenssen
- Marbio, UiT–The Arctic University of Norway, Breivika, Tromsø, Norway
| | | | - Espen H. Hansen
- Marbio, UiT–The Arctic University of Norway, Breivika, Tromsø, Norway
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25
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Koeninger L, Osbelt L, Berscheid A, Wendler J, Berger J, Hipp K, Lesker TR, Pils MC, Malek NP, Jensen BAH, Brötz-Oesterhelt H, Strowig T, Jan Wehkamp. Curbing gastrointestinal infections by defensin fragment modifications without harming commensal microbiota. Commun Biol 2021; 4:47. [PMID: 33420317 PMCID: PMC7794397 DOI: 10.1038/s42003-020-01582-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 11/20/2020] [Indexed: 01/30/2023] Open
Abstract
The occurrence and spread of multidrug-resistant pathogens, especially bacteria from the ESKAPE panel, increases the risk to succumb to untreatable infections. We developed a novel antimicrobial peptide, Pam-3, with antibacterial and antibiofilm properties to counter this threat. The peptide is based on an eight-amino acid carboxyl-terminal fragment of human β-defensin 1. Pam-3 exhibited prominent antimicrobial activity against multidrug-resistant ESKAPE pathogens and additionally eradicated already established biofilms in vitro, primarily by disrupting membrane integrity of its target cell. Importantly, prolonged exposure did not result in drug-resistance to Pam-3. In mouse models, Pam-3 selectively reduced acute intestinal Salmonella and established Citrobacter infections, without compromising the core microbiota, hence displaying an added benefit to traditional broad-spectrum antibiotics. In conclusion, our data support the development of defensin-derived antimicrobial agents as a novel approach to fight multidrug-resistant bacteria, where Pam-3 appears as a particularly promising microbiota-preserving candidate.
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Affiliation(s)
- Louis Koeninger
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany.
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
| | - Anne Berscheid
- Department for Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Judith Wendler
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Jürgen Berger
- Max-Planck Institute for Developmental Biology, Electron Microscopy, Tübingen, Germany
| | - Katharina Hipp
- Max-Planck Institute for Developmental Biology, Electron Microscopy, Tübingen, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marina C Pils
- Mouse Pathology and Histology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nisar P Malek
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Benjamin A H Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Human Genomics and Metagenomics in Metabolism, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heike Brötz-Oesterhelt
- Department for Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, Tübingen, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence - Resolving Infection Susceptibility, Hannover, Germany
| | - Jan Wehkamp
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, Tübingen, Germany
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26
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Piroozmand F, Mohammadipanah F, Faridbod F. Emerging biosensors in detection of natural products. Synth Syst Biotechnol 2020; 5:293-303. [PMID: 32954023 PMCID: PMC7484522 DOI: 10.1016/j.synbio.2020.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 01/10/2023] Open
Abstract
Natural products (NPs) are a valuable source in the food, pharmaceutical, agricultural, environmental, and many other industrial sectors. Their beneficial properties along with their potential toxicities make the detection, determination or quantification of NPs essential for their application. The advanced instrumental methods require time-consuming sample preparation and analysis. In contrast, biosensors allow rapid detection of NPs, especially in complex media, and are the preferred choice of detection when speed and high throughput are intended. Here, we review diverse biosensors reported for the detection of NPs. The emerging approaches for improving the efficiency of biosensors, such as microfluidics, nanotechnology, and magnetic beads, are also discussed. The simultaneous use of two detection techniques is suggested as a robust strategy for precise detection of a specific NP with structural complexity in complicated matrices. The parallel detection of a variety of NPs structures or biological activities in a mixture of extract in a single detection phase is among the anticipated future advancements in this field which can be achieved using multisystem biosensors applying multiple flow cells, sensing elements, and detection mechanisms on miniaturized folded chips.
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Affiliation(s)
- Firoozeh Piroozmand
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Farnoush Faridbod
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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27
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Schäfer AB, Wenzel M. A How-To Guide for Mode of Action Analysis of Antimicrobial Peptides. Front Cell Infect Microbiol 2020; 10:540898. [PMID: 33194788 PMCID: PMC7604286 DOI: 10.3389/fcimb.2020.540898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a promising alternative to classical antibiotics in the fight against multi-resistant bacteria. They are produced by organisms from all domains of life and constitute a nearly universal defense mechanism against infectious agents. No drug can be approved without information about its mechanism of action. In order to use them in a clinical setting, it is pivotal to understand how AMPs work. While many pore-forming AMPs are well-characterized in model membrane systems, non-pore-forming peptides are often poorly understood. Moreover, there is evidence that pore formation may not happen or not play a role in vivo. It is therefore imperative to study how AMPs interact with their targets in vivo and consequently kill microorganisms. This has been difficult in the past, since established methods did not provide much mechanistic detail. Especially, methods to study membrane-active compounds have been scarce. Recent advances, in particular in microscopy technology and cell biological labeling techniques, now allow studying mechanisms of AMPs in unprecedented detail. This review gives an overview of available in vivo methods to investigate the antibacterial mechanisms of AMPs. In addition to classical mode of action classification assays, we discuss global profiling techniques, such as genomic and proteomic approaches, as well as bacterial cytological profiling and other cell biological assays. We cover approaches to determine the effects of AMPs on cell morphology, outer membrane, cell wall, and inner membrane properties, cellular macromolecules, and protein targets. We particularly expand on methods to examine cytoplasmic membrane parameters, such as composition, thickness, organization, fluidity, potential, and the functionality of membrane-associated processes. This review aims to provide a guide for researchers, who seek a broad overview of the available methodology to study the mechanisms of AMPs in living bacteria.
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Affiliation(s)
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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28
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Emami K, Wu LJ, Errington J. A Small Molecule Inhibitor of CTP Synthetase Identified by Differential Activity on a Bacillus subtilis Mutant Deficient in Class A Penicillin-Binding Proteins. Front Microbiol 2020; 11:2001. [PMID: 32973723 PMCID: PMC7479849 DOI: 10.3389/fmicb.2020.02001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/28/2020] [Indexed: 12/03/2022] Open
Abstract
In the course of screening for compounds with differential growth inhibition activity on a mutant of Bacillus subtilis lacking all four class A penicillin-binding proteins (Δ4), we came across an isoquinoline derivative, IQ-1 carboxylic acid (IQC) with relatively high activity on the mutant compared to the wild type strain. Treated cells were slightly elongated and had altered chromosome morphology. Mutants of Δ4 resistant to IQC were isolated and subjected to whole genome sequencing. Most of the mutants were affected in the gene, pyrG, encoding CTP synthetase (CTPS). Purified wild type CTPS was inhibited in vitro by IQC. Two of the three mutant proteins purified showed decreased sensitivity to IQC in vitro. Finally, inhibition by IQC was rescued by addition of cytidine but not uridine to the growth medium, consistent with the notion that IQC acts by reducing the synthesis of CTP or a related compound. IQC provides a promising new starting point for antibiotic inhibitors of CTPS.
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Affiliation(s)
- Kaveh Emami
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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29
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Revilla-Guarinos A, Dürr F, Popp PF, Döring M, Mascher T. Amphotericin B Specifically Induces the Two-Component System LnrJK: Development of a Novel Whole-Cell Biosensor for the Detection of Amphotericin-Like Polyenes. Front Microbiol 2020; 11:2022. [PMID: 32973732 PMCID: PMC7472640 DOI: 10.3389/fmicb.2020.02022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/30/2020] [Indexed: 11/13/2022] Open
Abstract
The rise of drug-resistant fungal pathogens urges for the development of new tools for the discovery of novel antifungal compounds. Polyene antibiotics are potent agents against fungal infections in humans and animals. They inhibit the growth of fungal cells by binding to sterols in the cytoplasmic membrane that subsequently causes pore formation and eventually results in cell death. Many polyenes are produced by Streptomycetes and released into the soil environment, where they can then target fungal hyphae. While not antibacterial, these compounds could nevertheless be also perceived by bacteria sharing the same habitat and serve as signaling molecules. We therefore addressed the question of how polyenes such as amphotericin B are perceived by the soil bacterium, Bacillus subtilis. Global transcriptional profiling identified a very narrow and specific response, primarily resulting in strong upregulation of the lnrLMN operon, encoding an ABC transporter previously associated with linearmycin resistance. Its strong and specific induction prompted a detailed analysis of the lnrL promoter element and its regulation. We demonstrate that the amphotericin response strictly depends on the two-component system LnrJK and that the target of LnrK-dependent gene regulation, the lnrLMN operon, negatively affects LnrJK-dependent signal transduction. Based on this knowledge, we developed a novel whole-cell biosensor, based on a PlnrL-lux fusion reporter construct in a lnrLMN deletion mutant background. This highly sensitive and dynamic biosensor is ready to be applied for the discovery or characterization of novel amphotericin-like polyenes, hopefully helping to increase the repertoire of antimycotic and antiparasitic polyenes available to treat human and animal infections.
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Affiliation(s)
- Ainhoa Revilla-Guarinos
- Department of General Microbiology, Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Franziska Dürr
- Department of General Microbiology, Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Philipp F Popp
- Department of General Microbiology, Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Maximilian Döring
- Department of General Microbiology, Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Thorsten Mascher
- Department of General Microbiology, Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
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30
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Lautenschläger N, Popp PF, Mascher T. Development of a novel heterologous β-lactam-specific whole-cell biosensor in Bacillus subtilis. J Biol Eng 2020; 14:21. [PMID: 32765644 PMCID: PMC7394692 DOI: 10.1186/s13036-020-00243-4] [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: 01/24/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
Background Whole-cell biosensors are a powerful and easy-to-use screening tool for the fast and sensitive detection of chemical compounds, such as antibiotics. β-Lactams still represent one of the most important antibiotic groups in therapeutic use. They interfere with late stages of the bacterial cell wall biosynthesis and result in irreversible perturbations of cell division and growth, ultimately leading to cell lysis. In order to simplify the detection of these antibiotics from solutions, solid media or directly from producing organisms, we aimed at developing a novel heterologous whole-cell biosensor in Bacillus subtilis, based on the β-lactam-induced regulatory system BlaR1/BlaI from Staphylococcus aureus. Results The BlaR1/BlaI system was heterologously expressed in B. subtilis and combined with the luxABCDE operon of Photorhabdus luminescens under control of the BlaR1/BlaI target promoter to measure the output of the biosensor. A combination of codon adaptation, constitutive expression of blaR1 and blaI and the allelic replacement of penP increased the inducer spectrum and dynamic range of the biosensor. β-Lactams from all four classes induced the target promoter PblaZ in a concentration-dependent manner, with a dynamic range of 7- to 53-fold. We applied our biosensor to a set of Streptomycetes soil isolates and demonstrated its potential to screen for the production of β-lactams. In addition to the successful implementation of a highly sensitive β-lactam biosensor, our results also provide the first experimental evidence to support previous suggestions that PenP functions as a β-lactamase in B. subtilis. Conclusion We have successfully established a novel heterologous whole-cell biosensor in B. subtilis that is highly sensitive for a broad spectrum of β-lactams from all four chemical classes. Therefore, it increases the detectable spectrum of compounds with respect to previous biosensor designs. Our biosensor can readily be applied for identifying β-lactams in liquid or on solid media, as well as for identifying potential β-lactam producers.
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Affiliation(s)
- Nina Lautenschläger
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Philipp F Popp
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
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31
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Vadakedath N, Halami PM. Characterization and mode of action of a potent bio-preservative from food-gradeBacillus licheniformisMCC 2016. Prep Biochem Biotechnol 2019; 49:334-343. [DOI: 10.1080/10826068.2019.1566141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Nithya Vadakedath
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Prakash M. Halami
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysore, India
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Mosaei H, Molodtsov V, Kepplinger B, Harbottle J, Moon CW, Jeeves RE, Ceccaroni L, Shin Y, Morton-Laing S, Marrs ECL, Wills C, Clegg W, Yuzenkova Y, Perry JD, Bacon J, Errington J, Allenby NEE, Hall MJ, Murakami KS, Zenkin N. Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis. Mol Cell 2018; 72:263-274.e5. [PMID: 30244835 PMCID: PMC6202310 DOI: 10.1016/j.molcel.2018.08.028] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/19/2018] [Accepted: 08/17/2018] [Indexed: 01/07/2023]
Abstract
Antibiotic-resistant bacterial pathogens pose an urgent healthcare threat, prompting a demand for new medicines. We report the mode of action of the natural ansamycin antibiotic kanglemycin A (KglA). KglA binds bacterial RNA polymerase at the rifampicin-binding pocket but maintains potency against RNA polymerases containing rifampicin-resistant mutations. KglA has antibiotic activity against rifampicin-resistant Gram-positive bacteria and multidrug-resistant Mycobacterium tuberculosis (MDR-M. tuberculosis). The X-ray crystal structures of KglA with the Escherichia coli RNA polymerase holoenzyme and Thermus thermophilus RNA polymerase-promoter complex reveal an altered-compared with rifampicin-conformation of KglA within the rifampicin-binding pocket. Unique deoxysugar and succinate ansa bridge substituents make additional contacts with a separate, hydrophobic pocket of RNA polymerase and preclude the formation of initial dinucleotides, respectively. Previous ansa-chain modifications in the rifamycin series have proven unsuccessful. Thus, KglA represents a key starting point for the development of a new class of ansa-chain derivatized ansamycins to tackle rifampicin resistance.
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Affiliation(s)
- Hamed Mosaei
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Vadim Molodtsov
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Bernhard Kepplinger
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK,Demuris Limited, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - John Harbottle
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Christopher William Moon
- TB Research Group, National Infection Service, Public Health England, Manor Farm Road, Porton, Salisbury SP4 0JG, UK
| | - Rose Elizabeth Jeeves
- TB Research Group, National Infection Service, Public Health England, Manor Farm Road, Porton, Salisbury SP4 0JG, UK
| | - Lucia Ceccaroni
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephanie Morton-Laing
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Corinne Wills
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - William Clegg
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - John David Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Joanna Bacon
- TB Research Group, National Infection Service, Public Health England, Manor Farm Road, Porton, Salisbury SP4 0JG, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK,Demuris Limited, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | | | - Michael John Hall
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA,Corresponding author
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK,Corresponding author
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Kepplinger B, Morton-Laing S, Seistrup KH, Marrs ECL, Hopkins AP, Perry JD, Strahl H, Hall MJ, Errington J, Allenby NEE. Mode of Action and Heterologous Expression of the Natural Product Antibiotic Vancoresmycin. ACS Chem Biol 2018; 13:207-214. [PMID: 29185696 DOI: 10.1021/acschembio.7b00733] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Antibiotics that interfere with the bacterial cytoplasmic membrane have long-term potential for the treatment of infectious diseases as this mode of action is anticipated to result in low resistance frequency. Vancoresmycin is an understudied natural product antibiotic consisting of a terminal tetramic acid moiety fused to a linear, highly oxygenated, stereochemically complex polyketide chain. Vancoresmycin shows minimum inhibitory concentrations (MICs) from 0.125 to 2 μg/mL against a range of clinically relevant, antibiotic-resistant Gram-positive bacteria. Through a comprehensive mode-of-action study, utilizing Bacillus subtilis reporter strains, DiSC3(5) depolarization assays, and fluorescence microscopy, we have shown that vancoresmycin selectively targets the cytoplasmic membrane of Gram-positive bacteria via a non-pore-forming, concentration-dependent depolarization mechanism. Whole genome sequencing of the producing strain allowed identification of the 141 kbp gene cluster encoding for vancoresmycin biosynthesis and a preliminary model for its biosynthesis. The size and complex structure of vancoresmycin could confound attempts to generate synthetic analogues. To overcome this problem and facilitate future studies, we identified, cloned, and expressed the 141 kbp biosynthetic gene cluster in Streptomyces coelicolor M1152. Elucidation of the mode-of-action of vancoresmycin, together with the heterologous expression system, will greatly facilitate further studies of this and related molecules.
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Affiliation(s)
- Bernhard Kepplinger
- Centre for Bacterial Cell Biology, Newcastle University
, Newcastle upon Tyne NE2 4BN, United Kingdom
- Demuris Limited , Newcastle Biomedicine Bio-Incubators
, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Stephanie Morton-Laing
- Demuris Limited , Newcastle Biomedicine Bio-Incubators
, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Kenneth Holst Seistrup
- Centre for Bacterial Cell Biology, Newcastle University
, Newcastle upon Tyne NE2 4BN, United Kingdom
| | | | - Adam Paul Hopkins
- Demuris Limited , Newcastle Biomedicine Bio-Incubators
, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - John David Perry
- Microbiology Department, Freeman Hospital
, Newcastle upon Tyne NE7 7DN, United Kingdom
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Newcastle University
, Newcastle upon Tyne NE2 4BN, United Kingdom
| | - Michael John Hall
- School of Chemistry, Newcastle University
, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Newcastle University
, Newcastle upon Tyne NE2 4BN, United Kingdom
- Demuris Limited , Newcastle Biomedicine Bio-Incubators
, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicholas Edward Ellis Allenby
- Demuris Limited , Newcastle Biomedicine Bio-Incubators
, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
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34
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Saising J, Nguyen MT, Härtner T, Ebner P, Al Mamun Bhuyan A, Berscheid A, Muehlenkamp M, Schäkermann S, Kumari N, Maier ME, Voravuthikunchai SP, Bandow J, Lang F, Brötz-Oesterhelt H, Götz F. Rhodomyrtone (Rom) is a membrane-active compound. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1114-1124. [PMID: 29317198 DOI: 10.1016/j.bbamem.2018.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/15/2017] [Accepted: 01/04/2018] [Indexed: 12/24/2022]
Abstract
Particularly in Asia medicinal plants with antimicrobial activity are used for therapeutic purpose. One such plant-derived antibiotic is rhodomyrtone (Rom) isolated from Rhodomyrtus tomentosa leaves. Rom shows high antibacterial activity against a wide range of Gram-positive bacteria, however, its mode of action is still unclear. Reporter gene assays and proteomic profiling experiments in Bacillus subtilis indicate that Rom does not address classical antibiotic targets like translation, transcription or DNA replication, but acts at the cytoplasmic membrane. In Staphylococcus aureus, Rom decreases the membrane potential within seconds and at low doses, causes release of ATP and even the excretion of cytoplasmic proteins (ECP), but does not induce pore-formation as for example nisin. Lipid staining revealed that Rom induces local membrane damage. Rom's antimicrobial activity can be antagonized in the presence of a very narrow spectrum of saturated fatty acids (C15:0, C16:0, or C18:0) that most likely contribute to counteract the membrane damage. Gram-negative bacteria are resistant to Rom, presumably due to reduced penetration through the outer membrane and its neutralization by LPS. Rom is cytotoxic for many eukaryotic cells and studies with human erythrocytes showed that Rom induces eryptosis accompanied by erythrocyte shrinkage, cell membrane blebbing, and membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Rom's distinctive interaction with the cytoplasmic membrane reminds on the amphipathic, alpha-helical peptides, the phenol-soluble modulins (PSMs), and renders Rom an important tool for the investigation of membrane physiology.
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Affiliation(s)
- Jongkon Saising
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany; School of Health Science, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
| | - Minh-Thu Nguyen
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany; School of Biological and Food Technology, Hanoi University of Science and Technology, Hanoi, Viet Nam
| | - Thomas Härtner
- Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Patrick Ebner
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | | | - Anne Berscheid
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
| | - Melanie Muehlenkamp
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
| | | | - Nimerta Kumari
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Martin E Maier
- Institut für Organische Chemie, Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | | | - Julia Bandow
- Applied Microbiology, Ruhr University Bochum, Bochum, Germany
| | - Florian Lang
- Departments of Cardiology, Vascular Medicine & Physiology, University of Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.
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35
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Mokhlesi A, Stuhldreier F, Wex KW, Berscheid A, Hartmann R, Rehberg N, Sureechatchaiyan P, Chaidir C, Kassack MU, Kalscheuer R, Brötz-Oesterhelt H, Wesselborg S, Stork B, Daletos G, Proksch P. Cyclic Cystine-Bridged Peptides from the Marine Sponge Clathria basilana Induce Apoptosis in Tumor Cells and Depolarize the Bacterial Cytoplasmic Membrane. JOURNAL OF NATURAL PRODUCTS 2017; 80:2941-2952. [PMID: 29094598 DOI: 10.1021/acs.jnatprod.7b00477] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Investigation of the sponge Clathria basilana collected in Indonesia afforded five new peptides, including microcionamides C (1) and D (2), gombamides B (4), C (5), and D (6), and an unusual amide, (E)-2-amino-3-methyl-N-styrylbutanamide (7), along with 11 known compounds, among them microcionamide A (3). The structures of the new compounds were elucidated by one- and two-dimensional NMR spectroscopy as well as by high-resolution mass spectrometry. The absolute configurations of the constituent amino acid residues in 1-7 were determined by Marfey's analysis. Microcionamides A, C, and D (1-3) showed in vitro cytotoxicity against lymphoma (Ramos) and leukemia cell lines (HL-60, Nomo-1, Jurkat J16), as well as against a human ovarian carcinoma cell line (A2780) with IC50 values ranging from 0.45 to 28 μM. Mechanistic studies showed that compounds 1-3 rapidly induce apoptotic cell death in Jurkat J16 and Ramos cells and that 1 and 2 potently block autophagy upon starvation conditions, thereby impairing pro-survival signaling of cancer cells. In addition, microcionamides C and A (1 and 3) inhibited bacterial growth of Staphylococcus aureus and Enterococcus faecium with minimal inhibitory concentrations between 6.2 and 12 μM. Mechanistic studies indicate dissipation of the bacterial membrane potential.
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Affiliation(s)
- Amin Mokhlesi
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
- Department of Marine Biology, Faculty of Marine Sciences, Tarbiat Modares University , Noor, Iran
| | - Fabian Stuhldreier
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Katharina W Wex
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen , Auf der Morgenstelle 28/E8, 72076 Tübingen, Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen , Auf der Morgenstelle 28/E8, 72076 Tübingen, Germany
| | - Rudolf Hartmann
- Institute of Complex Systems: Strukturbiochemie, Forschungszentrum Jülich , Wilhelm-Johnenstrasse, 52428 Jülich, Germany
| | - Nidja Rehberg
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Parichat Sureechatchaiyan
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Chaidir Chaidir
- Center for Pharmaceutical and Medical Technology, Agency for the Assessment and Application Technology , 10340 Jakarta, Indonesia
| | - Matthias U Kassack
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen , Auf der Morgenstelle 28/E8, 72076 Tübingen, Germany
| | - Sebastian Wesselborg
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Georgios Daletos
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Peter Proksch
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University , Universitätsstraße 1, D-40225 Düsseldorf, Germany
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36
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Dhusia K, Bajpai A, Ramteke PW. Overcoming antibiotic resistance: Is siderophore Trojan horse conjugation an answer to evolving resistance in microbial pathogens? J Control Release 2017; 269:63-87. [PMID: 29129658 DOI: 10.1016/j.jconrel.2017.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 01/11/2023]
Abstract
Comparative study of siderophore biosynthesis pathway in pathogens provides potential targets for antibiotics and host drug delivery as a part of computationally feasible microbial therapy. Iron acquisition using siderophore models is an essential and well established model in all microorganisms and microbial infections a known to cause great havoc to both plant and animal. Rapid development of antibiotic resistance in bacterial as well as fungal pathogens has drawn us at a verge where one has to get rid of the traditional way of obstructing pathogen using single or multiple antibiotic/chemical inhibitors or drugs. 'Trojan horse' strategy is an answer to this imperative call where antibiotic are by far sneaked into the pathogenic cell via the siderophore receptors at cell and outer membrane. This antibiotic once gets inside, generates a 'black hole' scenario within the opportunistic pathogens via iron scarcity. For pathogens whose siderophore are not compatible to smuggle drug due to their complex conformation and stiff valence bonds, there is another approach. By means of the siderophore biosynthesis pathways, potential targets for inhibition of these siderophores in pathogenic bacteria could be achieved and thus control pathogenic virulence. Method to design artificial exogenous siderophores for pathogens that would compete and succeed the battle of intake is also covered with this review. These manipulated siderophore would enter pathogenic cell like any other siderophore but will not disperse iron due to which iron inadequacy and hence pathogens control be accomplished. The aim of this review is to offer strategies to overcome the microbial infections/pathogens using siderophore.
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Affiliation(s)
- Kalyani Dhusia
- Deptartment of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Allahabad-211007 (U.P.), India
| | - Archana Bajpai
- Laboratory for Disease Systems Modeling, Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, 230-0045, Japan
| | - P W Ramteke
- Deptartment of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Allahabad-211007 (U.P.), India
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37
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New methodologies in screening of antibiotic residues in animal-derived foods: Biosensors. Talanta 2017; 175:435-442. [PMID: 28842013 DOI: 10.1016/j.talanta.2017.07.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/15/2017] [Accepted: 07/13/2017] [Indexed: 01/05/2023]
Abstract
Antibiotics are leading medicine asset for fighting against microbial infection, but also one of the important causes of death worldwide. Many antibiotics used as therapeutics and growth promotion agents in animals can lead to antibiotic residues in animal-derived food which harm the health of people. Hence, it is vital to screen antibiotic residues in animal derived foods. Typical methods for screening antibiotic residues are based on microbiological growth inhibition and immunological analyses. However these two methods have some disadvantages, such as poor sensitive, lack of specificity and etc. Therefore, it is necessary to develop simple, more efficient and high sensitive screening methods of antibiotic residues. These assays have been introduced for the screening of numerous food samples. Biosensors are emerging methods, applied in screening antibiotic residues in animal-derived foods. Two types of biosensors, whole-cell based biosensors and surface plasmon resonance-based sensors have been extensively used. Their advantages include portability, small sample requirement, high sensitivity and good specificity over the traditional screening methods.
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38
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Raschig J, Mailänder-Sánchez D, Berscheid A, Berger J, Strömstedt AA, Courth LF, Malek NP, Brötz-Oesterhelt H, Wehkamp J. Ubiquitously expressed Human Beta Defensin 1 (hBD1) forms bacteria-entrapping nets in a redox dependent mode of action. PLoS Pathog 2017; 13:e1006261. [PMID: 28323883 PMCID: PMC5376342 DOI: 10.1371/journal.ppat.1006261] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/31/2017] [Accepted: 02/26/2017] [Indexed: 11/19/2022] Open
Abstract
Ever since the discovery of endogenous host defense antimicrobial peptides it has been discussed how these evolutionary conserved molecules avoid to induce resistance and to remain effective. Human ß-defensin 1 (hBD1) is an ubiquitously expressed endogenous antimicrobial peptide that exhibits qualitatively distinct activities between its oxidized and reduced forms. Here, we explore these antimicrobial mechanisms. Surprisingly, using electron microscopy we detected a so far unknown net-like structure surrounding bacteria, which were treated with the reduced but not the oxidized form of hBD1. A transmigration assay demonstrated that hBD1-derived nets capture bacteria and inhibit bacterial transmigration independent of bacterial killing. The presence of nets could completely prevent migration of hBD1 resistant pathogens and are stable in the presence of human duodenal secretion with a high amount of proteases. In contrast to HD6, cysteins are necessary for net formation. This redox-dependent function serves as an additional mechanism of action for hBD1 and differs from net formation by other defensins such as Paneth cell-derived human α-defensin 6 (HD6). While hBD1red and hBD1ox have distinct antimicrobial profiles and functions, only the reduced form provides additional host protection by entrapping bacteria in extracellular net structures preventing bacterial invasion. Better understanding of the modes of action of endogenous host peptides will help to find new antimicrobial strategies.
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Affiliation(s)
- Judith Raschig
- Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Anne Berscheid
- Department for Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Jürgen Berger
- Max-Planck Institute for Developmental Biology, Electron Microscopy, Tuebingen, Germany
| | - Adam A. Strömstedt
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Lioba F. Courth
- Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | - Nisar P. Malek
- Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | - Heike Brötz-Oesterhelt
- Department for Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Jan Wehkamp
- Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
- * E-mail:
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39
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Branchini BR, Southworth TL. A Highly Sensitive Biosensor for ATP Using a Chimeric Firefly Luciferase. Methods Enzymol 2017; 589:351-364. [PMID: 28336069 DOI: 10.1016/bs.mie.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Firefly luciferases, which emit visible light in a highly specific ATP-dependent process, have been adapted for a variety of applications based on the detection of the enzymes or using the proteins to measure ATP levels. Based on studies of chimeric luciferases, we engineered a novel luciferase called PLG2 that has enhanced specific activity, and thermal and pH stability compared to the commonly used Photinus pyralis luciferase. We present here protocols for preparing a single assay mixture containing PLG2 that can be used to readily detect femtomole levels of ATP. Our methodology can be used with a variety of samples, including human and bacterial cells, where measurements of ATP can be used as a biosensor for the detection of viable cells.
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40
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Weinstein ZB, Zaman MH. Quantitative bioassay to identify antimicrobial drugs through drug interaction fingerprint analysis. Sci Rep 2017; 7:42644. [PMID: 28205640 PMCID: PMC5311984 DOI: 10.1038/srep42644] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/09/2017] [Indexed: 02/08/2023] Open
Abstract
Drug interaction analysis, which reports the extent to which the presence of one drug affects the efficacy of another, is a powerful tool to select potent combinatorial therapies and predict connectivity between cellular components. Combinatorial effects of drug pairs often vary even for drugs with similar mechanism of actions. Therefore, drug interaction fingerprinting may be harnessed to differentiate drug identities. We developed a method to analyze drug interactions for the application of identifying active pharmaceutical ingredients, an essential step to assess drug quality. We developed a novel approach towards the identification of active pharmaceutical ingredients by comparing drug interaction fingerprint similarity metrics such as correlation and Euclidean distance. To expedite this method, we used bioluminescent E. coli in a simplified checkerboard assay to generate unique drug interaction fingerprints of antimicrobial drugs. Of 30 antibiotics studied, 29 could be identified based on their drug interaction fingerprints. We present drug interaction fingerprint analysis as a cheap, sensitive and quantitative method towards substandard and counterfeit drug detection.
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Affiliation(s)
- Zohar B Weinstein
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Muhammad H Zaman
- Howard Hughes Medical Institute, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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41
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Schüller A, Matzner D, Lünse CE, Wittmann V, Schumacher C, Unsleber S, Brötz-Oesterhelt H, Mayer C, Bierbaum G, Mayer G. Activation of the glmS Ribozyme Confers Bacterial Growth Inhibition. Chembiochem 2017; 18:435-440. [PMID: 28012261 DOI: 10.1002/cbic.201600491] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 02/06/2023]
Abstract
The ever-growing number of pathogenic bacteria resistant to treatment with antibiotics call for the development of novel compounds with as-yet unexplored modes of action. Here, we demonstrate the in vivo antibacterial activity of carba-α-d-glucosamine (CGlcN). In this mode of action study, we provide evidence that CGlcN-mediated growth inhibition is due to glmS ribozyme activation, and we demonstrate that CGlcN hijacks an endogenous activation pathway, hence utilizing a prodrug mechanism. This is the first report describing antibacterial activity mediated by activating the self-cleaving properties of a ribozyme. Our results open the path towards a compound class with an entirely novel and distinct molecular mechanism.
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Affiliation(s)
- Anna Schüller
- University of Bonn, LIMES Institute, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Daniel Matzner
- University of Bonn, LIMES Institute, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Christina E Lünse
- University of Bonn, LIMES Institute, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany.,University of Leipzig, Institute for Biochemistry, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Valentin Wittmann
- University of Konstanz, Chemistry Department, Universitaetsstrasse 10, 78464, Konstanz, Germany
| | - Catherine Schumacher
- University of Düsseldorf, Institute for Pharmaceutical Biology, Universitätsstrasse 1, Bld. 26.23, Room 00.44, 40225, Düsseldorf, Germany
| | - Sandra Unsleber
- University of Tübingen, Interfaculty Institute for Microbiology and Infection Medicine, Department of Microbiology & Biotechnology, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- University of Tübingen, Interfaculty Institute for Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Christoph Mayer
- University of Tübingen, Interfaculty Institute for Microbiology and Infection Medicine, Department of Microbiology & Biotechnology, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Gabriele Bierbaum
- University of Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Strasse 25, 53127, Bonn, Germany
| | - Günter Mayer
- University of Bonn, LIMES Institute, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
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Webb AJ, Kelwick R, Freemont PS. Opportunities for applying whole-cell bioreporters towards parasite detection. Microb Biotechnol 2017; 10:244-249. [PMID: 28124438 PMCID: PMC5328813 DOI: 10.1111/1751-7915.12604] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/12/2016] [Accepted: 01/02/2017] [Indexed: 12/11/2022] Open
Affiliation(s)
- Alexander J Webb
- Centre for Synthetic Biology and Innovation, Imperial College London, London, SW7 2AZ, UK.,Section of Structural Biology, Department of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Richard Kelwick
- Centre for Synthetic Biology and Innovation, Imperial College London, London, SW7 2AZ, UK.,Section of Structural Biology, Department of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London, London, SW7 2AZ, UK.,Section of Structural Biology, Department of Medicine, Imperial College London, London, SW7 2AZ, UK
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44
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Kim H, Rha E, Seong W, Yeom SJ, Lee DH, Lee SG. A Cell-Cell Communication-Based Screening System for Novel Microbes with Target Enzyme Activities. ACS Synth Biol 2016; 5:1231-1238. [PMID: 27452868 DOI: 10.1021/acssynbio.5b00287] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The development of synthetic biological devices has increased rapidly in recent years and the practical benefits of such biological devices are becoming increasingly clear. Here, we further improved the design of a previously reported high-throughput genetic enzyme screening system by investigating device-compatible biological components and phenol-mediated cell-cell communication, both of which increased the efficiency and practicality of the screening device without requiring the use of flow cytometry analysis. A sensor cell was designed to detect novel microbes with target enzyme activities on solid media by forming clear, circular colonies with fluorescence around the unknown microbes producing target enzymes. This mechanism of detection was enabled by the combination of pre-effector phenolic substrate treatment in the presence of target enzyme-producing microbes and control of the growth and fluorescence of remote sensor cells via phenol-mediated cell-cell communication. The sensor cells were applied to screen soil bacteria with phosphatase activity using phenyl phosphate as phenolic substrates. The sensor cells facilitated successful visualization of phosphatase activity in unknown microbes, which were identified by 16S rRNA analysis. Enzyme activity assays confirmed that the proposed screening technique was able to find 23 positive clones out of 33 selected colonies. Since many natural enzymatic reactions produce phenolic compounds from phenol-derived substrates, we anticipate that the proposed technique may have broad applications in the assessment and screening of novel microbes with target enzymes of interest. This method also can provide insights into the identification of novel enzymes for which screening assays are not yet available.
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Affiliation(s)
- Haseong Kim
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Eugene Rha
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Wonjae Seong
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
- Biosystems
and Bioengineering Program, University of Science and Technology, 217 Gajung-ro, Yuseong-gu, Daejeon, South Korea
| | - Soo-Jin Yeom
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Dae-Hee Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
- Biosystems
and Bioengineering Program, University of Science and Technology, 217 Gajung-ro, Yuseong-gu, Daejeon, South Korea
| | - Seung-Goo Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
- Biosystems
and Bioengineering Program, University of Science and Technology, 217 Gajung-ro, Yuseong-gu, Daejeon, South Korea
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45
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Osterman IA, Bogdanov AA, Dontsova OA, Sergiev PV. Techniques for Screening Translation Inhibitors. Antibiotics (Basel) 2016; 5:antibiotics5030022. [PMID: 27348012 PMCID: PMC5039519 DOI: 10.3390/antibiotics5030022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 02/03/2023] Open
Abstract
The machinery of translation is one of the most common targets of antibiotics. The development and screening of new antibiotics usually proceeds by testing antimicrobial activity followed by laborious studies of the mechanism of action. High-throughput methods for new antibiotic screening based on antimicrobial activity have become routine; however, identification of molecular targets is usually a challenge. Therefore, it is highly beneficial to combine primary screening with the identification of the mechanism of action. In this review, we describe a collection of methods for screening translation inhibitors, with a special emphasis on methods which can be performed in a high-throughput manner.
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Affiliation(s)
- Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Alexey A Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Olga A Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Petr V Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
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Wolf D, Mascher T. The applied side of antimicrobial peptide-inducible promoters from Firmicutes bacteria: expression systems and whole-cell biosensors. Appl Microbiol Biotechnol 2016; 100:4817-29. [PMID: 27102123 DOI: 10.1007/s00253-016-7519-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 11/28/2022]
Abstract
The cell envelope is an essential bacterial structure that consists of the cytoplasmic membrane, the cell wall, and-in Gram-negative bacteria-the outer membrane. Because of its crucial functions, it represents a prime antibiotic target. Monitoring and maintaining its integrity are therefore keys to survival, especially in competitive environments where antibiotics represent one means of suppressing the growth of competitors. Resistance against external antibiotic threat, as well as auto-immunity against self-produced antibiotics, is often mediated by two-component systems (2CSs). They respond to antibiotic threat by inducing gene expression that results in the production of specific resistance determinants. The underlying transcriptional control is exhibited at the level of specific target promoters, which usually share a number of relevant features: They are tightly controlled and only induced in the presence of specific (sets of) antibiotics. This induction is dose dependent and often very sensitive, that is, it occurs well below inhibitory antibiotic concentrations. Because of these characteristics, a number of well-characterized cell envelope stress-inducible promoters have been developed for two different applied purposes: first, as whole-cell biosensors for antibiotic detection and mechanism-of-action studies, and second, as antibiotic-inducible expression systems for biotechnological purposes. The current state of research in both fields will be discussed in this review, focusing on 2CS-regulated promoters from Firmicutes bacteria that are induced to mediate resistance against antimicrobial peptides (AMPs) targeting the cell envelope.
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Affiliation(s)
- Diana Wolf
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany.
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Affiliation(s)
- Xianting Ding
- School of Biomedical Engineering, Institute for Personalized Medicine, Shanghai Jiao Tong University, Med-X Research Institute, Shanghai, China
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48
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Harrison PL, Abdel-Rahman MA, Strong PN, Tawfik MM, Miller K. Characterisation of three alpha-helical antimicrobial peptides from the venom of Scorpio maurus palmatus. Toxicon 2016; 117:30-6. [PMID: 27019370 DOI: 10.1016/j.toxicon.2016.03.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/04/2016] [Accepted: 03/23/2016] [Indexed: 11/19/2022]
Abstract
Scorpion venoms provide a rich source of anti-microbial peptides. Here we characterise three from the venom of Scorpion maurus palmatus. Smp13 is biologically inactive, despite sharing homology with other antimicrobial peptides, probably because it lacks a typically charged structure. Both Smp-24 and Smp-43 have broad spectrum antimicrobial activity, disrupting bacterial membranes. In addition, there is evidence that Smp24 may inhibit DNA synthesis in Bacillus subtilis. Smp24 haemolysed red blood cells but in contrast, Smp43 was non-haemolytic. The introduction of a flexible Gly-Val-Gly hinge into the middle of Smp24 did not alter the haemolytic activity of Smp24 (as might have been predicted from earlier studies with Pandinin2 (Pin2), although C-terminal truncation of Smp-24 reduced its haemolytic activity, in agreement with earlier Pin 2 studies. Smp24 and its derivatives, as well as Smp-43, were all cytotoxic (ATP release assay) toward mammalian HepG2 liver cells. Our results highlight the beneficial effect of helical-hinge-helical conformation on promoting prokaryotic selectivity of long chain scorpion AMPs, as well as the importance of examining a wide range of mammalian cell types in cytotoxicity testing.
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Affiliation(s)
- Patrick L Harrison
- Biomedical Research Centre, Biosciences Division, Sheffield Hallam University, Sheffield, UK
| | | | - Peter N Strong
- Biomedical Research Centre, Biosciences Division, Sheffield Hallam University, Sheffield, UK
| | - Mohamed M Tawfik
- Biomedical Research Centre, Biosciences Division, Sheffield Hallam University, Sheffield, UK
| | - Keith Miller
- Biomedical Research Centre, Biosciences Division, Sheffield Hallam University, Sheffield, UK.
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Helmann JD. Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope. Curr Opin Microbiol 2016; 30:122-132. [PMID: 26901131 DOI: 10.1016/j.mib.2016.02.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 01/20/2023]
Abstract
Bacillus subtilis provides a model for investigation of the bacterial cell envelope, the first line of defense against environmental threats. Extracytoplasmic function (ECF) sigma factors activate genes that confer resistance to agents that threaten the integrity of the envelope. Although their individual regulons overlap, σ(W) is most closely associated with membrane-active agents, σ(X) with cationic antimicrobial peptide resistance, and σ(V) with resistance to lysozyme. Here, I highlight the role of the σ(M) regulon, which is strongly induced by conditions that impair peptidoglycan synthesis and includes the core pathways of envelope synthesis and cell division, as well as stress-inducible alternative enzymes. Studies of these cell envelope stress responses provide insights into how bacteria acclimate to the presence of antibiotics.
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Affiliation(s)
- John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
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50
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Myronovskyi M, Luzhetskyy A. Native and engineered promoters in natural product discovery. Nat Prod Rep 2016; 33:1006-19. [DOI: 10.1039/c6np00002a] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transcriptional activation of biosynthetic gene clusters.
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Affiliation(s)
- Maksym Myronovskyi
- Helmholtz-Institute for Pharmaceutical Research Saarland
- 66123 Saarbrücken
- Germany
| | - Andriy Luzhetskyy
- Helmholtz-Institute for Pharmaceutical Research Saarland
- 66123 Saarbrücken
- Germany
- Department of Pharmaceutical Biotechnology
- Saarland University
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