1
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Li XQ, Cheng XJ, Wu J, Wu KF, Liu T. Targeted inhibition of the PI3K/AKT/mTOR pathway by (+)-anthrabenzoxocinone induces cell cycle arrest, apoptosis, and autophagy in non-small cell lung cancer. Cell Mol Biol Lett 2024; 29:58. [PMID: 38649803 PMCID: PMC11036658 DOI: 10.1186/s11658-024-00578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Non-small cell lung cancer (NSCLC), characterized by low survival rates and a high recurrence rate, is a major cause of cancer-related mortality. Aberrant activation of the PI3K/AKT/mTOR signaling pathway is a common driver of NSCLC. Within this study, the inhibitory activity of (+)-anthrabenzoxocinone ((+)-ABX), an oxygenated anthrabenzoxocinone compound derived from Streptomyces, against NSCLC is demonstrated for the first time both in vitro and in vivo. Mechanistically, it is confirmed that the PI3K/AKT/mTOR signaling pathway is targeted and suppressed by (+)-ABX, resulting in the induction of S and G2/M phase arrest, apoptosis, and autophagy in NSCLC cells. Additionally, the augmentation of intracellular ROS levels by (+)-ABX is revealed, further contributing to the inhibition of the signaling pathway and exerting inhibitory effects on tumor growth. The findings presented in this study suggest that (+)-ABX possesses the potential to serve as a lead compound for the treatment of NSCLC.
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Affiliation(s)
- Xiao-Qian Li
- The Third Affiliated Hospital of Zunyi Medical University, The First People's Hospital of Zunyi), Scientific Research Center, Guizhou, 563002, People's Republic of China
| | - Xiao-Ju Cheng
- The Third Affiliated Hospital of Zunyi Medical University, The First People's Hospital of Zunyi), Scientific Research Center, Guizhou, 563002, People's Republic of China
| | - Jie Wu
- The Third Affiliated Hospital of Zunyi Medical University, The First People's Hospital of Zunyi), Scientific Research Center, Guizhou, 563002, People's Republic of China
| | - Kai-Feng Wu
- The Third Affiliated Hospital of Zunyi Medical University, The First People's Hospital of Zunyi), Scientific Research Center, Guizhou, 563002, People's Republic of China.
| | - Tie Liu
- The Third Affiliated Hospital of Zunyi Medical University, The First People's Hospital of Zunyi), Scientific Research Center, Guizhou, 563002, People's Republic of China.
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China.
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2
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Radović Jakovljević M, Grujičić D, Stanković M, Milošević-Djordjević O. Artemisia vulgaris L., Artemisia alba Turra and their constituents reduce mitomycin C-induced genomic instability in human peripheral blood lymphocytes in vitro. Drug Chem Toxicol 2024; 47:156-165. [PMID: 36476306 DOI: 10.1080/01480545.2022.2154358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/23/2022] [Accepted: 11/27/2022] [Indexed: 12/13/2022]
Abstract
This study aimed to evaluate the effect of aqueous and acetone extracts from Artemisia vulgaris L. (AV) and Artemisia alba Turra (AA), and two major polyphenols compounds (3,5-dihydroxybenzoic acid and quercetin-3-O-glucopyranoside) presented in both extracts of the plants against mitomycin C (MMC)-induced genomic instability. Genomic instability was measured using cytokinesis block micronucleus (MN) assay in human peripheral blood lymphocytes (PBLs) in vitro by analyzing two biomarkers - MN and nuclear division index (NDI). Extracts were tested in a concentration-dependent manner (10-250 µg/mL), while 3,5-dihydroxybenzoic acid and quercetin-3-O-glucopyranoside were tested in three different concentrations, in combination with 0.5 µg/mL of MMC. Aqueous and acetone extracts obtained from both plants significantly reduced MMC-induced MN frequency in PBLs, compared to positive control cells (p < 0.05). Extracts from AV did not affect NDI, whereas the concentrations of 10-100 μg/mL of aqueous and acetone AA extracts significantly elevated MMC-decreased NDI values in comparison to positive control cells (p < 0.05). Combined treatment of 3,5-dihydroxybenzoic acid and MMC showed a significant reduction of MMC-induced MN frequency, while quercetin-3-O-glucopyranoside increased MN frequency compared to positive control cells (p < 0.05). Both compounds decreased NDI values but only at the highest tested concentration of quercetin-3-O-glucopyranoside it was of greater significance. In conclusion, all extracts from AV and AA and 3,5-dihydroxybenzoic acid showed protective effect, whereby aqueous AA demonstrated the highest protective effect on MMC- induced genomic instability, while quercetin-3-O-glucopyranoside showed co-mutagen effect.
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Affiliation(s)
| | - Darko Grujičić
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Kragujevac, Serbia
| | - Milan Stanković
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Kragujevac, Serbia
| | - Olivera Milošević-Djordjević
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Kragujevac, Serbia
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Kragujevac, Serbia
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3
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Sharma DK, Soni I, Misra HS, Rajpurohit YS. Natural transformation-specific DprA coordinate DNA double-strand break repair pathways in heavily irradiated D. radiodurans. Appl Environ Microbiol 2024; 90:e0194823. [PMID: 38193676 PMCID: PMC10880594 DOI: 10.1128/aem.01948-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/02/2023] [Indexed: 01/10/2024] Open
Abstract
Deinococcus radiodurans exhibits remarkable survival under extreme conditions, including ionizing radiation, desiccation, and various DNA-damaging agents. It employs unique repair mechanisms, such as single-strand annealing (SSA) and extended synthesis-dependent strand annealing (ESDSA), to efficiently restore damaged genome. In this study, we investigate the role of the natural transformation-specific protein DprA in DNA repair pathways following acute gamma radiation exposure. Our findings demonstrate that the absence of DprA leads to rapid repair of gamma radiation-induced DNA double-strand breaks primarily occur through SSA repair pathway. Additionally, our findings suggest that the DprA protein may hinder both the SSA and ESDSA repair pathways, albeit in distinct manners. Overall, our results highlight the crucial function of DprA in the selection between SSA and ESDSA pathways for DNA repair in heavily irradiated D. radiodurans.IMPORTANCEDeinococcus radiodurans exhibits an extraordinary ability to endure and thrive in extreme environments, including exposure to radiation, desiccation, and damaging chemicals, as well as intense UV radiation. The bacterium has evolved highly efficient repair mechanisms capable of rapidly mending hundreds of DNA fragments in its genome. Our research indicates that natural transformation (NT)-specific dprA genes play a pivotal role in regulating DNA repair in response to radiation. Remarkably, we found that DprA is instrumental in selecting DNA double-strand break repair pathways, a novel function that has not been reported before. This unique regulatory mechanism highlights the indispensable role of DprA beyond its native function in NT and underscores its ubiquitous presence across various bacterial species, regardless of their NT proficiency. These findings shed new light on the resilience and adaptability of Deinococcus radiodurans, opening avenues for further exploration into its exceptional survival strategies.
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Affiliation(s)
- Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Ishu Soni
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Hari S. Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
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4
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Camus A, Espinosa E, Zapater Baras P, Singh P, Quenech’Du N, Vickridge E, Modesti M, Barre FX, Espéli O. The SMC-like RecN protein is at the crossroads of several genotoxic stress responses in Escherichia coli. Front Microbiol 2023; 14:1146496. [PMID: 37168111 PMCID: PMC10165496 DOI: 10.3389/fmicb.2023.1146496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Introduction DNA damage repair (DDR) is an essential process for living organisms and contributes to genome maintenance and evolution. DDR involves different pathways including Homologous recombination (HR), Nucleotide Excision Repair (NER) and Base excision repair (BER) for example. The activity of each pathway is revealed with particular drug inducing lesions, but the repair of most DNA lesions depends on concomitant or subsequent action of the multiple pathways. Methods In the present study, we used two genotoxic antibiotics, mitomycin C (MMC) and Bleomycin (BLM), to decipher the interplays between these different pathways in E. coli. We combined genomic methods (TIS and Hi-SC2) and imaging assays with genetic dissections. Results We demonstrate that only a small set of DDR proteins are common to the repair of the lesions induced by these two drugs. Among them, RecN, an SMC-like protein, plays an important role by controlling sister chromatids dynamics and genome morphology at different steps of the repair processes. We further demonstrate that RecN influence on sister chromatids dynamics is not equivalent during the processing of the lesions induced by the two drugs. We observed that RecN activity and stability requires a pre-processing of the MMC-induced lesions by the NER but not for BLM-induced lesions. Discussion Those results show that RecN plays a major role in rescuing toxic intermediates generated by the BER pathway in addition to its well-known importance to the repair of double strand breaks by HR.
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Affiliation(s)
- Adrien Camus
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
| | - Elena Espinosa
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | | | - Parul Singh
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
| | - Nicole Quenech’Du
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
| | - Elise Vickridge
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Mauro Modesti
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR 7258, INSERM U1068, Institut Paoli-Calmettes, Aix Marseille University, Marseille, France
| | - François Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Olivier Espéli
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
- *Correspondence: Olivier Espéli,
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5
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Paz MM, Champeil E. Insight Into Factors Governing Formation, Synthesis and Stereochemical Configuration of DNA Adducts Formed by Mitomycins. CHEM REC 2023; 23:e202200193. [PMID: 36251922 DOI: 10.1002/tcr.202200193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/19/2022] [Indexed: 01/24/2023]
Abstract
Mitomycin C, (MC), an antitumor drug used in the clinics, is a DNA alkylating agent. Inert in its native form, MC is reduced to reactive mitosenes in cellulo which undergo nucleophilic attack by DNA bases to form monoadducts as well as interstrand crosslinks (ICLs). These properties constitute the molecular basis for the cytotoxic effects of the drug. The mechanism of DNA alkylation by mitomycins has been studied for the past 30 years and, until recently, the consensus was that drugs of the mitomycins family mainly target CpG sequences in DNA. However, that paradigm was recently challenged. Here, we relate the latest research on both MC and dicarbamoylmitomycin C (DMC), a synthetic derivative of MC which has been used to investigate the regioselectivity of mitomycins DNA alkylation as well as the relationship between mitomycins reductive activation pathways and DNA adducts stereochemical configuration. We also review the different synthetic routes to access mitomycins nucleoside adducts and oligonucleotides containing MC/DMC DNA adducts located at a single position. Finally, we briefly describe the DNA structural modifications induced by MC and DMC adducts and how site specifically modified oligonucleotides have been used to elucidate the role each adduct plays in the drugs cytotoxicity.
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Affiliation(s)
- Manuel M Paz
- Instituto de Materiais (iMATUS), Departamento de Química Orgánica, Facultad de Química, Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, 15782, Spain
| | - Elise Champeil
- Department of sciences, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
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6
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Payne-Dwyer AL, Syeda AH, Shepherd JW, Frame L, Leake MC. RecA and RecB: probing complexes of DNA repair proteins with mitomycin C in live Escherichia coli with single-molecule sensitivity. J R Soc Interface 2022; 19:20220437. [PMID: 35946163 PMCID: PMC9363994 DOI: 10.1098/rsif.2022.0437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 01/02/2023] Open
Abstract
The RecA protein and RecBCD complex are key bacterial components for the maintenance and repair of DNA. RecBCD is a helicase-nuclease that uses homologous recombination to resolve double-stranded DNA breaks. It also facilitates coating of single-stranded DNA with RecA to form RecA filaments, a vital step in the double-stranded break DNA repair pathway. However, questions remain about the mechanistic roles of RecA and RecBCD in live cells. Here, we use millisecond super-resolved fluorescence microscopy to pinpoint the spatial localization of fluorescent reporters of RecA or RecB at physiological levels of expression in individual live Escherichia coli cells. By introducing the DNA cross-linker mitomycin C, we induce DNA damage and quantify the resulting steady state changes in stoichiometry, cellular protein copy number and molecular mobilities of RecA and RecB. We find that both proteins accumulate in molecular hotspots to effect repair, resulting in RecA stoichiometries equivalent to several hundred molecules that assemble largely in dimeric subunits before DNA damage, but form periodic subunits of approximately 3-4 molecules within mature filaments of several thousand molecules. Unexpectedly, we find that the physiologically predominant forms of RecB are not only rapidly diffusing monomers, but slowly diffusing dimers.
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Affiliation(s)
- Alex L. Payne-Dwyer
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York YO10 5DD, UK
| | - Aisha H. Syeda
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York YO10 5DD, UK
| | - Jack W. Shepherd
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York YO10 5DD, UK
| | - Lewis Frame
- School of Natural Sciences, University of York, York YO10 5DD, UK
| | - Mark C. Leake
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York YO10 5DD, UK
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7
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Wozniak KJ, Burby PE, Nandakumar J, Simmons LA. Structure and kinase activity of bacterial cell cycle regulator CcrZ. PLoS Genet 2022; 18:e1010196. [PMID: 35576203 PMCID: PMC9135335 DOI: 10.1371/journal.pgen.1010196] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/26/2022] [Accepted: 04/09/2022] [Indexed: 11/24/2022] Open
Abstract
CcrZ is a recently discovered cell cycle regulator that connects DNA replication initiation with cell division in pneumococci and may have a similar function in related bacteria. CcrZ is also annotated as a putative kinase, suggesting that CcrZ homologs could represent a novel family of bacterial kinase-dependent cell cycle regulators. Here, we investigate the CcrZ homolog in Bacillus subtilis and show that cells lacking ccrZ are sensitive to a broad range of DNA damage. We demonstrate that increased expression of ccrZ results in over-initiation of DNA replication. In addition, increased expression of CcrZ activates the DNA damage response. Using sensitivity to DNA damage as a proxy, we show that the negative regulator for replication initiation (yabA) and ccrZ function in the same pathway. We show that CcrZ interacts with replication initiation proteins DnaA and DnaB, further suggesting that CcrZ is important for replication timing. To understand how CcrZ functions, we solved the crystal structure bound to AMP-PNP to 2.6 Å resolution. The CcrZ structure most closely resembles choline kinases, consisting of a bilobal structure with a cleft between the two lobes for binding ATP and substrate. Inspection of the structure reveals a major restructuring of the substrate-binding site of CcrZ relative to the choline-binding pocket of choline kinases, consistent with our inability to detect activity with choline for this protein. Instead, CcrZ shows activity on D-ribose and 2-deoxy-D-ribose, indicating adaptation of the choline kinase fold in CcrZ to phosphorylate a novel substrate. We show that integrity of the kinase active site is required for ATPase activity in vitro and for function in vivo. This work provides structural, biochemical, and functional insight into a newly identified, and conserved group of bacterial kinases that regulate DNA replication initiation.
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Affiliation(s)
- Katherine J. Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter E. Burby
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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8
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Zacarias O, Petrovic AG, Abzalimov R, Pradhan P, Champeil E. Synthesis of Oligonucleotides Containing Trans Mitomycin C DNA Adducts at N 6 of Adenine and N 2 of Guanine. Chemistry 2021; 27:14263-14272. [PMID: 34319608 PMCID: PMC8516704 DOI: 10.1002/chem.202102338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 11/09/2022]
Abstract
Mitomycin C, (MC), an antitumor drug, is a DNA alkylating agent currently used in the clinics. Inert in its native form, MC is reduced to reactive mitosenes, which undergo nucleophilic attack by guanine or adenine bases in DNA to form monoadducts as well as interstrand crosslinks (ICLs). Although ICLs are considered the most cytotoxic lesions, the role of each individual adduct in the drug's cytotoxicity is still not fully understood. Synthetic routes have been developed to access modified oligonucleotides containing dG MC-monoadducts and dG-MC-dG ICL at a single position of their base sequences to investigate the biological effects of these adducts. However, until now, oligonucleotides containing monoadducts formed by MC at the adenine base had not been available, thus preventing the examination of the role played by these lesions in the toxicity of MC. Here, we present a route to access these substrates. Structural proof of the adducted oligonucleotides were provided by enzymatic digestion to nucleosides and high-resolution mass spectral analysis. Additionally, parent oligonucleotides containing a dG monoadduct and a dG-MC-dG ICL were also produced. The stability and physical properties of all substrates were compared via CD spectroscopy and UV melting temperature studies. Finally, virtual models were created to explore the conformational space and structural features of these MC-DNA complexes.
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Affiliation(s)
- Owen Zacarias
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Ana G Petrovic
- New York Institute of Technology, 1855 Broadway, EGGC 405 A, New York, NY, 10023, USA
| | - Rinat Abzalimov
- City University of New York, Advanced Research Center, 85 St Nicholas Terrace, New York, NY, 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Padmanava Pradhan
- The City College, 138th Street at Convent Avenue, New York, New York, 10031, USA
| | - Elise Champeil
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
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9
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Korry BJ, Lee SYE, Chakrabarti AK, Choi AH, Ganser C, Machan JT, Belenky P. Genotoxic Agents Produce Stressor-Specific Spectra of Spectinomycin Resistance Mutations Based on Mechanism of Action and Selection in Bacillus subtilis. Antimicrob Agents Chemother 2021; 65:e0089121. [PMID: 34339280 PMCID: PMC8448107 DOI: 10.1128/aac.00891-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
Mutagenesis is integral for bacterial evolution and the development of antibiotic resistance. Environmental toxins and stressors are known to elevate the rate of mutagenesis through direct DNA toxicity, known as stress-associated mutagenesis, or via a more general stress-induced process that relies on intrinsic bacterial pathways. Here, we characterize the spectra of mutations induced by an array of different stressors using high-throughput sequencing to profile thousands of spectinomycin-resistant colonies of Bacillus subtilis. We found 69 unique mutations in the rpsE and rpsB genes, and that each stressor leads to a unique and specific spectrum of antibiotic-resistance mutations. While some mutations clearly reflected the DNA damage mechanism of the stress, others were likely the result of a more general stress-induced mechanism. To determine the relative fitness of these mutants under a range of antibiotic selection pressures, we used multistrain competitive fitness experiments and found an additional landscape of fitness and resistance. The data presented here support the idea that the environment in which the selection is applied (mutagenic stressors that are present), as well as changes in local drug concentration, can significantly alter the path to spectinomycin resistance in B. subtilis.
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Affiliation(s)
- Benjamin J. Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Stella Ye Eun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Amit K. Chakrabarti
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Ashley H. Choi
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Collin Ganser
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Jason T. Machan
- Department of Orthopedics, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Surgery, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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10
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Fallon AM. Assessment of mitotically inactivated mosquito cell feeder layers produced with mitomycin C. In Vitro Cell Dev Biol Anim 2021; 57:583-586. [PMID: 34184209 DOI: 10.1007/s11626-021-00597-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 11/24/2022]
Affiliation(s)
- Ann M Fallon
- Department of Entomology, University of Minnesota, 1980 Folwell Ave, St. Paul, MN, 55108, USA.
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11
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Xu Y, Jin X, Zhang J, Wang K, Jin X, Xu D, Tian X, Liu L. Antitumor Activity of a Novel Double-Targeted System for Folate Receptor-Mediated Delivery of Mitomycin C. ACS OMEGA 2020; 5:26864-26870. [PMID: 33111012 PMCID: PMC7581226 DOI: 10.1021/acsomega.0c04042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
In this study, we designed, formulated, and investigated the potential antitumor activity of a folate receptor (FR)-mediated double-targeted drug delivery system. The system comprised of the FR ligand folic acid (FA), glycine-phenylalanine-leucine-glycine (Gly-Phe-Leu-Gly, GFLG), which can be specifically cleaved by cathepsin B, and the anticancer drug mitomycin C (MMC). The antitumor effect of FA-GFLG-MMC was compared to that of MMC. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay revealed that FA-GFLG-MMC has a significantly higher inhibitory effect on HeLa, SiHa, and PC9 cells (high FR expression) than that on 16HBE and A549 cells (low FR expression). Furthermore, FA-GFLG-MMC inhibited cancer cell proliferation in a dose-dependent manner. Free MMC was toxic to both cancer and normal cells. Apoptosis of the HeLa, SiHa, and PC9 cells was higher than that of the A549 cells; however, the apoptotic effect on 16HBE cells was minimal. Proapoptotic protein bcl-2-associated X-protein (BAX) and antiapoptotic protein BCL-2 play critical roles in cellular defense and apoptotic signal transduction. BAX/BCL-2 ratio is used to determine the intensity of an apoptotic signal and assess whether a cell will survive or undergo apoptosis. BAX and BCL-2 expression in cells treated with 5 μM FA-GFLG-MMC was studied by Western blotting. FA-GFLG-MMC increased the BAX/BCL-2 ratio in HeLa, SiHa, and PC9 cells. The results show that FA-GFLG-MMC can effectively inhibit tumor cell proliferation by inducing apoptosis. Therefore, the system developed can enhance the delivery of anticancer drugs to cancer cells and thereby reduce their toxic effects on normal cells.
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Affiliation(s)
- Yan Xu
- Center
of Morphological Experiment, Yanbian University, Yanji 133002, Jilin, China
| | - Xiangmei Jin
- Department
of Chemistry, Yanbian University, Yanji 133002, Jilin, China
| | - Jun Zhang
- Center
of Morphological Experiment, Yanbian University, Yanji 133002, Jilin, China
| | - Kun Wang
- Department
of Chemistry, Yanbian University, Yanji 133002, Jilin, China
| | - Xiaoyan Jin
- Department
of Chemistry, Yanbian University, Yanji 133002, Jilin, China
| | - Dongyuan Xu
- Center
of Morphological Experiment, Yanbian University, Yanji 133002, Jilin, China
| | - Xizhe Tian
- Department
of Chemistry, Yanbian University, Yanji 133002, Jilin, China
| | - Lan Liu
- Department
of Pathology, Yanbian University Hospital, Yanji 133000, Jilin, China
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12
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Klimova AN, Sandler SJ. An Epistasis Analysis of recA and recN in Escherichia coli K-12. Genetics 2020; 216:381-393. [PMID: 32816866 PMCID: PMC7536844 DOI: 10.1534/genetics.120.303476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/11/2020] [Indexed: 12/26/2022] Open
Abstract
RecA is essential for double-strand-break repair (DSBR) and the SOS response in Escherichia coli K-12. RecN is an SOS protein and a member of the Structural Maintenance of Chromosomes family of proteins thought to play a role in sister chromatid cohesion/interactions during DSBR. Previous studies have shown that a plasmid-encoded recA4190 (Q300R) mutant had a phenotype similar to ∆recN (mitomycin C sensitive and UV resistant). It was hypothesized that RecN and RecA physically interact, and that recA4190 specifically eliminated this interaction. To test this model, an epistasis analysis between recA4190 and ∆recN was performed in wild-type and recBC sbcBC cells. To do this, recA4190 was first transferred to the chromosome. As single mutants, recA4190 and ∆recN were Rec+ as measured by transductional recombination, but were 3-fold and 10-fold decreased in their ability to do I-SceI-induced DSBR, respectively. In both cases, the double mutant had an additive phenotype relative to either single mutant. In the recBC sbcBC background, recA4190 and ∆recN cells were very UVS (sensitive), Rec-, had high basal levels of SOS expression and an altered distribution of RecA-GFP structures. In all cases, the double mutant had additive phenotypes. These data suggest that recA4190 (Q300R) and ∆recN remove functions in genetically distinct pathways important for DNA repair, and that RecA Q300 was not important for an interaction between RecN and RecA in vivorecA4190 (Q300R) revealed modest phenotypes in a wild-type background and dramatic phenotypes in a recBC sbcBC strain, reflecting greater stringency of RecA's role in that background.
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Affiliation(s)
- Anastasiia N Klimova
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Massachusetts 01003
| | - Steven J Sandler
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Massachusetts 01003
- Department of Microbiology, University of Massachusetts Amherst, Massachusetts 01003
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Abilev SK, Kotova VY, Smirnova SV, Shapiro TN, Zavilgelsky GB. Specific Lux Biosensors of Escherichia coli Containing pRecA::lux, pColD::lux, and pDinI::lux Plasmids for Detection of Genotoxic Agents. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Ibrahim MA, Yasui M, Saha LK, Sasanuma H, Honma M, Takeda S. Enhancing the sensitivity of the thymidine kinase assay by using DNA repair-deficient human TK6 cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:602-610. [PMID: 32243652 PMCID: PMC7384079 DOI: 10.1002/em.22371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 05/17/2023]
Abstract
The OECD guidelines define the bioassays of identifying mutagenic chemicals, including the thymidine kinase (TK) assay, which specifically detects the mutations that inactivate the TK gene in the human TK6 lymphoid line. However, the sensitivity of this assay is limited because it detects mutations occurring only in the TK gene but not any other genes. Moreover, the limited sensitivity of the conventional TK assay is caused by the usage of DNA repair-proficient wild-type cells, which are capable of accurately repairing DNA damage induced by chemicals. Mutagenic chemicals produce a variety of DNA lesions, including base lesions, sugar damage, crosslinks, and strand breaks. Base damage causes point mutations and is repaired by the base excision repair (BER) and nucleotide excision repair (NER) pathways. To increase the sensitivity of TK assay, we simultaneously disrupted two genes encoding XRCC1, an important BER factor, and XPA, which is essential for NER, generating XRCC1 -/- /XPA -/- cells from TK6 cells. We measured the mutation frequency induced by four typical mutagenic agents, methyl methane sulfonate (MMS), cis-diamminedichloro-platinum(II) (cisplatin, CDDP), mitomycin-C (MMC), and cyclophosphamide (CP) by the conventional TK assay using wild-type TK6 cells and also by the TK assay using XRCC1 -/- /XPA -/- cells. The usage of XRCC1 -/- /XPA -/- cells increased the sensitivity of detecting the mutagenicity by 8.6 times for MMC, 8.5 times for CDDP, and 2.6 times for MMS in comparison with the conventional TK assay. In conclusion, the usage of XRCC1 -/- /XPA -/- cells will significantly improve TK assay.
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Affiliation(s)
| | - Manabu Yasui
- Division of Genetics and MutagenesisNational Institute of Health SciencesKawasakiKanagawaJapan
| | - Liton Kumar Saha
- Department of Radiation GeneticsKyoto University, Graduate School of MedicineKyotoJapan
- Developmental Therapeutics Branch, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Hiroyuki Sasanuma
- Department of Radiation GeneticsKyoto University, Graduate School of MedicineKyotoJapan
| | - Masamitsu Honma
- Division of Genetics and MutagenesisNational Institute of Health SciencesKawasakiKanagawaJapan
| | - Shunichi Takeda
- Department of Radiation GeneticsKyoto University, Graduate School of MedicineKyotoJapan
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Serment-Guerrero J, Dominguez-Monroy V, Davila-Becerril J, Morales-Avila E, Fuentes-Lorenzo JL. Induction of the SOS response of Escherichia coli in repair-defective strains by several genotoxic agents. Mutat Res 2020; 854-855:503196. [PMID: 32660820 DOI: 10.1016/j.mrgentox.2020.503196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/07/2020] [Accepted: 04/21/2020] [Indexed: 11/16/2022]
Abstract
DNA is exposed to the attack of several exogenous agents that modify its chemical structure, so cells must repair those changes in order to survive. Alkylating agents introduce methyl or ethyl groups in most of the cyclic or exocyclic nitrogen atoms of the ring and exocyclic oxygen available in DNA bases producing damage that can induce the SOS response in Escherichia coli and many other bacteria. Likewise, ultraviolet light produces mainly cyclobutane pyrimidine dimers that arrest the progression of the replication fork and triggers such response. The need of some enzymes (such as RecO, ExoI and RecJ) in processing injuries produced by gamma radiation prior the induction of the SOS response has been reported before. In the present work, several repair-defective strains of E. coli were treated with methyl methanesulfonate, ethyl methanesulfonate, mitomycin C or ultraviolet light. Both survival and SOS induction (by means of the Chromotest) were tested. Our results indicate that the participation of these genes depends on the type of injury caused by a genotoxin on DNA.
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Affiliation(s)
- Jorge Serment-Guerrero
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares, La Marquesa, Estado de México, Mexico.
| | - Viridiana Dominguez-Monroy
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares, La Marquesa, Estado de México, Mexico
| | - Jenny Davila-Becerril
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares, La Marquesa, Estado de México, Mexico
| | - Enrique Morales-Avila
- Facultad de Química, Universidad Autónoma del Estado de México, Toluca, Estado de México, Mexico
| | - Jorge Luis Fuentes-Lorenzo
- Laboratorio de Microbiología y Mutagénesis Ambiental, Grupo de Investigación en Microbiología y Genética, Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia
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16
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Ma L, Sun S, Yuan Z, Deng Z, Tang Y, Yu Y. Three putative DNA replication/repair elements encoding genes confer self-resistance to distamycin in Streptomyces netropsis. Acta Biochim Biophys Sin (Shanghai) 2020; 52:91-96. [PMID: 31833535 DOI: 10.1093/abbs/gmz133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/18/2022] Open
Abstract
Distamycin (DST) is a well-characterized DNA minor groove binder with antivirus activity and antitumor potency. Two separate gene clusters (a 28-kb cluster and a 7-kb cluster) have recently been identified to coordinately encode the biosynthetic machinery of DST in Streptomyces netropsis. Here we report a gene cassette, which is linked to the aforementioned smaller dst gene cluster and plays an important role in the self-resistance to DST in S. netropsis. This cassette consists of three uncharacterized genes that might be implicated in DNA replication/repair. Knockout of the cassette led to the decrease in the production of DST, while heterologous expression of part of the cassette in S. lividans made it become resistant to both DST and mitomycin C, another DNA-binding agent. More interestingly, homologs of these three genes were found in genomes of other actinomyces that produce DNA-binding antibiotics, suggesting that a novel common mechanism in addition to pumping may enable these strains to resist the cytotoxic metabolites they produced.
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Affiliation(s)
- Lie Ma
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Siyao Sun
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Ziyu Yuan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Zixin Deng
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yajie Tang
- Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yi Yu
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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17
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Köstner N, Jürgens K, Labrenz M, Herndl GJ, Winter C. Uneven host cell growth causes lysogenic virus induction in the Baltic Sea. PLoS One 2019; 14:e0220716. [PMID: 31386696 PMCID: PMC6684075 DOI: 10.1371/journal.pone.0220716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/22/2019] [Indexed: 12/04/2022] Open
Abstract
In the Baltic Sea redoxcline, lysogenic viruses infecting prokaryotes have rarely been detected using the commonly used inducing agent mitomycin C. However, it is well known that not all viruses are induceable by mitomycin C and growing evidence suggests that changes in trophic conditions may trigger the induction of lysogenic viruses. We hypothesized that using antibiotics to simulate a strong change in trophic conditions for antibiotica-resistant cells due to reduced competition for resources might lead to the induction of lysogenic viruses into the lytic cycle within these cells. This hypothesis was tested by incubating prokaryotes obtained throughout the Baltic Sea redoxcline in seawater with substantially reduced numbers of viruses. We used a mixture of the protein synthesis-inhibiting antibiotics streptomycin and erythromycin to induce the desired changes in trophic conditions for resistant cells and at the same time ensuring that no progeny viruses were formed in sensitive cells. No inducible lysogenic viruses could be detected in incubations amended with mitomycin C. Yet, the presence of streptomycin and erythromycin increased virus-induced mortality of prokaryotes by 56–930% compared to controls, resulting in the induction of lysogenic viruses equivalent to 2–14% of in situ prokaryotic abundance. The results indicate the existence of a previously unrecognized induction mechanism for lysogenic viruses in the Baltic Sea redoxcline, as the mode of action distinctly differs between the used antibiotics (no virus production within affected cells) and mitomycin C (lysogenic viruses are produced within affected cells). Obtaining accurate experimental data on levels of lysogeny in prokaryotic host cells remains challenging, as relying on mitomycin C alone may severely underestimate lysogeny.
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Affiliation(s)
- Nicole Köstner
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Klaus Jürgens
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock-Warnemünde, Germany
| | - Matthias Labrenz
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock-Warnemünde, Germany
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, AB Den Burg, The Netherlands
| | - Christian Winter
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- * E-mail:
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18
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Nero TM, Dalia TN, Wang JCY, Kysela DT, Bochman ML, Dalia AB. ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species. Nucleic Acids Res 2019; 46:6099-6111. [PMID: 29722872 PMCID: PMC6158740 DOI: 10.1093/nar/gky343] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 04/19/2018] [Indexed: 12/16/2022] Open
Abstract
Acquisition of foreign DNA by natural transformation is an important mechanism of adaptation and evolution in diverse microbial species. Here, we characterize the mechanism of ComM, a broadly conserved AAA+ protein previously implicated in homologous recombination of transforming DNA (tDNA) in naturally competent Gram-negative bacterial species. In vivo, we found that ComM was required for efficient comigration of linked genetic markers in Vibrio cholerae and Acinetobacter baylyi, which is consistent with a role in branch migration. Also, ComM was particularly important for integration of tDNA with increased sequence heterology, suggesting that its activity promotes the acquisition of novel DNA sequences. In vitro, we showed that purified ComM binds ssDNA, oligomerizes into a hexameric ring, and has bidirectional helicase and branch migration activity. Based on these data, we propose a model for tDNA integration during natural transformation. This study provides mechanistic insight into the enigmatic steps involved in tDNA integration and uncovers the function of a protein required for this conserved mechanism of horizontal gene transfer.
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Affiliation(s)
- Thomas M Nero
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Triana N Dalia
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - David T Kysela
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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19
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Rozelle AL, Kumar RN, Lee S. Photo-induced DNA interstrand cross-links formed by a coumarin-modified nucleoside. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:236-247. [PMID: 30922158 DOI: 10.1080/15257770.2018.1515439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Coumarins are a class of naturally occurring compounds that have been shown to form photochemical DNA interstrand cross-links (ICLs). However, study of a coumarin base has not been explored. Using nucleophilic substitution and phosphoramidite chemistry, we synthesized a coumarin base-containing oligonucleotide. Upon exposure to long-wave ultraviolet light, the coumarin-modified oligonucleotide formed ICLs with complementary oligonucleotide containing dT and dC opposite the coumarin base, presumably through a [2 + 2] cycloaddition mechanism. Moderate yields with both bases were observed; though, dT has a higher reactivity than dC. Overall, this work provides new means for biochemical characterization of ICLs formed by coumarins.
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Affiliation(s)
- Aaron Leland Rozelle
- a Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy, The University of Texas at Austin , Austin , Texas , 78712 , USA
| | - Rayala Naveen Kumar
- a Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy, The University of Texas at Austin , Austin , Texas , 78712 , USA
| | - Seongmin Lee
- a Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy, The University of Texas at Austin , Austin , Texas , 78712 , USA
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20
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Cheng SY, Vargas A, Lee JY, Clement CC, Champeil E. Involvement of Akt in mitomycin C and its analog triggered cytotoxicity in MCF-7 and K562 cancer cells. Chem Biol Drug Des 2018; 92:2022-2034. [PMID: 30091208 PMCID: PMC6251731 DOI: 10.1111/cbdd.13374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/13/2018] [Accepted: 07/22/2018] [Indexed: 01/13/2023]
Abstract
Mitomycin C (MC) is a well-known DNA alkylating agent. MC analog, 10-decarbamoyl mitomycin C (DMC), unlike MC, has stronger effects on cancer with p53 mutation. We previously demonstrated that MC/DMC could activate p21WAF1/CIP1 in MCF-7 (p53-proficient) and K562 (p53-deficient) cells in a p53-independent mode. This study aimed to elucidate the upstream signaling pathway of p21WAF1/CIP1 activation triggered by MC/DMC. Besides p53, Akt plays an important role on deactivating p21WAF1/CIP1 . The results showed that MC/DMC inhibited Akt in MCF-7 cells, but not in K562 cells. By knocking down p53, the Akt inhibition in MCF-7 cells was alleviated. This implied that the deactivated Akt caused by MC/DMC was p53-dependent. With Akt activator (SC79), p21WAF1/CIP1 activation triggered by MC/DMC in MCF-7 cells was not reduced. This indicated that Akt inhibition triggered by MC/DMC was not associated with MC/DMC-induced p21WAF1/CIP1 activation. Label-free quantitative proteomic profiling analysis revealed that DMC has a stronger effect on down-regulating the PI3K/Akt signaling pathway in MCF-7 cells as compared to MC. No significant effect of MC/DMC on PI3K/Akt in K562 cells was observed. In summary, MC/DMC regulate Akt activation in a p53-dependent manner. This Akt deactivation is not associated with p21WAF1/CIP1 activation in response to MC/DMC.
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Affiliation(s)
- Shu-Yuan Cheng
- Department of Sciences, John Jay College of Criminal Justice, The City University of New York, New York City, New York
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York City, New York
| | - Anayatzinc Vargas
- Department of Sciences, John Jay College of Criminal Justice, The City University of New York, New York City, New York
| | - Ji-Young Lee
- Department of Sciences, John Jay College of Criminal Justice, The City University of New York, New York City, New York
| | - Cristina C Clement
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
- Chemistry Department, Lehman College, City University of New York, Bronx, New York
| | - Elise Champeil
- Department of Sciences, John Jay College of Criminal Justice, The City University of New York, New York City, New York
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21
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Burby PE, Simmons LA. A bacterial DNA repair pathway specific to a natural antibiotic. Mol Microbiol 2018; 111:338-353. [PMID: 30379365 DOI: 10.1111/mmi.14158] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2018] [Indexed: 12/17/2022]
Abstract
All organisms possess DNA repair pathways that are used to maintain the integrity of their genetic material. Although many DNA repair pathways are well understood, new pathways continue to be discovered. Here, we report an antibiotic specific DNA repair pathway in Bacillus subtilis that is composed of a previously uncharacterized helicase (mrfA) and exonuclease (mrfB). Deletion of mrfA and mrfB results in sensitivity to the DNA damaging agent mitomycin C, but not to any other type of DNA damage tested. We show that MrfAB function independent of canonical nucleotide excision repair, forming a novel excision repair pathway. We demonstrate that MrfB is a metal-dependent exonuclease and that the N-terminus of MrfB is required for interaction with MrfA. We determined that MrfAB failed to unhook interstrand cross-links in vivo, suggesting that MrfAB are specific to the monoadduct or the intrastrand cross-link. A phylogenetic analysis uncovered MrfAB homologs in diverse bacterial phyla, and cross-complementation indicates that MrfAB function is conserved in closely related species. B. subtilis is a soil dwelling organism and mitomycin C is a natural antibiotic produced by the soil bacterium Streptomyces lavendulae. The specificity of MrfAB suggests that these proteins are an adaptation to environments with mitomycin producing bacteria.
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Affiliation(s)
- Peter E Burby
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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22
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Aguilar W, Paz MM, Vargas A, Zheng M, Cheng SY, Champeil E. Interdependent Sequence Selectivity and Diastereoselectivity in the Alkylation of DNA by Decarbamoylmitomycin C. Chemistry 2018; 24:13278-13289. [PMID: 29958326 PMCID: PMC7152928 DOI: 10.1002/chem.201802038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/27/2018] [Indexed: 02/01/2023]
Abstract
Mitomycin C (MC), an antitumor drug, and decarbamoylmitomycin C (DMC), a derivative of MC, alkylate DNA and form deoxyguanosine monoadducts and interstrand crosslinks (ICLs). Interestingly, in mammalian culture cells, MC forms primarily deoxyguanosine adducts with a 1"-R stereochemistry at the guanine-mitosene bond (1"-α) whereas DMC forms mainly adducts with a 1"-S stereochemistry (1"-β). The molecular basis for the stereochemical configuration exhibited by DMC has been investigated using biomimetic synthesis. Here, we present the results of our studies on the monoalkylation of DNA by DMC. We show that the formation of 1"-β-deoxyguanosine adducts requires bifunctional reductive activation of DMC, and that monofunctional activation only produces 1"-α-adducts. The stereochemistry of the deoxyguanosine adducts formed is also dependent on the regioselectivity of DNA alkylation and on the overall DNA CG content. Additionally, we found that temperature plays a determinant role in the regioselectivity of duplex DNA alkylation by mitomycins: At 0 °C, both deoxyadenosine (dA) and deoxyguanosine (dG) alkylation occur whereas at 37 °C, mitomycins alkylate dG preferentially. The new reaction protocols developed in our laboratory to investigate DMC-DNA alkylation raise the possibility that oligonucleotides containing DMC 1"-β-deoxyguanosine adducts at a specific site may be synthesized by a biomimetic approach.
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Affiliation(s)
- William Aguilar
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Manuel M Paz
- Departamento de Química Orgánica, Facultade de Química, Universidade de Santiago de Compostela, 15782, Santiago, de Compostela, Spain
| | - Anayatzinc Vargas
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Maggie Zheng
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Shu-Yuan Cheng
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Elise Champeil
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City, University of New York, New York, NY, 10016, USA
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23
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Validation of the 3D Skin Comet assay using full thickness skin models: Transferability and reproducibility. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 827:27-41. [DOI: 10.1016/j.mrgentox.2018.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/18/2017] [Accepted: 01/09/2018] [Indexed: 12/21/2022]
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24
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Shanmughapriya V, Richard S, Nagarajan T, Munavar MH. Ascribing a novel role for tmRNA of Escherichia coli in resistance to mitomycin C. Future Microbiol 2017; 12:1381-1395. [PMID: 29027471 DOI: 10.2217/fmb-2016-0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM The ssrA mutants were found to be more sensitive to mitomycin C (MMC) and our aim was to study this phenomenon in detail. MATERIALS & METHODS Strains were constructed by P1 transduction. pssrA+ plasmid was constructed by PCR-based cloning and transformation was done by CaCl2 method. Relative viability analyses were done to assess the extent of viability of strains in relevant conditions. Gram staining was used for microscopic analysis. RESULTS ssrA mutants become sensitive specifically to MMC, that too in a strain-specific manner. Precise tagging function of SsrA is necessary for conferring resistance to MMC. sulA::kan restored the viability of ssrA::cat mutants in a strain-specific manner. CONCLUSION This study for the first time implicates SsrA in progression of efficient cell division and resistance to MMC.
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Affiliation(s)
- Vinod Shanmughapriya
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional & Organismal Genomics, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Stephen Richard
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional & Organismal Genomics, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.,Faculty of Medicine, Technion - Israel Institute of Technology, Bat Galim, Haifa 31096, Israel
| | - Tamilmaran Nagarajan
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional & Organismal Genomics, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - M Hussain Munavar
- Department of Molecular Biology, School of Biological Sciences, Centre for Advanced Studies in Functional & Organismal Genomics, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
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25
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Inactivation of genes involved in base excision repair of Corynebacterium glutamicum and survival of the mutants in presence of various mutagens. Arch Microbiol 2017; 199:1043-1054. [PMID: 28391506 DOI: 10.1007/s00203-017-1377-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/27/2017] [Accepted: 04/01/2017] [Indexed: 10/19/2022]
Abstract
Base Excision Repair (BER) is considered as the most active DNA repair pathway in vivo, which is initiated by recognition of the nucleotide lesions and excision of the damaged DNA base. The genome of Corynebacterium glutamicum ATCC 13032 contains various DNA glycosylases encoding genes (ung, fpg/mutM, tagI, alkA, mutY), two AP-endonuclease encoding genes (nei and nth) and an exonuclease encoding gene xth. To investigate the role of these genes during DNA repair in C. glutamicum, mutants with deletions of one or more genes in BER pathway were created. After treatment with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), mitomycin C (MMC), zeocin and UV-light, we characterised the function of the different BER genes by determination of the survival capability. DNA lesions caused by MNNG strongly reduced survival of the tagI, mutY and alkA mutants but had a negligible effect on the ung and mutM mutants. The endonucleases Nth and Nei turned out to be essential for the repair of base modifications caused by MMC while UV-light and zeocin did not seem to address the BER. So far, BER in C. glutamicum appears to be very similar to that in E. coli.
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Management of E. coli sister chromatid cohesion in response to genotoxic stress. Nat Commun 2017; 8:14618. [PMID: 28262707 PMCID: PMC5343486 DOI: 10.1038/ncomms14618] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 01/13/2017] [Indexed: 11/08/2022] Open
Abstract
Aberrant DNA replication is a major source of the mutations and chromosomal rearrangements associated with pathological disorders. In bacteria, several different DNA lesions are repaired by homologous recombination, a process that involves sister chromatid pairing. Previous work in Escherichia coli has demonstrated that sister chromatid interactions (SCIs) mediated by topological links termed precatenanes, are controlled by topoisomerase IV. In the present work, we demonstrate that during the repair of mitomycin C-induced lesions, topological links are rapidly substituted by an SOS-induced sister chromatid cohesion process involving the RecN protein. The loss of SCIs and viability defects observed in the absence of RecN were compensated by alterations in topoisomerase IV, suggesting that the main role of RecN during DNA repair is to promote contacts between sister chromatids. RecN also modulates whole chromosome organization and RecA dynamics suggesting that SCIs significantly contribute to the repair of DNA double-strand breaks (DSBs).
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Napolitano T, Cheng SY, Nielsen B, Choi C, Aguilar W, Paz MM, Sapse AM, Champeil E. Acetone promoted 1,4-migration of an alkoxycarbonyl group on a syn-1,2-diamine. Tetrahedron Lett 2017; 58:597-601. [DOI: 10.1016/j.tetlet.2016.12.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cheng SY, Seo J, Huang BT, Napolitano T, Champeil E. Mitomycin C and decarbamoyl mitomycin C induce p53-independent p21WAF1/CIP1 activation. Int J Oncol 2016; 49:1815-1824. [PMID: 27666201 PMCID: PMC5063421 DOI: 10.3892/ijo.2016.3703] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/16/2016] [Indexed: 12/16/2022] Open
Abstract
Mitomycin C (MC), a commonly used anticancer drug, induces DNA damage via DNA alkylation. Decarbamoyl mitomycin C (DMC), another mitomycin lacking the carbamate at C10, generates similar lesions as MC. Interstrand cross-links (ICLs) are believed to be the lesions primarily responsible for the cytotoxicity of MC and DMC. The major ICL generated by MC (α-ICL) has a trans stereochemistry at the guanine-drug linkage whereas the major ICL from DMC (β-ICL) has the opposite, cis, stereochemistry. In addition, DMC can provoke strong p53-independent cell death. Our hypothesis is that the stereochemistry of the major unique β-ICL generated by DMC is responsible for this p53-independent cell death signaling. p53 gene is inactively mutated in more than half of human cancers. p21WAF1/CIP1 known as a major effector of p53 is involved in p53-dependent and -independent control of cell proliferation and death. This study revealed the role of p21WAF1/CIP1 on MC and DMC triggered cell damage. MCF-7 (p53-proficient) and K562 (p53-deficient) cells were used. Cell cycle distributions were shifted to the G1/S phase in MCF-7 treated with MC and DMC, but were shifted to the S phase in K562. p21WAF1/CIP1 activation was observed in both cells treated with MC and DMC, and DMC triggered more significant activation. Knocking down p53 in MCF-7 did not attenuate MC and DMC induced p21WAF1/CIP1 activation. The α-ICL itself was enough to cause p21WAF1/CIP1 activation.
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Affiliation(s)
- Shu-Yuan Cheng
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, NY 10019, USA
| | - Jiwon Seo
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, NY 10019, USA
| | - Bik Tzu Huang
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, NY 10019, USA
| | - Tanya Napolitano
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, NY 10019, USA
| | - Elise Champeil
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, NY 10019, USA
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Wang Y, Lin Z, Fan H, Peng X. Photoinduced DNA Interstrand Cross-Link Formation by Naphthalene Boronates via a Carbocation. Chemistry 2016; 22:10382-6. [DOI: 10.1002/chem.201601504] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Yibin Wang
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Zechao Lin
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Heli Fan
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
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Yang S, Xu H, Wang J, Liu C, Lu H, Liu M, Zhao Y, Tian B, Wang L, Hua Y. Cyclic AMP Receptor Protein Acts as a Transcription Regulator in Response to Stresses in Deinococcus radiodurans. PLoS One 2016; 11:e0155010. [PMID: 27182600 PMCID: PMC4868304 DOI: 10.1371/journal.pone.0155010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/22/2016] [Indexed: 11/24/2022] Open
Abstract
The cyclic AMP receptor protein family of transcription factors regulates various metabolic pathways in bacteria, and also play roles in response to environmental changes. Here, we identify four homologs of the CRP family in Deinococcus radiodurans, one of which tolerates extremely high levels of oxidative stress and DNA-damaging reagents. Transcriptional levels of CRP were increased under hydrogen peroxide (H2O2) treatment during the stationary growth phase, indicating that CRPs function in response to oxidative stress. By constructing all CRP single knockout mutants, we found that the dr0997 mutant showed the lowest tolerance toward H2O2, ultraviolet radiation, ionizing radiation, and mitomycin C, while the phenotypes of the dr2362, dr0834, and dr1646 mutants showed slight or no significant differences from those of the wild-type strain. Taking advantage of the conservation of the CRP-binding site in many bacteria, we found that transcription of 18 genes, including genes encoding chromosome-partitioning protein (dr0998), Lon proteases (dr0349 and dr1974), NADH-quinone oxidoreductase (dr1506), thiosulfate sulfurtransferase (dr2531), the DNA repair protein UvsE (dr1819), PprA (dra0346), and RecN (dr1447), are directly regulated by DR0997. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses showed that certain genes involved in anti-oxidative responses, DNA repair, and various cellular pathways are transcriptionally attenuated in the dr0997 mutant. Interestingly, DR0997 also regulate the transcriptional levels of all CRP genes in this bacterium. These data suggest that DR0997 contributes to the extreme stress resistance of D. radiodurans via its regulatory role in multiple cellular pathways, such as anti-oxidation and DNA repair pathways.
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Affiliation(s)
- Su Yang
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Hong Xu
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Jiali Wang
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Chengzhi Liu
- Laboratory of Microbiology and Genomics, Zhejiang Institute of Microbiology, Hangzhou, China
| | - Huizhi Lu
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Mengjia Liu
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Ye Zhao
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Bing Tian
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Liangyan Wang
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
- * E-mail: (YH); (LW)
| | - Yuejin Hua
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
- * E-mail: (YH); (LW)
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Wang S, Liu K, Xiao L, Yang L, Li H, Zhang F, Lei L, Li S, Feng X, Li A, He J. Characterization of a novel DNA glycosylase from S. sahachiroi involved in the reduction and repair of azinomycin B induced DNA damage. Nucleic Acids Res 2015; 44:187-97. [PMID: 26400161 PMCID: PMC4705692 DOI: 10.1093/nar/gkv949] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/13/2015] [Indexed: 01/27/2023] Open
Abstract
Azinomycin B is a hybrid polyketide/nonribosomal peptide natural product and possesses antitumor activity by interacting covalently with duplex DNA and inducing interstrand crosslinks. In the biosynthetic study of azinomycin B, a gene (orf1) adjacent to the azinomycin B gene cluster was found to be essential for the survival of the producer, Streptomyces sahachiroi ATCC33158. Sequence analyses revealed that Orf1 belongs to the HTH_42 superfamily of conserved bacterial proteins which are widely distributed in pathogenic and antibiotic-producing bacteria with unknown functions. The protein exhibits a protective effect against azinomycin B when heterologously expressed in azinomycin-sensitive strains. EMSA assays showed its sequence nonspecific binding to DNA and structure-specific binding to azinomycin B-adducted sites, and ChIP assays revealed extensive association of Orf1 with chromatin in vivo. Interestingly, Orf1 not only protects target sites by protein–DNA interaction but is also capable of repairing azinomycin B-mediated DNA cross-linking. It possesses the DNA glycosylase-like activity and specifically repairs DNA damage induced by azinomycin B through removal of both adducted nitrogenous bases in the cross-link. This bifunctional protein massively binds to genomic DNA to reduce drug attack risk as a novel DNA binding protein and triggers the base excision repair system as a novel DNA glycosylase.
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Affiliation(s)
- Shan Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Le Xiao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - LiYuan Yang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - FeiXue Zhang
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Lei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - ShengQing Li
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - AiYing Li
- State Key Laboratory of Microbial Technology, Shandong University Helmholtz Joint Institute of Biotechnology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Stationary-Phase Persisters to Ofloxacin Sustain DNA Damage and Require Repair Systems Only during Recovery. mBio 2015; 6:e00731-15. [PMID: 26330511 PMCID: PMC4556807 DOI: 10.1128/mbio.00731-15] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Chronic infections are a serious health care problem, and bacterial persisters have been implicated in infection reoccurrence. Progress toward finding antipersister therapies has been slow, in part because of knowledge gaps regarding the physiology of these rare phenotypic variants. Evidence shows that growth status is important for survival, as nongrowing cultures can have 100-fold more persisters than growing populations. However, additional factors are clearly important, as persisters remain rare even in nongrowing populations. What features, beyond growth inhibition, allow persisters to survive antibiotic stress while the majority of their kin succumb to it remains an open question. To investigate this, we used stationary phase as a model nongrowing environment to study Escherichia coli persistence to ofloxacin. Given that the prevailing model of persistence attributes survival to transient dormancy and antibiotic target inactivity, we anticipated that persisters would suffer less damage than their dying kin. However, using genetic mutants, flow cytometry, fluorescence-activated cell sorting, and persistence assays, we discovered that nongrowing ofloxacin persisters experience antibiotic-induced damage that is indistinguishable from that of nonpersisters. Consistent with this, we found that these persisters required DNA repair for survival and that repair machinery was unnecessary until the posttreatment recovery period (after ofloxacin removal). These findings suggest that persistence to ofloxacin is not engendered solely by reduced antibiotic target corruption, demonstrate that what happens following antibiotic stress can be critical to the persistence phenotype, and support the notion that inhibition of DNA damage repair systems could be an effective strategy to eliminate fluoroquinolone persisters. In the absence of resistant mutants, infection reoccurrences can still occur because of persisters, rare bacterial cells that survive antibiotic treatments to repopulate infection sites. Persister survival is attributed to a transient state of dormancy in which a cell’s growth and metabolism are significantly reduced and many essential processes are thought to be inactive. Thus, dormancy is believed to protect persisters from antibiotic-induced damage and death. In this work, we show that in nongrowing populations, persisters to ofloxacin experience the same level of antibiotic-induced damage as cells that succumb to the treatment and that their survival critically depends on repair of this damage after the conclusion of treatment. These findings reveal that persistence to ofloxacin is not engendered solely by reduced antibiotic target corruption and highlight that processes following antibiotic stress are important to survival. We hypothesize that effective antipersister therapies may be developed on the basis of this knowledge.
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Lopes-Kulishev CO, Alves IR, Valencia EY, Pidhirnyj MI, Fernández-Silva FS, Rodrigues TR, Guzzo CR, Galhardo RS. Functional characterization of two SOS-regulated genes involved in mitomycin C resistance in Caulobacter crescentus. DNA Repair (Amst) 2015; 33:78-89. [DOI: 10.1016/j.dnarep.2015.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 06/24/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
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Kwan BW, Chowdhury N, Wood TK. Combatting bacterial infections by killing persister cells with mitomycin C. Environ Microbiol 2015; 17:4406-14. [PMID: 25858802 DOI: 10.1111/1462-2920.12873] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/04/2015] [Indexed: 11/29/2022]
Abstract
Persister cells are a multi-drug tolerant subpopulation of bacteria that contribute to chronic and recalcitrant clinical infections such as cystic fibrosis and tuberculosis. Persisters are metabolically dormant, so they are highly tolerant to all traditional antibiotics which are mainly effective against actively growing cells. Here, we show that the FDA-approved anti-cancer drug mitomycin C (MMC) eradicates persister cells through a growth-independent mechanism. MMC is passively transported and bioreductively activated, leading to spontaneous cross-linking of DNA, which we verify in both active and dormant cells. We find MMC effectively eradicates cells grown in numerous different growth states (e.g. planktonic cultures and highly robust biofilm cultures) in both rich and minimal media. Additionally, MMC is a potent bactericide for a broad range of bacterial persisters, including commensal Escherichia coli K-12 as well as pathogenic species of E. coli, Staphylococcus aureus and Pseudomonas aeruginosa. We also demonstrate the efficacy of MMC in an animal model and a wound model, substantiating the clinical applicability of MMC against bacterial infections. Therefore, MMC is the first broad-spectrum compound capable of eliminating persister cells, meriting investigation as a new approach for the treatment of recalcitrant infections.
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Affiliation(s)
- Brian W Kwan
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Nityananda Chowdhury
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802-4400, USA
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Han Y, Chen W, Kuang Y, Sun H, Wang Z, Peng X. UV-Induced DNA Interstrand Cross-Linking and Direct Strand Breaks from a New Type of Binitroimidazole Analogue. Chem Res Toxicol 2015; 28:919-26. [PMID: 25844639 DOI: 10.1021/tx500522r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Four novel photoactivated binitroimidazole prodrugs were synthesized. These agents produced DNA interstrand cross-links (ICLs) and direct strand breaks (DSB) upon UV irradiation, whereas no or very few DNA ICLs and DSBs were observed without UV treatment. Although these four molecules (1-4) contain the same binitroimidazole moiety, they bear four different leaving groups, which resulted in their producing different yields of DNA damage. Compound 4, with nitrogen mustard as a leaving group, showed the highest ICL yield. Surprisingly, compounds 1-3, without any alkylating functional group, also induced DNA ICL formation, although they did so with lower yields, which suggested that the binitroimidazole moiety released from UV irradiation of 1-3 is capable of cross-linking DNA. The DNA cross-linked products induced by these compounds were completely destroyed upon 1.0 M piperidine treatment at 90 °C (leading to cleavage at dG sites), which revealed that DNA cross-linking mainly occurred via alkylation of dGs. We proposed a possible mechanism by which alkylating agents were released from these compounds. HRMS and NMR analysis confirmed that free nitrogen mustards were generated by UV irradiation of 4. Suppression of DNA ICL and DSB formation by a radical trap, TEMPO, indicated the involvement of free radicals in the photo reactions of 3 and 4 with DNA. On the basis of these data, we propose that UV irradiation of compounds 1-4 generated a binitroimidazole intermediate that cross-links DNA. The higher ICL yield observed with 4 resulted from the amine effector nitrogen mustard released from UV irradiation.
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Affiliation(s)
- Yanyan Han
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Wenbing Chen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Yunyan Kuang
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Huabing Sun
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Zhiqiang Wang
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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Amount of colicin release in Escherichia coli is regulated by lysis gene expression of the colicin E2 operon. PLoS One 2015; 10:e0119124. [PMID: 25751274 PMCID: PMC4353708 DOI: 10.1371/journal.pone.0119124] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/09/2015] [Indexed: 12/02/2022] Open
Abstract
The production of bacteriocins in response to worsening environmental conditions is one means of bacteria to outcompete other microorganisms. Colicins, one class of bacteriocins in Escherichia coli, are effective against closely related Enterobacteriaceae. Current research focuses on production, release and uptake of these toxins by bacteria. However, little is known about the quantitative aspects of these dynamic processes. Here, we quantitatively study expression dynamics of the Colicin E2 operon in E. coli on a single cell level using fluorescence time-lapse microscopy. DNA damage, triggering SOS response leads to the heterogeneous expression of this operon including the cea gene encoding the toxin, Colicin E2, and the cel gene coding for the induction of cell lysis and subsequent colicin release. Advancing previous whole population investigations, our time-lapse experiments reveal that at low exogenous stress levels all cells eventually respond after a given time (heterogeneous timing). This heterogeneous timing is lost at high stress levels, at which a synchronized stress response of all cells 60 min after induction via stress can be observed. We further demonstrate, that the amount of colicin released is dependent on cel (lysis) gene expression, independent of the applied exogenous stress level. A heterogeneous response in combination with heterogeneous timing can be biologically significant. It might enable a bacterial population to endure low stress levels, while at high stress levels an immediate and synchronized population wide response can give single surviving cells of the own species the chance to take over the bacterial community after the stress has ceased.
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Sun H, Fan H, Peng X. Quantitative DNA interstrand cross-link formation by coumarin and thymine: structure determination, sequence effect, and fluorescence detection. J Org Chem 2014; 79:11359-69. [PMID: 25372021 DOI: 10.1021/jo5014756] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The coumarin analogues have been widely utilized in medicine, biology, biochemistry, and material sciences. Here, we report a detailed study on the reactivity of coumarins toward DNA. A series of coumarin analogues were synthesized and incorporated into oligodeoxynucleotides. A photoinduced [2 + 2] cycloaddition occurs between the coumarin moiety and the thymidine upon 350 nm irradiation forming both syn- and anti-cyclobutane adducts (17 and 18), which are photoreversible by 254/350 nm irradiation in DNA. Quantitative DNA interstrand cross-link (ICL) formation was observed with the coumarin moieties containing a flexible two-carbon or longer chain. DNA cross-linking by coumarins shows a kinetic preference when flanked by an A:T base pair as opposed to a G:C pair. An efficient photoinduced electron transfer between coumarin and dG slows down ICL formation. ICL formation quenches the fluorescence of coumarin, which, for the first time, enables fast, easy, and real-time monitoring of DNA cross-linking and photoreversibility via fluorescence spectroscopy. It can be used to detect the transversion mutation between pyrimidines and purines. Overall, this work provides new insights into the biochemical properties and possible toxicity of coumarins. A quantitative, fluorescence-detectable, and photoswitchable DNA cross-linking reaction of the coumarin moieties can potentially serve as mechanistic probes and tools for bioresearch without disrupting native biological environment.
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Affiliation(s)
- Huabing Sun
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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A novel toxicogenomics-based approach to categorize (non-)genotoxic carcinogens. Arch Toxicol 2014; 89:2413-27. [DOI: 10.1007/s00204-014-1368-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
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Ghosh S, Greenberg MM. Nucleotide excision repair of chemically stabilized analogues of DNA interstrand cross-links produced from oxidized abasic sites. Biochemistry 2014; 53:5958-65. [PMID: 25208227 PMCID: PMC4172206 DOI: 10.1021/bi500914d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nucleotide excision repair is a primary pathway in cells for coping with DNA interstrand cross-links (ICLs). Recently, C4'-oxidized (C4-AP) and C5'-oxidized abasic sites (DOB) that are produced following hydrogen atom abstraction from the DNA backbone were found to produce ICLs. Because some of the ICLs derived from C4-AP and DOB are too unstable to characterize in biochemical processes, chemically stable analogues were synthesized [Ghosh, S., and Greenberg, M. M. (2014) J. Org. Chem. 79, 5948-5957]. UvrABC incision of DNA substrates containing stabilized analogues of the ICLs derived from C4-AP and DOB was examined. The incision pattern for the ICL related to the C4'-oxidized abasic site was typical for UvrABC substrates. UvrABC cleaved both strands of the substrate containing the C4-AP ICL analogue, but it was a poor substrate. UvrABC incised <30% of the C4-AP ICL analogue over an 8 h period, raising the possibility that this cross-link will be inefficiently repaired in cells. Furthermore, double-strand breaks were not detected upon incision of an internally labeled hairpin substrate containing the C4-AP ICL analogue. UvrABC incised the stabilized analogue of the DOB ICL more efficiently (~20% in 1 h). Furthermore, the incision pattern was unique, and the cross-linked substrate was converted into a single product, a double-strand break. The template strand was exclusively incised on the template strand on the 3'-side of the cross-linked dA. Although the outcomes of the interaction between UvrABC and these two cross-linked substrates are different from one another, they provide additional examples of how seemingly simple lesions (C4-AP and DOB) can potentially exert significant deleterious effects on biochemical processes.
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Affiliation(s)
- Souradyuti Ghosh
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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Ghosh S, Greenberg MM. Synthesis of cross-linked DNA containing oxidized abasic site analogues. J Org Chem 2014; 79:5948-57. [PMID: 24949656 PMCID: PMC4084848 DOI: 10.1021/jo500944g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA interstrand cross-links are an important family of DNA damage that block replication and transcription. Recently, it was discovered that oxidized abasic sites react with the opposing strand of DNA to produce interstrand cross-links. Some of the cross-links between 2'-deoxyadenosine and the oxidized abasic sites, 5'-(2-phosphoryl-1,4-dioxobutane) (DOB) and the C4-hydroxylated abasic site (C4-AP), are formed reversibly. Chemical instability hinders biochemical, structural, and physicochemical characterization of these cross-linked duplexes. To overcome these limitations, we developed methods for preparing stabilized analogues of DOB and C4-AP cross-links via solid-phase oligonucleotide synthesis. Oligonucleotides of any sequence are attainable by synthesizing phosphoramidites in which the hydroxyl groups of the cross-linked product were orthogonally protected using photochemically labile and hydrazine labile groups. Selective unmasking of a single hydroxyl group precedes solid-phase synthesis of one arm of the cross-linked DNA. The method is compatible with commercially available phosphoramidites and other oligonucleotide synthesis reagents. Cross-linked duplexes containing as many as 54 nt were synthesized on solid-phase supports. Subsequent enzyme ligation of one cross-link product provided a 60 bp duplex, which is suitable for nucleotide excision repair studies.
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Affiliation(s)
- Souradyuti Ghosh
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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Haque MM, Sun H, Liu S, Wang Y, Peng X. Photoswitchable Formation of a DNA Interstrand Cross-Link by a Coumarin-Modified Nucleotide. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Haque MM, Sun H, Liu S, Wang Y, Peng X. Photoswitchable formation of a DNA interstrand cross-link by a coumarin-modified nucleotide. Angew Chem Int Ed Engl 2014; 53:7001-5. [PMID: 24840115 DOI: 10.1002/anie.201310609] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/19/2014] [Indexed: 11/08/2022]
Abstract
A coumarin-modified pyrimidine nucleoside (1) has been synthesized using a Cu(I)-catalyzed click reaction and incorporated into oligodeoxynucleotides (ODNs). Interstrand cross-links are produced upon irradiation of ODNs containing 1 at 350 nm. Cross-linking occurs through a [2+2] cycloaddition reaction with the opposing thymidine, 2'-deoxycytidine, or 2'-deoxyadenosine. A much higher reactivity was observed with dT than dC or dA. Irradiation of the dT-1 and dC-1 cross-linked products at 254 nm leads to a reversible ring-opening reaction, while such phenomena were not observed with dA-1 adducts. The reversible reaction is ultrafast and complete within 50-90 s. Consistent photoswitching behavior was observed over 6 cycles of irradiation at 350 nm and 254 nm. To the best of our knowledge, this is the first example of photoswitchable interstrand cross-linking formation induced by a modified pyrimidine nucleoside.
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Affiliation(s)
- Mohammad Mojibul Haque
- Department of Chemistry and Biochemistry, University of Wisconsin Milwaukee, 3210 N. Cramer St., Milwaukee, WI 53211 (USA)
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Chen W, Han Y, Peng X. Aromatic nitrogen mustard-based prodrugs: activity, selectivity, and the mechanism of DNA cross-linking. Chemistry 2014; 20:7410-8. [PMID: 24806710 DOI: 10.1002/chem.201400090] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 12/26/2022]
Abstract
Three novel H2O2-activated aromatic nitrogen mustard prodrugs (6-8) are reported. These compounds contain a DNA alkylating agent connected to a H2O2-responsive trigger by different electron-withdrawing linkers so that they are inactive towards DNA but can be triggered by H2O2 to release active species. The activity and selectivity of these compounds towards DNA were investigated by measuring DNA interstrand cross-link (ICL) formation in the presence or absence of H2O2. An electron-withdrawing linker unit, such as a quaternary ammonia salt (6), a carboxyamide (7), and a carbonate group (8), is sufficient to deactivate the aromatic nitrogen mustard resulting in less than 1.5 % cross-linking formation. However, H2O2 can restore the activity of the effectors by converting a withdrawing group to a donating group, therefore increasing the cross-linking efficiency (>20 %). The stability and reaction sites of the ICL products were determined, which revealed that alkylation induced by 7 and 8 not only occurred at the purine sites but also at the pyrimidine site. For the first time, we isolated and characterized the monomer adducts formed between the canonical nucleosides and the aromatic nitrogen mustard (15) which supported that nitrogen mustards reacted with dG, dA, and dC. The activation mechanism was studied by NMR spectroscopic analysis. An in vitro cytotoxicity assay demonstrated that compound 7 with a carboxyamide linker dramatically inhibited the growth of various cancer cells with a GI50 of less than 1 μM, whereas compound 6 with a charged linker did not show any obvious toxicity in all cell lines tested. These data indicated that a neutral carboxyamide linker is preferable for developing nitrogen mustard prodrugs. Our results showed that 7 is a potent anticancer prodrug that can serve as a model compound for further development. We believe these novel aromatic nitrogen mustards will inspire further and effective applications.
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Affiliation(s)
- Wenbing Chen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St, Milwaukee, WI 53211 (USA)
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Greenberg MM. Looking beneath the surface to determine what makes DNA damage deleterious. Curr Opin Chem Biol 2014; 21:48-55. [PMID: 24762292 DOI: 10.1016/j.cbpa.2014.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 02/07/2023]
Abstract
Apurinic/apyrimidinic and oxidized abasic sites are chemically reactive DNA lesions that are produced by a variety of damaging agents. The effects of these molecules that lack a Watson-Crick base on polymerase enzymes are well documented. More recently, multiple consequences of the electrophilic nature of abasic lesions have been revealed. Members of this family of DNA lesions have been shown to inactivate repair enzymes and undergo spontaneous transformation into more deleterious forms of damage. Abasic site reactivity provides insight into the chemical basis for the cytotoxicity of DNA damaging agents that produce them and are valuable examples of how looking beneath the surface of seemingly simple molecules can reveal biologically relevant chemical complexity.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400N, Charles Street, Baltimore, MD 21218, United States.
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Hou D, Greenberg MM. DNA interstrand cross-linking upon irradiation of aryl halide C-nucleotides. J Org Chem 2014; 79:1877-84. [PMID: 24559326 DOI: 10.1021/jo4028227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
γ-Radiolysis kills cells by damaging DNA via radical processes. Many of the radical pathways are O2 dependent, which results in a reduction in the cytotoxicity of ionizing radiation in hypoxic tumor cells. Consequently, there is a need for chemical agents that increase DNA damage by ionizing radiation under O2-deficient conditions. Modified nucleotides that are incorporated in DNA and produce highly reactive σ-radicals are useful as radiosensitizing agents. Aryl halide C-nucleotides (4-6) were incorporated into oligonucleotides by solid-phase synthesis. Duplex DNA containing 4-6 forms interstrand cross-links upon γ-radiolysis under anaerobic conditions or UV irradiation. Deep Vent (exo(-)) DNA polymerase accepted the nucleotide triphosphate of C-nucleotide 6 as a substrate and preferentially incorporated it opposite pyrimidines, but no further extension was detected. Incorporation of 6 in extended products by Deep Vent (exo(-)) during PCR or by Sequenase during copying of single stranded DNA plasmid was undetectable. Aryl halide nucleotide analogues that produce DNA interstrand cross-links under anaerobic conditions upon irradiation are potentially useful as radiosensitizing agents, but further research is needed to identify molecules that are incorporated by DNA polymerases and do not block further polymerization for this approach to be useful in cells.
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Affiliation(s)
- Dianjie Hou
- Department of Chemistry Johns Hopkins University 3400 North Charles Street, Baltimore, Maryland 21218, United States
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Greenberg MM. Abasic and oxidized abasic site reactivity in DNA: enzyme inhibition, cross-linking, and nucleosome catalyzed reactions. Acc Chem Res 2014; 47:646-55. [PMID: 24369694 DOI: 10.1021/ar400229d] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abasic lesions are a family of DNA modifications that lack Watson-Crick bases. The parent member of this family, the apurinic/apyrimidinic lesion (AP), occurs as an intermediate during DNA repair, following nucleobase alkylation, and from random hydrolysis of native nucleotides. In a given day, each cell produces between 10000 and 50000 AP lesions. A variety of oxidants including γ-radiolysis produce oxidized abasic sites, such as C4-AP, from the deoxyribose backbone. A number of potent, cytotoxic antitumor agents, such as bleomycin and the enediynes (e.g., calicheamicin, esperamicin, and neocarzinostatin) also lead to oxidized abasic sites in DNA. The absence of Watson-Crick bases prevents DNA polymerases from properly determining which nucleotide to incorporate opposite abasic lesions. Consequently, several studies have revealed that (oxidized) abasic sites are highly mutagenic. Abasic lesions are also chemically unstable, are prone to strand scission, and possess electrophilic carbonyl groups. However, researchers have only uncovered the consequences of the inherent reactivity of these electrophiles within the past decade. The development of solid phase synthesis methods for oligonucleotides that both place abasic sites in defined positions and circumvent their inherent alkaline lability has facilitated this research. Chemically synthesized oligonucleotides containing abasic lesions provide substrates that have allowed researchers to discover a range of interesting chemical properties of potential biological importance. For instance, abasic lesions form DNA-DNA interstrand cross-links, a particularly important family of DNA damage because they block replication and transcription absolutely. In addition, bacterial repair enzymes can convert an interstrand cross-link derived from C4-AP into a double-strand break, the most deleterious form of DNA damage. Oxidized abasic lesions can also inhibit DNA repair enzymes that remove damaged nucleotides. DNA polymerase β, an enzyme that is irreversibly inactivated, is vitally important in base excision repair and is overproduced in some tumor cells. Nucleosome core particles, the monomeric components that make up chromatin, accentuate the chemical instability of abasic lesions. In experiments using synthetic nucleosome core particles containing abasic sites, the histone proteins catalyze strand cleavage at the sites that incorporate these lesions. Furthermore, in the presence of the C4-AP lesion, strand scission is accompanied by modification of the histone protein. The reactivity of (oxidized) abasic lesions illustrates how seemingly simple nucleic acid modifications can have significant biochemical effects and may provide a chemical basis for the cytotoxicity of the chemotherapeutic agents that produce them.
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Affiliation(s)
- Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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A replication-inhibited unsegregated nucleoid at mid-cell blocks Z-ring formation and cell division independently of SOS and the SlmA nucleoid occlusion protein in Escherichia coli. J Bacteriol 2013; 196:36-49. [PMID: 24142249 DOI: 10.1128/jb.01230-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromosome replication and cell division of Escherichia coli are coordinated with growth such that wild-type cells divide once and only once after each replication cycle. To investigate the nature of this coordination, the effects of inhibiting replication on Z-ring formation and cell division were tested in both synchronized and exponentially growing cells with only one replicating chromosome. When replication elongation was blocked by hydroxyurea or nalidixic acid, arrested cells contained one partially replicated, compact nucleoid located mid-cell. Cell division was strongly inhibited at or before the level of Z-ring formation. DNA cross-linking by mitomycin C delayed segregation, and the accumulation of about two chromosome equivalents at mid-cell also blocked Z-ring formation and cell division. Z-ring inhibition occurred independently of SOS, SlmA-mediated nucleoid occlusion, and MinCDE proteins and did not result from a decreased FtsZ protein concentration. We propose that the presence of a compact, incompletely replicated nucleoid or unsegregated chromosome masses at the normal mid-cell division site inhibits Z-ring formation and that the SOS system, SlmA, and MinC are not required for this inhibition.
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Couvé S, Ishchenko AA, Fedorova OS, Ramanculov EM, Laval J, Saparbaev M. Direct DNA Lesion Reversal and Excision Repair in Escherichia coli. EcoSal Plus 2013; 5. [PMID: 26442931 DOI: 10.1128/ecosalplus.7.2.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Indexed: 06/05/2023]
Abstract
Cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that inevitably lead to DNA damage: structural and chemical modifications of primary DNA sequence. These DNA lesions are either cytotoxic, because they block DNA replication and transcription, or mutagenic due to the miscoding nature of the DNA modifications, or both, and are believed to contribute to cell lethality and mutagenesis. Studies on DNA repair in Escherichia coli spearheaded formulation of principal strategies to counteract DNA damage and mutagenesis, such as: direct lesion reversal, DNA excision repair, mismatch and recombinational repair and genotoxic stress signalling pathways. These DNA repair pathways are universal among cellular organisms. Mechanistic principles used for each repair strategies are fundamentally different. Direct lesion reversal removes DNA damage without need for excision and de novo DNA synthesis, whereas DNA excision repair that includes pathways such as base excision, nucleotide excision, alternative excision and mismatch repair, proceeds through phosphodiester bond breakage, de novo DNA synthesis and ligation. Cell signalling systems, such as adaptive and oxidative stress responses, although not DNA repair pathways per se, are nevertheless essential to counteract DNA damage and mutagenesis. The present review focuses on the nature of DNA damage, direct lesion reversal, DNA excision repair pathways and adaptive and oxidative stress responses in E. coli.
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Paz MM, Pritsos CA. The Molecular Toxicology of Mitomycin C. ADVANCES IN MOLECULAR TOXICOLOGY VOLUME 6 2012. [DOI: 10.1016/b978-0-444-59389-4.00007-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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