1
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Gouws AC, Kruger HG, Gheysens O, Zeevaart JR, Govender T, Naicker T, Ebenhan T. Antibiotic-Derived Radiotracers for Positron Emission Tomography: Nuclear or "Unclear" Infection Imaging? Angew Chem Int Ed Engl 2022; 61:e202204955. [PMID: 35834311 PMCID: PMC9826354 DOI: 10.1002/anie.202204955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Indexed: 01/11/2023]
Abstract
The excellent features of non-invasive molecular imaging, its progressive technology (real-time, whole-body imaging and quantification), and global impact by a growing infrastructure for positron emission tomography (PET) scanners are encouraging prospects to investigate new concepts, which could transform clinical care of complex infectious diseases. Researchers are aiming towards the extension beyond the routinely available radiopharmaceuticals and are looking for more effective tools that interact directly with causative pathogens. We reviewed and critically evaluated (challenges or pitfalls) antibiotic-derived PET radiopharmaceutical development efforts aimed at infection imaging. We considered both radiotracer development for infection imaging and radio-antibiotic PET imaging supplementing other tools for pharmacologic drug characterization; overall, a total of 20 original PET radiotracers derived from eleven approved antibiotics.
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Affiliation(s)
- Arno Christiaan Gouws
- Catalysis and Peptide Research UnitUniversity of KwaZulu-NatalDurban4000South Africa
| | | | - Olivier Gheysens
- Department of Nuclear MedicineCliniques Universitaires Saint-Luc, and Institute of Clinical and Experimental ResearchUniversité Catholique de LouvainBrusselsBelgium
| | - Jan Rijn Zeevaart
- Nuclear Medicine Research Infrastructure NPCPretoria0001South Africa
- RadiochemistryThe South African Nuclear Energy CorporationBrits0420South Africa
- Preclinical Drug Development PlatformNorth West UniversityPotchefstroom2520South Africa
| | | | - Tricia Naicker
- Catalysis and Peptide Research UnitUniversity of KwaZulu-NatalDurban4000South Africa
| | - Thomas Ebenhan
- Nuclear Medicine Research Infrastructure NPCPretoria0001South Africa
- Preclinical Drug Development PlatformNorth West UniversityPotchefstroom2520South Africa
- Department of Nuclear MedicineUniversity of PretoriaPretoria0001South Africa
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2
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Paulowski L, Beckham KSH, Johansen MD, Berneking L, Van N, Degefu Y, Staack S, Sotomayor FV, Asar L, Rohde H, Aldridge BB, Aepfelbacher M, Parret A, Wilmanns M, Kremer L, Combrink K, Maurer FP. C25-modified rifamycin derivatives with improved activity against Mycobacterium abscessus. PNAS NEXUS 2022; 1:pgac130. [PMID: 36714853 PMCID: PMC9802118 DOI: 10.1093/pnasnexus/pgac130] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
Infections caused by Mycobacterium abscessus are difficult to treat due to its intrinsic resistance to most antibiotics. Formation of biofilms and the capacity of M. abscessus to survive inside host phagocytes further complicate eradication. Herein, we explored whether addition of a carbamate-linked group at the C25 position of rifamycin SV blocks enzymatic inactivation by ArrMab, an ADP-ribosyltransferase conferring resistance to rifampicin (RMP). Unlike RMP, 5j, a benzyl piperidine rifamycin derivative with a morpholino substituted C3 position and a naphthoquinone core, is not modified by purified ArrMab. Additionally, we show that the ArrMab D82 residue is essential for catalytic activity. Thermal profiling of ArrMab in the presence of 5j, RMP, or rifabutin shows that 5j does not bind to ArrMab. We found that the activity of 5j is comparable to amikacin against M. abscessus planktonic cultures and pellicles. Critically, 5j also exerts potent antimicrobial activity against M. abscessus in human macrophages and shows synergistic activity with amikacin and azithromycin.
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Affiliation(s)
| | | | | | | | - Nhi Van
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Yonatan Degefu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Sonja Staack
- European Molecular Biology Laboratory, 22607 Hamburg, Germany
| | - Flor Vasquez Sotomayor
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany,Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lucia Asar
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Annabel Parret
- European Molecular Biology Laboratory, 22607 Hamburg, Germany,Charles River Laboratories, 2340 Beerse, Belgium
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, 22607 Hamburg, Germany,University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 34293 Montpellier, France,INSERM, Institut de Recherche en Infectiologie de Montpellier, 34293 Montpellier, France
| | - Keith Combrink
- Department of Chemistry and Biochemistry, Texas A&M International University, Laredo, TX 77843, USA,Department of Chemistry, Blinn College, Bryan Campus, Brenham, TX 77833, USA
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3
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Gouws AC, Kruger HG, Gheysens O, Zeevaart JR, Govender T, Naiker T, Ebenhan T. Antibiotic‐Derived Radiotracers for Positron Emission Tomography: Nuclear or ‘Unclear’ Infection Imaging? Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Arno Christiaan Gouws
- University of KwaZulu-Natal School of Health Sciences Catalysis and Peptide Research Unit SOUTH AFRICA
| | - Hendrik Gerhardus Kruger
- University of KwaZulu-Natal School of Health Sciences Catalysis and Peptide Research Unit SOUTH AFRICA
| | - Olivier Gheysens
- Cliniques Universitaires Saint-Luc Department of Nuclear Medicine BELGIUM
| | - Jan Rijn Zeevaart
- North-West University Potchefstroom Campus: North-West University Preclinical Drug Development Platform SOUTH AFRICA
| | | | - Tricia Naiker
- University of KwaZulu-Natal School of Health Sciences Catalysis and Peptide Research Unit SOUTH AFRICA
| | - Thomas Ebenhan
- University of Pretoria Nuclear Medicine Steve Biko and Malherbe St 0001 Pretoria SOUTH AFRICA
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4
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Chen J, Zhang H, Guo Q, He S, Xu L, Zhang Z, Ma J, Chu H. In Vitro Activity of Rifabutin against Mycobacterium abscessus, Including Clarithromycin-Insusceptible Multidrug-Resistant Clinical Isolates. Clin Exp Pharmacol Physiol 2022; 49:767-775. [PMID: 35531776 DOI: 10.1111/1440-1681.13651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Abstract
The antibiotic options available for Mycobacterium abscessus (M. abscessus) infection are limited and no definitive therapeutic strategies have been formulated. The recent discovery that rifabutin is active against M. abscessus has raised interest in using rifabutin to treat this intractable disease. In this study, we evaluated the in vitro activity of rifabutin against 194 M. abscessus clinical isolates collected during 2012 January to 2017 December. As respected, rifabutin demonstrated considerably lower MICs against M. abscessus, with an MIC50 of 2μg/ml and MIC90 of 4μg/ml, respectively. Notably, the anti-M.abscessus activity was even stronger among clarithromycin-insusceptible strains. In addition, M. abscessus isolates with a rough morphotype were more sensitive to rifabutin compared with those forming smooth colonies when considered as a whole or in separate subspecies. Results from synergistic experiments revealed that the in vitro activity of rifabutin was significantly enhanced by the addition of amikacin, suggesting a promising strategy for M. abscessus infection combination treatment. Finally, five and three mutation patterns in rpoB and arr, respectively, were identified among the 194 strains through whole genome sequencing. However, none of them conferred rifabutin resistance. Our study is among the first to report the susceptibility of M. abscessus to rifabutin in vitro with a large amount of clinical isolates, suggesting that rifabutin is active, both alone and in combination, against M. abscessus and is worth considering as part of a combination treatment regimen for M. abscessus infections.
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Affiliation(s)
- Jianhui Chen
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Haonan Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Qi Guo
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Siyuan He
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Liyun Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhemin Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jian Ma
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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5
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Blocking Bacterial Naphthohydroquinone Oxidation and ADP-Ribosylation Improves Activity of Rifamycins against Mycobacterium abscessus. Antimicrob Agents Chemother 2021; 65:e0097821. [PMID: 34228543 PMCID: PMC8370238 DOI: 10.1128/aac.00978-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rifampicin is an effective drug for treating tuberculosis (TB) but is not used to treat Mycobacterium abscessus infections due to poor in vitro activity. While rifabutin, another rifamycin, has better anti-M. abscessus activity, its activity is far from the nanomolar potencies of rifamycins against Mycobacterium tuberculosis. Here, we asked (i) why is rifabutin more active against M. abscessus than rifampicin, and (ii) why is rifabutin's anti-M. abscessus activity poorer than its anti-TB activity? Comparative analysis of naphthoquinone- versus naphthohydroquinone-containing rifamycins suggested that the improved activity of rifabutin over rifampicin is linked to its less readily oxidizable naphthoquinone core. Although rifabutin is resistant to bacterial oxidation, metabolite and genetic analyses showed that this rifamycin is metabolized by the ADP-ribosyltransferase ArrMab like rifampicin, preventing it from achieving the nanomolar activity that it displays against M. tuberculosis. Based on the identified dual mechanism of intrinsic rifamycin resistance, we hypothesized that rifamycins more potent than rifabutin should contain the molecule's naphthoquinone core plus a modification that blocks ADP-ribosylation at its C-23. To test these predictions, we performed a blinded screen of a diverse collection of 189 rifamycins and identified two molecules more potent than rifabutin. As predicted, these compounds contained both a more oxidatively resistant naphthoquinone core and C-25 modifications that blocked ADP-ribosylation. Together, this work revealed dual bacterial metabolism as the mechanism of intrinsic resistance of M. abscessus to rifamycins and provides proof of concept for the repositioning of rifamycins for M. abscessus disease by developing derivatives that resist both bacterial oxidation and ADP-ribosylation.
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6
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Iwasaki RS, Batey RT. SPRINT: a Cas13a-based platform for detection of small molecules. Nucleic Acids Res 2020; 48:e101. [PMID: 32797156 PMCID: PMC7515716 DOI: 10.1093/nar/gkaa673] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/15/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
Recent efforts in biological engineering have made detection of nucleic acids in samples more rapid, inexpensive and sensitive using CRISPR-based approaches. We expand one of these Cas13a-based methods to detect small molecules in a one-batch assay. Using SHERLOCK-based profiling of in vitrotranscription (SPRINT), in vitro transcribed RNA sequence-specifically triggers the RNase activity of Cas13a. This event activates its non-specific RNase activity, which enables cleavage of an RNA oligonucleotide labeled with a quencher/fluorophore pair and thereby de-quenches the fluorophore. This fluorogenic output can be measured to assess transcriptional output. The use of riboswitches or proteins to regulate transcription via specific effector molecules is leveraged as a coupled assay that transforms effector concentration into fluorescence intensity. In this way, we quantified eight different compounds, including cofactors, nucleotides, metabolites of amino acids, tetracycline and monatomic ions in samples. In this manner, hundreds of reactions can be easily quantified in a few hours. This increased throughput also enables detailed characterization of transcriptional regulators, synthetic compounds that inhibit transcription, or other coupled enzymatic reactions. These SPRINT reactions are easily adaptable to portable formats and could therefore be used for the detection of analytes in the field or at point-of-care situations.
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Affiliation(s)
- Roman S Iwasaki
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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7
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Ganapathy US, Dartois V, Dick T. Repositioning rifamycins for Mycobacterium abscessus lung disease. Expert Opin Drug Discov 2019; 14:867-878. [PMID: 31195849 DOI: 10.1080/17460441.2019.1629414] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: The treatment of Mycobacterium abscessus lung disease faces significant challenges due to intrinsic antibiotic resistance. New drugs are needed to cure this incurable disease. The key anti-tubercular rifamycin, rifampicin, suffers from low potency against M. abscessus and is not used clinically. Recently, another member of the rifamycin class, rifabutin, was shown to be active against the opportunistic pathogen. Areas covered: In this review, the authors discuss the rifamycins as a reemerging drug class for treating M. abscessus infections. The authors focus on the differential potency of rifampicin and rifabutin against M. abscessus in the context of intrinsic antibiotic resistance and bacterial uptake and metabolism. Reports of rifamycin-based drug synergies and rifamycin potentiation by host-directed therapy are evaluated. Expert opinion: While repurposing rifabutin for M. abscessus lung disease may provide some immediate relief, the repositioning (chemical optimization) of rifamycins offers long-term potential for improving clinical outcomes. Repositioning will require a multifaceted approach involving renewed screening of rifamycin libraries, medicinal chemistry to improve 'bacterial cell pharmacokinetics', better models of bacterial pathophysiology and infection, and harnessing of drug synergies and host-directed therapy towards the development of a better drug regimen.
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Affiliation(s)
- Uday S Ganapathy
- a Center for Discovery and Innovation, Hackensack Meridian Health , Nutley , NJ , USA
| | - Véronique Dartois
- a Center for Discovery and Innovation, Hackensack Meridian Health , Nutley , NJ , USA
| | - Thomas Dick
- a Center for Discovery and Innovation, Hackensack Meridian Health , Nutley , NJ , USA
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8
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Miropolskaya N, Feklistov A, Nikiforov V, Kulbachinskiy A. Site-specific aptamer inhibitors of Thermus RNA polymerase. Biochem Biophys Res Commun 2017; 495:110-115. [PMID: 29097207 DOI: 10.1016/j.bbrc.2017.10.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 10/28/2017] [Indexed: 11/19/2022]
Abstract
Bacterial RNA polymerase (RNAP) is an RNA-synthesizing molecular machine and a target for antibiotics. In transcription, RNAP can interact with DNA sequence-specifically, during promoter recognition by the σ-containing holoenzyme, or nonspecifically, during productive RNA elongation by the core RNAP. We describe high-affinity single-stranded DNA aptamers that are specifically recognized by the core RNAP from Thermus aquaticus. The aptamers interact with distinct epitopes inside the RNAP main channel, including the rifamycin pocket, and sense the binding of other RNAP ligands such as rifamycin and the σA subunit. The aptamers inhibit RNAP activity and can thus be used for functional studies of transcription and development of novel RNAP inhibitors.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Andrey Feklistov
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vadim Nikiforov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia.
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9
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Patel MB, Garrad EC, Stavri A, Gokel MR, Negin S, Meisel JW, Cusumano Z, Gokel GW. Hydraphiles enhance antimicrobial potency against Escherichia coli, Pseudomonas aeruginosa, and Bacillus subtilis. Bioorg Med Chem 2016; 24:2864-70. [PMID: 27166575 DOI: 10.1016/j.bmc.2016.04.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/19/2016] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
Hydraphiles are synthetic amphiphiles that form ion-conducting pores in liposomal membranes. These pores exhibit open-close behavior when studied by planar bilayer conductance techniques. In previous work, we showed that when co-administered with various antibiotics to the DH5α strain of Escherichia coli, they enhanced the drug's potency. We report here potency enhancements at low concentrations of hydraphiles for the structurally and mechanistically unrelated antibiotics erythromycin, kanamycin, rifampicin, and tetracycline against Gram negative E. coli (DH5α and K-12) and Pseudomonas aeruginosa, as well as Gram positive Bacillus subtilis. Earlier work suggested that potency increases correlated to ion transport function. The data presented here comport with the function of hydraphiles to enhance membrane permeability in addition to, or instead of, their known function as ion conductors.
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Affiliation(s)
- Mohit B Patel
- Center for Nanoscience, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA; Department of Biology, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA
| | - Evan C Garrad
- Department of Biology, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA
| | - Ariel Stavri
- Department of Biology, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA
| | - Michael R Gokel
- Upaya Pharmaceuticals, LLC, 4633 World Pkwy. Cir., Berkeley, MO 63134, USA; Center for Nanoscience, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA
| | - Saeedeh Negin
- Center for Nanoscience, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA; Department of Chemistry & Biochemistry, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA
| | - Joseph W Meisel
- Center for Nanoscience, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA; Department of Chemistry & Biochemistry, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA
| | - Zachary Cusumano
- Department of Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - George W Gokel
- Center for Nanoscience, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA; Department of Chemistry & Biochemistry, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA; Department of Biology, University of Missouri-St. Louis, 1 University Blvd., St. Louis, MO 63121, USA; Upaya Pharmaceuticals, LLC, 4633 World Pkwy. Cir., Berkeley, MO 63134, USA.
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10
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Zheng X, Bi C, Li Z, Podariu M, Hage DS. Analytical methods for kinetic studies of biological interactions: A review. J Pharm Biomed Anal 2015; 113:163-80. [PMID: 25700721 PMCID: PMC4516701 DOI: 10.1016/j.jpba.2015.01.042] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 01/13/2023]
Abstract
The rates at which biological interactions occur can provide important information concerning the mechanism and behavior of these processes in living systems. This review discusses several analytical methods that can be used to examine the kinetics of biological interactions. These techniques include common or traditional methods such as stopped-flow analysis and surface plasmon resonance spectroscopy, as well as alternative methods based on affinity chromatography and capillary electrophoresis. The general principles and theory behind these approaches are examined, and it is shown how each technique can be utilized to provide information on the kinetics of biological interactions. Examples of applications are also given for each method. In addition, a discussion is provided on the relative advantages or potential limitations of each technique regarding its use in kinetic studies.
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Affiliation(s)
- Xiwei Zheng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Cong Bi
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Zhao Li
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Maria Podariu
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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11
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Negin S, Gokel MR, Patel MB, Sedinkin SL, Osborn DC, Gokel GW. The aqueous medium-dimethylsulfoxide conundrum in biological studies. RSC Adv 2015. [DOI: 10.1039/c4ra15217d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A series of straight and branched chain pyrogallol[4]arenes was studied and found to be essentially nontoxic to two strains of E. coli.
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Affiliation(s)
- Saeedeh Negin
- Center for Nanoscience
- University of Missouri-St. Louis
- St. Louis
- USA
- Dept. of Chemistry
| | - Michael R. Gokel
- Center for Nanoscience
- University of Missouri-St. Louis
- St. Louis
- USA
| | - Mohit B. Patel
- Dept. of Chemistry
- University of Missouri-St. Louis
- St. Louis
- USA
- Department of Biology
| | - Sergey L. Sedinkin
- Center for Nanoscience
- University of Missouri-St. Louis
- St. Louis
- USA
- Dept. of Chemistry
| | - David C. Osborn
- Center for Nanoscience
- University of Missouri-St. Louis
- St. Louis
- USA
| | - George W. Gokel
- Center for Nanoscience
- University of Missouri-St. Louis
- St. Louis
- USA
- Dept. of Chemistry
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12
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Gokel GW, Negin S. Synthetic ion channels: from pores to biological applications. Acc Chem Res 2013; 46:2824-33. [PMID: 23738778 DOI: 10.1021/ar400026x] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this Account, we describe the development of several diverse families of synthetic, membrane-active amphiphiles that form pores and facilitate transport within membrane bilayers. For the most part, the compounds are amphiphiles that insert into the bilayer and form pores either on their own or by self-assembly. The first family of synthetic ion channels prepared in our lab, the hydraphiles, used crown ethers as head groups and as a polar central element. In a range of biophysical studies, we showed that the hydraphiles formed unimolecular pores that spanned the bilayer. They mediated the transport of Na(+) and K(+) but were blocked by Ag(+). The hydraphiles are nonrectifying and disrupt ion homeostasis. As a result, these synthetic ion channels are toxic to various bacteria and yeast, a feature that has been used therapeutically in direct injection chemotherapy. We also developed a family of amphiphilic heptapeptide ion transporters that selected Cl(-) >10-fold over K(+) and showed voltage dependent gating. The formed pores were approximately dimeric, and variations in the N- and C-terminal anchor chains and the acids affected transport rates. Surprisingly, the longer N-terminal anchor chains led to less transport but greater Cl(-) selectivity. A proline residue, which is present in the ClC protein channel's conductance pore, proved to be critical for Cl(-) transport selectivity. Pyrogallol[4]arenes are macrocycles formed by acid-catalyzed condensation of four 1,2,3- trihydroxybenzenes with four aldehydes. The combination of 12 hydroxyl groups on one face of the macrocycle and four pendant alkyl chains conferred considerable amphiphilicity to these compounds. The pyrogallol[4]arenes inserted into bilayer membranes and conducted ions. Based on our experimental evidence, the ions passed through a self-assembled pore comprising four or five amphiphiles rather than passing through the central opening of a single macrocycle. Pyrogallol[4]arenes constructed with branched chains are also amphiphilic and active in membranes. The pyrogallol[4]arene with 3-pentyl sidechains formed a unique nanotube assembly and functioned as an ion channel in bilayer membranes. Finally, we showed that dianilides of either isophthalic or dipicolinic acids, compounds which have been extensively studied as anion binders, can self-assemble to form pores within bilayers. We called these dianilides tris-arenes and have shown that they readily bind to phosphate anions. These structures also mediated the transport of DNA plasmids through vital bilayer membranes in the bacterium Escherichia coli and in the yeast Saccharomyces cerevisiae . This transformation or transfection process occurred readily and without any apparent toxicity or mutagenicity.
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Affiliation(s)
- George W. Gokel
- Departments of †Chemistry & Biochemistry and ‡Biology, §Center for Nanoscience, University of Missouri—St. Louis, St. Louis, Missouri 63121, United States
| | - Saeedeh Negin
- Departments of †Chemistry & Biochemistry and ‡Biology, §Center for Nanoscience, University of Missouri—St. Louis, St. Louis, Missouri 63121, United States
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13
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Dey A, Chatterji D. Tracing the Variation in Physiological Response to Rifampicin Across the Microbial Spectrum. ACTA ACUST UNITED AC 2012. [DOI: 10.4167/jbv.2012.42.2.87] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Abhinav Dey
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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14
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Dey A, Verma AK, Chatterji D. Molecular insights into the mechanism of phenotypic tolerance to rifampicin conferred on mycobacterial RNA polymerase by MsRbpA. MICROBIOLOGY-SGM 2011; 157:2056-2071. [PMID: 21415119 DOI: 10.1099/mic.0.047480-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The protein MsRbpA from Mycobacterium smegmatis rescues RNA polymerase (RNAP) from the inhibitory effect of rifampicin (Rif). We have reported previously that MsRbpA interacts with the β-subunit of RNAP and that the effect of MsRbpA on Rif-resistant (Rif(R)) RNAP is minimal. Here we attempted to gain molecular insights into the mechanism of action of this protein with respect to its role in rescuing RNAP from Rif-mediated transcription inhibition. Our experimental approach comprised multiple-round transcription assays, fluorescence spectroscopy, MS and surface plasmon resonance in order to meet the above objective. Based on our molecular studies we propose here that Rif is released from its binding site in the RNAP-Rif complex in the presence of MsRbpA. Biophysical studies reveal that the location of MsRbpA on RNAP is at the junction of the β- and β'-subunits, close to the Rif-binding site and the (i+1) site on RNAP.
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Affiliation(s)
- Abhinav Dey
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Amit Kumar Verma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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15
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Liu L, Xu Y, Shea C, Fowler JS, Hooker JM, Tonge PJ. Radiosynthesis and bioimaging of the tuberculosis chemotherapeutics isoniazid, rifampicin and pyrazinamide in baboons. J Med Chem 2010; 53:2882-91. [PMID: 20205479 DOI: 10.1021/jm901858n] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The front-line tuberculosis (TB) chemotherapeutics isoniazid (INH), rifampicin (RIF), and pyrazinamide (PZA) have been labeled with carbon-11 and the biodistribution of each labeled drug has been determined in baboons using positron emission tomography (PET). Each radiosynthesis and formulation has been accomplished in 1 h, using [(11)C]CH(3)I to label RIF and [(11)C]HCN to label INH and PZA. Following iv administration, INH, PZA, RIF, and/or their radiolabeled metabolites clear rapidly from many tissues; however, INH, PZA, and/or their radiolabeled metabolites accumulate in the bladder while RIF and/or its radiolabeled metabolites accumulates in the liver and gall bladder, consistent with the known routes of excretion of the drugs. In addition, the biodistribution data demonstrate that the ability of the three drugs and their radiolabeled metabolites to cross the blood-brain barrier decreases in the order PZA > INH > RIF, although in all cases the estimated drug concentrations are greater than the minimum inhibitory concentration (MIC) values for inhibiting bacterial growth of Mycobacterium tuberculosis (MTB). The pharmacokinetic (PK) and drug distribution data have important implications for treatment of disseminated TB in the brain and pave the way for imaging the distribution of the pathogen in vivo.
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Affiliation(s)
- Li Liu
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
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16
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Tremblay JM, Unruh JR, Johnson CK, Yarbrough LR. Mechanism of interaction of PITPα with membranes: Conformational changes in the C-terminus associated with membrane binding. Arch Biochem Biophys 2005; 444:112-20. [PMID: 16309627 DOI: 10.1016/j.abb.2005.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 09/02/2005] [Accepted: 09/09/2005] [Indexed: 10/25/2022]
Abstract
Eukaryotic phosphatidylinositol transfer proteins (PITPs) are composed predominantly of small ( approximately 32 kDa) soluble proteins that bind and transfer a single phospholipid, normally phosphatidylinositol or phosphatidycholine. Two forms, PITPalpha and PITPbeta, which share approximately 80% amino acid sequence similarity, are known. Rat PITPalpha was labeled at specific single reactive Cys residues with I-AEDANS and used to examine PITP-membrane interactions. Upon binding to phospholipid vesicles, PITP labeled with AEDANS at the C-terminus, a region postulated to be involved in membrane binding, shows significant decreases in both steady-state and dynamic fluorescence anisotropy. In contrast, PITPs labeled with AEDANS at sites located distal to the C-terminus show increases in both steady-state and dynamic anisotropy. These results suggest that interaction of PITP with membrane surfaces leads to significant alterations in conformation and perhaps melting of the C-terminal helix.
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Affiliation(s)
- Jacqueline M Tremblay
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, 66160-7421, USA
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17
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Kulbachinskiy A, Feklistov A, Krasheninnikov I, Goldfarb A, Nikiforov V. Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. ACTA ACUST UNITED AC 2005; 271:4921-31. [PMID: 15606780 DOI: 10.1111/j.1432-1033.2004.04461.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The process of transcription is accompanied by complex structural rearrangements of RNAP. Despite the recent progress in structural studies of RNAP, detailed mechanisms of conformational changes of RNAP that occur at different stages of transcription remain unknown. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. Using in vitro selection methods, we obtained 13 classes of ssDNA aptamers against Escherichia coli core RNAP. The minimal nucleic acid scaffold (an oligonucleotide construct imitating DNA and RNA in elongation complex), rifampicin and the sigma70-subunit inhibited binding of the aptamers to RNAP core but did not affect the dissociation rate of preformed RNAP-aptamer complexes. We argue that these ligands sterically block access of the aptamers to their binding sites within the main RNAP channel. In contrast, transcript cleavage factor GreB increased the rate of dissociation of preformed RNAP-aptamer complexes. This suggested that GreB that binds RNAP outside the main channel actively disrupts RNAP-aptamer complexes by inducing conformational changes in the channel. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme.
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18
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Zenkin N, Kulbachinskiy A, Bass I, Nikiforov V. Different rifampin sensitivities of Escherichia coli and Mycobacterium tuberculosis RNA polymerases are not explained by the difference in the beta-subunit rifampin regions I and II. Antimicrob Agents Chemother 2005; 49:1587-90. [PMID: 15793146 PMCID: PMC1068591 DOI: 10.1128/aac.49.4.1587-1590.2005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis RNA polymerase is 1,000-fold more sensitive to rifampin than Escherichia coli RNA polymerase. Chimeric E. coli RNA polymerase in which the beta-subunit segment encompassing rifampin regions I and II (amino acids [aa] 463 through 590) was replaced with the corresponding region from M. tuberculosis (aa 382 through 509) did not show an increased sensitivity to the antibiotic. Thus, the difference in amino acid sequence between the rifampin regions I and II of the two species does not account for the difference in rifampin sensitivity of the two polymerases.
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Affiliation(s)
- N Zenkin
- Institute of Molecular Genetics, Kurchatov Sq. 2, Moscow 123182, Russia
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19
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Knight JL, Mekler V, Mukhopadhyay J, Ebright RH, Levy RM. Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophys J 2004; 88:925-38. [PMID: 15542547 PMCID: PMC1305165 DOI: 10.1529/biophysj.104.050187] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We are developing distance-restrained docking strategies for modeling macromolecular complexes that combine available high-resolution structures of the components and intercomponent distance restraints derived from systematic fluorescence resonance energy transfer (FRET) measurements. In this article, we consider the problem of docking small-molecule ligands within macromolecular complexes. Using simulated FRET data, we have generated a series of benchmarks that permit estimation of model accuracy based on the quantity and quality of FRET-derived distance restraints, including the number, random error, systematic error, distance distribution, and radial distribution of FRET-derived distance restraints. We find that expected model accuracy is 10 A or better for models based on: i), > or =20 restraints with up to 15% random error and no systematic error, or ii), > or =20 restraints with up to 15% random error, up to 10% systematic error, and a symmetric radial distribution of restraints. Model accuracies can be improved to 5 A or better by increasing the number of restraints to > or =40 and/or by optimizing the distance distribution of restraints. Using experimental FRET data, we have defined the positions of the binding sites within bacterial RNA polymerase of the small-molecule inhibitors rifampicin (Rif) and rifamycin SV (Rif SV). The inferred binding sites for Rif and Rif SV were located with accuracies of, respectively, 7 and 10 A relative to the crystallographically defined binding site for Rif. These accuracies agree with expectations from the benchmark simulations and suffice to indicate that the binding sites for Rif and Rif SV are located within the RNA polymerase active-center cleft, overlapping the binding site for the RNA-DNA hybrid.
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Affiliation(s)
- Jennifer L Knight
- Department of Chemistry and Chemical Biology and the BioMaPS Institute for Quantitative Biology, and Howard Hughes Medical Institute, Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA
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20
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Sakakibara Y. Rifampin-induced initiation of chromosome replication in dnaR-deficient Escherichia coli cells. J Bacteriol 1996; 178:1242-7. [PMID: 8631698 PMCID: PMC177795 DOI: 10.1128/jb.178.5.1242-1247.1996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The dnaR130 mutant of Escherichia coli, which was thermosensitive in initiation of chromosome replication, was capable of thermoresistant DNA synthesis in the presence of rifampin at a low concentration that allowed almost normal RNA synthesis. The DNA synthesis in the presence of the drug depended on protein synthesis at the high temperature. The protein synthesis in the dnaR-deficient cells provided a potential for thermoresistant DNA synthesis to be induced at a high dose of the drug that almost completely prevented RNA synthesis. The induced synthesis was synchronously initiated from oriC and proceeded semiconservatively toward terC. The replication depended on the dnaA function, which was essential for normal initiation of replication from oriC. The capability for drug-induced replication was abolished by certain rifampin resistance mutations in the beta subunit of RNA polymerase. Thus, the drug can induce the dnaA-dependent initiation of replication in the dnaR-deficient cells through its effect on RNA polymerase. This result implies that the dnaR product is involved in the transcription obligatory for the initiation of replication of the bacterial chromosome.
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Affiliation(s)
- Y Sakakibara
- Department of Biochemistry and Cellular Biology, National Institute of Health, Tokyo, Japan
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21
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Logan K, Zhang J, Davis EA, Ackerman S. Drug inhibitors of RNA polymerase II transcription. DNA (MARY ANN LIEBERT, INC.) 1989; 8:595-604. [PMID: 2574659 DOI: 10.1089/dna.1989.8.595] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Transcription by RNA polymerase II occurs after formation of a transcription complex. This complex is assembled in stages by the interaction of transcription factors with the template and/or with each other. We report on the ability of six drugs to inhibit the assembly of the RNA polymerase II transcription complex. Assembly of the complex on the adenovirus major late promoter requires several transcription factors. The normal assembly process requires that the DNA first interact with TFIIA, then with TFIID, and finally with at least four additional transcription factors (one of which is RNA polymerase II). We observed that streptolydigin (10 micrograms/ml) inhibits association of ILA and IID, and at higher concentrations (100 micrograms/ml) inhibits that IIA/IID complex from binding to DNA. Streptovaricin (100 micrograms/ml) appears to inhibit the IIA/IID interaction with DNA and prevents reinitiation (at 500 micrograms/ml). Adriamycin (1 microgram/ml) inhibits the interaction of TFIID with the IIA/DNA complex and inhibits an additional event immediately prior to, or during, elongation. Daunorubicin may be an elongation inhibitor. Heparin at 10 micrograms/ml inhibits further assembly after the IIA/IID/DNA complex has formed, and at 100 micrograms/ml also inhibits a late event in the assembly process and blocks reinitiation. Rifamycin AF/013 (100 micrograms/ml) inhibits the early events necessary to form the IIA/IID/DNA complex and (at 10 micrograms/ml) an assembly event following formation of the IIA/IID/DNA complex. Therefore, these compounds should be useful as probes for further examination of the assembly process.
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Affiliation(s)
- K Logan
- Biology Department, University of Massachusetts, Boston 02125
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22
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Kundzicz H, Davis EA, Ackerman S. RNA polymerase II transcription complexes are destabilized by ATP or GTP. Biochem Biophys Res Commun 1989; 162:1133-9. [PMID: 2764922 DOI: 10.1016/0006-291x(89)90791-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In vitro transcription by RNA polymerase II requires hydrolysis of the beta-gamma bond of ATP after the transcription complex forms, prior to RNA synthesis. It was observed that the presence of ATP during transcription complex formation inhibits subsequent transcription when the remaining 3 rNTPs are added. We now report that ATP or GTP inhibits transcription if either is present during transcription complex formation to added to preformed complexes. This inhibition is not due to purine rNTP degradation and occurs if as little as 2 mM ATP or 50 mM GTP is added to forming or preformed complexes. Deoxy derivatives of ATP inhibit similarly. AMP-PNP, a beta-gamma imido derivative, neither satisfies the energy requirement nor inhibits transcription if added to incubations of forming or of preformed transcription complexes.
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Affiliation(s)
- H Kundzicz
- Biology Department, University of Massachusetts, Boston 02125
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23
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Akimoto S, Sakikawa T, Ono K, Ono T, Ohnishi Y. Transcriptional regulation of F plasmid gene srnB: rifampicin-promoted in vitro readthrough of a terminator in the leader region. Mol Microbiol 1989; 3:787-96. [PMID: 2747521 DOI: 10.1111/j.1365-2958.1989.tb00227.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
srnB is an F-plasmid encoded gene, otherwise silent, whose expression is induced by added rifampicin, leading to the release of cellular Mg2+ and degradation of stable RNA. In the absence of rifampicin, transcripts from the srnB gene were relatively short. S1 nuclease mapping revealed that the short mRNA species terminated within the leader, at the 3' end of a potential stem-and-loop structure. A deletion in the stem-loop resulted in constitutive synthesis of the mRNA that extended beyond the termination site into the structural gene. Even with the wild-type gene, transcription continued beyond the terminator sequence in the presence of added rifampicin. Most of the transcripts synthesized in the presence of rifampicin were long enough to encode the srnB protein. We hypothesize from these results that RNA polymerase associated with rifampicin can read through the terminator to induce srnB expression.
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Affiliation(s)
- S Akimoto
- Department of Bacteriology, School of Medicine, University of Tokushima, Japan
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24
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Cella L, Heumann H, Baer G, Werel W. Mechanism of inhibition of DNA-dependent RNA polymerase of Escherichia coli by rifamycins. Eur J Med Chem 1989. [DOI: 10.1016/0223-5234(89)90103-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Newman AJ, Ma JC, Howe KM, Garner I, Hayward RS. Evidence that rifampicin can stimulate readthrough of transcriptional terminators in Escherichia coli, including the attenuator of the rpoBC operon. Nucleic Acids Res 1982; 10:7409-24. [PMID: 6296775 PMCID: PMC327014 DOI: 10.1093/nar/10.22.7409] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genes encoding the beta and beta' subunits of RNA polymerase in E.coli, rpoB and rpoC, lie downstream of at least two ribosomal protein genes, rplJ (encoding L10) and rplL (L7/12), in a common operon. All four genes are served by promoter PL10, and an attenuator (partial terminator) of transcription, t1, lies between rplJL and rpoBC. Treatment of E.coli with rifampicin, under conditions producing partial inhibition of general RNA synthesis, can stimulate transcription of rpoBC. We have investigated the locus of this effect by fusing PL10 and t1 separately to galK, in suitable plasmids. Our studies of these fusions, and similar fusions involving transcriptional terminators derived from coliphage T7, indicate that low concentrations of rifampicin cause increased readthrough of several different transcriptional terminators in E.coli in vivo, including rpo t1. We discuss whether or not this unspecific mechanism is solely responsible for the observed stimulatory effects of the drug on rpoBC transcription.
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26
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Wu CW, Tweedy N. Mechanistic aspects of promoter binding and chain initiation by RNA polymerase. Mol Cell Biochem 1982; 47:129-49. [PMID: 6755217 DOI: 10.1007/bf00229597] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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27
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Kinsella L, Hsu CY, Schulz W, Dennis D. RNA polymerase: correlation between transcript length, abortive product synthesis, and formation of a stable ternary complex. Biochemistry 1982; 21:2719-23. [PMID: 7093217 DOI: 10.1021/bi00540a022] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In order to investigate the relationship between the stability of the ternary complex RNA polymerase-T7 D111 DNA-RNA product and the length of the bound RNA product, we have developed a protocol for the production of stable ternary complexes of known length and composition. The assembly of the ternary complex is achieved by utilizing a dinucleotide tetraphosphate (pppApU) as a selective primer, which is augmented by one or more appropriate nucleotides. The labeled products were characterized by autoradiography of gel electrophoresis patterns, which were then quantified. The criterion for stability is the protection from perturbations (a salt-jump or a rifampicin challenge), which effectively inhibit initiation. The formation of a bound ribotetranucleotide ternary complex confers stability and terminates abortive product synthesis.
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28
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Kessler C, Mi H, Hartman GR. Competition of rifampicin with binding of substrate and RNA to RNA polymerase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 122:515-8. [PMID: 6174335 DOI: 10.1111/j.1432-1033.1982.tb06467.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The rate of formation of dinucleoside tetraphosphate, pppApU, from ATP and UTP by RNA polymerase on the A1 promoter of the mutant D111 of bacteriophage T7 is distinctly and specifically reduced not only by the third template-directed nucleotide, CTP, but also by CMP. The inhibitory effect of CMP is not changed when the enzyme contains prebound rifampicin. The synthesis of pppApU is also strongly reduced after preincubation of the enzyme with RNA. This inhibitory effect of RNA is, however, distinctly diminished by rifampicin bound to the enzyme prior to the addition of RNA. On the other hand RNA can suppress the specific binding of the antibiotic to the RNA polymerase subassembly alpha 2 beta.
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29
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Dillwith JW, Lewis RA. Mechanism of inhibition of Escherichia coli RNA polymerase by captan. Biochem J 1982; 201:145-51. [PMID: 6177315 PMCID: PMC1163619 DOI: 10.1042/bj2010145] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Captan (N-trichloromethylthiocyclohex-4-ene-1,2-dicarboximide) was shown to inhibit RNA synthesis in vitro catalysed by Escherichia coli RNA polymerase. Incorporation of [gamma-32P]ATP and [gamma-32P]GTP was inhibited by captan to the same extent as overall RNA synthesis. The ratio of [3H]UTP incorporation to that of [gamma-32P]ATP or of [gamma-32P]GTP in control and captan-treated samples indicated that initiation was inhibited, but the length of RNA chains being synthesized was not altered by captan treatment. Limited-substrate assays in which re-initiation of RNA chains did not occur also showed that captan had no effect on the elongation reaction. Studies which measured the interaction of RNA polymerase with template DNA revealed that the binding of enzyme to DNA was inhibited by captan. Glycerol-gradient sedimentation of the captan-treated RNA polymerase indicated that the inhibition of the enzyme was irreversible and did not result in dissociation of its subunits. These data are consistent with a mechanism in which RNA polymerase activity was irreversibly altered by captan, resulting in an inability of the enzyme to bind to the template. This interaction was probably at the DNA-binding site on the polymerase and did not involve reaction of captan with the DNA template.
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30
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Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. I. Characterization of core enzyme open complexes. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(18)43428-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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31
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Stenesh J, Madison JB. Stability of bacterial messenger RNA in mesophiles and thermophiles. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 565:154-60. [PMID: 508760 DOI: 10.1016/0005-2787(79)90091-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The decay of [3H]uridine-labeled mRNA was measured in the mesophile, Bacillus licheniformis (grown at 37 degrees C and 46 degrees C), and in the thermophile, Bacillus stearothermophilus (grown at 46 degrees C and 55 degrees C). For each organism, the half-life of the mRNA decreased as the growth temperature was increased. The stability index (half-life of mRNA/doubling time of cells), however, was remarkably constant for each organism regardless of the growth temperature. It is concluded that these results support the concept that kinetic considerations play a significant role in the explanation of thermophily.
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32
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Studies of RNA chain initiation by Escherichia coli RNA polymerase bound to T7 DNA. Direct analysis of the kinetics and extent of RNA chain initiation at T7 promoter A1. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)36034-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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33
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DeLorbe WJ, Surzycki S, Gussin G. Inactivation of E. coli RNA polymerase by polyriboinosinic acid: heterogeneity of RS complexes. MOLECULAR & GENERAL GENETICS : MGG 1979; 173:51-9. [PMID: 381842 DOI: 10.1007/bf00267690] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polyriboinosinic acid (poly I) inhibits initiation of transcription by binary complexes formed between Adenovirus 2 DNA and E. coli RNA polymerase holoenzyme. In the presence of poly I, just as in the presence of rifampicin, initiation of transcription exhibits a sigmoidal dependence on the temperature at which the binary complexes are formed. This indicates that I (closed) complexes between Ad 2 DNA and RNA polymerase are rapidly inactivated by poly I, but that RS (open) complexes are relatively resistant. However, even among the RS complexes, at least two classes can be distinguished on the basis of the degree to which they are resistant to poly I: RS-1 complexes are somewhat sensitive to poly I (half-time of inactivation approximately 10 min) while RS-2 complexes are almost completely resistant to the inhibitor (half-time of inactivation approximately 10 h). For both types of RS complex, the degree of sensitivity to poly I is ionic strength-dependent.
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34
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35
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36
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Blumenthal RM, Dennis PP. Gene expression in Escherichia coli B/r during partial rifampicin-mediated restrictions of transcription initiation. MOLECULAR & GENERAL GENETICS : MGG 1978; 165:79-86. [PMID: 362168 DOI: 10.1007/bf00270379] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The antibiotic rifampicin inhibits transcription initiation, but not the elongation and completion of nascent RNA transcripts. Addition of low concentrations of rifampicin only partially blocks initiation but at the same time specifically alters the general pattern of transcription in the culture. The transcription of genes specifying the beta and beta' subunits of RNA polymerase, and to a lesser extent of the genes specifying the RNA and protein components of the ribosome, was specifically stimulated relative to total transcription. In contrast, the transcription of the lactose operon was selectively reduced. These results are consistent with the ideas that the level of expression of the genes specifying the beta and beta' subunits is sensitive to the general rate of RNA synthesis in the culture, and that the expression of the beta and beta' RNA polymerase genes is related to the expression of ribosome component genes.
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37
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Wehrli W. Kinetic studies of the interaction between rifampicin and DNA-dependent RNA polymerase of Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 80:325-30. [PMID: 336370 DOI: 10.1111/j.1432-1033.1977.tb11886.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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38
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Stender W, Scheit KH. Studies of the topography of the binding site of DNA-dependent RNA polymerase from Escherichia coli for the antibiotic rifamycin SV. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 76:591-600. [PMID: 330165 DOI: 10.1111/j.1432-1033.1977.tb11629.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Fujii DK, Fulco AJ. Biosynthesis of unsaturated fatty acids by bacilli. Hyperinduction and modulation of desaturase synthesis. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40303-6] [Citation(s) in RCA: 37] [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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