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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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2
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Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes (Basel) 2021; 12:genes12070963. [PMID: 34202810 PMCID: PMC8305020 DOI: 10.3390/genes12070963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.
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Methanothermobacter thermautotrophicus strain ΔH as a potential microorganism for bioconversion of CO2 to methane. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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4
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Tian Y, Zhang H, Zheng L, Li S, Hao H, Huang H. Effect of Zn Addition on the Cd-Containing Anaerobic Fermentation Process: Biodegradation and Microbial Communities. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16162998. [PMID: 31434308 PMCID: PMC6720270 DOI: 10.3390/ijerph16162998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 12/20/2022]
Abstract
Anaerobic fermentation is considered as a cost-effective way of biomass waste disposal. However, the compound heavy metals contained in the biomass may induce complex effects on anaerobic fermentation, which limit the utilization of metal-contaminated biowaste. In this study, the impacts of Cd and Zn addition on biogas properties, process stability, substrate biodegradation, enzyme activity, and microbial properties were studied. The results showed that the addition of Cd together with Zn (Cd+Zn) increased the maximum daily and cumulative biogas yields, and brought forward the gas production peak compared with the Cd-added group. Taking the whole fermentation process into account, the promotion effects of adding Zn into the Cd-containing fermentation system on biogas yields were mainly attributable to better process stability, higher average NH4+-N concentration in the later stage of fermentation, reduced COD (p < 0.05), and increased biodegradability of lignocelluloses (p < 0.01), especially cellulose (p < 0.05) and lignin (p < 0.01). Meanwhile, the addition of Zn promoted the coenzyme M activity (p < 0.05), and increased the absolute abundance of Methanothermobacter. The bacteria communities during the fermentation process were responsible for the degradation of lignocelluloses. The results demonstrated that the addition of appropriate Zn into the Cd-containing fermentation system enhanced the efficiency of anaerobic fermentation and utilization of biowaste.
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Affiliation(s)
- Yonglan Tian
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
| | - Huayong Zhang
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China.
| | - Lei Zheng
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
| | - Shusen Li
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
| | - He Hao
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
| | - Hai Huang
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
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Zhang H, Han X, Tian Y, Li Y, Yang K, Hao H, Chai Y, Xu X. Process analysis of anaerobic fermentation of Phragmites australis straw and cow dung exposing to elevated chromium (VI) concentrations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 224:414-424. [PMID: 30075309 DOI: 10.1016/j.jenvman.2018.07.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic fermentation is considered as a cost-effective way of biomass waste disposal. Chromium (Cr) is one of the heavy metals that often been blamed for unsatisfactory operation or failure of anaerobic fermentation. The impact of Cr (added as K2Cr2O7) on mesophilic anaerobic fermentation of Phragmites australis straw and cow dung was demonstrated by investigating the biogas properties, process stability, substrate degradation and enzyme activities during the fermentation process. The results showed that 30, 100 and 500 mg/L Cr6+ addition increased the cumulative biogas yields by up to 19.00%, 14.85% and 7.68% respectively, and brought forward the daily biogas yield peak. Meanwhile, the methane (CH4) content in the 30 (52.47%) and 100 (40.57%) mg/L Cr6+-added groups were generally higher than the control group (37.70%). Higher pH values (close to pH 7) and lower oxidation-reduction potential (ORP) values in the Cr6+-added groups after the 15th day indicated the better process stability compared to the control group. Taking the whole fermentation process into account, the promoting effect of Cr6+ addition on biogas yields was mainly attributable to better process stability, the enhanced degradation of lignin and hemicellulose, the transformation of intermediates into VFA, the higher coenzyme F420 activities and the efficient generation of CH4. These results demonstrate that an appropriate addition of Cr6+ could enhance the anaerobic fermentation which support the regulations utilizing of the Cr6+ contaminated biowaste.
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Affiliation(s)
- Huayong Zhang
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, China.
| | - Xiaoxi Han
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, China
| | - Yonglan Tian
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, China
| | - Ying Li
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, China
| | - Kun Yang
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, China
| | - He Hao
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, China
| | - Yang Chai
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, China
| | - Xiang Xu
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, China
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Identification of the Radical SAM Enzymes Involved in the Biosynthesis of Methanopterin and Coenzyme F 420 in Methanogens. Methods Enzymol 2018; 606:461-483. [DOI: 10.1016/bs.mie.2018.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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AlMatar M, AlMandeal H, Var I, Kayar B, Köksal F. New drugs for the treatment of Mycobacterium tuberculosis infection. Biomed Pharmacother 2017; 91:546-558. [PMID: 28482292 DOI: 10.1016/j.biopha.2017.04.105] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 03/29/2017] [Accepted: 04/23/2017] [Indexed: 12/25/2022] Open
Abstract
Tuberculosis presents a grave challenge to health, globally instigating 1.5 million mortalities each year. Following the breakthrough of first-line anti-TB medication, the number of mortalities reduced greatly; nonetheless, the swift appearance of tuberculosis which was drug-resistant, as well as the capability of the bacterium to survive and stay dormant are a considerable problem for public health. In order to address this issue, several novel possible candidates for tuberculosis therapy have been subjected to clinical trials of late. The novel antimycobacterial agents are acquired from different categories of medications, operate through a range of action systems, and are at various phases of advancement. We therefore talk about the present methods of treating tuberculosis and novel anti-TB agents with their action method, in order to advance awareness of these new compounds and medications.
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Affiliation(s)
- Manaf AlMatar
- Department of Biotechnology, Institute of Natural and Applied Sciences (Fen Bilimleri Enstitüsü), Cukurova University, Adana, Turkey.
| | - Husam AlMandeal
- Universitätsklinikum des Saarlandes, Gebäude 90, Kirrberger Straße, D-66421, Homburg, Germany
| | - Işıl Var
- Department of Food Engineering, Agricultural Faculty, Cukurova University, Adana, Turkey
| | - Begüm Kayar
- Department of Medical Microbiology, Faculty of Medicine, Çukurova University, Adana, Turkey
| | - Fatih Köksal
- Department of Medical Microbiology, Faculty of Medicine, Çukurova University, Adana, Turkey
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8
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Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. Microbiol Mol Biol Rev 2016; 80:451-93. [PMID: 27122598 DOI: 10.1128/mmbr.00070-15] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
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Villahermosa D, Corzo A, Garcia-Robledo E, González JM, Papaspyrou S. Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms. PLoS One 2016; 11:e0149096. [PMID: 26872267 PMCID: PMC4752510 DOI: 10.1371/journal.pone.0149096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/27/2016] [Indexed: 11/18/2022] Open
Abstract
Nitrate decreases sulfide release in wastewater treatment plants (WWTP), but little is known on how it affects the microzonation and kinetics of related microbial processes within the biofilm. The effect of nitrate addition on these properties for sulfate reduction, sulfide oxidation, and oxygen respiration were studied with the use of microelectrodes in microaerophilic wastewater biofilms. Mass balance calaculations and community composition analysis were also performed. At basal WWTP conditions, the biofilm presented a double-layer system. The upper microaerophilic layer (~300 μm) showed low sulfide production (0.31 μmol cm-3 h-1) and oxygen consumption rates (0.01 μmol cm-3 h-1). The anoxic lower layer showed high sulfide production (2.7 μmol cm-3 h-1). Nitrate addition decreased net sulfide production rates, caused by an increase in sulfide oxidation rates (SOR) in the upper layer, rather than an inhibition of sulfate reducing bacteria (SRB). This suggests that the indigenous nitrate reducing-sulfide oxidizing bacteria (NR-SOB) were immediately activated by nitrate. The functional vertical structure of the biofilm changed to a triple-layer system, where the previously upper sulfide-producing layer in the absence of nitrate split into two new layers: 1) an upper sulfide-consuming layer, whose thickness is probably determined by the nitrate penetration depth within the biofilm, and 2) a middle layer producing sulfide at an even higher rate than in the absence of nitrate in some cases. Below these layers, the lower net sulfide-producing layer remained unaffected. Net SOR varied from 0.05 to 0.72 μmol cm-3 h-1 depending on nitrate and sulfate availability. Addition of low nitrate concentrations likely increased sulfate availability within the biofilm and resulted in an increase of both net sulfate reduction and net sulfide oxidation by overcoming sulfate diffusional limitation from the water phase and the strong coupling between SRB and NR-SOB syntrophic relationship.
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Affiliation(s)
- Desirée Villahermosa
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n, 11510-Puerto Real, Cádiz, Spain
| | - Alfonso Corzo
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n, 11510-Puerto Real, Cádiz, Spain
- * E-mail:
| | - Emilio Garcia-Robledo
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n, 11510-Puerto Real, Cádiz, Spain
| | - Juan M. González
- Instituto de Recursos Naturales y Agrobiología, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012-Sevilla, Spain
| | - Sokratis Papaspyrou
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n, 11510-Puerto Real, Cádiz, Spain
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10
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Shea MT, Walter ME, Duszenko N, Ducluzeau AL, Aldridge J, King SK, Buan NR. pNEB193-derived suicide plasmids for gene deletion and protein expression in the methane-producing archaeon, Methanosarcina acetivorans. Plasmid 2016; 84-85:27-35. [PMID: 26876941 DOI: 10.1016/j.plasmid.2016.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 02/10/2016] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
Gene deletion and protein expression are cornerstone procedures for studying metabolism in any organism, including methane-producing archaea (methanogens). Methanogens produce coenzymes and cofactors not found in most bacteria, therefore it is sometimes necessary to express and purify methanogen proteins from the natural host. Protein expression in the native organism is also useful when studying post-translational modifications and their effect on gene expression or enzyme activity. We have created several new suicide plasmids to complement existing genetic tools for use in the methanogen, Methanosarcina acetivorans. The new plasmids are derived from the commercially available Escherichia coli plasmid, pNEB193, and cannot replicate autonomously in methanogens. The designed plasmids facilitate markerless gene deletion, gene transcription, protein expression, and purification of proteins with cleavable affinity tags from the methanogen, M. acetivorans.
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Affiliation(s)
- Mitchell T Shea
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Mary E Walter
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nikolas Duszenko
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Anne-Lise Ducluzeau
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Jared Aldridge
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Shannon K King
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nicole R Buan
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
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Lanz ND, Booker SJ. Auxiliary iron-sulfur cofactors in radical SAM enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1316-34. [PMID: 25597998 DOI: 10.1016/j.bbamcr.2015.01.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 11/19/2022]
Abstract
A vast number of enzymes are now known to belong to a superfamily known as radical SAM, which all contain a [4Fe-4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5'-deoxyadenosyl radical. The 5'-deoxyadenosyl radical then abstracts a target substrate hydrogen atom, initiating a wide variety of radical-based transformations. A subset of radical SAM enzymes contains one or more additional iron-sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of radical SAM enzymes that harbor auxiliary iron-sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
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12
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Raoof A, Depledge P, Hamilton NM, Hamilton NS, Hitchin JR, Hopkins GV, Jordan AM, Maguire LA, McGonagle AE, Mould DP, Rushbrooke M, Small HF, Smith KM, Thomson GJ, Turlais F, Waddell ID, Waszkowycz B, Watson AJ, Ogilvie DJ. Toxoflavins and deazaflavins as the first reported selective small molecule inhibitors of tyrosyl-DNA phosphodiesterase II. J Med Chem 2013; 56:6352-70. [PMID: 23859074 DOI: 10.1021/jm400568p] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently discovered enzyme tyrosyl-DNA phosphodiesterase 2 (TDP2) has been implicated in the topoisomerase-mediated repair of DNA damage. In the clinical setting, it has been hypothesized that TDP2 may mediate drug resistance to topoisomerase II (topo II) inhibition by etoposide. Therefore, selective pharmacological inhibition of TDP2 is proposed as a novel approach to overcome intrinsic or acquired resistance to topo II-targeted drug therapy. Following a high-throughput screening (HTS) campaign, toxoflavins and deazaflavins were identified as the first reported sub-micromolar and selective inhibitors of this enzyme. Toxoflavin derivatives appeared to exhibit a clear structure-activity relationship (SAR) for TDP2 enzymatic inhibition. However, we observed a key redox liability of this series, and this, alongside early in vitro drug metabolism and pharmacokinetics (DMPK) issues, precluded further exploration. The deazaflavins were developed from a singleton HTS hit. This series showed distinct SAR and did not display redox activity; however low cell permeability proved to be a challenge.
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Affiliation(s)
- Ali Raoof
- Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester M20 4BX, U.K.
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13
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Decamps L, Philmus B, Benjdia A, White R, Begley TP, Berteau O. Biosynthesis of F0, Precursor of the F420 Cofactor, Requires a Unique Two Radical-SAM Domain Enzyme and Tyrosine as Substrate. J Am Chem Soc 2012; 134:18173-6. [DOI: 10.1021/ja307762b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laure Decamps
- Institut National de la Recherche Agronomique, UMR 1319 Micalis, F-78350
Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, F-78350 Jouy-en-Josas,
France
| | - Benjamin Philmus
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Alhosna Benjdia
- Department
of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse
29, 69120 Heidelberg, Germany
| | - Robert White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United
States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Olivier Berteau
- Institut National de la Recherche Agronomique, UMR 1319 Micalis, F-78350
Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, F-78350 Jouy-en-Josas,
France
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14
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More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:973848. [PMID: 21559116 PMCID: PMC3087415 DOI: 10.1155/2011/973848] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 12/07/2010] [Accepted: 02/18/2011] [Indexed: 12/19/2022]
Abstract
The hydrogenotrophic methanogens Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus can easily be mass cultured. They have therefore been used almost exclusively to study the biochemistry of methanogenesis from H2 and CO2, and the genomes of these two model organisms have been sequenced. The close relationship of the two organisms is reflected in their genomic architecture and coding potential. Within the 1,607 protein coding sequences (CDS) in common, we identified approximately 200 CDS required for the synthesis of the enzymes, coenzymes, and prosthetic groups involved in CO2 reduction to methane and in coupling this process with the phosphorylation of ADP. Approximately 20 additional genes, such as those for the biosynthesis of F430 and methanofuran and for the posttranslational modifications of the two methyl-coenzyme M reductases, remain to be identified.
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Choi KP, Kendrick N, Daniels L. Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F(420) and FO biosynthesis. J Bacteriol 2002; 184:2420-8. [PMID: 11948155 PMCID: PMC134996 DOI: 10.1128/jb.184.9.2420-2428.2002] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using the nitroimidazopyran-based antituberculosis drug PA-824 as a selective agent, transposon-generated Mycobacterium bovis strain BCG (M. bovis) mutants that could not make coenzyme F(420) were identified. Four independent mutants that could not make F(420) or the biosynthesis intermediate FO were examined more closely. These mutants contained transposons inserted in the M. bovis homologue of the Mycobacterium tuberculosis gene Rv1173, which we have named fbiC. Complementation of an M. bovis FbiC(-) mutant with fbiC restored the F(420) phenotype. These data demonstrate that fbiC is essential for F(420) production and that FbiC participates in a portion of the F(420) biosynthetic pathway between pyrimidinedione and FO. Homologues of fbiC were found in all 11 microorganisms that have been fully sequenced and that are known to make F(420). Four of these homologues (all from members of the aerobic actinomycetes) coded for proteins homologous over the entire length of the M. bovis FbiC, but in seven microorganisms two separate genes were found to code for proteins homologous with either the N-terminal or C-terminal portions of the M. bovis FbiC. Histidine-tagged FbiC overexpressed in Escherichia coli produced a fusion protein of the molecular mass predicted from the M. bovis BCG sequence (approximately 95,000 Da), as well as three other histidine-tagged proteins of significantly smaller size, which are thought to be proteolysis products of the FbiC fusion protein.
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Affiliation(s)
- Kwang-Pil Choi
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
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16
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Choi KP, Bair TB, Bae YM, Daniels L. Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F(420) biosynthesis by Mycobacterium bovis BCG. J Bacteriol 2001; 183:7058-66. [PMID: 11717263 PMCID: PMC95553 DOI: 10.1128/jb.183.24.7058-7066.2001] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three transposon Tn5367 mutagenesis vectors (phAE94, pPR28, and pPR29) were used to create a collection of insertion mutants of Mycobacterium bovis strain BCG. A strategy to select for transposon-generated mutants that cannot make coenzyme F(420) was developed using the nitroimidazopyran-based antituberculosis drug PA-824. One-third of 134 PA-824-resistant mutants were defective in F(420) accumulation. Two mutants that could not make F(420)-5,6 but which made the biosynthesis intermediate FO were examined more closely. These mutants contained transposons inserted in two adjacent homologues of Mycobacterium tuberculosis genes, which we have named fbiA and fbiB for F(420) biosynthesis. Homologues of fbiA were found in all seven microorganisms that have been fully sequenced and annotated and that are known to make F(420). fbiB homologues were found in all but one such organism. Complementation of the fbiA mutant with fbiAB and complementation of the fbiB mutant with fbiB both restored the F(420)-5,6 phenotype. Complementation of the fbiA mutant with fbiA or fbiB alone did not restore the F(420)-5,6 phenotype, but the fbiA mutant complemented with fbiA produced F(420)-2,3,4 at levels similar to F(420)-5,6 made by the wild-type strain, but produced much less F(420)-5. These data demonstrate that both genes are essential for normal F(420)-5,6 production and suggest that the fbiA mutation has a partial polar effect on fbiB. Reverse transcription-PCR data demonstrated that fbiA and fbiB constitute an operon. However, very low levels of fbiB mRNA are produced by the fbiA mutant, suggesting that a low-level alternative start site is located upstream of fbiB. The specific reactions catalyzed by FbiA and FbiB are unknown, but both function between FO and F(420)-5,6, since FO is made by both mutants.
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Affiliation(s)
- K P Choi
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
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Ebert S, Rieger PG, Knackmuss HJ. Function of coenzyme F420 in aerobic catabolism of 2,4, 6-trinitrophenol and 2,4-dinitrophenol by Nocardioides simplex FJ2-1A. J Bacteriol 1999; 181:2669-74. [PMID: 10217752 PMCID: PMC93703 DOI: 10.1128/jb.181.9.2669-2674.1999] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,4,6-Trinitrophenol (picric acid) and 2,4-dinitrophenol were readily biodegraded by the strain Nocardioides simplex FJ2-1A. Aerobic bacterial degradation of these pi-electron-deficient aromatic compounds is initiated by hydrogenation at the aromatic ring. A two-component enzyme system was identified which catalyzes hydride transfer to picric acid and 2,4-dinitrophenol. Enzymatic activity was dependent on NADPH and coenzyme F420. The latter could be replaced by an authentic preparation of coenzyme F420 from Methanobacterium thermoautotrophicum. One of the protein components functions as a NADPH-dependent F420 reductase. A second component is a hydride transferase which transfers hydride from reduced coenzyme F420 to the aromatic system of the nitrophenols. The N-terminal sequence of the F420 reductase showed high homology with an F420-dependent NADP reductase found in archaea. In contrast, no N-terminal similarity to any known protein was found for the hydride-transferring enzyme.
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Affiliation(s)
- S Ebert
- Institut für Mikrobiologie der Universität Stuttgart, Stuttgart, Germany
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Abstract
Methanococcus vannielii is capable of degrading purines to the extent that each of these purines may serve as the sole nitrogen source for growth. Results presented here demonstrate that purine degradation by M. vannielii is accomplished by a route similar to that described for clostridia. Various characteristics of the purine-degrading pathway of M. vannielii are described. Additionally, it is shown that M. vannielii does not extensively degrade exogenously supplied guanine if that compound is present at levels near or lower than those required to supply the cellular guanine requirement. Under those conditions, M. vannielii incorporates the intact guanine molecule into its guanine nucleotide pool. The benefits of a purine-degrading pathway to methanogens are discussed.
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Affiliation(s)
- E DeMoll
- Department of Microbiology and Immunology, Chandler Medical Center, University of Kentucky, Lexington 40536-0084
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Abstract
The incorporation of 13C- and 14C-labeled precursors into 5-deaza-7,8-didemethyl-8-hydroxyriboflavin (factor F0) was studied with growing cells of Methanobacterium thermoautotrophicum. 5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione was incorporated into the deazaflavin and into riboflavin without dilution. Tyrosine and 4-hydroxyphenylpyruvate were incorporated into the deazaflavin and into cellular protein. 4-Hydroxybenzaldehyde was not incorporated. A reaction mechanism is proposed for the formation of the deazaflavin chromophore from 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione and tyrosine or 4-hydroxyphenylpyruvate.
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Affiliation(s)
- B Reuke
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Garching, Germany
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Wächtershäuser G. Groundworks for an evolutionary biochemistry: the iron-sulphur world. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1992; 58:85-201. [PMID: 1509092 DOI: 10.1016/0079-6107(92)90022-x] [Citation(s) in RCA: 359] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Eisenreich W, Schwarzkopf B, Bacher A. Biosynthesis of nucleotides, flavins, and deazaflavins in Methanobacterium thermoautotrophicum. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)92866-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
The biosynthetic pathway for the generation of the methylated pterin in methanopterins was determined for the methanogenic bacteria Methanococcus volta and Methanobacterium formicicum. Extracts of M. volta were found to readily cleave L-7,8-dihydroneopterin to 7,8-dihydro-6-(hydroxymethyl)pterin, which was confirmed to be a precursor of the pterin portion of the methanopterin. [methylene-2H]-6-(Hydroxymethyl)pterin was incorporated into methanopterin by growing cells of M. volta to an extent of 30%. Both the C-11 and C-12 methyl groups of methanopterin originate from [methyl-2H3]methionine, as confirmed by the incorporation of two C2H3 groups into 6-ethyl-7-methylpterin, a pterin-containing fragment derived from methanopterin. Cells grown in the presence of [methylene-2H]-6-(hydroxymethyl)pterin, [ethyl-2H4]-6-[1 (RS)-hydroxyethyl]pterin, [methyl-2H3]-6- (hydroxymethyl)-7-methylpterin, [ethyl-2H4, methyl-2H3]-6-[1 (RS)-hydroxyethyl]-7-methylpterin, and [1-ethyl-3H]-6-[1 (RS)-hydroxyethyl]-7-methylpterin showed that only the non-7-methylated pterins were incorporated into methanopterin. Cells extracts of M. formicicum readily condensed synthetic [methylene-3H]-7,8-H2-6-(hydroxymethyl)pterin-PP with methaniline to generate demethylated methanopterin, which is then methylated to methanopterin by the cell extract in the presence of S-adenosylmethionine. These observations indicate that the pterin portion of methanopterin is biosynthetically derived from 7,8-H2-6-(hydroxymethyl)pterin, which is coupled to methaniline by a pathway analogous to the biosynthesis of folic acid. This pathway for the biosynthesis of methanopterin represents the first example of the modification of the specificity of a coenzyme through a methylation reaction.
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Affiliation(s)
- R H White
- Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061
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Biosynthesis of coenzyme F420 and methanopterin in Methanobacterium thermoautotrophicum. Arch Microbiol 1990. [DOI: 10.1007/bf00249078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Conversion of d-xylose into xylitol by immobilized cells of Candida pelliculosa and Methanobacterium sp. HU. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/0922-338x(89)90255-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Regeneration and retention of NADP (H) for xylitol production in an ionized membrane reactor. Biotechnol Lett 1985. [DOI: 10.1007/bf01040204] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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