1
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Garg K, Bhandari RK, Shafiq N, Jain S, Jaswal S, Chawla D, Mallayasamy S, Khurana S, Batcha JSD. Population pharmacokinetics of ciprofloxacin in newborns with early onset neonatal sepsis and suspected meningitis. Pediatr Res 2024; 95:1273-1278. [PMID: 38062257 DOI: 10.1038/s41390-023-02941-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 04/24/2024]
Abstract
BACKGROUND Neonatal Sepsis accounts for significant proportion of neonatal mortality globally. Ciprofloxacin can be used as an effective antimicrobial against common causative agents of neonatal sepsis. However, there is only limited information about its pharmacokinetic distribution in plasma and Cerebrospinal fluid (CSF) of neonates. METHODS Plasma and CSF samples were taken using a sparse sampling technique from neonates who received at least one dose of intravenous ciprofloxacin. Ciprofloxacin levels were analysed using high-performance liquid chromatography (HPLC). Population pharmacokinetic analysis was conducted using a non-linear mixed-effects modelling using Pumas® (Pharmaceutical Modelling and Simulation) package (Version 2.0). RESULTS 53 neonates were enroled in the study of whom; 9 (17%) had meningitis. The median concentration of ciprofloxacin in CSF was 1.4 (0.94-2.06) ug/ml and plasma was 2.94 (1.8-5.0) ug/ml. A one-compartment model with first-order elimination fitted the data. Body weight was found to be a significant covariate on volume of distribution (Vd). Simulations based on the final model suggest that dose of 10 mg/kg, intravenous b.d may not be able to achieve the desirable indices. CONCLUSIONS One compartment model with weight as a covariate explained the available data. Further studies with modified sampling strategy, larger sample size and variable dose levels are needed.
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Affiliation(s)
- Kunal Garg
- Department of Neonatology, Government Medical College and Hospital, Chandigarh, India
| | - Ritika Kondel Bhandari
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Nusrat Shafiq
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Suksham Jain
- Department of Neonatology, Government Medical College and Hospital, Chandigarh, India
| | - Shivani Jaswal
- Department of Biochemistry, Government Medical College and Hospital, Chandigarh, India
| | - Deepak Chawla
- Department of Neonatology, Government Medical College and Hospital, Chandigarh, India
| | - Surulivelrajan Mallayasamy
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Supreet Khurana
- Department of Neonatology, Government Medical College and Hospital, Chandigarh, India.
| | - Jaya Shree Dilli Batcha
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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2
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Weber-Theen A, Dören L. Chronic toxicity of pharmaceuticals to the benthic green alga Closterium ehrenbergii. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116025. [PMID: 38290309 DOI: 10.1016/j.ecoenv.2024.116025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/30/2023] [Accepted: 01/24/2024] [Indexed: 02/01/2024]
Abstract
Pharmaceuticals in the environment have emerged to a topic of global concern. Since these substances are designed to be biologically active, hazardous effects on non-target organisms are frequently reported. Here, the effects of five pharmaceuticals, one radiocontrast agent, and one degradation product on the freshwater green alga Closterium ehrenbergii were evaluated after chronic exposure of 168 h. Growth and maximum quantum yield (FV/FM) were used as endpoints and complemented by the assessment of morphology and chlorophyll fluorescence. We found that the tested antibiotics Ciprofloxacin and Ofloxacin impaired chloroplast integrity, resulting in a reduction of FV/FM from 0.1 mg/L. The disintegration of chloroplasts at higher concentrations (c = 0.3 and 0.8 mg/L, respectively) was visualized by brightfield and fluorescence microscopy. In contrast, Sulfamethoxazole interfered with cell division, leading to malformation of cells from 0.8 mg/L. Furthermore, the antibiotics exhibited a latency period of 72 h after which they started to reveal their true effects. Therefore, the importance of long-term toxicity testing is outlined in order to avoid underestimation of toxic effects of pharmaceuticals. Based on the EC10 values obtained, the antibiotics were considered to meet the criteria for classification as toxic to aquatic life with long lasting effects. The other test substances were found to exert no effects on C. ehrenbergii or only at very high concentrations and were classified as nontoxic.
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Affiliation(s)
- Andreas Weber-Theen
- Department of Environmental Engineering, Laboratories of Ecotoxicology and Analytical Chemistry, RheinMain University of Applied Sciences, P.O. Box 3251, 65022 Wiesbaden, Germany; Department of Experimental Phycology and Culture Collection of Algae, Georg-August-University, Göttingen, Germany.
| | - László Dören
- Department of Environmental Engineering, Laboratories of Ecotoxicology and Analytical Chemistry, RheinMain University of Applied Sciences, P.O. Box 3251, 65022 Wiesbaden, Germany
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3
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Lin JY, Liu YC, Tseng YH, Chan MT, Chang CC. TALE-based organellar genome editing and gene expression in plants. PLANT CELL REPORTS 2024; 43:61. [PMID: 38336900 DOI: 10.1007/s00299-024-03150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
KEY MESSAGE TALE-based editors provide an alternative way to engineer the organellar genomes in plants. We update and discuss the most recent developments of TALE-based organellar genome editing in plants. Gene editing tools have been widely used to modify the nuclear genomes of plants for various basic research and biotechnological applications. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 editing platform is the most commonly used technique because of its ease of use, fast speed, and low cost; however, it encounters difficulty when being delivered to plant organelles for gene editing. In contrast, protein-based editing technologies, such as transcription activator-like effector (TALE)-based tools, could be easily delivered, expressed, and targeted to organelles in plants via Agrobacteria-mediated nuclear transformation. Therefore, TALE-based editors provide an alternative way to engineer the organellar genomes in plants since the conventional chloroplast transformation method encounters technical challenges and is limited to certain species, and the direct transformation of mitochondria in higher plants is not yet possible. In this review, we update and discuss the most recent developments of TALE-based organellar genome editing in plants.
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Affiliation(s)
- Jer-Young Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yu-Chang Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan
| | - Yan-Hao Tseng
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan.
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Ching-Chun Chang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
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4
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Dar A, Godara P, Prusty D, Bashir M. Plasmodium falciparum topoisomerases: Emerging targets for anti-malarial therapy. Eur J Med Chem 2024; 265:116056. [PMID: 38171145 DOI: 10.1016/j.ejmech.2023.116056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
Different metabolic pathways like DNA replication, transcription, and recombination generate topological constrains in the genome. These topological constraints are resolved by essential molecular machines known as topoisomerases. To bring changes in DNA topology, the topoisomerases create a single or double-stranded nick in the template DNA, hold the nicked ends to let the tangled DNA pass through, and finally re-ligate the breaks. The DNA nicking and re-ligation activities as well as ATPase activities (when present) in topoisomerases are subjected to inhibition by several anticancer and antibacterial drugs, thus establishing these enzymes as successful targets in anticancer and antibacterial therapies. The anti-topoisomerase drugs interfere with the functioning of these enzymes and result in the accumulation of DNA tangles or lethal genomic breaks, thereby promoting host cell (or organism) death. The potential of topoisomerases in the human malarial parasite, Plasmodium falciparum in antimalarial drug development has received little attention so far. Interestingly, the parasite genome encodes orthologs of topoisomerases found in eukaryotes, prokaryotes, and archaea, thus, providing an enormous opportunity for investigating these enzymes for antimalarial therapeutics. This review focuses on the features of Plasmodium falciparum topoisomerases (PfTopos) with respect to their closer counterparts in other organisms. We will discuss overall advances and basic challenges with topoisomerase research in Plasmodium falciparum and our attempts to understand the interaction of PfTopos with classical and new-generation topoisomerase inhibitors using in silico molecular docking approach. The recent episodes of parasite resistance against artemisinin, the only effective antimalarial drug at present, further highlight the significance of investigating new drug targets including topoisomerases in antimalarial therapeutics.
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Affiliation(s)
- Ashraf Dar
- Department of Biochemistry, University of Kashmir, Srinagar, 190006, India.
| | - Priya Godara
- Central University of Rajasthan, Ajmer, Rajasthan, India
| | | | - Masarat Bashir
- COTS, Sheri-Kashmir University of Agricultural Sciences and Technology, Mirgund, Srinagar, India
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5
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Diyah NW, Indriani DA, Dessidianti R, Siswandono S. In silico analysis of luteolin derivatives as antibacterial agents targeting DNA gyrase and CTX-M-15 extended-spectrum β-lactamase of Escherichia coli. J Adv Pharm Technol Res 2024; 15:29-36. [PMID: 38389968 PMCID: PMC10880919 DOI: 10.4103/japtr.japtr_217_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/14/2023] [Accepted: 10/06/2023] [Indexed: 02/24/2024] Open
Abstract
Luteolin exhibited antibacterial activity against Escherichia coli and its chemical structure similar to that of ciprofloxacin (CPF) which works by inhibiting DNA gyrase. Filtrate from passion fruit extract containing luteolin and its derivatives could inhibit extended-spectrum β-lactamase (ESBL)-producing E. coli. Antibacterial compounds that can also inhibit ESBL will be valuable compounds to overcome the problem of resistant bacteria. This study aimed to ensure the potency of luteolin and luteolin derivatives targeting DNA gyrase and ESBL by in silico approach. Docking simulation of ligands L1-L14 was performed using AutoDock Vina, and pharmacokinetics and toxicity (absorption, distribution, metabolism, excretion, and toxicity) profiles were predicted by pKCSM online. The docking result revealed higher binding affinity on DNA gyrase (PDB.1KZN) of 12 luteolin derivatives (energy <-7.6 kcal/mol) compared to CPF and higher affinity (energy <-6.27 kcal/mol) of all compounds than clavulanic acid against ESBL CTX-M-15 (PDB.4HBU). The compounds could be absorbed through the human intestine moderately, which showed low permeability to blood-brain barrier, nontoxic and nonhepatotoxic. The most active luteolin glycoside (L6) is capable to inhibit DNA gyrase and ESBL from E. coli which provided the potential against resistant bacteria and was promoted as lead compounds to be developed further.
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Affiliation(s)
- Nuzul Wahyuning Diyah
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
| | - Dwi Ayu Indriani
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
| | - Rachma Dessidianti
- Study Program of Pharmacy, Faculty of Health Science, Universitas Muhammadiyah Surabaya, Surabaya, Indonesia
| | - Siswandono Siswandono
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
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6
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Narciso A, Barra Caracciolo A, De Carolis C. Overview of Direct and Indirect Effects of Antibiotics on Terrestrial Organisms. Antibiotics (Basel) 2023; 12:1471. [PMID: 37760767 PMCID: PMC10525971 DOI: 10.3390/antibiotics12091471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotics (ABs) have made it possible to treat bacterial infections, which were in the past untreatable and consequently fatal. Regrettably, their use and abuse among humans and livestock led to antibiotic resistance, which has made them ineffective in many cases. The spread of antibiotic resistance genes (ARGs) and bacteria is not limited to nosocomial environments, but also involves water and soil ecosystems. The environmental presence of ABs and ARGs is a hot topic, and their direct and indirect effects, are still not well known or clarified. A particular concern is the presence of antibiotics in agroecosystems due to the application of agro-zootechnical waste (e.g., manure and biosolids), which can introduce antibiotic residues and ARGs to soils. This review provides an insight of recent findings of AB direct and indirect effects on terrestrial organisms, focusing on plant and invertebrates. Possible changing in viability and organism growth, AB bioaccumulation, and shifts in associated microbiome composition are reported. Oxidative stress responses of plants (such as reactive oxygen species production) to antibiotics are also described.
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Affiliation(s)
- Alessandra Narciso
- Water Research Institute, National Research Council (IRSA-CNR), SP 35d, km 0.7 Montelibretti, 00010 Rome, Italy; (A.N.); (C.D.C.)
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Anna Barra Caracciolo
- Water Research Institute, National Research Council (IRSA-CNR), SP 35d, km 0.7 Montelibretti, 00010 Rome, Italy; (A.N.); (C.D.C.)
| | - Chiara De Carolis
- Water Research Institute, National Research Council (IRSA-CNR), SP 35d, km 0.7 Montelibretti, 00010 Rome, Italy; (A.N.); (C.D.C.)
- Department of Environmental Biology, La Sapienza’ University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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7
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Butler G, Bos J, Austin RH, Amend SR, Pienta KJ. Escherichia coli survival in response to ciprofloxacin antibiotic stress correlates with increased nucleoid length and effective misfolded protein management. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230338. [PMID: 37564061 PMCID: PMC10410211 DOI: 10.1098/rsos.230338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023]
Abstract
The evolution of antibiotic resistance is a fundamental problem in disease management but is rarely quantified on a single-cell level owing to challenges associated with capturing the spatial and temporal variation across a population. To evaluate cell biological phenotypic responses, we tracked the single-cell dynamics of filamentous bacteria through time in response to ciprofloxacin antibiotic stress. We measured the degree of phenotypic variation in nucleoid length and the accumulation of protein damage under ciprofloxacin antibiotic and quantified the impact on bacterial survival. Increased survival was correlated with increased nucleoid length and the variation in this response was inversely correlated with antibiotic concentration. Survival time was also increased through clearance of misfolded proteins, an unexpected mechanism of stress relief deployed by the filamentous bacteria. Our results reveal a diverse range of survival tactics employed by bacteria in response to ciprofloxacin and suggest potential evolutionary routes to resistance.
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Affiliation(s)
- George Butler
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Julia Bos
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Department of Physics, Princeton University, Princeton, NJ, USA
| | | | - Sarah R. Amend
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kenneth J. Pienta
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
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8
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Mackie ERR, Barrow AS, Giel MC, Hulett MD, Gendall AR, Panjikar S, Soares da Costa TP. Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity. Commun Biol 2023; 6:550. [PMID: 37217566 DOI: 10.1038/s42003-023-04895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.
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Affiliation(s)
- Emily R R Mackie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Marie-Claire Giel
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark D Hulett
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Anthony R Gendall
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC, 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia.
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9
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Spencer AC, Panda SS. DNA Gyrase as a Target for Quinolones. Biomedicines 2023; 11:371. [PMID: 36830908 PMCID: PMC9953508 DOI: 10.3390/biomedicines11020371] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Bacterial DNA gyrase is a type II topoisomerase that can introduce negative supercoils to DNA substrates and is a clinically-relevant target for the development of new antibacterials. DNA gyrase is one of the primary targets of quinolones, broad-spectrum antibacterial agents and are used as a first-line drug for various types of infections. However, currently used quinolones are becoming less effective due to drug resistance. Common resistance comes in the form of mutation in enzyme targets, with this type being the most clinically relevant. Additional mechanisms, conducive to quinolone resistance, are arbitrated by chromosomal mutations and/or plasmid-gene uptake that can alter quinolone cellular concentration and interaction with the target, or affect drug metabolism. Significant synthetic strategies have been employed to modify the quinolone scaffold and/or develop novel quinolones to overcome the resistance problem. This review discusses the development of quinolone antibiotics targeting DNA gyrase to overcome bacterial resistance and reduce toxicity. Moreover, structural activity relationship (SAR) data included in this review could be useful for the development of future generations of quinolone antibiotics.
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Affiliation(s)
| | - Siva S. Panda
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA
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10
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Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stępień Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Süssmuth RD, Ghilarov D. Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin. Nat Catal 2023; 6:52-67. [PMID: 36741192 PMCID: PMC9886550 DOI: 10.1038/s41929-022-00904-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/30/2022] [Indexed: 01/24/2023]
Abstract
The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between Escherichia coli topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and E. coli topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.
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Affiliation(s)
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Iraj Behroz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Marcel Kulike
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Zuzanna Pakosz-Stępień
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Lukasz Mazurek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Maria Kunert
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | | | - Bernhard Loll
- moloX GmbH, Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - John B Weston
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,John Innes Centre, Norwich Research Park, Norwich, UK
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11
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Kitamura RSA, Brito JCM, Silva de Assis HC, Gomes MP. Physiological responses and phytoremediation capacity of floating and submerged aquatic macrophytes exposed to ciprofloxacin. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:622-639. [PMID: 35904744 DOI: 10.1007/s11356-022-22253-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Ciprofloxacin (Cipro) water contamination is a global concern, having reached disturbing concentrations and threatening the aquatic ecosystems. We investigated the physiological responses and Cipro-phytoremediation capacity of one floating (Salvinia molesta D.S. Mitchell) and one submerged (Egeria densa Planch.) species of aquatic macrophytes. The plants were exposed to increased concentrations of Cipro (0, 1, 10, and 100 µg.Cipro.L-1) in artificially contaminated water for 96 and 168 h. Although the antibiotic affected the activities of mitochondrial electron transport chain enzymes, the resulting increases in H2O2 concentrations were not associated with oxidative damage or growth reductions, mainly due to the activation of antioxidant systems for both species. In addition to being tolerant to Cipro, after only 96 h, plants were able to reclaim more than 58% of that from the media. The phytoremediation capacity did not differ between the species, however, while S. molesta bioaccumulate, E. densa appears to metabolize Cipro in their tissues. Both macrophytes are indicated for Cipro-phytoremediation projects.
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Affiliation(s)
- Rafael Shinji Akiyama Kitamura
- Laboratório de Fisiologia de Plantas Sob Estresse, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal Do Paraná, Avenida Coronel Francisco H. Dos Santos, 100, Centro Politécnico Jardim das Américas, C.P. 19031, Curitiba , Paraná, 81531-980, Brazil
- Laboratório de Toxicologia Ambiental, Departamento de Farmacologia, Setor de Ciências Biológicas, Universidade Federal Do Paraná, Avenida Coronel Francisco H. Dos Santos, 100, Centro Politécnico Jardim das Américas, C.P. 19031, Curitiba , Paraná, 81531-980, Brazil
- Ecology and Conservation Program Post-Graduation, Federal University of Paraná, Avenue Coronel Francisco Heráclito dos Santos, 100, Jardim das Américas, Curitiba , Paraná, 81531-980, Brazil
| | - Júlio César Moreira Brito
- Fundação Ezequiel Dias, Rua Conde Pereira Carneiro, 80, Belo Horizonte, Minas Gerais, 30510-010, Brazil
| | - Helena Cristina Silva de Assis
- Laboratório de Toxicologia Ambiental, Departamento de Farmacologia, Setor de Ciências Biológicas, Universidade Federal Do Paraná, Avenida Coronel Francisco H. Dos Santos, 100, Centro Politécnico Jardim das Américas, C.P. 19031, Curitiba , Paraná, 81531-980, Brazil
| | - Marcelo Pedrosa Gomes
- Laboratório de Fisiologia de Plantas Sob Estresse, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal Do Paraná, Avenida Coronel Francisco H. Dos Santos, 100, Centro Politécnico Jardim das Américas, C.P. 19031, Curitiba , Paraná, 81531-980, Brazil.
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12
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Duke SO, Dayan FE. The search for new herbicide mechanisms of action: Is there a 'holy grail'? PEST MANAGEMENT SCIENCE 2022; 78:1303-1313. [PMID: 34796620 DOI: 10.1002/ps.6726] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/18/2021] [Indexed: 05/26/2023]
Abstract
New herbicide modes of action (MOAs) are in great demand because of the burgeoning evolution of resistance of weeds to existing commercial herbicides. This need has been exacerbated by the almost complete lack of introduction of herbicides with new MOAs for almost 40 years. There are many highly phytotoxic compounds with MOAs not represented by commercial herbicides, but neither these compounds nor structural analogues have been developed as herbicides for a variety of reasons. Natural products provide knowledge of many MOAs that are not being utilized by commercial herbicides. Other means of identifying new herbicide targets are discussed, including pharmaceutical target sites and metabolomic and proteomic information, as well as the use of artificial intelligence and machine learning to predict herbicidal compounds with new MOAs. Information about several newly discovered herbicidal compounds with new MOAs is summarized. The currently increased efforts of both established companies and start-up companies are likely to result in herbicides with new MOAs that can be used in herbicide resistance management within the next decade. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Stephen O Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Oxford, MS, USA
| | - Franck E Dayan
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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13
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Rei Liao JY, Friso G, Forsythe ES, Michel EJS, Williams AM, Boguraev SS, Ponnala L, Sloan DB, van Wijk KJ. Proteomics, phylogenetics, and co-expression analyses indicate novel interactions in the plastid CLP chaperone-protease system. J Biol Chem 2022; 298:101609. [PMID: 35065075 PMCID: PMC8889267 DOI: 10.1016/j.jbc.2022.101609] [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: 10/28/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/20/2022] Open
Abstract
The chloroplast chaperone CLPC1 unfolds and delivers substrates to the stromal CLPPRT protease complex for degradation. We previously used an in vivo trapping approach to identify interactors with CLPC1 in Arabidopsis thaliana by expressing a STREPII-tagged copy of CLPC1 mutated in its Walker B domains (CLPC1-TRAP) followed by affinity purification and mass spectrometry. To create a larger pool of candidate substrates, adaptors, or regulators, we carried out a far more sensitive and comprehensive in vivo protein trapping analysis. We identified 59 highly enriched CLPC1 protein interactors, in particular proteins belonging to families of unknown functions (DUF760, DUF179, DUF3143, UVR-DUF151, HugZ/DUF2470), as well as the UVR domain proteins EXE1 and EXE2 implicated in singlet oxygen damage and signaling. Phylogenetic and functional domain analyses identified other members of these families that appear to localize (nearly) exclusively to plastids. In addition, several of these DUF proteins are of very low abundance as determined through the Arabidopsis PeptideAtlas http://www.peptideatlas.org/builds/arabidopsis/ showing that enrichment in the CLPC1-TRAP was extremely selective. Evolutionary rate covariation indicated that the HugZ/DUF2470 family coevolved with the plastid CLP machinery suggesting functional and/or physical interactions. Finally, mRNA-based coexpression networks showed that all 12 CLP protease subunits tightly coexpressed as a single cluster with deep connections to DUF760-3. Coexpression modules for other trapped proteins suggested specific functions in biological processes, e.g., UVR2 and UVR3 were associated with extraplastidic degradation, whereas DUF760-6 is likely involved in senescence. This study provides a strong foundation for discovery of substrate selection by the chloroplast CLP protease system.
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Affiliation(s)
- Jui-Yun Rei Liao
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Evan S Forsythe
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Elena J S Michel
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Alissa M Williams
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sasha S Boguraev
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | | | - Daniel B Sloan
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA.
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14
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Huang CH, Liu YC, Shen JY, Lu FI, Shaw SY, Huang HJ, Chang CC. Repairing TALEN-mediated double-strand break by microhomology-mediated recombination in tobacco plastids generates abundant subgenomic DNA. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111028. [PMID: 34763881 DOI: 10.1016/j.plantsci.2021.111028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Transcription activator-like effector nuclease (TALEN) technology has been widely used to edit nuclear genomes in plants but rarely for editing organellar genomes. In addition, ciprofloxacin, commonly used to cause the double-strand break of organellar DNA for studying the repair mechanism in plants, confers no organellar selectivity and site-specificity. To demonstrate the feasibility of TALEN-mediated chloroplast DNA editing and to use it for studying the repair mechanism in plastids, we developed a TALEN-mediated editing technology fused with chloroplast transit peptide (cpTALEN) to site-specifically edit the rpoB gene via Agrobacteria-mediated transformation of tobacco leaf. Transgenic plants showed various degrees of chlorotic phenotype. Repairing damaged plastid DNA resulted in point mutation, large deletion and small inversion surrounding the rpoB gene by homologous recombination and/or microhomology-mediated recombination. In an albino line, microhomology-mediated recombination via a pair of 12-bp direct repeats between rpoC2 and ycf2 genes generated the chimeric ycf2-rpoC2 subgenome, with the level about 3- to 5-fold higher for subgenomic DNA than ycf2. Additionally, the expression of chimeric ycf2-rpoC2 transcripts versus ycf2 mRNA agreed well with the level of corresponding DNA. The ycf2-rpoC2 subgenomic DNA might independently and preferentially replicate in plastids.
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Affiliation(s)
- Chih-Hao Huang
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Chang Liu
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Jia-Yi Shen
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Fu-I Lu
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shyh-Yu Shaw
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan; Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ching-Chun Chang
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
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15
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Bellin L, Scherer V, Dörfer E, Lau A, Vicente AM, Meurer J, Hickl D, Möhlmann T. Cytosolic CTP Production Limits the Establishment of Photosynthesis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:789189. [PMID: 34917117 PMCID: PMC8669480 DOI: 10.3389/fpls.2021.789189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
CTP synthases (CTPS) comprise a protein family of the five members CTPS1-CTPS5 in Arabidopsis, all located in the cytosol. Specifically, downregulation of CTPS2 by amiRNA technology results in plants with defects in chlorophyll accumulation and photosynthetic performance early in development. CTP and its deoxy form dCTP are present at low levels in developing seedlings. Thus, under conditions of fast proliferation, the synthesis of CTP (dCTP) can become a limiting factor for RNA and DNA synthesis. The higher sensitivity of ami-CTPS2 lines toward the DNA-Gyrase inhibitor ciprofloxacin, together with reduced plastid DNA copy number and 16S and 23S chloroplast ribosomal RNA support this view. High expression and proposed beneficial biochemical features render CTPS2 the most important isoform for early seedling development. In addition, CTPS2 was identified as an essential enzyme in embryo development before, as knock-out mutants were embryo lethal. In line with this, ami-CTPS2 lines also exhibited reduced seed numbers per plant.
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Affiliation(s)
- Leo Bellin
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Vanessa Scherer
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Eva Dörfer
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Anne Lau
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Alexandre Magno Vicente
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Daniel Hickl
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Torsten Möhlmann
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Kaiserslautern, Germany
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16
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Okolo EN, Ugwu DI, Ezema BE, Ndefo JC, Eze FU, Ezema CG, Ezugwu JA, Ujam OT. New chalcone derivatives as potential antimicrobial and antioxidant agent. Sci Rep 2021; 11:21781. [PMID: 34741131 PMCID: PMC8571407 DOI: 10.1038/s41598-021-01292-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/14/2021] [Indexed: 01/11/2023] Open
Abstract
Seven chalcone derivatives were synthesized by the Claisen-Schmidt condensation. The structures of the compounds were confirmed by spectral data (Ultraviolet/visible, infrared, nuclear magnetic resonance and mass spectroscopy). The compounds were tested for their in silico and in vitro antimicrobial and antioxidant activities. The molecular docking assessments showed that all the compounds exhibited good binding affinity with the target microorganism proteins but, compounds 6e and 6g showed better binding affinity compared with the standards. The antimicrobial test revealed that all the compounds screened were active against Staphylococcus aureus and Bacillus subtilis and had minimum inhibitory concentrations (MIC) between 0.4 and 0.6 mg/mL. Compounds 6a, 6c and 6d had moderate activities on Salmonella typhi. Compounds 6b and 6c had moderate activity on Escherichia coli. Compound 6c had moderate activity on Aspergillus niger while compounds 6a and 6e had poor activity. All the compounds except compound 6e had no inhibition against Pseudomonas aeruginosa. The in-vitro antioxidant activity was assessed using ethylenediaminetetraacetate (EDTA) as the standard. Compounds 6c, 6e and 6g gave excellent inhibitory activity better than the standard. Compound 6a gave good activity at 500 μg/mL and 1000 μg/mL concentrations but, below the standard at 250 μg/mL and no inhibition at 125 μg/mL. Compound 6d had good inhibition at 500 μg/mL and 1000 μg/mL but, no inhibition at 125 μg/mL and 250 μg/mL. Compound 6b was found to be inactive in all the concentrations. Absorption, distribution, metabolism and excretion properties of the compounds were assessed using SwissADME. The results of lead likeness showed that compound 6e is a lead-like molecule.
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Affiliation(s)
- Emelda N Okolo
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - David I Ugwu
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria.
| | - Benjamin E Ezema
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - Joseph C Ndefo
- Department of Science Laboratory Technology, University of Nigeria, Nsukka, Nigeria
| | - Florence U Eze
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - Chidimma G Ezema
- National Center for Energy Research and Development, University of Nigeria, Nsukka, Nigeria
| | - James A Ezugwu
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - Oguejiofo T Ujam
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
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17
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Schatz-Daas D, Fertet A, Lotfi F, Gualberto JM. Assessment of Mitochondrial DNA Copy Number, Stability, and Repair in Arabidopsis. Methods Mol Biol 2021; 2363:301-319. [PMID: 34545500 DOI: 10.1007/978-1-0716-1653-6_20] [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: 02/23/2023]
Abstract
Mitochondrial functions depend on the proper maintenance and expression of the mitochondrial genome (mtDNA). Therefore, understanding mtDNA replication and repair requires methods to assess its integrity. Mutations or chemical treatments that affect processes involved in the maintenance or stability of the mtDNA can affect its global copy number, but also the relative abundance of different genomic regions or the frequency of illegitimate recombination across repeated sequences. These can be conveniently tested by quantitative PCR (qPCR). Arabidopsis thaliana offers several advantages for studying these processes, because of the extensive collections of mutants, natural accessions and other genetic resources available from stock centers. Here we describe protocols we routinely use to explore changes in mtDNA copy number and relative stoichiometry in Arabidopsis mutants of genes involved in the replication, repair and recombination of the mtDNA.
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Affiliation(s)
- Déborah Schatz-Daas
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Arnaud Fertet
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Frédérique Lotfi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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18
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Wallace MD, Debowski AW, Sukhoverkov KV, Mylne JS, Stubbs KA. Herbicidal activity of fluoroquinolone derivatives. PLANT DIRECT 2021; 5:e348. [PMID: 34541445 PMCID: PMC8438536 DOI: 10.1002/pld3.348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Development of herbicides with novel modes of action is crucial for weed control and to hinder herbicide resistance. An attractive novel herbicidal target is plant DNA gyrase, which has been demonstrated to be effectively inhibited by the known antimicrobial ciprofloxacin. Despite this good herbicidal activity, ciprofloxacin is not suitable as a herbicide due to its antimicrobial activity; therefore, a diverse library of analogues was analyzed to gain insight into the aspects required for herbicidal activity. This analysis revealed that significant structural modifications were tolerated and that the fluoride at C-6 and a cyclic amino group at C-7 were not crucial for herbicidal activity. The analysis also revealed that these modifications also affected the antibacterial activity with one compound demonstrating good herbicidal activity and weak antibacterial activity, against both Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Michael D. Wallace
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Aleksandra W. Debowski
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Biomedical SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Kirill V. Sukhoverkov
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaCrawleyWAAustralia
| | - Joshua S. Mylne
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaCrawleyWAAustralia
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | - Keith A. Stubbs
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
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19
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Abstract
Malaria persists as a major health problem due to the spread of drug resistance and the lack of effective vaccines. DNA gyrase is a well-validated and extremely effective therapeutic target in bacteria, and it is also known to be present in the apicoplast of malarial species, including Plasmodium falciparum. This raises the possibility that it could be a useful target for novel antimalarials. To date, characterization and screening of this gyrase have been hampered by difficulties in cloning and purification of the GyrA subunit, which is necessary together with GyrB for reconstitution of the holoenzyme. To overcome this, we employed a library of compounds with specificity for P. falciparum GyrB and assessed them in activity tests utilizing P. falciparum GyrB together with Escherichia coli GyrA to reconstitute a functional hybrid enzyme. Two inhibitory compounds were identified that preferentially inhibited the supercoiling activity of the hybrid enzyme over the E. coli enzyme. Of these, purpurogallin (PPG) was found to disrupt DNA binding to the hybrid gyrase complex and thus reduce the DNA-induced ATP hydrolysis of the enzyme. Binding studies indicated that PPG showed higher-affinity binding to P. falciparum GyrB than to the E. coli protein. We suggest that PPG achieves its inhibitory effect on gyrase through interaction with P. falciparum GyrB leading to disruption of DNA binding and, consequently, reduction of DNA-induced ATPase activity. The compound also showed an inhibitory effect against the malaria parasite in vitro and may be of interest for further development as an antimalarial agent.
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20
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Alamdari K, Fisher KE, Tano DW, Rai S, Palos K, Nelson ADL, Woodson JD. Chloroplast quality control pathways are dependent on plastid DNA synthesis and nucleotides provided by cytidine triphosphate synthase two. THE NEW PHYTOLOGIST 2021; 231:1431-1448. [PMID: 33993494 DOI: 10.1111/nph.17467] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Reactive oxygen species (ROS) produced in chloroplasts cause oxidative damage, but also signal to initiate chloroplast quality control pathways, cell death, and gene expression. The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant produces the ROS singlet oxygen in chloroplasts that activates such signaling pathways, but the mechanisms are largely unknown. Here we characterize one fc2 suppressor mutation and map it to CYTIDINE TRIPHOSPHATE SYNTHASE TWO (CTPS2), which encodes one of five enzymes in Arabidopsis necessary for de novo cytoplasmic CTP (and dCTP) synthesis. The ctps2 mutation reduces chloroplast transcripts and DNA content without similarly affecting mitochondria. Chloroplast nucleic acid content and singlet oxygen signaling are restored by exogenous feeding of the dCTP precursor deoxycytidine, suggesting ctps2 blocks signaling by limiting nucleotides for chloroplast genome maintenance. An investigation of CTPS orthologs in Brassicaceae showed CTPS2 is a member of an ancient lineage distinct from CTPS3. Complementation studies confirmed this analysis; CTPS3 was unable to compensate for CTPS2 function in providing nucleotides for chloroplast DNA and signaling. Our studies link cytoplasmic nucleotide metabolism with chloroplast quality control pathways. Such a connection is achieved by a conserved clade of CTPS enzymes that provide nucleotides for chloroplast function, thereby allowing stress signaling to occur.
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Affiliation(s)
- Kamran Alamdari
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Karen E Fisher
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - David W Tano
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Snigdha Rai
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Kyle Palos
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Jesse D Woodson
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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21
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Duan S, Hu L, Dong B, Jin HL, Wang HB. Signaling from Plastid Genome Stability Modulates Endoreplication and Cell Cycle during Plant Development. Cell Rep 2021; 32:108019. [PMID: 32783941 DOI: 10.1016/j.celrep.2020.108019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/08/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023] Open
Abstract
Plastid-nucleus genome coordination is crucial for plastid activity, but the mechanisms remain unclear. By treating Arabidopsis plants with the organellar genome-damaging agent ciprofloxacin, we found that plastid genome instability can alter endoreplication and the cell cycle. Similar results are observed in the plastid genome instability mutants of reca1why1why3. Cell division and embryo development are disturbed in the reca1why1why3 mutant. Notably, SMR5 and SMR7 genes, which encode cell-cycle kinase inhibitors, are upregulated in plastid genome instability plants, and the mutation of SMR7 can restore the endoreplication and growth phenotype of reca1why1why3 plants. Furthermore, we establish that the DNA damage response transcription factor SOG1 mediates the alteration of endoreplication and cell cycle triggered by plastid genome instability. Finally, we demonstrate that reactive oxygen species produced in plastids are important for plastid-nucleus genome coordination. Our findings uncover a molecular mechanism for the coordination of plastid and nuclear genomes during plant growth and development.
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Affiliation(s)
- Sujuan Duan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China; Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China
| | - Lili Hu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
| | - Beibei Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
| | - Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China.
| | - Hong-Bin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China; Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China.
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22
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Adetutu A, Olaniyi TD, Owoade OA. GC-MS analysis and in silico assessment of constituents of Psidium guajava leaf extract against DNA gyrase of Salmonella enterica serovar Typhi. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Sutormin DA, Galivondzhyan AK, Polkhovskiy AV, Kamalyan SO, Severinov KV, Dubiley SA. Diversity and Functions of Type II Topoisomerases. Acta Naturae 2021; 13:59-75. [PMID: 33959387 PMCID: PMC8084294 DOI: 10.32607/actanaturae.11058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 11/29/2022] Open
Abstract
The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect - supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Affiliation(s)
- D. A. Sutormin
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - A. K. Galivondzhyan
- Lomonosov Moscow State University, Moscow, 119991 Russia
- Institute of Molecular Genetics RAS, Moscow, 123182 Russia
| | - A. V. Polkhovskiy
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - S. O. Kamalyan
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - K. V. Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
- Waksman Institute for Microbiology, Piscataway, New Jersey, 08854 USA
| | - S. A. Dubiley
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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24
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Ramachandran B, Srinivasadesikan V, Chou TM, Jeyakanthan J, Lee SL. Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of Staphylococcus aureus. J Biomol Struct Dyn 2020; 40:4314-4327. [PMID: 33308046 DOI: 10.1080/07391102.2020.1856184] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The flavonoid derivatives possess various biological activities such as antimicrobial, anti-inflammatory and anticancer activities. The aim of present study is to identify the potential molecule from flavonoid derivatives against Staphylococcus aureus using atomistic simulation namely Molecular Docking, Quantum Chemical and Molecular Dynamics. The molecules Cpd58, Cpd65 and Cpd70 are identified as potential molecules through molecular docking approaches by exploring through the N - H…O hydrogen bonding interactions with Asn31 and Glu35 of Gyrase B. To confirm the intramolecular charge transfer in the flavonoid derivatives, Frontier Molecular Orbital (FMO) calculation was performed at M06/6-31g(d) level in gas phase. The lowest HOMO-LUMO gap was calculated for Cpd58, Cpd65 and Cpd70 among the selected compounds used in this study. Molecular dynamics simulation were carried out for Cpd58 and Cpd70 for a time period of 50 ns and found to be stable throughout the analysis. Therefore, the identified compounds are found to be a potent inhibitor for GyrB of S. aureus that can be validated by experimental studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Balajee Ramachandran
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Venkatesan Srinivasadesikan
- Division of Chemistry, Department of Sciences & Humanities, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Andhra Pradesh, India
| | - Tsz-Min Chou
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Shyi-Long Lee
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan
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25
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Hall CJ, Mackie ER, Gendall AR, Perugini MA, Soares da Costa TP. Review: amino acid biosynthesis as a target for herbicide development. PEST MANAGEMENT SCIENCE 2020; 76:3896-3904. [PMID: 32506606 DOI: 10.1002/ps.5943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
There are three amino acid biosynthesis pathways that are targeted by current herbicides, namely those leading to the production of aromatic amino acids, branched chain amino acids and glutamine. However, their efficacy is diminishing as a result of the increasing number of resistant weeds. Indeed, resistance to most classes of herbicides is on the rise, posing a significant threat to the utility of current herbicides to sustain effective weed management. This review provides an overview of potential herbicide targets within amino acid biosynthesis that remain unexploited commercially, and recent inhibitor discovery efforts. Despite contemporary approaches to herbicide discovery, such as chemical repurposing and the use of omics technologies, there have been no new products introduced to the market that inhibit amino acid biosynthesis over the past three decades. This highlights the chasm that exists between identifying a potent inhibitor and introducing a commercial herbicide. The unpredictability of a mode of action at the systemic level, as well as poor physicochemical properties, often contribute to a lack of progression beyond the target inhibition stage. Nevertheless, it will be important to overcome these obstacles for the development of new herbicides to protect our agricultural industry and ensure food security for an increasing world population. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Emily Rr Mackie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
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26
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Metwally NH, Abdallah SO, Mohsen MMA. Design, green one-pot synthesis and molecular docking study of novel N,N-bis(cyanoacetyl)hydrazines and bis-coumarins as effective inhibitors of DNA gyrase and topoisomerase IV. Bioorg Chem 2020; 97:103672. [PMID: 32145481 DOI: 10.1016/j.bioorg.2020.103672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/24/2020] [Accepted: 02/14/2020] [Indexed: 12/15/2022]
Abstract
A novel, quick, environmentally safe, and one-pot synthesis of a series of N,N-bis(cyanoacetyl)hydrazine derivatives, bis-imino-2H-chromenes and bis-2-oxo-2H-chromene derivatives have been designed. Some selected newly synthesized compounds were investigated in vitro for their antibacterial activity. Compound 5j is the most toxic compound against Staphylococcus aureus with activity index 171%, followed by compound 15b with activity index 136% compared to standard drug ampicillin. Moreover, compound 15a is the most toxic compound against Escherichia coli with activity index 111% compared to standard drug gentamicin. Minimum inhibitory concentration (MIC) was carried out for compounds with high antibacterial activity. Compound 5j has good MIC (7.8 μg/ml) against Staphylococcus aureus while 15a has good MIC (31.25 μg/ml) against Streptococcus mutans which is better than MIC of the standard drug ampicillin (MIC = 62.5 μg/ml). Compounds 5j, 5k, 15a, 15b and 15e which have good MIC values were introduced to enzyme assay against DNA gyrase and topoisomerase IV. The results showed that compound 15a can strongly inhibit DNA gyrase and topoisomerase IV (IC50 = 27.30 and 25.52 μM respectively), compared to methotrexate as the standard drug (IC50 = 29.01 and 23.55 μM respectively). Structure-activity relationships were also discussed based on the biological and docking simulation results.
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27
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Brieba LG. Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System. PLANTS 2019; 8:plants8120533. [PMID: 31766564 PMCID: PMC6963530 DOI: 10.3390/plants8120533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
Abstract
Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.
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Affiliation(s)
- Luis Gabriel Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato C.P. 36821, Mexico
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28
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Yan Y, Xu X, Shi C, Yan W, Zhang L, Wang G. Ecotoxicological effects and accumulation of ciprofloxacin in Eichhornia crassipes under hydroponic conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:30348-30355. [PMID: 31435908 DOI: 10.1007/s11356-019-06232-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Antibiotic residues pose a threat to the health of aquatic organisms. The effects and accumulation of antibiotic ciprofloxacin (CIP) in a floating macrophyte (Eichhornia crassipes) under hydroponic conditions were investigated. It was found that E. crassipes exposure to CIP (< 1000 μg L-1) could maintain a stable photosynthesis efficiency. In response to CIP stress, catalase and peroxidase activities of leaves were 7.24-37.51 nmol min-1 g-1 and 98.46-173.16 U g-1, respectively. The presence of CIP did not inhibit the growth of the plant. After 14 days of exposure, tender leaves became white and withered, ascribed to the decline of chlorophyll content and chlorophyll fluorescence parameters. The CIP concentrations, absorbed by E. crassipes, were highest in the roots, followed by white aerial parts and green aerial parts at CIP concentrations of 100 and 1000 μg L-1. These findings demonstrated that E. crassipes could absorb and tolerate CIP in a limited time-scale and imply an alternative solution for phytoremediation in water bodies contaminated with antibiotics.
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Affiliation(s)
- Yan Yan
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China
| | - Xiaoguang Xu
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China
| | - Chenfei Shi
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China
| | - Wang Yan
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China
| | - Limin Zhang
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China.
| | - Guoxiang Wang
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China.
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29
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Dayan FE. Current Status and Future Prospects in Herbicide Discovery. PLANTS 2019; 8:plants8090341. [PMID: 31514265 PMCID: PMC6783942 DOI: 10.3390/plants8090341] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022]
Abstract
Herbicides represent about 60% of the pesticides (by volume) used worldwide. The success of herbicides can be attributed in part to a relatively steady discovery of one unique mechanisms of action (MOA) every two years from the early 1950s to the mid-1980s. While this situation changed dramatically after the introduction of glyphosate-resistant crops, evolution of resistance to glyphosate has renewed the agrichemical industry interest in new chemistry interacting with novel target sites. This review analyses recent characterization of new herbicide target sites, the chemical classes developed to inhibit these target sites, and where appropriate the innovative technologies used in these discovery programs.
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Affiliation(s)
- Franck E Dayan
- Department of Bioagricultural Sciences and Pest Management, 1177 Campus Delivery, Colorado State University, Fort Collins, CO 80523, USA.
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30
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Hashimi SM. Albicidin, a potent DNA gyrase inhibitor with clinical potential. J Antibiot (Tokyo) 2019; 72:785-792. [PMID: 31451755 DOI: 10.1038/s41429-019-0228-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/23/2019] [Accepted: 08/14/2019] [Indexed: 11/09/2022]
Abstract
The emergence of multiple antibiotic-resistant bacteria is a serious global problem which requires the development of new effective antimicrobial therapeutics. Albicidin produced by the sugarcane pathogen Xanthomonas albilineans is a potent DNA gyrase inhibitor with inhibitory effects significantly better than most DNA gyrase inhibitors. Albicidin acts primarily by inhibiting the religation of the cleaved DNA intermediate during the gyrase catalytic sequence similar to quinolones. The clinical realization of albicidin has been hampered by limited production and its unsolved structure. In this review, the relationship between albicidin and sugarcane leaf-scald disease is described. Furthermore, the biosynthesis and resistance mechanisms of albicidin are discussed. Finally, recent efforts to solve the structure and produce albicidin in a heterologous host and chemically are summarized.
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Affiliation(s)
- Saeed Mujahid Hashimi
- Department of Basic Science, Biology Unit, Deanship of Preparatory Year and Supporting Studies, and Department of Stem Cell Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34212, Saudi Arabia.
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31
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Yan Y, Chen Y, Xu X, Zhang L, Wang G. Effects and Removal of the Antibiotic Sulfadiazine by Eichhornia crassipes: Potential Use for Phytoremediation. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2019; 103:342-347. [PMID: 31222425 DOI: 10.1007/s00128-019-02656-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/15/2019] [Indexed: 06/09/2023]
Abstract
The antibiotic sulfadiazine (SDZ) is a challenging threat to the health of aquatic organisms, as it frequently occurs in aquatic ecosystems. Tolerance mechanisms and accumulation of SDZ in a floating macrophyte (Eichhornia crassipes) under hydroponic conditions were investigated in this study to provide more insight into the SDZ removal process. Results show that the presence of 1 mg L-1 SDZ decreased the quickest and ranged from 669.45 to 165.34 μg L-1 from days 5 to 25. Exposing E. crassipes to SDZ ( < 1 mg L-1) maintained stable leaf photosynthetic efficiency. The overall increase in superoxide dismutase and peroxidase activities with SDZ treatments indicated that leaves were resistant. SDZ was absorbed by E. crassipes, following the sequence of root > aerial parts under all treatments. These findings suggest that E. crassipes has the ability to phytoremediation SDZ contaminated water.
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Affiliation(s)
- Yan Yan
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China
| | - Yun Chen
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China
| | - Xiaoguang Xu
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China
| | - Limin Zhang
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China.
| | - Guoxiang Wang
- School of Environment, Nanjing Normal University, 1, Wenyuan Road, Xianlin University District, Nanjing, 210023, People's Republic of China.
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32
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Khan SA, Asiri AM, Basisi HM, Asad M, Zayed ME, Sharma K, Wani MY. Synthesis and evaluation of Quinoline-3-carbonitrile derivatives as potential antibacterial agents. Bioorg Chem 2019; 88:102968. [DOI: 10.1016/j.bioorg.2019.102968] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/26/2019] [Accepted: 04/29/2019] [Indexed: 12/24/2022]
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Pérez Di Giorgio JA, Lepage É, Tremblay-Belzile S, Truche S, Loubert-Hudon A, Brisson N. Transcription is a major driving force for plastid genome instability in Arabidopsis. PLoS One 2019; 14:e0214552. [PMID: 30943245 PMCID: PMC6447228 DOI: 10.1371/journal.pone.0214552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Though it is an essential process, transcription can be a source of genomic instability. For instance, it may generate RNA:DNA hybrids as the nascent transcript hybridizes with the complementary DNA template. These hybrids, called R-loops, act as a major cause of replication fork stalling and DNA breaks. In this study, we show that lowering transcription and R-loop levels in plastids of Arabidopsis thaliana reduces DNA rearrangements and mitigates plastid genome instability phenotypes. This effect can be observed on a genome-wide scale, as the loss of the plastid sigma transcription factor SIG6 prevents DNA rearrangements by favoring conservative repair in the presence of ciprofloxacin-induced DNA damage or in the absence of plastid genome maintenance actors such as WHY1/WHY3, RECA1 and POLIB. Additionally, resolving R-loops by the expression of a plastid-targeted exogenous RNAse H1 produces similar results. We also show that highly-transcribed genes are more susceptible to DNA rearrangements, as increased transcription of the psbD operon by SIG5 correlates with more locus-specific rearrangements. The effect of transcription is not specific to Sigma factors, as decreased global transcription levels by mutation of heat-stress-induced factor HSP21, mutation of nuclear-encoded polymerase RPOTp, or treatment with transcription-inhibitor rifampicin all prevent the formation of plastid genome rearrangements, especially under induced DNA damage conditions.
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Affiliation(s)
| | - Étienne Lepage
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Samuel Tremblay-Belzile
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Sébastien Truche
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Audrey Loubert-Hudon
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Normand Brisson
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
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34
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Sutormin D, Rubanova N, Logacheva M, Ghilarov D, Severinov K. Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome. Nucleic Acids Res 2019; 47:1373-1388. [PMID: 30517674 PMCID: PMC6379681 DOI: 10.1093/nar/gky1222] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/19/2018] [Accepted: 11/23/2018] [Indexed: 12/31/2022] Open
Abstract
An important antibiotic target, DNA gyrase is an essential bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA polymerases. By altering the superhelical density, gyrase may regulate expression of bacterial genes. The information about how gyrase is distributed along genomic DNA and whether its distribution is affected by drugs is scarce. During catalysis, gyrase cleaves both DNA strands forming a covalently bound intermediate. By exploiting the ability of several topoisomerase poisons to stabilize this intermediate we developed a ChIP-Seq-based approach to locate, with single nucleotide resolution, DNA gyrase cleavage sites (GCSs) throughout the Escherichia coli genome. We identified an extended gyrase binding motif with phased 10-bp G/C content variation, indicating that bending ability of DNA contributes to gyrase binding. We also found that GCSs are enriched in extended regions located downstream of highly transcribed operons. Transcription inhibition leads to redistribution of gyrase suggesting that the enrichment is functionally significant. Our method can be applied for precise mapping of prokaryotic and eukaryotic type II topoisomerases cleavage sites in a variety of organisms and paves the way for future studies of various topoisomerase inhibitors.
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Affiliation(s)
- Dmitry Sutormin
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Natalia Rubanova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Maria Logacheva
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Malopolska Centre of Biotechnology, Jagiellonian University, 30387 Cracow, Poland
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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35
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Pedroza-García JA, Nájera-Martínez M, Mazubert C, Aguilera-Alvarado P, Drouin-Wahbi J, Sánchez-Nieto S, Gualberto JM, Raynaud C, Plasencia J. Role of pyrimidine salvage pathway in the maintenance of organellar and nuclear genome integrity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:430-446. [PMID: 30317699 DOI: 10.1111/tpj.14128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
Nucleotide biosynthesis proceeds through a de novo pathway and a salvage route. In the salvage route, free bases and/or nucleosides are recycled to generate the corresponding nucleotides. Thymidine kinase (TK) is the first enzyme in the salvage pathway to recycle thymidine nucleosides as it phosphorylates thymidine to yield thymidine monophosphate. The Arabidopsis genome contains two TK genes -TK1a and TK1b- that show similar expression patterns during development. In this work, we studied the respective roles of the two genes during early development and in response to genotoxic agents targeting the organellar or the nuclear genome. We found that the pyrimidine salvage pathway is crucial for chloroplast development and genome replication, as well as for the maintenance of its integrity, and is thus likely to play a crucial role during the transition from heterotrophy to autotrophy after germination. Interestingly, defects in TK activity could be partially compensated by supplementation of the medium with sugar, and this effect resulted from both the availability of a carbon source and the activation of the nucleotide de novo synthesis pathway, providing evidence for a compensation mechanism between two routes of nucleotide biosynthesis that depend on nutrient availability. Finally, we found differential roles of the TK1a and TK1b genes during the plant response to genotoxic stress, suggesting that different pools of nucleotides exist within the cells and are required to respond to different types of DNA damage. Altogether, our results highlight the importance of the pyrimidine salvage pathway, both during plant development and in response to genotoxic stress.
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Affiliation(s)
- José-Antonio Pedroza-García
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Manuela Nájera-Martínez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
| | - Christelle Mazubert
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Paulina Aguilera-Alvarado
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
| | - Jeannine Drouin-Wahbi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Sobeida Sánchez-Nieto
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
| | - José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084, Strasbourg, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Javier Plasencia
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
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36
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Le Ret M, Belcher S, Graindorge S, Wallet C, Koechler S, Erhardt M, Williams-Carrier R, Barkan A, Gualberto JM. Efficient Replication of the Plastid Genome Requires an Organellar Thymidine Kinase. PLANT PHYSIOLOGY 2018; 178:1643-1656. [PMID: 30305373 PMCID: PMC6288739 DOI: 10.1104/pp.18.00976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/01/2018] [Indexed: 05/17/2023]
Abstract
Thymidine kinase (TK) is a key enzyme of the salvage pathway that recycles thymidine nucleosides to produce deoxythymidine triphosphate. Here, we identified the single TK of maize (Zea mays), denoted CPTK1, as necessary in the replication of the plastidial genome (cpDNA), demonstrating the essential function of the salvage pathway during chloroplast biogenesis. CPTK1 localized to both plastids and mitochondria, and its absence resulted in an albino phenotype, reduced cpDNA copy number and a severe deficiency in plastidial ribosomes. Mitochondria were not affected, indicating they are less reliant on the salvage pathway. Arabidopsis (Arabidopsis thaliana) TKs, TK1A and TK1B, apparently resulted from a gene duplication after the divergence of monocots and dicots. Similar but less-severe effects were observed for Arabidopsis tk1a tk1b double mutants in comparison to those in maize cptk1 TK1B was important for cpDNA replication and repair in conditions of replicative stress but had little impact on the mitochondrial phenotype. In the maize cptk1 mutant, the DNA from the small single-copy region of the plastidial genome was reduced to a greater extent than other regions, suggesting preferential abortion of replication in this region. This was accompanied by the accumulation of truncated genomes that resulted, at least in part, from unfaithful microhomology-mediated repair. These and other results suggest that the loss of normal cpDNA replication elicits the mobilization of new replication origins around the rpoB (beta subunit of plastid-encoded RNA polymerase) transcription unit and imply that increased transcription at rpoB is associated with the initiation of cpDNA replication.
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Affiliation(s)
- Monique Le Ret
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Susan Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Stéfanie Graindorge
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Clémentine Wallet
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Mathieu Erhardt
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
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37
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Soczek KM, Grant T, Rosenthal PB, Mondragón A. CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage. eLife 2018; 7:41215. [PMID: 30457554 PMCID: PMC6286129 DOI: 10.7554/elife.41215] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/09/2018] [Indexed: 11/13/2022] Open
Abstract
Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.
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Affiliation(s)
- Katarzyna M Soczek
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Tim Grant
- Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom
| | - Peter B Rosenthal
- Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom.,Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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38
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Fuchs LK, Jenkins G, Phillips DW. Anthropogenic Impacts on Meiosis in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1429. [PMID: 30323826 PMCID: PMC6172301 DOI: 10.3389/fpls.2018.01429] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/07/2018] [Indexed: 05/18/2023]
Abstract
As the human population grows and continues to encroach on the natural environment, organisms that form part of such ecosystems are becoming increasingly exposed to exogenous anthropogenic factors capable of changing their meiotic landscape. Meiotic recombination generates much of the genetic variation in sexually reproducing species and is known to be a highly conserved pathway. Environmental stresses, such as variations in temperature, have long been known to change the pattern of recombination in both model and crop plants, but there are other factors capable of causing genome damage, infertility and meiotic abnormalities. Our agrarian expansion and our increasing usage of agrochemicals unintentionally affect plants via groundwater contamination or spray drift; our industrial developments release heavy metals into the environment; pathogens are spread by climate change and a globally mobile population; imperfect waste treatment plants are unable to remove chemical and pharmaceutical residues from sewage leading to the release of xenobiotics, all with potentially deleterious meiotic effects. In this review, we discuss the major classes of exogenous anthropogenic factors known to affect meiosis in plants, namely environmental stresses, agricultural inputs, heavy metals, pharmaceuticals and pathogens. The possible evolutionary fate of plants thrust into their new anthropogenically imposed environments are also considered.
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Affiliation(s)
| | | | - Dylan W. Phillips
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
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39
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Synthesis of spiro[indoline-3,4′-pyrano[3,2-c]quinolone]-3′-carbonitriles. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-017-2078-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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40
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Wallace MD, Waraich NF, Debowski AW, Corral MG, Maxwell A, Mylne JS, Stubbs KA. Developing ciprofloxacin analogues against plant DNA gyrase: a novel herbicide mode of action. Chem Commun (Camb) 2018; 54:1869-1872. [DOI: 10.1039/c7cc09518j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The development of ciprofloxacin analogues against plant DNA gyrase, a novel herbicidal target, with increased herbicidal activity and diminished antibacterial activity is described.
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Affiliation(s)
- Michael D. Wallace
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
| | - Nidda F. Waraich
- Department of Biological Chemistry
- John Innes Centre
- Norwich Research Park
- Norwich
- UK
| | - Aleksandra W. Debowski
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
- School of Biomedical Sciences
| | - Maxime G. Corral
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
- ARC Centre of Excellence in Plant Energy Biology
| | - Anthony Maxwell
- Department of Biological Chemistry
- John Innes Centre
- Norwich Research Park
- Norwich
- UK
| | - Joshua S. Mylne
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
- ARC Centre of Excellence in Plant Energy Biology
| | - Keith A. Stubbs
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
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41
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Le Page G, Gunnarsson L, Snape J, Tyler CR. Integrating human and environmental health in antibiotic risk assessment: A critical analysis of protection goals, species sensitivity and antimicrobial resistance. ENVIRONMENT INTERNATIONAL 2017; 109:155-169. [PMID: 28964562 DOI: 10.1016/j.envint.2017.09.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/04/2017] [Accepted: 09/10/2017] [Indexed: 05/21/2023]
Abstract
Antibiotics are vital in the treatment of bacterial infectious diseases but when released into the environment they may impact non-target organisms that perform vital ecosystem services and enhance antimicrobial resistance development with significant consequences for human health. We evaluate whether the current environmental risk assessment regulatory guidance is protective of antibiotic impacts on the environment, protective of antimicrobial resistance, and propose science-based protection goals for antibiotic manufacturing discharges. A review and meta-analysis was conducted of aquatic ecotoxicity data for antibiotics and for minimum selective concentration data derived from clinically relevant bacteria. Relative species sensitivity was investigated applying general linear models, and predicted no effect concentrations were generated for toxicity to aquatic organisms and compared with predicted no effect concentrations for resistance development. Prokaryotes were most sensitive to antibiotics but the range of sensitivities spanned up to several orders of magnitude. We show reliance on one species of (cyano)bacteria and the 'activated sludge respiration inhibition test' is not sufficient to set protection levels for the environment. Individually, neither traditional aquatic predicted no effect concentrations nor predicted no effect concentrations suggested to safeguard for antimicrobial resistance, protect against environmental or human health effects (via antimicrobial resistance development). Including data from clinically relevant bacteria and also more species of environmentally relevant bacteria in the regulatory framework would help in defining safe discharge concentrations for antibiotics for patient use and manufacturing that would protect environmental and human health. It would also support ending unnecessary testing on metazoan species.
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Affiliation(s)
- Gareth Le Page
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Lina Gunnarsson
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Jason Snape
- AstraZeneca, Global Environment, Alderley Park, Macclesfield, Cheshire SK10 4TF, UK; School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK.
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42
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Neoteric advancement in TB drugs and an overview on the anti-tubercular role of peptides through computational approaches. Microb Pathog 2017; 114:80-89. [PMID: 29174699 DOI: 10.1016/j.micpath.2017.11.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 11/21/2022]
Abstract
Tuberculosis (TB) is a devastating threat to human health whose treatment without the emergence of drug resistant Mycobacterium tuberculosis (M. tuberculosis) is the million-dollar question at present. The pathogenesis of M. tuberculosis has been extensively studied which represents unique defence strategies by infecting macrophages. Several anti-tubercular drugs with varied mode of action and administration from diversified sources have been used for the treatment of TB that later contributed to the emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB). However, few of potent anti-tubercular drugs are scheduled for clinical trials status in 2017-2018. Peptides of varied origins such as human immune cells and non-immune cells, bacteria, fungi, and venoms have been widely investigated as anti-tubercular agents for the replacement of existing anti-tubercular drugs in future. In the present review, we spotlighted not only on the mechanisms of action and mode of administration of currently available anti-tubercular drugs but also the recent comprehensive report of World Health Organization (WHO) on TB epidemic, diagnosis, prevention, and treatment. The major excerpt of the study also inspects the direct contribution of different computational tools during drug designing strategies against M. tuberculosis in order to grasp the interplay between anti-tubercular peptides and targeted bacterial protein. The potentiality of some of these anti-tubercular peptides as therapeutic agents unlocks a new portal for achieving the goal of end TB strategy.
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43
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Yang Z, Hou Q, Cheng L, Xu W, Hong Y, Li S, Sun Q. RNase H1 Cooperates with DNA Gyrases to Restrict R-Loops and Maintain Genome Integrity in Arabidopsis Chloroplasts. THE PLANT CELL 2017; 29:2478-2497. [PMID: 28939594 PMCID: PMC5774575 DOI: 10.1105/tpc.17.00305] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/05/2017] [Accepted: 09/20/2017] [Indexed: 05/19/2023]
Abstract
Maintaining organellar genome integrity is essential for eukaryotic cells, and many factors can threaten genome integrity. R-loops are DNA:RNA duplexes produced during transcription, with the nontemplated DNA forming a single-stranded region. R-loops function in the regulation of transcription, DNA replication, and DNA repair, but can also be susceptible to lesions that form double-stranded breaks and thus induce genome instability. From investigating the function of a plant chloroplast-localized R-loop removing enzyme AtRNH1C, we have found that it is responsible for plastid R-loop homeostasis, chloroplast genome instability, and development. Interactome analysis revealed that AtRNH1C associates with multiple chloroplast-localized DNA and RNA metabolism-related proteins, including the core DNA gyrases complex. The interaction between AtRNH1C and AtGyrases was critical for R-loop homeostasis in chloroplast and important to release the transcription-replication conflicts in the highly transcribed and replication originated cp-rDNA regions and thus to reduce the DNA damage. Our results reveal the plastid R-loop accumulation leads to chloroplast DNA instability and provide insight into the maintenance of genome integrity in chloroplasts, in which the evolutionarily conserved RNase H1 and DNA gyrase proteins are involved.
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Affiliation(s)
- Zhuo Yang
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Quancan Hou
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lingling Cheng
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xu
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuai Li
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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44
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Gualberto JM, Newton KJ. Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:225-252. [PMID: 28226235 DOI: 10.1146/annurev-arplant-043015-112232] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified. They are involved mainly in pathways of DNA repair by homologous recombination and mismatch repair, which appear to be essential for the faithful replication of the mitogenome. Mutations leading to the loss of any of these activities release error-prone repair pathways, resulting in increased ectopic recombination, genome instability, and heteroplasmy. We review the present state of knowledge of the genes and pathways underlying mitochondrial genome stability.
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Affiliation(s)
- José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France;
| | - Kathleen J Newton
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211;
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45
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Corral MG, Leroux J, Stubbs KA, Mylne JS. Herbicidal properties of antimalarial drugs. Sci Rep 2017; 7:45871. [PMID: 28361906 PMCID: PMC5374466 DOI: 10.1038/srep45871] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022] Open
Abstract
The evolutionary relationship between plants and the malarial parasite Plasmodium falciparum is well established and underscored by the P. falciparum apicoplast, an essential chloroplast-like organelle. As a result of this relationship, studies have demonstrated that herbicides active against plants are also active against P. falciparum and thus could act as antimalarial drug leads. Here we show the converse is also true; many antimalarial compounds developed for human use are highly herbicidal. We found that human antimalarial drugs (e.g. sulfadiazine, sulfadoxine, pyrimethamine, cycloguanil) were lethal to the model plant Arabidopsis thaliana at similar concentrations to market herbicides glufosinate and glyphosate. Furthermore, the physicochemical properties of these herbicidal antimalarial compounds were similar to commercially used herbicides. The implications of this finding that many antimalarial compounds are herbicidal proffers two novel applications: (i) using the genetically tractable A. thaliana to reveal mode-of-action for understudied antimalarial drugs, and (ii) co-opting antimalarial compounds as a new source for much needed herbicide lead molecules.
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Affiliation(s)
- Maxime G Corral
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia.,The ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Julie Leroux
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia.,The ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia.,The ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
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46
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Malik M, Mustaev A, Schwanz HA, Luan G, Shah N, Oppegard LM, de Souza EC, Hiasa H, Zhao X, Kerns RJ, Drlica K. Suppression of gyrase-mediated resistance by C7 aryl fluoroquinolones. Nucleic Acids Res 2016; 44:3304-16. [PMID: 26984528 PMCID: PMC4838383 DOI: 10.1093/nar/gkw161] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/02/2016] [Indexed: 11/16/2022] Open
Abstract
Fluoroquinolones form drug-topoisomerase-DNA complexes that rapidly block transcription and replication. Crystallographic and biochemical studies show that quinolone binding involves a water/metal-ion bridge between the quinolone C3-C4 keto-acid and amino acids in helix-4 of the target proteins, GyrA (gyrase) and ParC (topoisomerase IV). A recent cross-linking study revealed a second drug-binding mode in which the other end of the quinolone, the C7 ring system, interacts with GyrA. We report that addition of a dinitrophenyl (DNP) moiety to the C7 end of ciprofloxacin (Cip-DNP) reduced protection due to resistance substitutions in Escherichia coli GyrA helix-4, consistent with the existence of a second drug-binding mode not evident in X-ray structures of drug-topoisomerase-DNA complexes. Several other C7 aryl fluoroquinolones behaved in a similar manner with particular GyrA mutants. Treatment of E. coli cultures with Cip-DNP selectively enriched an uncommon variant, GyrA-A119E, a change that may impede binding of the dinitrophenyl group at or near the GyrA-GyrA interface. Collectively the data support the existence of a secondary quinolone-binding mode in which the quinolone C7 ring system interacts with GyrA; the data also identify C7 aryl derivatives as a new way to obtain fluoroquinolones that overcome existing GyrA-mediated quinolone resistance.
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Affiliation(s)
- Muhammad Malik
- Public Heath Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Science, 225 Warren Street, Newark, NJ 07103, USA
| | - Arkady Mustaev
- Public Heath Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Science, 225 Warren Street, Newark, NJ 07103, USA
| | - Heidi A Schwanz
- University of Iowa, Division of Medicinal & Natural Products Chemistry, College of Pharmacy, Iowa City, IA 52246, USA
| | - Gan Luan
- Public Heath Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Science, 225 Warren Street, Newark, NJ 07103, USA
| | - Nirali Shah
- Public Heath Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Science, 225 Warren Street, Newark, NJ 07103, USA
| | - Lisa M Oppegard
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Ernane C de Souza
- University of Iowa, Division of Medicinal & Natural Products Chemistry, College of Pharmacy, Iowa City, IA 52246, USA
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Xilin Zhao
- Public Heath Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Science, 225 Warren Street, Newark, NJ 07103, USA Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Science, 225 Warren Street, Newark, NJ 07103, USA State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Robert J Kerns
- University of Iowa, Division of Medicinal & Natural Products Chemistry, College of Pharmacy, Iowa City, IA 52246, USA
| | - Karl Drlica
- Public Heath Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Science, 225 Warren Street, Newark, NJ 07103, USA Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Science, 225 Warren Street, Newark, NJ 07103, USA
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