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Sagurna L, Heinrich S, Kaufmann LS, Rückert-Reed C, Busche T, Wolf A, Eickhoff J, Klebl B, Kalinowski J, Bandow JE. Characterization of the Antibacterial Activity of Quinone-Based Compounds Originating from the Alnumycin Biosynthetic Gene Cluster of a Streptomyces Isolate. Antibiotics (Basel) 2023; 12:1116. [PMID: 37508212 PMCID: PMC10376017 DOI: 10.3390/antibiotics12071116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Bacteria of the genus Streptomyces produce various specialized metabolites. Single biosynthetic gene clusters (BGCs) can give rise to different products that can vary in terms of their biological activities. For example, for alnumycin and the shunt product K115, antimicrobial activity was described, while no antimicrobial activity was detected for the shunt product 1,6-dihydro 8-propylanthraquinone. To investigate the antibacterial activity of 1,6-dihydro 8-propylanthraquinone, we produced alnumycin and 1,6-dihydro 8-propylanthraquinone from a Streptomyces isolate containing the alnumycin BGC. The strain was cultivated in liquid glycerol-nitrate-casein medium (GN), and both compounds were isolated using an activity and mass spectrometry-guided purification. The structures were validated via nuclear magnetic resonance (NMR) spectroscopy. A minimal inhibitory concentration (MIC) test revealed that 1,6-dihydro 8-propylanthraquinone exhibits antimicrobial activity against E. coli ΔtolC, B. subtilis, an S. aureus type strain, and a vancomycin intermediate-resistance S. aureus strain (VISA). Activity of 1,6-dihydro 8-propylanthraquinone against E. coli ΔtolC was approximately 10-fold higher than that of alnumycin. We were unable to confirm gyrase inhibition for either compound and believe that the modes of action of both compounds are worth reinvestigating.
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Affiliation(s)
- Leonie Sagurna
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Sascha Heinrich
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Lara-Sophie Kaufmann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Christian Rückert-Reed
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany
| | | | - Jan Eickhoff
- Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
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Drlica K, Hiasa H, Kerns R, Malik M, Mustaev A, Zhao X. Quinolones: action and resistance updated. Curr Top Med Chem 2009; 9:981-98. [PMID: 19747119 PMCID: PMC3182077 DOI: 10.2174/156802609789630947] [Citation(s) in RCA: 235] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 07/30/2009] [Indexed: 11/22/2022]
Abstract
The quinolones trap DNA gyrase and DNA topoisomerase IV on DNA as complexes in which the DNA is broken but constrained by protein. Early studies suggested that drug binding occurs largely along helix-4 of the GyrA (gyrase) and ParC (topoisomerase IV) proteins. However, recent X-ray crystallography shows drug intercalating between the -1 and +1 nucleotides of cut DNA, with only one end of the drug extending to helix-4. These two models may reflect distinct structural steps in complex formation. A consequence of drug-enzyme-DNA complex formation is reversible inhibition of DNA replication; cell death arises from subsequent events in which bacterial chromosomes are fragmented through two poorly understood pathways. In one pathway, chromosome fragmentation stimulates excessive accumulation of highly toxic reactive oxygen species that are responsible for cell death. Quinolone resistance arises stepwise through selective amplification of mutants when drug concentrations are above the MIC and below the MPC, as observed with static agar plate assays, dynamic in vitro systems, and experimental infection of rabbits. The gap between MIC and MPC can be narrowed by compound design that should restrict the emergence of resistance. Resistance is likely to become increasingly important, since three types of plasmid-borne resistance have been reported.
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Affiliation(s)
- Karl Drlica
- Public Health Research Institute, New Jersey Medical School, UMDNJ, 225 Warren Street, Newark, NJ 07103, USA.
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Affiliation(s)
- Karl Drlica
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, 225 Warren St., Newark, NJ 07103, USA.
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Grompone G, Bidnenko V, Ehrlich SD, Michel B. PriA is essential for viability of the Escherichia coli topoisomerase IV parE10(Ts) mutant. J Bacteriol 2004; 186:1197-9. [PMID: 14762016 PMCID: PMC344234 DOI: 10.1128/jb.186.4.1197-1199.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The parE10(Ts) mutation, which renders Escherichia coli thermosensitive for growth by inactivation of the essential E. coli topoisomerase topo IV, is lethal at all temperatures when PriA, the main replication restart protein, is absent. This lethality is suppressed by the activation of a PriA-independent replication restart pathway (dnaC809 mutation). This result suggests that topo IV acts prior to full-chromosome replication completion.
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Affiliation(s)
- Gianfranco Grompone
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, 78352 Jouy en Josas, France
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Brunetti R, Prosseda G, Beghetto E, Colonna B, Micheli G. The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains. Biochimie 2001; 83:873-82. [PMID: 11698109 DOI: 10.1016/s0300-9084(01)01331-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
We have investigated the major Escherichia coli histone-like proteins (H-NS, HU, FIS, and IHF) as putative factors involved in the maintenance of the overall DNA looped arrangement of the bacterial nucleoid. The long-range architecture of the chromosome has been studied by means of an assay based on in vivo genomic fragmentation mediated by endogenous DNA gyrase in the presence of oxolinic acid. The fragmentation products were analysed by CHEF electrophoresis. The results indicate that in vivo a large fraction of the bacterial chromatin constitutes an adequate substrate for the enzyme. DNA fragments released upon oxo-treatment span a size range from about 1000 kb to a limit-size of about 50 kb. The latter value is in excellent agreement with the average size reported for bacterial chromosomal domains. The DNA gyrase-mediated fragmentation does not appear to be significantly altered in strains depleted in histone-like proteins as compared to an E. coli wild type strain. This suggests that these proteins may not represent critical determinants for the maintenance of the supercoiled loop organisation of the E. coli chromosome.
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Affiliation(s)
- R Brunetti
- Centro Acidi Nucleici C.N.R., Università La Sapienza, P. le A. Moro 5, Rome 00185, Italy
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Abstract
For many years, DNA gyrase was thought to be responsible both for unlinking replicated daughter chromosomes and for controlling negative superhelical tension in bacterial DNA. However, in 1990 a homolog of gyrase, topoisomerase IV, that had a potent decatenating activity was discovered. It is now clear that topoisomerase IV, rather than gyrase, is responsible for decatenation of interlinked chromosomes. Moreover, topoisomerase IV is a target of the 4-quinolones, antibacterial agents that had previously been thought to target only gyrase. The key event in quinolone action is reversible trapping of gyrase-DNA and topoisomerase IV-DNA complexes. Complex formation with gyrase is followed by a rapid, reversible inhibition of DNA synthesis, cessation of growth, and induction of the SOS response. At higher drug concentrations, cell death occurs as double-strand DNA breaks are released from trapped gyrase and/or topoisomerase IV complexes. Repair of quinolone-induced DNA damage occurs largely via recombination pathways. In many gram-negative bacteria, resistance to moderate levels of quinolone arises from mutation of the gyrase A protein and resistance to high levels of quinolone arises from mutation of a second gyrase and/or topoisomerase IV site. For some gram-positive bacteria, the situation is reversed: primary resistance occurs through changes in topoisomerase IV while gyrase changes give additional resistance. Gyrase is also trapped on DNA by lethal gene products of certain large, low-copy-number plasmids. Thus, quinolone-topoisomerase biology is providing a model for understanding aspects of host-parasite interactions and providing ways to investigate manipulation of the bacterial chromosome by topoisomerases.
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Affiliation(s)
- K Drlica
- Public Health Research Institute, New York, New York 10016, USA.
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Drlica K, Kreiswirth B. 4-quinolones and the physiology of DNA gyrase. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 1994; 29A:263-83. [PMID: 7826862 DOI: 10.1016/s1054-3589(08)60549-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- K Drlica
- Public Health Research Institute, New York University School of Medicine, New York 10016
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Abstract
Two DNA topoisomerases control the level of negative supercoiling in bacterial cells. DNA gyrase introduces supercoils, and DNA topoisomerase I prevents supercoiling from reaching unacceptably high levels. Perturbations of supercoiling are corrected by the substrate preferences of these topoisomerases with respect to DNA topology and by changes in expression of the genes encoding the enzymes. However, supercoiling changes when the growth environment is altered in ways that also affect cellular energetics. The ratio of [ATP] to [ADP], to which gyrase is sensitive, may be involved in the response of supercoiling to growth conditions. Inside cells, supercoiling is partitioned into two components, superhelical tension and restrained supercoils. Shifts in superhelical tension elicited by nicking or by salt shock do not rapidly change the level of restrained supercoiling. However, a steady-state change in supercoiling caused by mutation of topA does alter both tension and restrained supercoils. This communication between the two compartments may play a role in the control of supercoiling.
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Affiliation(s)
- K Drlica
- Public Health Research Institute, New York, New York 10016
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Abstract
DNA gyrase is an essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed-circular DNA. Gyrase belongs to a class of enzymes known as topoisomerases that are involved in the control of topological transitions of DNA. The mechanism by which gyrase is able to influence the topological state of DNA molecules is of inherent interest from an enzymological standpoint. In addition, much attention has been focused on DNA gyrase as the intracellular target of a number of antibacterial agents as a paradigm for other DNA topoisomerases. In this review we summarize the current knowledge concerning DNA gyrase by addressing a wide range of aspects of the study of this enzyme.
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Affiliation(s)
- R J Reece
- Department of Biochemistry, University of Leicester, UK
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Condemine G, Smith CL. Transcription regulates oxolinic acid-induced DNA gyrase cleavage at specific sites on the E. coli chromosome. Nucleic Acids Res 1990; 18:7389-96. [PMID: 2175434 PMCID: PMC332877 DOI: 10.1093/nar/18.24.7389] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Prominent DNA gyrase-mediated cleavage sites, induced by oxolinic acid, occur at specific, but infrequent, locations on the Escherichia coli chromosome. These sites, which we call toposites, may represent high affinity DNA gyrase binding sites or may mark chromosomal regions that accumulate superhelical stress. Toposites are usually grouped in 5 to 10 kb clusters that are mostly 50 to 100 kb apart. The total number of clusters on the chromosome is between 50 and 100. The location of sites depends on the local sequence. The extent of DNA gyrase cleavage at toposites can be strongly modulated by transcription occurring at as far as 35 kb away.
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Affiliation(s)
- G Condemine
- Laboratoire de Microbiologie, INSA Bat 406, Villeurbanne, France
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Affiliation(s)
- K Drlica
- Public Health Research Institute, New York, NY 10016
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