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Nedal A, Ræder SB, Dalhus B, Helgesen E, Forstrøm RJ, Lindland K, Sumabe BK, Martinsen JH, Kragelund BB, Skarstad K, Bjørås M, Otterlei M. Peptides containing the PCNA interacting motif APIM bind to the β-clamp and inhibit bacterial growth and mutagenesis. Nucleic Acids Res 2020; 48:5540-5554. [PMID: 32347931 PMCID: PMC7261172 DOI: 10.1093/nar/gkaa278] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/08/2023] Open
Abstract
In the fight against antimicrobial resistance, the bacterial DNA sliding clamp, β-clamp, is a promising drug target for inhibition of DNA replication and translesion synthesis. The β-clamp and its eukaryotic homolog, PCNA, share a C-terminal hydrophobic pocket where all the DNA polymerases bind. Here we report that cell penetrating peptides containing the PCNA-interacting motif APIM (APIM-peptides) inhibit bacterial growth at low concentrations in vitro, and in vivo in a bacterial skin infection model in mice. Surface plasmon resonance analysis and computer modeling suggest that APIM bind to the hydrophobic pocket on the β-clamp, and accordingly, we find that APIM-peptides inhibit bacterial DNA replication. Interestingly, at sub-lethal concentrations, APIM-peptides have anti-mutagenic activities, and this activity is increased after SOS induction. Our results show that although the sequence homology between the β-clamp and PCNA are modest, the presence of similar polymerase binding pockets in the DNA clamps allows for binding of the eukaryotic binding motif APIM to the bacterial β-clamp. Importantly, because APIM-peptides display both anti-mutagenic and growth inhibitory properties, they may have clinical potential both in combination with other antibiotics and as single agents.
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Affiliation(s)
- Aina Nedal
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Synnøve B Ræder
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Emily Helgesen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Rune J Forstrøm
- Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Kim Lindland
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Balagra K Sumabe
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Jacob H Martinsen
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Kirsten Skarstad
- Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
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Bøyum A, Forstrøm RJ, Sefland I, Sand KL, Benestad HB. Intricacies of redoxome function demonstrated with a simple in vitro chemiluminescence method, with special reference to vitamin B12 as antioxidant. Scand J Immunol 2015; 80:390-7. [PMID: 25345916 PMCID: PMC4285856 DOI: 10.1111/sji.12220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 08/21/2014] [Indexed: 11/27/2022]
Abstract
The homeostatic control of the redox system (the redoxome) in mammalian cells depends upon a large number of interacting molecules, which tend to buffer the electronegativity of cells against oxidants or reductants. Some of these components kill – at high concentration – microbes and by-stander normal cells, elaborated by professional phagocytes. We examined whether a simple, in vitro chemiluminescence set-up, utilizing redox components from human polymorphonuclear neutrophils (PMN) and red blood cells (RBC), could clarify some unexplained workings of the redoxome. PMN or purified myeloperoxidase (MPO) triggers formation of reactive oxygen species (ROS), quantified by light emission from oxidized luminol. Both PMN and RBC can generate abundant amounts of ROS, necessitating the presence of a high-capacity redoxome to keep the cellular electronegativity within physiological limits. We obtained proof-of-principle evidence that our assay could assess redox effects, but also demonstrated the intricacies of redox reactions. Simple dose–responses were found, as for the PMN proteins S100A9 (A9) and S100A8 (A8), and the system also revealed the reducing capacity of vitamin B12 (Cbl) and lutein. However, increased concentrations of oxidants in the assay mixture could decrease the chemiluminescence. Even more remarkable, A9 and NaOCl together stimulated the MPO response, but alone they inhibited MPO chemiluminescence. Biphasic responses were also recorded for some dose–response set-ups and are tentatively explained by a ‘balance hypothesis’ for the redoxome.
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Affiliation(s)
- A Bøyum
- Department of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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Abstract
Abasic (AP) sites are formed spontaneously and are inevitably intermediates during base excision repair of DNA base damages. AP sites are both mutagenic and cytotoxic and key enzymes for their removal are AP endonucleases. However, AP endonuclease independent repair initiated by DNA glycosylases performing β,δ-elimination cleavage of the AP sites has been described in mammalian cells. Here, we describe another AP endonuclease independent repair pathway for removal of AP sites in Schizosaccharomyces pombe that is initiated by a bifunctional DNA glycosylase, Nth1 and followed by cleavage of the baseless sugar residue by tyrosyl phosphodiesterase Tdp1. We propose that repair is completed by the action of a polynucleotide kinase, a DNA polymerase and finally a DNA ligase to seal the gap. A fission yeast double mutant of the major AP endonuclease Apn2 and Tdp1 shows synergistic increase in MMS sensitivity, substantiating that Apn2 and Tdp1 process the same substrate. These results add new knowledge to the complex cellular response to AP sites, which could be exploited in chemotherapy where synthetic lethality is a key strategy of treatment.
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Affiliation(s)
- Line Nilsen
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, PO Box 4950 Nydalen, N-0424 Oslo, Norway
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Osenbroch PØ, Auk-Emblem P, Halsne R, Strand J, Forstrøm RJ, van der Pluijm I, Eide L. Accumulation of mitochondrial DNA damage and bioenergetic dysfunction in CSB defective cells. FEBS J 2009; 276:2811-21. [PMID: 19389114 DOI: 10.1111/j.1742-4658.2009.07004.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cockayne syndrome (CS) is a complex, progressive disease that involves neurological and developmental impairment and premature aging. The majority of CS patients have mutations in the CSB gene. The CSB protein is involved in multiple DNA repair pathways and CSB mutated cells are sensitive to a broad spectrum of genotoxic agents. We tested the hypothesis that sensitivity to such genotoxins could be mediated by mitochondrial dysfunction as a consequence of the CSB mutation. mtDNA from csb(m/m) mice accumulates oxidative damage including 8-oxoguanine, and cells from this mouse are hypersensitive to the mitochondrial oxidant menadione. Inhibitors of mitochondrial complexes and the glycolysis inhibitor 2-deoxyglucose kill csb(m/m) cells more efficiently than wild-type cells, via a mechanism that does not correlate with mtDNA damage formation. Menadione depletes cellular ATP, and recovery after depletion is slower in csb(m/m) cells. The bioenergetic alteration in csb(m/m) cells parallels the simpler organization of supercomplexes consisting of complexes I, III and IV in addition to partially disassembled complex V in the inner mitochondrial membrane. Exposing wild-type cells to DNA intercalating agents induces complex alterations, suggesting a link between mtDNA integrity, respiratory complexes and mitochondrial function. Thus, mitochondrial dysfunction may play a role in the pathology of CS.
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Affiliation(s)
- Pia Ø Osenbroch
- Institute of Clinical Biochemistry, Faculty division Rikshospitalet, University of Oslo, Norway
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Yndestad A, Neurauter CG, Oie E, Forstrøm RJ, Vinge LE, Eide L, Luna L, Aukrust P, Bjørås M. Up-regulation of myocardial DNA base excision repair activities in experimental heart failure. Mutat Res 2009; 666:32-8. [PMID: 19481677 DOI: 10.1016/j.mrfmmm.2009.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 03/11/2009] [Accepted: 03/19/2009] [Indexed: 01/20/2023]
Abstract
Base excision repair (BER) is the major pathway to counteract the genotoxic effect of endogenous DNA damaging agents. The present study investigated the enzymatic activities and gene transcription of DNA glycosylases initiating BER in an experimental heart failure (HF) model. Rats were subjected to myocardial infarction or sham-operated. Twenty-eight days after surgical intervention cell-free protein extracts, total RNA and genomic DNA were isolated to analyze DNA glycosylase and AP-endonuclease activities, transcript levels of DNA glycosylases and accumulation of oxidative DNA damage. The capacity to remove major oxidation products (e.g., formamidopyrimidine and 5-hydroxycytosine) was significantly increased in the border zone of infarcted area, while the capacity to remove the highly mutagenic 8-oxoguanine residue was enhanced both in non-infarcted and infarcted areas of left ventricle (LV). DNA glycosylase activities towards 3-methyladenine and uracil were up-regulated in infarcted and non-infarcted areas of LV, indicating that generation of alkylated and deaminated base lesions on DNA increase during HF. Finally, we found no difference in accumulation of oxidative DNA damage in myocardial tissue between rats with post-myocardial infarction and sham-operated rats. This up-regulation of activities, initiating the BER pathway, could play an important role during HF by counteracting the effect of genotoxic stress, structural damage of tissue and myocardial remodeling.
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Affiliation(s)
- Arne Yndestad
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, University of Oslo, N-0027 Oslo, Norway
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