1
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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. BIOLOGY 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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2
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Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stępień Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Süssmuth RD, Ghilarov D. Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin. Nat Catal 2023; 6:52-67. [PMID: 36741192 PMCID: PMC9886550 DOI: 10.1038/s41929-022-00904-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/30/2022] [Indexed: 01/24/2023]
Abstract
The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between Escherichia coli topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and E. coli topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.
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Affiliation(s)
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Iraj Behroz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Marcel Kulike
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Zuzanna Pakosz-Stępień
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Lukasz Mazurek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Maria Kunert
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | | | - Bernhard Loll
- moloX GmbH, Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - John B Weston
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,John Innes Centre, Norwich Research Park, Norwich, UK
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3
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Marković KG, Grujović MŽ, Koraćević MG, Nikodijević DD, Milutinović MG, Semedo-Lemsaddek T, Djilas MD. Colicins and Microcins Produced by Enterobacteriaceae: Characterization, Mode of Action, and Putative Applications. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11825. [PMID: 36142096 PMCID: PMC9517006 DOI: 10.3390/ijerph191811825] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Enterobacteriaceae are widely present in many environments related to humans, including the human body and the food that they consume, from both plant or animal origin. Hence, they are considered relevant members of the gastrointestinal tract microbiota. On the other hand, these bacteria are also recognized as putative pathogens, able to impair human health and, in food, they are considered indicators for the microbiological quality and hygiene status of a production process. Nevertheless, beneficial properties have also been associated with Enterobacteriaceae, such as the ability to synthesize peptides and proteins, which can have a role in the structure of microbial communities. Among these antimicrobial molecules, those with higher molecular mass are called colicins, while those with lower molecular mass are named microcins. In recent years, some studies show an emphasis on molecules that can help control the development of pathogens. However, not enough data are available on this subject, especially related to microcins. Hence, this review gathers and summarizes current knowledge on colicins and microcins, potential usage in the treatment of pathogen-associated diseases and cancer, as well as putative applications in food biotechnology.
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Affiliation(s)
- Katarina G. Marković
- Institute for Information Technologies, Department of Science, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Mirjana Ž. Grujović
- Institute for Information Technologies, Department of Science, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Maja G. Koraćević
- Innovation Center, University of Niš, 18000 Niš, Serbia
- Faculty of Medicine, Department of Pharmacy, University of Niš, 18000 Niš, Serbia
| | - Danijela D. Nikodijević
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Milena G. Milutinović
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Teresa Semedo-Lemsaddek
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Milan D. Djilas
- Institute for Public Health of Vojvodina, Futoška 121, 21000 Novi Sad, Serbia
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4
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An Overview of Biofilm Formation-Combating Strategies and Mechanisms of Action of Antibiofilm Agents. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081110. [PMID: 35892912 PMCID: PMC9394423 DOI: 10.3390/life12081110] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022]
Abstract
Biofilm formation on surfaces via microbial colonization causes infections and has become a major health issue globally. The biofilm lifestyle provides resistance to environmental stresses and antimicrobial therapies. Biofilms can cause several chronic conditions, and effective treatment has become a challenge due to increased antimicrobial resistance. Antibiotics available for treating biofilm-associated infections are generally not very effective and require high doses that may cause toxicity in the host. Therefore, it is essential to study and develop efficient anti-biofilm strategies that can significantly reduce the rate of biofilm-associated healthcare problems. In this context, some effective combating strategies with potential anti-biofilm agents, including plant extracts, peptides, enzymes, lantibiotics, chelating agents, biosurfactants, polysaccharides, organic, inorganic, and metal nanoparticles, etc., have been reviewed to overcome biofilm-associated healthcare problems. From their extensive literature survey, it can be concluded that these molecules with considerable structural alterations might be applied to the treatment of biofilm-associated infections, by evaluating their significant delivery to the target site of the host. To design effective anti-biofilm molecules, it must be assured that the minimum inhibitory concentrations of these anti-biofilm compounds can eradicate biofilm-associated infections without causing toxic effects at a significant rate.
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5
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Mazurek Ł, Ghilarov D, Michalczyk E, Pakosz Z, Metelev M, Czyszczoń W, Wawro K, Behroz I, Dubiley S, Süssmuth RD, Heddle JG. Pentapeptide repeat protein QnrB1 requires ATP hydrolysis to rejuvenate poisoned gyrase complexes. Nucleic Acids Res 2021; 49:1581-1596. [PMID: 33434265 PMCID: PMC7897471 DOI: 10.1093/nar/gkaa1266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/16/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
DNA gyrase, a type II topoisomerase found predominantly in bacteria, is the target for a variety of 'poisons', namely natural product toxins (e.g. albicidin, microcin B17) and clinically important synthetic molecules (e.g. fluoroquinolones). Resistance to both groups can be mediated by pentapeptide repeat proteins (PRPs). Despite long-term studies, the mechanism of action of these protective PRPs is not known. We show that a PRP, QnrB1 provides specific protection against fluoroquinolones, which strictly requires ATP hydrolysis by gyrase. QnrB1 binds to the GyrB protein and stimulates ATPase activity of the isolated N-terminal ATPase domain of GyrB (GyrB43). We probed the QnrB1 binding site using site-specific incorporation of a photoreactive amino acid and mapped the crosslinks to the GyrB43 protein. We propose a model in which QnrB1 binding allosterically promotes dissociation of the fluoroquinolone molecule from the cleavage complex.
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Affiliation(s)
- Łukasz Mazurek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Zuzanna Pakosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | | | - Wojciech Czyszczoń
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Karolina Wawro
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Iraj Behroz
- Institute of Biological Chemistry, Technische Universität Berlin, Berlin, Germany
| | | | - Roderich D Süssmuth
- Institute of Biological Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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6
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Lu CH, McCloskey A, Chen FR, Nakayasu ES, Zhang LQ, Luo ZQ. Fic Proteins Inhibit the Activity of Topoisomerase IV by AMPylation in Diverse Bacteria. Front Microbiol 2020; 11:2084. [PMID: 32983060 PMCID: PMC7479194 DOI: 10.3389/fmicb.2020.02084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
The Fic (filamentation induced by cyclic AMP) domain is a widely distributed motif with a conserved sequence of HPFx[D/E]GN[G/K]R, some of which regulate cellular activity by catalyzing the transfer of the AMP moiety from ATP to protein substrates. Some Fic proteins, including Fic-1 from the soil bacterium Pseudomonas fluorescens strain 2P24, have been shown to inhibit bacterial DNA replication by AMPylating the subunit B of DNA gyrase (GyrB), but the biochemical activity and cellular target of most Fic proteins remain unknown. Here, we report that Fic-2, which is another Fic protein from strain 2P24 and Fic-1 AMPylate the topoisomerase IV ParE at Tyr109. We also examined Fic proteins from several phylogenetically diverse bacteria and found that those from Yersinia pseudotuberculosis and Staphylococcus aureus AMPylate ParE and GrlB, the counterpart of ParE in Gram-positive bacteria, respectively. Modification by Fic-1 of P. fluorescens and FicY of Y. pseudotuberculosis inhibits the relaxation activity of topoisomerase IV. Consistent with the inhibition of ParE activity, ectopic expression of these Fic proteins causes cell filamentation akin to the canonical par phenotype in which nucleoids are assembled in the center of elongated cells, a process accompanied by the induction of the SOS response. Our results establish that Fic proteins from diverse bacterial species regulate chromosome division and cell separation in bacteria by targeting ParE.
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Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agriculture Science, Kunming, China.,Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China.,Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Alix McCloskey
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Fu-Rong Chen
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ernesto S Nakayasu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Li-Qun Zhang
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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7
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Collin F, Maxwell A. The Microbial Toxin Microcin B17: Prospects for the Development of New Antibacterial Agents. J Mol Biol 2019; 431:3400-3426. [PMID: 31181289 PMCID: PMC6722960 DOI: 10.1016/j.jmb.2019.05.050] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 01/03/2023]
Abstract
Microcin B17 (MccB17) is an antibacterial peptide produced by strains of Escherichia coli harboring the plasmid-borne mccB17 operon. MccB17 possesses many notable features. It is able to stabilize the transient DNA gyrase-DNA cleavage complex, a very efficient mode of action shared with the highly successful fluoroquinolone drugs. MccB17 stabilizes this complex by a distinct mechanism making it potentially valuable in the fight against bacterial antibiotic resistance. MccB17 was the first compound discovered from the thiazole/oxazole-modified microcins family and the linear azole-containing peptides; these ribosomal peptides are post-translationally modified to convert serine and cysteine residues into oxazole and thiazole rings. These chemical moieties are found in many other bioactive compounds like the vitamin thiamine, the anti-cancer drug bleomycin, the antibacterial sulfathiazole and the antiviral nitazoxanide. Therefore, the biosynthetic machinery that produces these azole rings is noteworthy as a general method to create bioactive compounds. Our knowledge of MccB17 now extends to many aspects of antibacterial-bacteria interactions: production, transport, interaction with its target, and resistance mechanisms; this knowledge has wide potential applicability. After a long time with limited progress on MccB17, recent publications have addressed critical aspects of MccB17 biosynthesis as well as an explosion in the discovery of new related compounds in the thiazole/oxazole-modified microcins/linear azole-containing peptides family. It is therefore timely to summarize the evidence gathered over more than 40 years about this still enigmatic molecule and place it in the wider context of antibacterials.
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Affiliation(s)
- Frederic Collin
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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8
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Sutormin D, Rubanova N, Logacheva M, Ghilarov D, Severinov K. Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome. Nucleic Acids Res 2019; 47:1373-1388. [PMID: 30517674 PMCID: PMC6379681 DOI: 10.1093/nar/gky1222] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/19/2018] [Accepted: 11/23/2018] [Indexed: 12/31/2022] Open
Abstract
An important antibiotic target, DNA gyrase is an essential bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA polymerases. By altering the superhelical density, gyrase may regulate expression of bacterial genes. The information about how gyrase is distributed along genomic DNA and whether its distribution is affected by drugs is scarce. During catalysis, gyrase cleaves both DNA strands forming a covalently bound intermediate. By exploiting the ability of several topoisomerase poisons to stabilize this intermediate we developed a ChIP-Seq-based approach to locate, with single nucleotide resolution, DNA gyrase cleavage sites (GCSs) throughout the Escherichia coli genome. We identified an extended gyrase binding motif with phased 10-bp G/C content variation, indicating that bending ability of DNA contributes to gyrase binding. We also found that GCSs are enriched in extended regions located downstream of highly transcribed operons. Transcription inhibition leads to redistribution of gyrase suggesting that the enrichment is functionally significant. Our method can be applied for precise mapping of prokaryotic and eukaryotic type II topoisomerases cleavage sites in a variety of organisms and paves the way for future studies of various topoisomerase inhibitors.
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Affiliation(s)
- Dmitry Sutormin
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Natalia Rubanova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Maria Logacheva
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Malopolska Centre of Biotechnology, Jagiellonian University, 30387 Cracow, Poland
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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9
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Ghilarov D, Stevenson CEM, Travin DY, Piskunova J, Serebryakova M, Maxwell A, Lawson DM, Severinov K. Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol Cell 2019; 73:749-762.e5. [PMID: 30661981 PMCID: PMC6395948 DOI: 10.1016/j.molcel.2018.11.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/24/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
Abstract
The introduction of azole heterocycles into a peptide backbone is the principal step in the biosynthesis of numerous compounds with therapeutic potential. One of them is microcin B17, a bacterial topoisomerase inhibitor whose activity depends on the conversion of selected serine and cysteine residues of the precursor peptide to oxazoles and thiazoles by the McbBCD synthetase complex. Crystal structures of McbBCD reveal an octameric B4C2D2 complex with two bound substrate peptides. Each McbB dimer clamps the N-terminal recognition sequence, while the C-terminal heterocycle of the modified peptide is trapped in the active site of McbC. The McbD and McbC active sites are distant from each other, which necessitates alternate shuttling of the peptide substrate between them, while remaining tethered to the McbB dimer. An atomic-level view of the azole synthetase is a starting point for deeper understanding and control of biosynthesis of a large group of ribosomally synthesized natural products. Azole synthetase McbBCD is co-crystallized with its product, microcin B17 Crystal structure of McbBCD reveals an octameric assembly of B4C2D2 Two McbB subunits within each asymmetric unit interact to recognize a peptide Formation of each azole ring requires shuttling of peptide between two active centers
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Affiliation(s)
- Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland
| | | | - Dmitrii Y Travin
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Julia Piskunova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina Serebryakova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, UK.
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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10
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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11
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Shah P, Hsiao FSH, Ho YH, Chen CS. The proteome targets of intracellular targeting antimicrobial peptides. Proteomics 2016; 16:1225-37. [PMID: 26648572 DOI: 10.1002/pmic.201500380] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/30/2015] [Accepted: 12/03/2015] [Indexed: 01/28/2023]
Abstract
Antimicrobial peptides have been considered well-deserving candidates to fight the battle against microorganisms due to their broad-spectrum antimicrobial activities. Several studies have suggested that membrane disruption is the basic mechanism of AMPs that leads to killing or inhibiting microorganisms. Also, AMPs have been reported to interact with macromolecules inside the microbial cells such as nucleic acids (DNA/RNA), protein synthesis, essential enzymes, membrane septum formation and cell wall synthesis. Proteins are associated with many intracellular mechanisms of cells, thus protein targets may be specifically involved in mechanisms of action of AMPs. AMPs like pyrrhocoricin, drosocin, apidecin and Bac 7 are documented to have protein targets, DnaK and GroEL. Moreover, the intracellular targeting AMPs are reported to influence more than one protein targets inside the cell, suggesting for the multiple modes of actions. This complex mechanism of intracellular targeting AMPs makes them more difficult for the development of resistance. Herein, we have summarized the current status of AMPs in terms of their mode of actions, entry to cytoplasm and inhibition of macromolecules. To reveal the mechanism of action, we have focused on AMPs with intracellular protein targets. We have also included the use of high-throughput proteome microarray to determine the unidentified AMP protein targets in this review.
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Affiliation(s)
- Pramod Shah
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Felix Shih-Hsiang Hsiao
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Yu-Hsuan Ho
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
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12
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Abstract
DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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13
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Metelev MV, Ghilarov DA. Structure, function, and biosynthesis of thiazole/oxazole-modified microcins. Mol Biol 2014. [DOI: 10.1134/s0026893314010105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Majumdar KC, Sinha B. Coinage metals (Cu, Ag and Au) in the synthesis of natural products. RSC Adv 2014. [DOI: 10.1039/c3ra44336a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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15
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Collin F, Thompson RE, Jolliffe KA, Payne RJ, Maxwell A. Fragments of the bacterial toxin microcin B17 as gyrase poisons. PLoS One 2013; 8:e61459. [PMID: 23593482 PMCID: PMC3622597 DOI: 10.1371/journal.pone.0061459] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/09/2013] [Indexed: 11/18/2022] Open
Abstract
Fluoroquinolones are very important drugs in the clinical antibacterial arsenal; their success is principally due to their mode of action: the stabilisation of a gyrase-DNA intermediate (the cleavage complex), which triggers a chain of events leading to cell death. Microcin B17 (MccB17) is a modified peptide bacterial toxin that acts by a similar mode of action, but is unfortunately unsuitable as a therapeutic drug. However, its structure and mechanism could inspire the design of new antibacterial compounds that are needed to circumvent the rise in bacterial resistance to current antibiotics. Here we describe the investigation of the structural features responsible for MccB17 activity and the identification of fragments of the toxin that retain the ability to stabilise the cleavage complex.
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Affiliation(s)
- Frédéric Collin
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Robert E. Thompson
- School of Chemistry, The University of Sydney, New South Wales, Australia
| | | | - Richard J. Payne
- School of Chemistry, The University of Sydney, New South Wales, Australia
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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16
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Taylor JA, Mitchenall LA, Rejzek M, Field RA, Maxwell A. Application of a novel microtitre plate-based assay for the discovery of new inhibitors of DNA gyrase and DNA topoisomerase VI. PLoS One 2013; 8:e58010. [PMID: 23469129 PMCID: PMC3582512 DOI: 10.1371/journal.pone.0058010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 01/29/2013] [Indexed: 01/15/2023] Open
Abstract
DNA topoisomerases are highly exploited targets for antimicrobial drugs. The spread of antibiotic resistance represents a significant threat to public health and necessitates the discovery of inhibitors that target topoisomerases in novel ways. However, the traditional assays for topoisomerase activity are not suitable for the high-throughput approaches necessary for drug discovery. In this study we validate a novel assay for screening topoisomerase inhibitors. A library of 960 compounds was screened against Escherichia coli DNA gyrase and archaeal Methanosarcina mazei DNA topoisomerase VI. Several novel inhibitors were identified for both enzymes, and subsequently characterised in vitro and in vivo. Inhibitors from the M. mazei topoisomerase VI screen were tested for their ability to inhibit Arabidopsis topoisomerase VI in planta. The data from this work present new options for antibiotic drug discovery and provide insight into the mechanism of topoisomerase VI.
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Affiliation(s)
- James A. Taylor
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Lesley A. Mitchenall
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Robert A. Field
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
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17
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Enck S, Tremmel P, Eckhardt S, Marsch M, Geyer A. Stereoselective synthesis of highly functionalized thiopeptide thiazole fragments from uronic acid/cysteine condensation products: access to the core dipeptide of the thiazomycins and nocathiacins. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.06.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Collin F, Karkare S, Maxwell A. Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl Microbiol Biotechnol 2011; 92:479-97. [PMID: 21904817 PMCID: PMC3189412 DOI: 10.1007/s00253-011-3557-z] [Citation(s) in RCA: 371] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/08/2011] [Accepted: 08/18/2011] [Indexed: 12/17/2022]
Abstract
DNA gyrase is a type II topoisomerase that can introduce negative supercoils into DNA at the expense of ATP hydrolysis. It is essential in all bacteria but absent from higher eukaryotes, making it an attractive target for antibacterials. The fluoroquinolones are examples of very successful gyrase-targeted drugs, but the rise in bacterial resistance to these agents means that we not only need to seek new compounds, but also new modes of inhibition of this enzyme. We review known gyrase-specific drugs and toxins and assess the prospects for developing new antibacterials targeted to this enzyme.
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Affiliation(s)
- Frédéric Collin
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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19
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Ghilarov D, Serebryakova M, Shkundina I, Severinov K. A major portion of DNA gyrase inhibitor microcin B17 undergoes an N,O-peptidyl shift during synthesis. J Biol Chem 2011; 286:26308-18. [PMID: 21628468 PMCID: PMC3143593 DOI: 10.1074/jbc.m111.241315] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/12/2011] [Indexed: 11/06/2022] Open
Abstract
Microcin B17 (McB) is a 43-amino acid antibacterial peptide targeting the DNA gyrase. The McB precursor is ribosomally produced and then post-translationally modified by the McbBCD synthase. Active mature McB contains eight oxazole and thiazole heterocycles. Here, we show that a major portion of mature McB contains an additional unusual modification, a backbone ester bond connecting McB residues 51 and 52. The modification results from an N → O shift of the Ser(52) residue located immediately downstream of one of McB thiazole heterocycles. We speculate that the N,O-peptidyl shift undergone by Ser(52) is an intermediate of post-translational modification reactions catalyzed by the McbBCD synthase that normally lead to formation of McB heterocycles.
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Affiliation(s)
- Dmitry Ghilarov
- From the Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Marina Serebryakova
- From the Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- the Institute of Physicochemical Medicine Federal Medico-Biological Agency, Moscow, 119992 Russia, Russia
| | - Irina Shkundina
- From the Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- the Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Konstantin Severinov
- From the Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- the Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
- the Waksman Institute of Microbiology, Piscataway, New Jersey 08854, and
- the Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
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20
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Thompson RE, Jolliffe KA, Payne RJ. Total synthesis of microcin B17 via a fragment condensation approach. Org Lett 2011; 13:680-3. [PMID: 21235262 DOI: 10.1021/ol102916b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The total synthesis of the 43 amino acid antibacterial peptide Microcin B17 (MccB17) is described. The natural product was synthesized via a convergent approach from a heterocycle-derived peptide and peptide thioester fragments prepared via Fmoc-strategy solid phase peptide synthesis (SPPS). Final assembly was achieved in an efficient manner using two Ag(I)-assisted peptide ligation reactions to afford MccB17 in excellent overall yield.
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21
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Sissi C, Palumbo M. In front of and behind the replication fork: bacterial type IIA topoisomerases. Cell Mol Life Sci 2010; 67:2001-24. [PMID: 20165898 PMCID: PMC11115839 DOI: 10.1007/s00018-010-0299-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 01/26/2010] [Accepted: 02/01/2010] [Indexed: 01/03/2023]
Abstract
Topoisomerases are vital enzymes specialized in controlling DNA topology, in particular supercoiling and decatenation, to properly handle nucleic acid packing and cell dynamics. The type IIA enzymes act by cleaving both strands of a double helix and having another strand from the same or another molecule cross the DNA gate before a re-sealing event completes the catalytic cycle. Here, we will consider the two types of IIA prokaryotic topoisomerases, DNA Gyrase and Topoisomerase IV, as crucial regulators of bacterial cell cycle progression. Their synergistic action allows control of chromosome packing and grants occurrence of functional transcription and replication processes. In addition to displaying a fascinating molecular mechanism of action, which transduces chemical energy into mechanical energy by means of large conformational changes, these enzymes represent attractive pharmacological targets for antibacterial chemotherapy.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131, Padua, Italy.
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22
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Synthetic microcin C analogs targeting different aminoacyl-tRNA synthetases. J Bacteriol 2009; 191:6273-80. [PMID: 19684138 DOI: 10.1128/jb.00829-09] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcin C (McC) is a potent antibacterial agent produced by some strains of Escherichia coli. McC consists of a ribosomally synthesized heptapeptide with a modified AMP attached through a phosphoramidate linkage to the alpha-carboxyl group of the terminal aspartate. McC is a Trojan horse inhibitor: it is actively taken inside sensitive cells and processed there, and the product of processing, a nonhydrolyzable aspartyl-adenylate, inhibits translation by preventing aminoacylation of tRNA(Asp) by aspartyl-tRNA synthetase (AspRS). Changing the last residue of the McC peptide should result in antibacterial compounds with targets other than AspRS. However, mutations that introduce amino acid substitutions in the last position of the McC peptide abolish McC production. Here, we report total chemical synthesis of three McC-like compounds containing a terminal aspartate, glutamate, or leucine attached to adenosine through a nonhydrolyzable sulfamoyl bond. We show that all three compounds function in a manner similar to that of McC, but the first compound inhibits bacterial growth by targeting AspRS while the latter two inhibit, respectively, GluRS and LeuRS. Our approach opens a way for creation of new antibacterial Trojan horse agents that target any 1 of the 20 tRNA synthetases in the cell.
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23
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Abstract
DNA topoisomerases are enzymes that control the topological state of DNA in all cells; they have central roles in DNA replication and transcription. They are classified into two types, I and II, depending on whether they catalyze reactions involving the breakage of one or both strands of DNA. Structural and mechanistic distinctions have led to further classifications: IA, IB, IC, IIA, and IIB. The essence of the topoisomerase reaction is the ability of the enzymes to stabilize transient breaks in DNA, via the formation of tyrosyl-phosphate covalent intermediates. The essential nature of topoisomerases and their ability to stabilize DNA breaks has led to them being key targets for antibacterial and anticancer agents. This chapter reviews the basic features of topoisomerases focussing mainly on the prokaryotic enzymes. We highlight recent structural advances that have given new insight into topoisomerase mechanisms and into the molecular basis of the action of topoisomerase-specific drugs.
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24
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Abstract
The conventional notion that peptides are poor candidates for orally available drugs because of protease-sensitive peptide bonds, intrinsic hydrophilicity, and ionic charges contrasts with the diversity of antibiotic natural products with peptide-based frameworks that are synthesized and utilized by Nature. Several of these antibiotics, including penicillin and vancomycin, are employed to treat bacterial infections in humans and have been best-selling therapeutics for decades. Others might provide new platforms for the design of novel therapeutics to combat emerging antibiotic-resistant bacterial pathogens.
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Affiliation(s)
- Elizabeth M Nolan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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25
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The pentapeptide repeat proteins MfpAMt and QnrB4 exhibit opposite effects on DNA gyrase catalytic reactions and on the ternary gyrase-DNA-quinolone complex. J Bacteriol 2008; 191:1587-94. [PMID: 19060136 DOI: 10.1128/jb.01205-08] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MfpA(Mt) and QnrB4 are two newly characterized pentapeptide repeat proteins (PRPs) that interact with DNA gyrase. The mfpA(Mt) gene is chromosome borne in Mycobacterium tuberculosis, while qnrB4 is plasmid borne in enterobacteria. We expressed and purified the two PRPs and compared their effects on DNA gyrase, taking into account host specificity, i.e., the effect of MfpA(Mt) on M. tuberculosis gyrase and the effect of QnrB4 on Escherichia coli gyrase. Whereas QnrB4 inhibited E. coli gyrase activity only at concentrations higher than 30 microM, MfpA(Mt) inhibited all catalytic reactions of the M. tuberculosis gyrase described for this enzyme (supercoiling, cleavage, relaxation, and decatenation) with a 50% inhibitory concentration of 2 microM. We showed that the D87 residue in GyrA has a major role in the MfpA(Mt)-gyrase interaction, as D87H and D87G substitutions abolished MfpA(Mt) inhibition of M. tuberculosis gyrase catalytic reactions, while A83S modification did not. Since MfpA(Mt) and QnrB4 have been involved in resistance to fluoroquinolones, we measured the inhibition of the quinolone effect in the presence of each PRP. QnrB4 reversed quinolone inhibition of E. coli gyrase at 0.1 microM as described for other Qnr proteins, but MfpA(Mt) did not modify M. tuberculosis gyrase inhibition by fluoroquinolones. Crossover experiments showed that MfpA(Mt) also inhibited E. coli gyrase function, while QnrB4 did not reverse quinolone inhibition of M. tuberculosis gyrase. In conclusion, our in vitro experiments showed that MfpA(Mt) and QnrB4 exhibit opposite effects on DNA gyrase and that these effects are protein and species specific.
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26
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Zavilgelsky GB, Rastorguev SM. DNA mimicry by proteins as effective mechanism for regulation of activity of DNA-dependent enzymes. BIOCHEMISTRY (MOSCOW) 2007; 72:913-9, 4 p. following 982. [DOI: 10.1134/s0006297907090015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Severinov K, Semenova E, Kazakov A, Kazakov T, Gelfand MS. Low-molecular-weight post-translationally modified microcins. Mol Microbiol 2007; 65:1380-94. [PMID: 17711420 DOI: 10.1111/j.1365-2958.2007.05874.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microcins are a class of ribosomally synthesized antibacterial peptides produced by Enterobacteriaceae and active against closely related bacterial species. While some microcins are active as unmodified peptides, others are heavily modified by dedicated maturation enzymes. Low-molecular-weight microcins from the post-translationally modified group target essential molecular machines inside the cells. In this review, available structural and functional data about three such microcins--microcin J25, microcin B17 and microcin C7-C51--are discussed. While all three low-molecular-weight post-translationally modified microcins are produced by Escherichia coli, inferences based on sequence and structural similarities with peptides encoded or produced by phylogenetically diverse bacteria are made whenever possible to put these compounds into a larger perspective.
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Affiliation(s)
- Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
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28
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Duquesne S, Destoumieux-Garzón D, Peduzzi J, Rebuffat S. Microcins, gene-encoded antibacterial peptides from enterobacteria. Nat Prod Rep 2007; 24:708-34. [PMID: 17653356 DOI: 10.1039/b516237h] [Citation(s) in RCA: 251] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microcins are gene-encoded antibacterial peptides, with molecular masses below 10 kDa, produced by enterobacteria. They are secreted under conditions of nutrient depletion and exert potent antibacterial activity against closely related species. Typical gene clusters encoding the microcin precursor, the self-immunity factor, the secretion proteins and frequently the post-translational modification enzymes are located either on plasmids or on the chromosome. In contrast to most of the antibiotics of microbial origin, which are non-ribosomally synthesized by multimodular enzymes termed peptide synthetases, microcins are ribosomally synthesized as precursors, which are further modified enzymatically. They form a restricted class of potent antibacterial peptides. Fourteen microcins have been reported so far, among which only seven have been isolated and characterized. Despite the low number of known representatives, microcins exhibit a diversity of structures and antibacterial mechanisms. This review provides an updated overview of microcin structures, antibacterial activities, genetic systems and biosyntheses, as well as of their mechanisms of action.
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Affiliation(s)
- Sophie Duquesne
- Laboratory of Chemistry and Biochemistry of Natural Substances, UMR 5154 CNRS, Department of Regulations, Development and Molecular Diversity, National Museum of Natural History, CP 54, 57 rue Cuvier, 75005, Paris, France
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29
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Parks WM, Bottrill AR, Pierrat OA, Durrant MC, Maxwell A. The action of the bacterial toxin, microcin B17, on DNA gyrase. Biochimie 2007; 89:500-7. [PMID: 17276574 DOI: 10.1016/j.biochi.2006.12.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Accepted: 12/22/2006] [Indexed: 11/29/2022]
Abstract
Microcin B17 (MccB17) is a peptide-based bacterial toxin that targets DNA gyrase, the bacterial enzyme that introduces supercoils into DNA. The site and mode of action of MccB17 on gyrase are unclear. We review what is currently known about MccB17-gyrase interactions and summarise approaches to understanding its mode of action that involve modification of the toxin. We describe experiments in which treatment of the toxin at high pH leads to the deamidation of two asparagine residues to aspartates. The modified toxin was found to be inactive in vivo and in vitro, suggesting that the Asn residues are essential for activity. Following on from these studies we have used molecular modelling to suggest a 3D structure for microcin B17. We discuss the implications of this model for MccB17 action and investigate the possibility that it binds metal ions.
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Affiliation(s)
- William M Parks
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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30
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Hashimi SM, Wall MK, Smith AB, Maxwell A, Birch RG. The phytotoxin albicidin is a novel inhibitor of DNA gyrase. Antimicrob Agents Chemother 2007; 51:181-7. [PMID: 17074789 PMCID: PMC1797663 DOI: 10.1128/aac.00918-06] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 09/20/2006] [Accepted: 10/20/2006] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas albilineans produces a family of polyketide-peptide compounds called albicidins which are highly potent antibiotics and phytotoxins as a result of their inhibition of prokaryotic DNA replication. Here we show that albicidin is a potent inhibitor of the supercoiling activity of bacterial and plant DNA gyrases, with 50% inhibitory concentrations (40 to 50 nM) less than those of most coumarins and quinolones. Albicidin blocks the religation of the cleaved DNA intermediate during the gyrase catalytic sequence and also inhibits the relaxation of supercoiled DNA by gyrase and topoisomerase IV. Unlike the coumarins, albicidin does not inhibit the ATPase activity of gyrase. In contrast to the quinolones, the albicidin concentration required to stabilize the gyrase cleavage complex increases 100-fold in the absence of ATP. The slow peptide poisons microcin B17 and CcdB also access ATP-dependent conformations of gyrase to block religation, but in contrast to albicidin, they do not inhibit supercoiling under routine assay conditions. Some mutations in gyrA, known to confer high-level resistance to quinolones or CcdB, confer low-level resistance or hypersensitivity to albicidin in Escherichia coli. Within the albicidin biosynthesis region in X. albilineans is a gene encoding a pentapeptide repeat protein designated AlbG that binds to E. coli DNA gyrase and that confers a sixfold increase in the level of resistance to albicidin in vitro and in vivo. These results demonstrate that DNA gyrase is the molecular target of albicidin and that X. albilineans encodes a gyrase-interacting protein for self-protection. The novel features of the gyrase-albicidin interaction indicate the potential for the development of new antibacterial drugs.
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Affiliation(s)
- Saeed M Hashimi
- Botany Department--SIB, The University of Queensland, Brisbane 4072, Australia
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31
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32
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Buchko GW, Ni S, Robinson H, Welsh EA, Pakrasi HB, Kennedy MA. Characterization of two potentially universal turn motifs that shape the repeated five-residues fold--crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142. Protein Sci 2006; 15:2579-95. [PMID: 17075135 PMCID: PMC2242410 DOI: 10.1110/ps.062407506] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 08/21/2006] [Accepted: 08/22/2006] [Indexed: 10/24/2022]
Abstract
The genome of the diurnal cyanobacterium Cyanothece sp. PCC 51142 has recently been sequenced and observed to contain 35 pentapeptide repeat proteins (PRPs). These proteins, while present throughout the prokaryotic and eukaryotic kingdoms, are most abundant in cyanobacteria. The sheer number of PRPs in cyanobacteria coupled with their predicted location in every cellular compartment argues for important, yet unknown, physiological and biochemical functions. To gain biochemical insights, the crystal structure for Rfr32, a 167-residue PRP with an N-terminal 29-residue signal peptide, was determined at 2.1 A resolution. The structure is dominated by 21 tandem pentapeptide repeats that fold into a right-handed quadrilateral beta-helix, or Rfr-fold, as observed for the tandem pentapeptide repeats in the only other PRP structure, the mycobacterial fluoroquinoline resistance protein MfpA from Mycobacterium tuberculosis. Sitting on top of the Rfr-fold are two short, antiparallel alpha-helices, bridged with a disulfide bond, that perhaps prevent edge-to-edge aggregation at the C terminus. Analysis of the main-chain (Phi,Psi) dihedral orientations for the pentapeptide repeats in Rfr32 and MfpA makes it possible to recognize the structural details for the two distinct types of four-residue turns adopted by the pentapeptide repeats in the Rfr-fold. These turns, labeled type II and type IV beta-turns, may be universal motifs that shape the Rfr-fold in all PRPs.
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Affiliation(s)
- Garry W Buchko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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33
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Smith AB, Maxwell A. A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site. Nucleic Acids Res 2006; 34:4667-76. [PMID: 16963775 PMCID: PMC1635281 DOI: 10.1093/nar/gkl636] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA gyrase is the only topoisomerase able to introduce negative supercoils into DNA. Absent in humans, gyrase is a successful target for antibacterial drugs. However, increasing drug resistance is a serious problem and new agents are urgently needed. The naturally-produced Escherichia coli toxin CcdB has been shown to target gyrase by what is predicted to be a novel mechanism. CcdB has been previously shown to stabilize the gyrase ‘cleavage complex’, but it has not been shown to inhibit the catalytic reactions of gyrase. We present data showing that CcdB does indeed inhibit the catalytic reactions of gyrase by stabilization of the cleavage complex and that the GyrA C-terminal DNA-wrapping domain and the GyrB N-terminal ATPase domain are dispensable for CcdB's action. We further investigate the role of specific GyrA residues in the action of CcdB by site-directed mutagenesis; these data corroborate a model for CcdB action based on a recent crystal structure of a CcdB–GyrA fragment complex. From this work, we are now able to present a model for CcdB action that explains all previous observations relating to CcdB–gyrase interaction. CcdB action requires a conformation of gyrase that is only revealed when DNA strand passage is taking place.
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Affiliation(s)
| | - Anthony Maxwell
- To whom correspondence should be addressed. Tel: +44 1603 450771; Fax: +44 1603 450018;
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34
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Metlitskaya A, Kazakov T, Kommer A, Pavlova O, Praetorius-Ibba M, Ibba M, Krasheninnikov I, Kolb V, Khmel I, Severinov K. Aspartyl-tRNA Synthetase Is the Target of Peptide Nucleotide Antibiotic Microcin C. J Biol Chem 2006; 281:18033-42. [PMID: 16574659 DOI: 10.1074/jbc.m513174200] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microcin C is a ribosome-synthesized heptapeptide that contains a modified adenosine monophosphate covalently attached to the C-terminal aspartate. Microcin C is a potent inhibitor of bacterial cell growth. Based on the in vivo kinetics of inhibition of macromolecular synthesis, Microcin C targets translation, through a mechanism that remained undefined. Here, we show that Microcin C is a subject of specific degradation inside the sensitive cell. The product of degradation, a modified aspartyl-adenylate containing an N-acylphosphoramidate linkage, strongly inhibits translation by blocking the function of aspartyl-tRNA synthetase.
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35
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Vetting MW, Hegde SS, Fajardo JE, Fiser A, Roderick SL, Takiff HE, Blanchard JS. Pentapeptide repeat proteins. Biochemistry 2006; 45:1-10. [PMID: 16388575 PMCID: PMC2566302 DOI: 10.1021/bi052130w] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pentapeptide repeat protein (PRP) family has more than 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S,T,A,V][D,N][L,F][S,T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral beta-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable similarity in size, shape, and electrostatics to DNA.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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Manjunatha UH, Maxwell A, Nagaraja V. A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism. Nucleic Acids Res 2005; 33:3085-94. [PMID: 15930158 PMCID: PMC1142348 DOI: 10.1093/nar/gki622] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
DNA gyrase is a DNA topoisomerase indispensable for cellular functions in bacteria. We describe a novel, hitherto unknown, mechanism of specific inhibition of Mycobacterium smegmatis and Mycobacterium tuberculosis DNA gyrase by a monoclonal antibody (mAb). Binding of the mAb did not affect either GyrA–GyrB or gyrase–DNA interactions. More importantly, the ternary complex of gyrase–DNA–mAb retained the ATPase activity of the enzyme and was competent to catalyse DNA cleavage–religation reactions, implying a new mode of action different from other classes of gyrase inhibitors. DNA gyrase purified from fluoroquinolone-resistant strains of M.tuberculosis and M.smegmatis were inhibited by the mAb. The absence of cross-resistance of the drug-resistant enzymes from two different sources to the antibody-mediated inhibition corroborates the new mechanism of inhibition. We suggest that binding of the mAb in the proximity of the primary dimer interface region of GyrA in the heterotetrameric enzyme appears to block the release of the transported segment after strand passage, leading to enzyme inhibition. The specific inhibition of mycobacterial DNA gyrase with the mAb opens up new avenues for designing novel lead molecules for drug discovery and for probing gyrase mechanism.
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Affiliation(s)
- Ujjini H Manjunatha
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, 560 012, India
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