1
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Maglangit F, Yu Y, Deng H. Bacterial pathogens: threat or treat (a review on bioactive natural products from bacterial pathogens). Nat Prod Rep 2021; 38:782-821. [PMID: 33119013 DOI: 10.1039/d0np00061b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to the second quarter of 2020 Threat or treat? While pathogenic bacteria pose significant threats, they also represent a huge reservoir of potential pharmaceuticals to treat various diseases. The alarming antimicrobial resistance crisis and the dwindling clinical pipeline urgently call for the discovery and development of new antibiotics. Pathogenic bacteria have an enormous potential for natural products drug discovery, yet they remained untapped and understudied. Herein, we review the specialised metabolites isolated from entomopathogenic, phytopathogenic, and human pathogenic bacteria with antibacterial and antifungal activities, highlighting those currently in pre-clinical trials or with potential for drug development. Selected unusual biosynthetic pathways, the key roles they play (where known) in various ecological niches are described. We also provide an overview of the mode of action (molecular target), activity, and minimum inhibitory concentration (MIC) towards bacteria and fungi. The exploitation of pathogenic bacteria as a rich source of antimicrobials, combined with the recent advances in genomics and natural products research methodology, could pave the way for a new golden age of antibiotic discovery. This review should serve as a compendium to communities of medicinal chemists, organic chemists, natural product chemists, biochemists, clinical researchers, and many others interested in the subject.
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Affiliation(s)
- Fleurdeliz Maglangit
- Department of Biology and Environmental Science, College of Science, University of the Philippines Cebu, Lahug, Cebu City, 6000, Philippines. and Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Hubei Province Engineering and Technology Research Centre for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
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2
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Design, synthesis and biological evaluation of novel hybrids of N-aryl pyrrothine-base α-pyrone as bacterial RNA polymerase inhibitors. Bioorg Med Chem Lett 2020; 30:127146. [DOI: 10.1016/j.bmcl.2020.127146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
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3
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Synthesis and biological evaluation of novel N-2,4-dimethoxyphenyl dithiolopyrrolone derivatives as bacterial RNA polymerase inhibitors. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02550-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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4
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Zhang X, Linder S, Bazzaro M. Drug Development Targeting the Ubiquitin-Proteasome System (UPS) for the Treatment of Human Cancers. Cancers (Basel) 2020; 12:cancers12040902. [PMID: 32272746 PMCID: PMC7226376 DOI: 10.3390/cancers12040902] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer cells are characterized by a higher rate of protein turnover and greater demand for protein homeostasis compared to normal cells. In this scenario, the ubiquitin-proteasome system (UPS), which is responsible for the degradation of over 80% of cellular proteins within mammalian cells, becomes vital to cancer cells, making the UPS a critical target for the discovery of novel cancer therapeutics. This review systematically categorizes all current reported small molecule inhibitors of the various essential components of the UPS, including ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), ubiquitin ligases (E3s), the 20S proteasome catalytic core particle (20S CP) and the 19S proteasome regulatory particles (19S RP), as well as their mechanism/s of action and limitations. We also discuss the immunoproteasome which is considered as a prospective therapeutic target of the next generation of proteasome inhibitors in cancer therapies.
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Affiliation(s)
- Xiaonan Zhang
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Oncology-Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden;
- Department of Immunology, Genetics, and Pathology, Uppsala University, 751 05 Uppsala, Sweden
| | - Stig Linder
- Department of Oncology-Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden;
- Department of Medical and Health Sciences, Linköping University, SE-58183 Linköping, Sweden
| | - Martina Bazzaro
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence:
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5
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Repurposing old drugs as new inhibitors of the ubiquitin-proteasome pathway for cancer treatment. Semin Cancer Biol 2019; 68:105-122. [PMID: 31883910 DOI: 10.1016/j.semcancer.2019.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/30/2019] [Accepted: 12/15/2019] [Indexed: 12/25/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays a central role in the degradation of cellular proteins. Targeting protein degradation has been validated as an effective strategy for cancer therapy since 2003. Several components of the UPS have been validated as potential anticancer targets, including 20S proteasomes, 19S proteasome-associated deubiquitinases (DUBs) and ubiquitin ligases (E3s). 20S proteasome inhibitors (such as bortezomib/BTZ and carfilzomib/CFZ) have been approved by the U.S. Food and Drug Administration (FDA) for the treatment of multiple myeloma (MM) and some other liquid tumors. Although survival of MM patients has been improved by the introduction of BTZ-based therapies, these clinical 20S proteasome inhibitors have several limitations, including emergence of resistance in MM patients, neuro-toxicities, and little efficacy in solid tumors. One of strategies to improve the current status of cancer treatment is to repurpose old drugs with UPS-inhibitory properties as new anticancer agents. Old drug reposition represents an attractive drug discovery approach compared to the traditional de novo drug discovery process which is time-consuming and costly. In this review, we summarize status of repurposed inhibitors of various UPS components, including 20S proteasomes, 19S-associated DUBs, and ubiquitin ligase E3s. The original and new mechanisms of action, molecular targets, and potential anticancer activities of these repurposed UPS inhibitors are reviewed, and their new uses including combinational therapies for cancer treatment are discussed.
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6
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Lauinger L, Li J, Shostak A, Cemel IA, Ha N, Zhang Y, Merkl PE, Obermeyer S, Stankovic-Valentin N, Schafmeier T, Wever WJ, Bowers AA, Carter KP, Palmer AE, Tschochner H, Melchior F, Deshaies RJ, Brunner M, Diernfellner A. Thiolutin is a zinc chelator that inhibits the Rpn11 and other JAMM metalloproteases. Nat Chem Biol 2017; 13:709-714. [PMID: 28459440 DOI: 10.1038/nchembio.2370] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/22/2017] [Indexed: 12/21/2022]
Abstract
Thiolutin is a disulfide-containing antibiotic and anti-angiogenic compound produced by Streptomyces. Its biological targets are not known. We show that reduced thiolutin is a zinc chelator that inhibits the JAB1/MPN/Mov34 (JAMM) domain-containing metalloprotease Rpn11, a deubiquitinating enzyme of the 19S proteasome. Thiolutin also inhibits the JAMM metalloproteases Csn5, the deneddylase of the COP9 signalosome; AMSH, which regulates ubiquitin-dependent sorting of cell-surface receptors; and BRCC36, a K63-specific deubiquitinase of the BRCC36-containing isopeptidase complex and the BRCA1-BRCA2-containing complex. We provide evidence that other dithiolopyrrolones also function as inhibitors of JAMM metalloproteases.
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Affiliation(s)
- Linda Lauinger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Jing Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Anton Shostak
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | | | - Nati Ha
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Yaru Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Philipp E Merkl
- Lehrstuhl Biochemie III, Biochemie Zentrum Regensburg, Universität Regensburg, Regensburg, Germany
| | - Simon Obermeyer
- Lehrstuhl Biochemie III, Biochemie Zentrum Regensburg, Universität Regensburg, Regensburg, Germany
| | - Nicolas Stankovic-Valentin
- Zentrum Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Walter J Wever
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kyle P Carter
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Amy E Palmer
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Herbert Tschochner
- Lehrstuhl Biochemie III, Biochemie Zentrum Regensburg, Universität Regensburg, Regensburg, Germany
| | - Frauke Melchior
- Zentrum Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - Michael Brunner
- Heidelberg University Biochemistry Center, Heidelberg, Germany
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7
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Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev 2016; 80:139-60. [PMID: 26764017 DOI: 10.1128/mmbr.00055-15] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
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8
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Li B, Wever WJ, Walsh CT, Bowers AA. Dithiolopyrrolones: biosynthesis, synthesis, and activity of a unique class of disulfide-containing antibiotics. Nat Prod Rep 2014; 31:905-23. [PMID: 24835149 PMCID: PMC4132845 DOI: 10.1039/c3np70106a] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Covering: up to 2014. Dithiolopyrrolone (DTP) group antibiotics were first isolated in the early half of the 20th century, but only recently has research been reawakened by insights gained from the synthesis and biosynthesis of this structurally intriguing class of molecules. DTPs are characterized by an electronically unique bicyclic structure, which contains a compact disulfide bridge between two ene-thiols. Points of diversity within the compound class occur outside of the bicyclic core, at the two amide nitrogens. Such modifications distinguish three of the most well studied members of the class, holomycin, thiolutin, and aureothricin; the DTP core has also more recently been identified in the marine antibiotic thiomarinol, in which it is linked to a marinolic acid moiety, analog of the FDA-approved topical antibiotic Bactroban® (GlaxoSmithKline). Dithiolopyrrolones exhibit relatively broad-spectrum antibiotic activity against many Gram-positive and Gram-negative bacteria, as well as strains of Mycobacterium tuberculosis. Additionally, they have been shown to exhibit potent and selective anti-cancer activity. Despite this promising profile, there is still much unknown about the mechanisms of action for DTPs. Early reports suggested that they inhibit yeast growth at the level of transcription and that this effect is largely responsible for their distinctive microbial static properties; a similar mechanism is supported in bacteria. Elucidation of biosynthetic pathways for holomycin in Streptomyces clavuligerus and Yersinia ruckeri and thiomarinol in Alteromonas rava sp. nov. SANK 73390, have contributed evidence suggesting that multiple mechanisms may be operative in the activity of these compounds. This review will comprehensively cover the history and development of dithiolopyrrolones with particular emphasis on the biosynthesis, synthesis, biological activity and mechanism of action.
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Affiliation(s)
- Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Walter J. Wever
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Christopher T. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 200 Longwood Ave., Boston, MA, 02115
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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9
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Abreu PA, Sousa TS, Jimenez PC, Wilke DV, Rocha DD, Freitas HPS, Pessoa ODL, La Clair JJ, Costa-Lotufo LV. Identification of pyrroloformamide as a cytokinesis modulator. Chembiochem 2014; 15:501-6. [PMID: 24478218 DOI: 10.1002/cbic.201300717] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Indexed: 12/26/2022]
Abstract
Discovered in the late 1940s, the pyrrolinonodithioles represent a family of potent disulfide-containing natural products. Although they are understood in a synthetic and biosynthetic context, the biological role of these materials remains unresolved. To date, their activity has been suggested to arise through regulating RNA metabolism, and more recently they have been suggested to function as backup thiols for detoxification. Using materials identified through a natural products program, we now identify the biological function of one member of this family, pyrroloformamide, as an antimitotic agent acting, in part, by disrupting cytokinesis.
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Affiliation(s)
- Paula A Abreu
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Rua Cel Nunes de Melo 1127, Fortaleza, Ceará, 60430-270 (Brazil)
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10
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Holomycin, a dithiolopyrrolone compound produced by Streptomyces clavuligerus. Appl Microbiol Biotechnol 2013; 98:1023-30. [DOI: 10.1007/s00253-013-5410-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/13/2013] [Accepted: 11/13/2013] [Indexed: 01/19/2023]
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11
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Qin Z, Huang S, Yu Y, Deng H. Dithiolopyrrolone natural products: isolation, synthesis and biosynthesis. Mar Drugs 2013; 11:3970-97. [PMID: 24141227 PMCID: PMC3826145 DOI: 10.3390/md11103970] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 12/24/2022] Open
Abstract
Dithiolopyrrolones are a class of antibiotics that possess the unique pyrrolinonodithiole (4H-[1,2] dithiolo [4,3-b] pyrrol-5-one) skeleton linked to two variable acyl groups. To date, there are approximately 30 naturally occurring dithiolopyrrolone compounds, including holomycin, thiolutin, and aureothricin, and more recently thiomarinols, a unique class of hybrid marine bacterial natural products containing a dithiolopyrrolone framework linked by an amide bridge with an 8-hydroxyoctanoyl chain linked to a monic acid. Generally, dithiolopyrrolone antibiotics have broad-spectrum antibacterial activity against various microorganisms, including Gram-positive and Gram-negative bacteria, and even parasites. Holomycin appeared to be active against rifamycin-resistant bacteria and also inhibit the growth of the clinical pathogen methicillin-resistant Staphylococcus aureus N315. Its mode of action is believed to inhibit RNA synthesis although the exact mechanism has yet to be established in vitro. A recent work demonstrated that the fish pathogen Yersinia ruckeri employs an RNA methyltransferase for self-resistance during the holomycin production. Moreover, some dithiolopyrrolone derivatives have demonstrated promising antitumor activities. The biosynthetic gene clusters of holomycin have recently been identified in S. clavuligerus and characterized biochemically and genetically. The biosynthetic gene cluster of thiomarinol was also identified from the marine bacterium Pseudoalteromonas sp. SANK 73390, which was uniquely encoded by two independent pathways for pseudomonic acid and pyrrothine in a novel plasmid. The aim of this review is to give an overview about the isolations, characterizations, synthesis, biosynthesis, bioactivities and mode of action of this unique family of dithiolopyrrolone natural products, focusing on the period from 1940s until now.
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Affiliation(s)
- Zhiwei Qin
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Sheng Huang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
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12
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Jiang CS, Müller WEG, Schröder HC, Guo YW. Disulfide- and multisulfide-containing metabolites from marine organisms. Chem Rev 2011; 112:2179-207. [PMID: 22176580 DOI: 10.1021/cr200173z] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cheng-Shi Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang High-Tech Park, Shanghai 201203, People's Republic of China
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13
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Dulev S, de Renty C, Mehta R, Minkov I, Schwob E, Strunnikov A. Essential global role of CDC14 in DNA synthesis revealed by chromosome underreplication unrecognized by checkpoints in cdc14 mutants. Proc Natl Acad Sci U S A 2009; 106:14466-71. [PMID: 19666479 PMCID: PMC2723162 DOI: 10.1073/pnas.0900190106] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Indexed: 12/27/2022] Open
Abstract
The CDC14 family of multifunctional evolutionarily conserved phosphatases includes major regulators of mitosis in eukaryotes and of DNA damage response in humans. The CDC14 function is also crucial for accurate chromosome segregation, which is exemplified by its absolute requirement in yeast for the anaphase segregation of nucleolar organizers; however the nature of this essential pathway is not understood. Upon investigation of the rDNA nondisjunction phenomenon, it was found that cdc14 mutants fail to complete replication of this locus. Moreover, other late-replicating genomic regions (10% of the genome) are also underreplicated in cdc14 mutants undergoing anaphase. This selective genome-wide replication defect is due to dosage insufficiency of replication factors in the nucleus, which stems from two defects, both contingent on the reduced CDC14 function in the preceding mitosis. First, a constitutive nuclear import defect results in a drastic dosage decrease for those replication proteins that are regulated by nuclear transport. Particularly, essential RPA subunits display both lower mRNA and protein levels, as well as abnormal cytoplasmic localization. Second, the reduced transcription of MBF and SBF-controlled genes in G1 leads to the reduction in protein levels of many proteins involved in DNA replication. The failure to complete replication of late replicons is the primary reason for chromosome nondisjunction upon CDC14 dysfunction. As the genome-wide slow-down of DNA replication does not trigger checkpoints [Lengronne A, Schwob E (2002) Mol Cell 9:1067-1078], CDC14 mutations pose an overwhelming challenge to genome stability, both generating chromosome damage and undermining the checkpoint control mechanisms.
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MESH Headings
- Active Transport, Cell Nucleus
- Anaphase/genetics
- Blotting, Western
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Nucleus/metabolism
- Chromatin Immunoprecipitation
- Chromosome Segregation
- Chromosomes, Fungal/genetics
- DNA Damage
- DNA Replication
- DNA, Fungal/biosynthesis
- DNA, Fungal/genetics
- DNA, Ribosomal/genetics
- G1 Phase/genetics
- Genes, Essential/genetics
- Genes, Essential/physiology
- Genome, Fungal/genetics
- Genome-Wide Association Study
- Models, Biological
- Mutation
- Protein Binding
- Protein Tyrosine Phosphatases/genetics
- Protein Tyrosine Phosphatases/metabolism
- Replication Protein A/genetics
- Replication Protein A/metabolism
- S Phase/genetics
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic
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Affiliation(s)
- Stanimir Dulev
- National Institutes of Health, National Institute of Child Health and Human Development, Bethesda, Maryland, 20892
- University of Plovdiv, Plovdiv 4000, Bulgaria
| | - Christelle de Renty
- Institute of Molecular Genetics, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, University Montpellier 2, 34293, France; and
| | - Rajvi Mehta
- National Institutes of Health, National Institute of Child Health and Human Development, Bethesda, Maryland, 20892
| | - Ivan Minkov
- University of Plovdiv, Plovdiv 4000, Bulgaria
| | - Etienne Schwob
- Institute of Molecular Genetics, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, University Montpellier 2, 34293, France; and
| | - Alexander Strunnikov
- National Institutes of Health, National Institute of Child Health and Human Development, Bethesda, Maryland, 20892
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14
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Ingram PJ, Stumpf MPH, Stark J. Nonidentifiability of the source of intrinsic noise in gene expression from single-burst data. PLoS Comput Biol 2008; 4:e1000192. [PMID: 18846201 PMCID: PMC2538572 DOI: 10.1371/journal.pcbi.1000192] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 08/25/2008] [Indexed: 12/03/2022] Open
Abstract
Over the last few years, experimental data on the fluctuations in gene activity
between individual cells and within the same cell over time have confirmed that
gene expression is a “noisy” process. This variation is in
part due to the small number of molecules taking part in some of the key
reactions that are involved in gene expression. One of the consequences of this
is that protein production often occurs in bursts, each due to a single promoter
or transcription factor binding event. Recently, the distribution of the number
of proteins produced in such bursts has been experimentally measured, offering a
unique opportunity to study the relative importance of different sources of
noise in gene expression. Here, we provide a derivation of the theoretical
probability distribution of these bursts for a wide variety of different models
of gene expression. We show that there is a good fit between our theoretical
distribution and that obtained from two different published experimental
datasets. We then prove that, irrespective of the details of the model, the
burst size distribution is always geometric and hence determined by a single
parameter. Many different combinations of the biochemical rates for the
constituent reactions of both transcription and translation will therefore lead
to the same experimentally observed burst size distribution. It is thus
impossible to identify different sources of fluctuations purely from protein
burst size data or to use such data to estimate all of the model parameters. We
explore methods of inferring these values when additional types of experimental
data are available. Recent experimental data showing fluctuations in gene activity between individual
cells and within the same cell over time confirm that gene expression is a
“noisy” process. This variation is partly due to the small
number of molecules involved in gene expression. One consequence is that protein
production often occurs in bursts, each due to the binding of a single
transcription factor. Recently, the distribution of the number of proteins
produced in such bursts has been experimentally measured, offering a unique
opportunity to study the relative importance of different sources of noise in
gene expression. We derive the theoretical probability distribution of these
bursts for a wide variety of gene expression models. We show a good fit between
our theoretical distribution and experimental data and prove that, irrespective
of the model details, the burst size distribution always has the same shape,
determined by a single parameter. As different combinations of the reaction
rates lead to the same observed distribution, it is impossible to estimate all
kinetic parameters from protein burst size data. When additional data, such as
protein equilibrium distributions, are available, these can be used to infer
additional parameters. We present one approach to this, demonstrating its
application to published data.
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Affiliation(s)
- Piers J Ingram
- Department of Mathematics, Imperial College London, London, United Kingdom.
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15
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Chopra I, Hesse L, O'Neill A. Exploiting current understanding of antibiotic action for discovery of new drugs. J Appl Microbiol 2002. [DOI: 10.1046/j.1365-2672.92.5s1.13.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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16
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Discovery and development of new anti-bacterial drugs. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0165-7208(02)80022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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17
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Oliva B, O'Neill A, Wilson JM, O'Hanlon PJ, Chopra I. Antimicrobial properties and mode of action of the pyrrothine holomycin. Antimicrob Agents Chemother 2001; 45:532-9. [PMID: 11158751 PMCID: PMC90323 DOI: 10.1128/aac.45.2.532-539.2001] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Holomycin, a member of the pyrrothine class of antibiotics, displayed broad-spectrum antibacterial activity, inhibiting a variety of gram-positive and gram-negative bacteria, with the exception of Enterobacter cloacae, Morganella morganii, and Pseudomonas aeruginosa. The antibiotic lacked activity against the eukaryotic microorganisms Saccharomyces cerevisiae and Candida kefyr. Holomycin exhibited a bacteriostatic response against Escherichia coli that was associated with rapid inhibition of RNA synthesis in whole cells. Inhibition of RNA synthesis could have been a secondary consequence of inhibiting tRNA aminoacylation, thereby inducing the stringent response. However, the levels of inhibition of RNA synthesis by holomycin were similar in a stringent and relaxed pair of E. coli strains that were isogenic except for the deletion of the relA gene. This suggests that inhibition of RNA synthesis by holomycin could reflect direct inhibition of DNA-dependent RNA polymerase. Examination of the effects of holomycin on the kinetics of the appearance of beta-galactosidase in induced E. coli cells was also consistent with inhibition of RNA polymerase at the level of RNA chain elongation. However, holomycin only weakly inhibited E. coli RNA polymerase in assays using synthetic poly(dA-dT) and plasmid templates. Furthermore, inhibition of RNA polymerase was observed only at holomycin concentrations in excess of those required to inhibit the growth of E. coli. It is possible that holomycin is a prodrug, requiring conversion in the cell to an active species that inhibits RNA polymerase.
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Affiliation(s)
- B Oliva
- Department of Experimental Medicine, University of L'Aquila, Coppito-67100, L'Aquila, Italy
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18
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O'Neill A, Oliva B, Storey C, Hoyle A, Fishwick C, Chopra I. RNA polymerase inhibitors with activity against rifampin-resistant mutants of Staphylococcus aureus. Antimicrob Agents Chemother 2000; 44:3163-6. [PMID: 11036042 PMCID: PMC101622 DOI: 10.1128/aac.44.11.3163-3166.2000] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A collection of rifampin-resistant mutants of Staphylococcus aureus with characterized RNA polymerase beta-subunit (rpoB) gene mutations was cross-screened against a number of other RNA polymerase inhibitors to correlate susceptibility with specific rpoB genotypes. The rpoB mutants were cross-resistant to streptolydigin and sorangicin A. In contrast, thiolutin, holomycin, corallopyronin A, and ripostatin A retained activity against the rpoB mutants. The second group of inhibitors may be of interest as drug development candidates.
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Affiliation(s)
- A O'Neill
- Antimicrobial Research Centre and Division of Microbiology, University of Leeds, Leeds LS2 9JT, United Kingdom
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Stachel HD, Nienaber J, Zoukas T. Kondensierte 1.2-Dithiole, I. Synthese von Thiolutin und verwandten Verbindungen. ACTA ACUST UNITED AC 1992. [DOI: 10.1002/jlac.199219920184] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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MacPherson J, Khachatourians G. Production of ß‐galactosidase in liquid cultures ofbeauveria bassiana. FOOD BIOTECHNOL 1991. [DOI: 10.1080/08905439109549789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Bergmann R. Thiolutin inhibits utilization of glucose and other carbon sources in cells of Escherichia coli. Antonie Van Leeuwenhoek 1989; 55:143-52. [PMID: 2662903 DOI: 10.1007/bf00404754] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Thiolutin was found to inhibit the utilization of glucose and other growth substrates in Escherichia coli. The inhibition was detected by a sharp drop of the respiration rate after addition of the antibiotic. The actual function affected was allocated to the cytoplasmic membrane of the bacterial cells by the following evidence: --spheroplasts were affected like intact cells, --individual reactions of either the electron transport chain or the glycolytic pathway were not inhibited, --glucose consumption in the culture stopped and the cells accumulated guanosine tetraphosphate as under starvation conditions, --activation of the cell's apo-glucose dehydrogenase restored respiration via bypassing the glucose phosphotransferase system. It was concluded that the transport of certain substrates across the membrane was inhibited.
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Affiliation(s)
- R Bergmann
- Institut für Allgemeine Botanik, Universität Hamburg, FRG
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Khachatourians GG, Holmlund PK, Dimmock JR. Some effects of 1-(2,4-Dichlorophenyl)-4-dimethylamino-methyl-1-nonen-3-one hydrochloride on Escherichia coli GK-19. J Pharm Sci 1984; 73:803-8. [PMID: 6204038 DOI: 10.1002/jps.2600730624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
1-(2,4-Dichlorophenyl)-4-dimethylaminomethyl-1-nonen-3-one hydrochloride (Id) was shown to inhibit the growth of Escherichia coli GK-19 at a concentration of 50 micrograms/mL in a medium of pH 6.5. Maximal antibacterial activity was found during the logarithmic growth phases rather than at the early stationary phase. Electron microscopy revealed that Id caused lysis, and inhibition of respiration and retardation of RNA and protein syntheses occurred in the bacteria with this compound at 50 micrograms/mL.
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23
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Joshi A, Verma M, Chakravorty M. Thiolutin-resistant mutants of Salmonella typhimurium. Antimicrob Agents Chemother 1982; 22:541-7. [PMID: 6758684 PMCID: PMC183790 DOI: 10.1128/aac.22.4.541] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Spontaneous mutants of Salmonella typhimurium isolated in our laboratory from thiolutin-containing tryptone agar plates are partially resistant to thiolutin in enriched media. In minimal media, they are not resistant. The mutants are not temperature sensitive but fail to support the development of phage P22 at higher temperatures (40 degrees C). Thiolutin did not interfere with RNA polymerase or nucleotide kinase in in vitro experiments. However, thiolutin did inhibit the rate of incorporation of exogenous uridine into the cellular pool and consequently the acid-precipitable material. It appears that one site of action of thiolutin is at the membrane level.
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Joshi A, Siddiqui JZ, Verma M, Chakravorty M. Participation of the host protein(s) in the morphogenesis of bacteriophage P22. MOLECULAR & GENERAL GENETICS : MGG 1982; 186:44-9. [PMID: 7050625 DOI: 10.1007/bf00422910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Spontaneous mutants of S. typhimurium resistant to thiolutin are conditionally non-permissive for phage P22 development (Joshi and Chakravorty 1979). At 40 degree C non-infective phage particles are produced. Phage development in two nonpermissive hosts (18/MC4 and 153/MC4) has been studied in detail. The steps at which the phage morphogenesis is interfered with differ in the two mutants. The electron micrograph of the particles produced in the mutant 18/MC4 reveals the presence of normal-looking particles; these particles contain phage DNA, adsorb to the permissive host but fail to inject their DNA. The particles produced in the mutant 153/MC4 which fail to adsorb to the host are found to be tail fibre-less. These observations indicate the involvement of host protein(s) in phage P22 morphogenesis.
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Sivasubramanian N, Jayaraman R. Mapping of two transcription mutations (tlnI and tlnII) conferring thiolutin resistance, adjacent to dnaZ and rho in Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1980; 180:609-15. [PMID: 7007825 DOI: 10.1007/bf00268068] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Two mutations in Escherichia coli conferring resistance to the transcription initiation inhibitor, thiolutin, have been mapped. One of these mutations (tln-I)( maps at 10.2 min on the genetic map and is cotransducible with dnaZ at a frequency of approximately 50%. The other mutation (tln-II) maps between metE and ilvD, probably close to rho, and is cotransducible with ilvD at a frequency of approximately 65%. The presence of both the mutations in the same cell confers resistance to thiolutin in minimal medium. Either one of them alone renders the cell 'conditionally auxotrophic' in the presence of the drug. The implications of these findings are discussed in relation to the mode of action of the thiolutin sensitive factors in transcription.
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26
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Barnsley PG, Sells BH. Synthesis of messenger RNA coding for individual ribosomal proteins during nutritional shift-up in Escherichia coli K-12. MOLECULAR & GENERAL GENETICS : MGG 1978; 160:41-9. [PMID: 347247 DOI: 10.1007/bf00275117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Gayda RC, Markovitz A. Altered bacteriophage lambda expression in cell division mutants capR(lon) of Escherichia coli K-12. MOLECULAR & GENERAL GENETICS : MGG 1978; 159:1-11. [PMID: 416333 DOI: 10.1007/bf00401741] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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28
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Barnsley PG, Sells BH. Functional inactivation rates of the messenger RNA molecules coding for the individual ribosomal proteins in Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1977; 153:121-7. [PMID: 329110 DOI: 10.1007/bf00264726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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Barnsley PG, Boyle SM, Sells BH. Synthesis of messenger RNA coding for elongation factors G and Ts during nutritional shift-up in Escherichia coli K-12. Biochem Biophys Res Commun 1976; 71:817-25. [PMID: 786293 DOI: 10.1016/0006-291x(76)90904-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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30
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Collmer A, Lamborg M. Arrangement and regulation of the nitrogen fixation genes in Klebsiella pneumoniae studied by depression kinetics. J Bacteriol 1976; 126:806-13. [PMID: 816785 PMCID: PMC233217 DOI: 10.1128/jb.126.2.806-813.1976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Events underlying depression of the nitrogen fixation (nif) genes in Klebsiella pneumoniae M5A1 were analyzed in vivo by comparing the effects of selective inhibitors of transcription and translation on subsequent nitrogenase activity (rate of acetylene reduction). When batch cultures were induced for depression, an 87-min lag separated ammonium ion/oxygen removal and the appearance of activity.
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Sivasubramanian N, Jayaraman R. Thiolutin resistant mutants of Escherichia coli are they RNA chain initiation mutants? MOLECULAR & GENERAL GENETICS : MGG 1976; 145:89-96. [PMID: 775314 DOI: 10.1007/bf00331562] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Four mutants of Escherichia coli KL16 resistant to the antibiotic Thiolutin have been isolated. This drug was earlier reported to be an inhibitor of RNA chain elongation. The first mutant, TLrI, is resistant only in rich or partially rich media: it can, however, grow in minimal medium containing the drug with a very long doubling time. The other mutants TLrII, TLrIIIa and TLrIIIb are resistant in rich as well as minimal media. beta-galactosidase could not be induced in TLrI and TLrII in the presence of thiolutin whereas the enzyme is constitutively synthesised in TLrIIIa and TLrIIIb irrespective of the drug. The mutants do not support the development of phage T4 in presence of the drug, if the drug is added along with the phage, but "escape" the inhibition if phage development is allowed to proceed for some time before the addition of the drug. The time of this escape is characteristic of the mutant. Even in a sensitive strain, T7 growth escapes inhibition very soon after infection, around the time the phage-specific RNA polymerase is synthesized. In the parent strain the kinetics of inhibition of beta-galactosidase induction resembles more the inhibition caused by rifampicin than by streptolydigin. It is proposed that thiolutin could be an inhibitor of RNA chain initiation and resistance might be due to mutation in the subunit(s)/factor(s) involved in initiation.
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32
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Abstract
Thiolutin reversibly inhibits growth and ribonucleic acid synthesis in
Saccharomyces cerevisiae
. It is now demonstrated that, at 5 μg/ml, thiolutin rapidly inhibits all incorporation of radioactive precursors into ribonucleic acid and protein in
Escherichia coli
, although the incorporation of deoxythymidine into deoxyribonucleic acid continues for some time. Concentrations of thiolutin of 5 μg/ml and above are bacteriostatic and do not lead to unbalanced growth, so that cell size remains constant. The antibiotic and its inhibitory effects are easily removed by washing, whereupon macromolecular synthesis and cell division resume unimpeded. These data are consistent with reversible inhibition of ribonucleic acid synthesis being the primary mode of action of thiolutin in
E. coli
, and suggest that thiolutin may be a useful tool for studies where such reversible inhibition is required.
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