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Arseniev A, Panfilov M, Pobegalov G, Potyseva A, Pavlinova P, Yakunina M, Lee J, Borukhov S, Severinov K, Khodorkovskii M. Single-molecule studies reveal the off-pathway elemental pause state as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.542125. [PMID: 37333075 PMCID: PMC10274647 DOI: 10.1101/2023.06.05.542125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of transcription elongation in ternary elongation complexes of RNAP (ECs) in the presence of Stl at a single-molecule level. We found that Stl induces long-lived stochastic pauses while the instantaneous velocity of transcription between the pauses is unaffected. Stl enhances the short-lived pauses associated with an off-pathway elemental paused state of the RNAP nucleotide addition cycle. Unexpectedly, we found that transcript cleavage factors GreA and GreB, which were thought to be Stl competitors, do not alleviate the streptolydigin-induced pausing; instead, they synergistically increase transcription inhibition by Stl. This is the first known instance of a transcriptional factor enhancing antibiotic activity. We propose a structural model of the EC-Gre-Stl complex that explains the observed Stl activities and provides insight into possible cooperative action of secondary channel factors and other antibiotics binding at the Stl-pocket. These results offer a new strategy for high-throughput screening for prospective antibacterial agents.
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Affiliation(s)
- Anatolii Arseniev
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Mikhail Panfilov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Alina Potyseva
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Polina Pavlinova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Jookyung Lee
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Konstantin Severinov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
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2
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Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH. Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles. Structure 2015; 23:1470-1481. [PMID: 26190576 DOI: 10.1016/j.str.2015.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 11/30/2022]
Abstract
CBR hydroxamidines are small-molecule inhibitors of bacterial RNA polymerase (RNAP) discovered through high-throughput screening of synthetic-compound libraries. CBR pyrazoles are structurally related RNAP inhibitors discovered through scaffold hopping from CBR hydroxamidines. CBR hydroxamidines and pyrazoles selectively inhibit Gram-negative bacterial RNAP and exhibit selective antibacterial activity against Gram-negative bacteria. Here, we report crystal structures of the prototype CBR hydroxamidine, CBR703, and a CBR pyrazole in complex with E. coli RNAP holoenzyme. In addition, we define the full resistance determinant for CBR703, show that the binding site and resistance determinant for CBR703 do not overlap the binding sites and resistance determinants of other characterized RNAP inhibitors, show that CBR703 exhibits no or minimal cross-resistance with other characterized RNAP inhibitors, and show that co-administration of CBR703 with other RNAP inhibitors results in additive antibacterial activities. The results set the stage for structure-based optimization of CBR inhibitors as antibacterial drugs.
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Affiliation(s)
- Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Xinyue Wang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shuang Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Deepankar Das
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Trevor Michalchuk
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Meliza Talaue
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Nancy Connell
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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3
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Resistance to rifampicin: a review. J Antibiot (Tokyo) 2014; 67:625-30. [PMID: 25118103 DOI: 10.1038/ja.2014.107] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 06/28/2014] [Accepted: 07/04/2014] [Indexed: 11/08/2022]
Abstract
Resistance to rifampicin (RIF) is a broad subject covering not just the mechanism of clinical resistance, nearly always due to a genetic change in the β subunit of bacterial RNA polymerase (RNAP), but also how studies of resistant polymerases have helped us understand the structure of the enzyme, the intricacies of the transcription process and its role in complex physiological pathways. This review can only scratch the surface of these phenomena. The identification, in strains of Escherichia coli, of the positions within β of the mutations determining resistance is discussed in some detail, as are mutations in organisms that are therapeutic targets of RIF, in particular Mycobacterium tuberculosis. Interestingly, changes in the same three codons of the consensus sequence occur repeatedly in unrelated RIF-resistant (RIF(r)) clinical isolates of several different bacterial species, and a single mutation predominates in mycobacteria. The utilization of our knowledge of these mutations to develop rapid screening tests for detecting resistance is briefly discussed. Cross-resistance among rifamycins has been a topic of controversy; current thinking is that there is no difference in the susceptibility of RNAP mutants to RIF, rifapentine and rifabutin. Also summarized are intrinsic RIF resistance and other resistance mechanisms.
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4
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Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH. Transcription inhibition by the depsipeptide antibiotic salinamide A. eLife 2014; 3:e02451. [PMID: 24843001 PMCID: PMC4029172 DOI: 10.7554/elife.02451] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 04/18/2014] [Indexed: 12/12/2022] Open
Abstract
We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center 'bridge-helix cap' comprising the 'bridge-helix N-terminal hinge', 'F-loop', and 'link region'. We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge.DOI: http://dx.doi.org/10.7554/eLife.02451.001.
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Affiliation(s)
- David Degen
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Yu Feng
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Yu Zhang
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | - Yon W Ebright
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | | | - Sukhendu Mandal
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Meliza Talaue
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, United States
| | - Nancy Connell
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, United States
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, United States
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5
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Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH. GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. eLife 2014; 3:e02450. [PMID: 24755292 PMCID: PMC3994528 DOI: 10.7554/elife.02450] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center ‘i’ and ‘i+1’ nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. DOI:http://dx.doi.org/10.7554/eLife.02450.001 As increasing numbers of bacteria become resistant to antibiotics, new drugs are needed to fight bacterial infections. To develop new antibacterial drugs, researchers need to understand how existing antibiotics work. There are many ways to kill bacteria, but one of the most effective is to target an enzyme called bacterial RNA polymerase. If bacterial RNA polymerase is prevented from working, bacteria cannot synthesize RNA and cannot survive. GE23077 (GE for short) is an antibiotic produced by bacteria found in soil. Although GE stops bacterial RNA polymerase from working, and thereby kills bacteria, it does not affect mammalian RNA polymerases, and so does not kill mammalian cells. Understanding how GE works could help with the development of new antibacterial drugs. Zhang et al. present results gathered from a range of techniques to show how GE inhibits bacterial RNA polymerase. These show that GE works by binding to a site on RNA polymerase that is different from the binding sites of previously characterized antibacterial drugs. The mechanism used to inhibit the RNA polymerase is also different. The newly identified binding site has several features that make it an unusually attractive target for development of antibacterial compounds. Bacteria can become resistant to an antibiotic if genetic mutations lead to changes in the site the antibiotic binds to. However, the site that GE binds to on RNA polymerase is essential for RNA polymerase to function and so cannot readily be changed without crippling the enzyme. Therefore, this type of antibiotic resistance is less likely to develop. In addition, the newly identified binding site for GE on RNA polymerase is located next to the binding site for a current antibacterial drug, rifampin. Zhang et al. therefore linked GE and rifampin to form a two-part (‘bipartite’) compound designed to bind simultaneously to the GE and the rifampin binding sites. This compound was able to inhibit drug-resistant RNA polymerases tens to thousands of times more potently than GE or rifampin alone. DOI:http://dx.doi.org/10.7554/eLife.02450.002
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Affiliation(s)
- Yu Zhang
- Waksman Institute, Rutgers University, Piscataway, United States
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6
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Antibiotic streptolydigin requires noncatalytic Mg2+ for binding to RNA polymerase. Antimicrob Agents Chemother 2013; 58:1420-4. [PMID: 24342645 PMCID: PMC3957892 DOI: 10.1128/aac.02248-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multisubunit RNA polymerase, an enzyme that accomplishes transcription in all living organisms, is a potent target for antibiotics. The antibiotic streptolydigin inhibits RNA polymerase by sequestering the active center in a catalytically inactive conformation. Here, we show that binding of streptolydigin to RNA polymerase strictly depends on a noncatalytic magnesium ion which is likely chelated by the aspartate of the bridge helix of the active center. Substitutions of this aspartate may explain different sensitivities of bacterial RNA polymerases to streptolydigin. These results provide the first evidence for the role of noncatalytic magnesium ions in the functioning of RNA polymerase and suggest new routes for the modification of existing and the design of new inhibitors of transcription.
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7
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Marvig RL, Johansen HK, Molin S, Jelsbak L. Genome analysis of a transmissible lineage of pseudomonas aeruginosa reveals pathoadaptive mutations and distinct evolutionary paths of hypermutators. PLoS Genet 2013; 9:e1003741. [PMID: 24039595 PMCID: PMC3764201 DOI: 10.1371/journal.pgen.1003741] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/08/2013] [Indexed: 11/18/2022] Open
Abstract
Genome sequencing of bacterial pathogens has advanced our understanding of their evolution, epidemiology, and response to antibiotic therapy. However, we still have only a limited knowledge of the molecular changes in in vivo evolving bacterial populations in relation to long-term, chronic infections. For example, it remains unclear what genes are mutated to facilitate the establishment of long-term existence in the human host environment, and in which way acquisition of a hypermutator phenotype with enhanced rates of spontaneous mutations influences the evolutionary trajectory of the pathogen. Here we perform a retrospective study of the DK2 clone type of P. aeruginosa isolated from Danish patients suffering from cystic fibrosis (CF), and analyze the genomes of 55 bacterial isolates collected from 21 infected individuals over 38 years. Our phylogenetic analysis of 8,530 mutations in the DK2 genomes shows that the ancestral DK2 clone type spread among CF patients through several independent transmission events. Subsequent to transmission, sub-lineages evolved independently for years in separate hosts, creating a unique possibility to study parallel evolution and identification of genes targeted by mutations to optimize pathogen fitness (pathoadaptive mutations). These genes were related to antibiotic resistance, the cell envelope, or regulatory functions, and we find that the prevalence of pathoadaptive mutations correlates with evolutionary success of co-evolving sub-lineages. The long-term co-existence of both normal and hypermutator populations enabled comparative investigations of the mutation dynamics in homopolymeric sequences in which hypermutators are particularly prone to mutations. We find a positive exponential correlation between the length of the homopolymer and its likelihood to acquire mutations and identify two homopolymer-containing genes preferentially mutated in hypermutators. This homopolymer facilitated differential mutagenesis provides a novel genome-wide perspective on the different evolutionary trajectories of hypermutators, which may help explain their emergence in CF infections. Pseudomonas aeruginosa is the dominating pathogen of chronic airway infections in patients with cystic fibrosis (CF). Although bacterial long-term persistence in CF hosts involves mutation and selection of genetic variants with increased fitness in the CF lung environment, our understanding of the within-host evolutionary processes is limited. Here, we performed a retrospective study of the P. aeruginosa DK2 clone type, which is a transmissible clone isolated from chronically infected Danish CF patients over a period of 38 years. Whole-genome analysis of DK2 isolates enabled a fine-grained reconstruction of the recent evolutionary history of the DK2 lineage and an identification of bacterial genes targeted by mutations to optimize pathogen fitness. The identification of such pathoadaptive genes gives new insight into how the pathogen evolves under the selective pressures of the host immune system and drug therapies. Furthermore, isolates with increased rates of mutation (hypermutator phenotype) emerged in the DK lineage. While this phenotype may accelerate evolution, we also show that hypermutators display differential mutagenesis of certain genes which enable them to follow alternative evolutionary pathways. Overall, our study identifies genes important for bacterial persistence and provides insight into the different mutational mechanisms that govern the adaptive genetic changes.
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Affiliation(s)
- Rasmus Lykke Marvig
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Søren Molin
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail: (SM); (LJ)
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail: (SM); (LJ)
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8
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Miropolskaya N, Nikiforov V, Klimasauskas S, Artsimovitch I, Kulbachinskiy A. Modulation of RNA polymerase activity through the trigger loop folding. Transcription 2012; 1:89-94. [PMID: 21326898 DOI: 10.4161/trns.1.2.12544] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 11/19/2022] Open
Abstract
Folding of the trigger loop of RNA polymerase promotes nucleotide addition through creating a closed, catalytically competent conformation of the active center. Here, we discuss the impact of adjacent RNA polymerase elements, including the F loop and the jaw domain, as well as external regulatory factors on the trigger loop folding and catalysis.
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9
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Pronin SV, Martinez A, Kuznedelov K, Severinov K, Shuman HA, Kozmin SA. Chemical synthesis enables biochemical and antibacterial evaluation of streptolydigin antibiotics. J Am Chem Soc 2011; 133:12172-84. [PMID: 21714556 PMCID: PMC3174773 DOI: 10.1021/ja2041964] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Inhibition of bacterial transcription represents an effective and clinically validated anti-infective chemotherapeutic strategy. We describe the evolution of our approach to the streptolydigin class of antibiotics that target bacterial RNA polymerases (RNAPs). This effort resulted in the synthesis and biological evaluation of streptolydigin, streptolydiginone, streptolic acid, and a series of new streptolydigin-based agents. Subsequent biochemical evaluation of RNAP inhibition demonstrated that the presence of both streptolic acid and tetramic acid subunits was required for activity of this class of antibiotics. In addition, we identified 10,11-dihydrostreptolydigin as a new RNAP-targeting agent, which was assembled with high synthetic efficiency of 15 steps in the longest linear sequence. Dihydrostreptolydigin inhibited three representative bacterial RNAPs and displayed in vitro antibacterial activity against S. salivarius . The overall increase in synthetic efficiency combined with substantial antibacterial activity of this fully synthetic antibiotic demonstrates the power of organic synthesis in enabling design and comprehensive in vitro pharmacological evaluation of new chemical agents that target bacterial transcription.
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Affiliation(s)
- Sergey V. Pronin
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607, United States
| | - Anthony Martinez
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607, United States
| | - Konstantin Kuznedelov
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Konstantin Severinov
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, United States
- Institutes of Gene Biology and Molecualr Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Howard A. Shuman
- Department of Microbiology, University of Chicago, Chicago, Illinois 60607, United States
| | - Sergey A. Kozmin
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607, United States
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10
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Yuzenkova Y, Tadigotla VR, Severinov K, Zenkin N. A new basal promoter element recognized by RNA polymerase core enzyme. EMBO J 2011; 30:3766-75. [PMID: 21792175 PMCID: PMC3173786 DOI: 10.1038/emboj.2011.252] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 06/29/2011] [Indexed: 11/23/2022] Open
Abstract
This study contributes to the understanding of gene-specific transcription by identifying a new promoter element that is contacted directly by an evolutionarily conserved loop within the largest subunit of the core RNA polymerase Bacterial promoters are recognized by RNA polymerase (RNAP) σ subunit, which specifically interacts with the −10 and −35 promoter elements. Here, we provide evidence that the β′ zipper, an evolutionarily conserved loop of the largest subunit of RNAP core, interacts with promoter spacer, a DNA segment that separates the −10 and −35 promoter elements, and facilitates the formation of stable closed promoter complex. Depending on the spacer sequence, the proposed interaction of the β′ zipper with the spacer can also facilitate open promoter complex formation and even substitute for interactions of the σ subunit with the −35 element. These results suggest that there exists a novel class of promoters that rely on interaction of the β′ zipper with promoter spacer, along with or instead of interactions of σ subunit with the −35 element, for their activity. Finally, our data suggest that sequence-dependent interactions of the β′ zipper with DNA can contribute to promoter-proximal σ-dependent RNAP pausing, a recently recognized important step of transcription control.
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Affiliation(s)
- Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, UK
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11
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Involvement of the beta subunit of RNA polymerase in resistance to streptolydigin and streptovaricin in the producer organisms Streptomyces lydicus and Streptomyces spectabilis. Antimicrob Agents Chemother 2010; 54:1684-92. [PMID: 20176899 DOI: 10.1128/aac.01406-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces lydicus NRRL2433 and S. spectabilis NRRL2494 produce two inhibitors of bacterial RNA polymerase: the 3-acyltetramic acid streptolydigin and the naphthalenic ansamycin streptovaricin, respectively. Both strains are highly resistant to their own antibiotics. Independent expression of the S. lydicus and S. spectabilis rpoB and rpoC genes, encoding the beta- and beta'-subunits of RNA polymerase, respectively, in S. albus showed that resistance is mediated by rpoB, with no effect of rpoC. Within the beta-subunit, resistance was confined to an amino acid region harboring the "rif region." Comparison of the beta-subunit amino acid sequences of this region from the producer strains and those of other streptomycetes and site-directed mutagenesis of specific differential residues located in it (L485 and D486 in S. lydicus and N474 and S475 in S. spectabilis) showed their involvement in streptolydigin and streptovaricin resistance. Other amino acids located close to the "Stl pocket" in the S. lydicus beta-subunit (L555, F593, and M594) were also found to exert influence on streptolydigin resistance.
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12
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Ho MX, Hudson BP, Das K, Arnold E, Ebright RH. Structures of RNA polymerase-antibiotic complexes. Curr Opin Struct Biol 2009; 19:715-23. [PMID: 19926275 DOI: 10.1016/j.sbi.2009.10.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 10/19/2009] [Accepted: 10/20/2009] [Indexed: 01/22/2023]
Abstract
Inhibition of bacterial RNA polymerase (RNAP) is an established strategy for antituberculosis therapy and broad-spectrum antibacterial therapy. Crystal structures of RNAP-inhibitor complexes are available for four classes of antibiotics: rifamycins, sorangicin, streptolydigin, and myxopyronin. The structures define three different targets, and three different mechanisms, for inhibition of bacterial RNAP: (1) rifamycins and sorangicin bind near the RNAP active center and block extension of RNA products; (2) streptolydigin interacts with a target that overlaps the RNAP active center and inhibits conformational cycling of the RNAP active center; and (3) myxopyronin interacts with a target remote from the RNAP active center and functions by interfering with opening of the RNAP active-center cleft to permit entry and unwinding of DNA and/or by interfering with interactions between RNAP and the DNA template strand. The structures enable construction of homology models of pathogen RNAP-antibiotic complexes, enable in silico screening for new antibacterial agents, and enable rational design of improved antibacterial agents.
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Affiliation(s)
- Mary X Ho
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, USA
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13
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Carlson JC, Li S, Burr DA, Sherman DH. Isolation and characterization of tirandamycins from a marine-derived Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2009; 72:2076-9. [PMID: 19883065 PMCID: PMC2873692 DOI: 10.1021/np9005597] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The novel dienoyl tetramic acids tirandamycin C (1) and tirandamycin D (2) with activity against vancomycin-resistant Enterococcus faecalis were isolated from the marine environmental isolate Streptomyces sp. 307-9, which also produces the previously identified compounds tirandamycins A (3) and B (4). Spectroscopic analysis of 1 and 2 indicated structural similarity to 3 and 4, with differences only in the pattern of pendant oxygenation on the bicyclic ketal system. The isolation of these putative biosynthetic intermediates was enabled by their sequestration on an adsorbent resin during early stationary-phase fermentation.
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Affiliation(s)
- Jacob C Carlson
- Life Sciences Institute and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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14
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Abstract
RNA polymerase (RNAP) is a complex molecular machine that governs gene expression and its regulation in all cellular organisms. To accomplish its function of accurately producing a full-length RNA copy of a gene, RNAP performs a plethora of chemical reactions and undergoes multiple conformational changes in response to cellular conditions. At the heart of this machine is the active center, the engine, which is composed of distinct fixed and moving parts that serve as the ultimate acceptor of regulatory signals and as the target of inhibitory drugs. Recent advances in the structural and biochemical characterization of RNAP explain the active center at the atomic level and enable new approaches to understanding the entire transcription mechanism, its exceptional fidelity and control.
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Affiliation(s)
- Evgeny Nudler
- Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA.
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15
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Svetlov V, Belogurov GA, Shabrova E, Vassylyev DG, Artsimovitch I. Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res 2007; 35:5694-705. [PMID: 17711918 PMCID: PMC2034486 DOI: 10.1093/nar/gkm600] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Efficient transcription of long polycistronic operons in bacteria frequently relies on accessory proteins but their molecular mechanisms remain obscure. RfaH is a cellular elongation factor that acts as a polarity suppressor by increasing RNA polymerase (RNAP) processivity. In this work, we provide evidence that RfaH acts by reducing transcriptional pausing at certain positions rather than by accelerating RNAP at all sites. We show that ‘fast’ RNAP variants are characterized by pause-free RNA chain elongation and are resistant to RfaH action. Similarly, the wild-type RNAP is insensitive to RfaH in the absence of pauses. In contrast, those enzymes that may be prone to falling into a paused state are hypersensitive to RfaH. RfaH inhibits pyrophosphorolysis of the nascent RNA and reduces the apparent Michaelis–Menten constant for nucleotides, suggesting that it stabilizes the post-translocated, active RNAP state. Given that the RfaH-binding site is located 75 Å away from the RNAP catalytic center, these results strongly indicate that RfaH acts allosterically. We argue that despite the apparent differences in the nucleic acid targets, the time of recruitment and the binding sites on RNAP, unrelated antiterminators (such as RfaH and λQ) utilize common strategies during both recruitment and anti-pausing modification of the transcription complex.
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Affiliation(s)
- Vladimir Svetlov
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
| | - Georgiy A. Belogurov
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
| | - Elena Shabrova
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
| | - Dmitry G. Vassylyev
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
- *To whom correspondence should be addressed. 614 292 6777614 292 8120
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16
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Villain-Guillot P, Bastide L, Gualtieri M, Leonetti JP. Progress in targeting bacterial transcription. Drug Discov Today 2007; 12:200-8. [PMID: 17331884 DOI: 10.1016/j.drudis.2007.01.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Revised: 01/05/2007] [Accepted: 01/23/2007] [Indexed: 01/25/2023]
Abstract
The bacterial RNA polymerase (RNAP) is an essential enzyme that is responsible for making RNA from a DNA template and is targeted by several antibiotics. Rifampicin was the first of such antibiotics to be described and is one of the most efficient anti-tuberculosis drugs in use. In the past five years, structural studies of bacterial RNAP and the resolution of several complexes of drugs bound to RNAP subunits have revealed molecular details of the drug-binding sites and the mechanism of drug action. This knowledge opens avenues for the development of antibiotics. Here these drugs are reviewed, together with their mechanisms and their potential interest for therapeutic applications.
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Affiliation(s)
- Philippe Villain-Guillot
- CNRS UMR 5236, UM1 UM2, Centre d'études d'agents pathogènes et Biotechnologies our la Santé, Av Charles Flahault, 34093 Montpellier, France
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17
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Friedman L, Alder JD, Silverman JA. Genetic changes that correlate with reduced susceptibility to daptomycin in Staphylococcus aureus. Antimicrob Agents Chemother 2006; 50:2137-45. [PMID: 16723576 PMCID: PMC1479123 DOI: 10.1128/aac.00039-06] [Citation(s) in RCA: 347] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Daptomycin is a lipopeptide antibiotic with potent activity against gram-positive bacteria. Complete-genome comparisons of laboratory-derived Staphylococcus aureus with decreased susceptibility to daptomycin and their susceptible parent were used to identify genes that contribute to reduced susceptibility to daptomycin. Selective pressure of growth in sublethal concentrations of daptomycin resulted in the accumulation of mutations over time correlating with incremental decreases in susceptibility. Single point mutations resulting in amino acid substitutions occurred in three distinct proteins: MprF, a lysylphosphatidylglycerol synthetase; YycG, a histidine kinase; and RpoB and RpoC, the beta and beta' subunits of RNA polymerase. Sequence analysis of mprF, yycF, yycG, rpoB, and rpoC in clinical isolates that showed treatment-emergent increases in daptomycin MICs revealed point mutations in mprF and a nucleotide insertion in yycG, suggesting a role for these genes in decreased susceptibility to daptomycin in the hospital setting.
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Affiliation(s)
- Lisa Friedman
- Cubist Pharmaceuticals, Inc., Lexington, MA 02421, USA.
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18
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Trinh V, Langelier MF, Archambault J, Coulombe B. Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol Mol Biol Rev 2006; 70:12-36. [PMID: 16524917 PMCID: PMC1393249 DOI: 10.1128/mmbr.70.1.12-36.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High-resolution crystallographic structures of multisubunit RNA polymerases (RNAPs) have increased our understanding of transcriptional mechanisms. Based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit RNA polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and eukaryotic enzymes. The observations support many previous hypotheses on the transcriptional process, including the implication of the bridge helix and the trigger loop in the processivity of RNAP, the importance of contacts between the RNAP jaw-lobe module and the downstream DNA in the establishment of a transcription bubble and selection of the transcription start site, the destabilizing effects of ppGpp on the open promoter complex, and the link between RNAP processivity and termination. This study also revealed novel, remarkable features of the RNA polymerase catalytic mechanisms that will require additional investigation, including the putative roles of fork loop 2 in the establishment of a transcription bubble, the trigger loop in start site selection, and the uncharacterized funnel domain in RNAP processivity.
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Affiliation(s)
- Vincent Trinh
- Gene Transcription Laboratory, Institut de Recherches Cliniques de Montréal, 110 Ave. des Pins Ouest, Montréal, Québec, Canada
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19
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Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 2005; 19:655-66. [PMID: 16167380 DOI: 10.1016/j.molcel.2005.07.020] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 A resolution structure of the Thermus thermophilus RNAP-Stl complex showed that, in full agreement with the available genetic data, the inhibitor binding site is located 20 A away from the RNAP active site and encompasses the bridge helix and the trigger loop, two elements that are considered to be crucial for RNAP catalytic center function. Structure-based biochemical experiments revealed additional determinants of Stl binding and demonstrated that Stl does not affect NTP substrate binding, DNA translocation, and phosphodiester bond formation. The RNAP-Stl complex structure, its comparison with the closely related substrate bound eukaryotic transcription elongation complexes, and biochemical analysis suggest an inhibitory mechanism in which Stl stabilizes catalytically inactive (preinsertion) substrate bound transcription intermediate, thereby blocking structural isomerization of RNAP to an active configuration. The results provide a basis for a design of new antibiotics utilizing the Stl-like mechanism.
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Affiliation(s)
- Dmitry Temiakov
- Department of Cell Biology, School of Osteopathic Medicine, University of Medicine and Dentistry of New Jersey, Stratford, New Jersey 08084, USA
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20
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Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark AD, Dharia C, Napoli A, Laptenko O, Lee J, Borukhov S, Ebright RH, Arnold E. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 2005; 122:541-52. [PMID: 16122422 PMCID: PMC2754413 DOI: 10.1016/j.cell.2005.07.017] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Revised: 06/03/2005] [Accepted: 07/13/2005] [Indexed: 11/17/2022]
Abstract
We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to but not overlapping the RNAP active center and stabilizes an RNAP-active-center conformational state with a straight-bridge helix. The results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations exist and that cycling between straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations is required for RNAP function. The results set bounds on models for RNAP function and suggest strategies for design of novel antibacterial agents.
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Affiliation(s)
- Steven Tuske
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Stefan G. Sarafianos
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Xinyue Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Brian Hudson
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Elena Sineva
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Jayanta Mukhopadhyay
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Jens J. Birktoft
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Olivier Leroy
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Sajida Ismail
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Arthur D. Clark
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Chhaya Dharia
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Andrew Napoli
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
| | - Oleg Laptenko
- Department of Cell Biology, UMDNJ, Stratford NJ 08084, USA
| | - Jookyung Lee
- Department of Cell Biology, UMDNJ, Stratford NJ 08084, USA
| | | | - Richard H. Ebright
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Eddy Arnold
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
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21
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Campbell EA, Pavlova O, Zenkin N, Leon F, Irschik H, Jansen R, Severinov K, Darst SA. Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J 2005; 24:674-82. [PMID: 15692574 PMCID: PMC549610 DOI: 10.1038/sj.emboj.7600499] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Accepted: 11/08/2004] [Indexed: 11/09/2022] Open
Abstract
A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP beta subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive to mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.
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Affiliation(s)
| | - Olga Pavlova
- Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers University, Piscataway, NJ, USA
- Department of Virology, Faculty of Biology, Moscow State University, Moscow, Russia
| | - Nikolay Zenkin
- Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Fred Leon
- The Rockefeller University, New York, NY, USA
| | - Herbert Irschik
- Department of Natural Products, Gesellschaft für Biotechnologische Forschung, Braunschweig, Germany
| | - Rolf Jansen
- Department of Natural Products, Gesellschaft für Biotechnologische Forschung, Braunschweig, Germany
| | - Konstantin Severinov
- Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Seth A Darst
- The Rockefeller University, New York, NY, USA
- Laboratory of Molecular Biophysics, The Rockefeller University, Box 224, 1230 York Avenue, New York, NY 10021, USA. Tel.: +1 212 327 7479; Fax: +1 212 327 7477; E-mail: or
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22
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MacDougall IJA, Lewis PJ, Griffith R. Homology modelling of RNA polymerase and associated transcription factors from Bacillus subtilis. J Mol Graph Model 2005; 23:297-303. [PMID: 15670950 DOI: 10.1016/j.jmgm.2004.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Revised: 09/29/2004] [Accepted: 10/11/2004] [Indexed: 10/26/2022]
Abstract
RNA polymerase (RNAP) is the central enzyme of transcription and requires interaction with transcription factors in vivo for correct processivity. Both the transcription initiation complex and the ternary elongation complex are stabilised by and require protein-protein interactions between the various components involved. These interactions may form the basis for rational design of small peptide mimics of one or more proteins involved in order to inhibit protein-protein interactions and thus transcription. Here, we present homology models of the model Gram positive organism Bacillus subtilis RNA polymerase in the core and holoenzyme forms. Interactions between RNA polymerase and the transcription factor sigmaA were investigated in order to design peptide mimics of the major interactions.
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Affiliation(s)
- Iain J A MacDougall
- School of Environmental and Life Sciences, The University of Newcastle, Biology Building, Callaghan, NSW 2308, Australia
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23
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Affiliation(s)
- Seth A Darst
- Rockefeller University, Box 224, 1230 York Avenue, New York, NY 10021, USA.
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24
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Artsimovitch I, Chu C, Lynch AS, Landick R. A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science 2003; 302:650-4. [PMID: 14576436 DOI: 10.1126/science.1087526] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
RNA polymerase (RNAP) is the central enzyme of gene expression. Despite availability of crystal structures, details of its nucleotide addition cycle remain obscure. We describe bacterial RNAP inhibitors (the CBR703 series) whose properties illuminate this mechanism. These compounds inhibit known catalytic activities of RNAP (nucleotide addition, pyrophosphorolysis, and Gre-stimulated transcript cleavage) but not translocation of RNA or DNA when translocation is uncoupled from catalysis. CBR703-resistance substitutions occur on an outside surface of RNAP opposite its internal active site. We propose that CBR703 compounds inhibit nucleotide addition allosterically by hindering movements of active site structures that are linked to the CBR703 binding site through a bridge helix.
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Affiliation(s)
- Irina Artsimovitch
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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25
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Yuzenkova J, Delgado M, Nechaev S, Savalia D, Epshtein V, Artsimovitch I, Mooney RA, Landick R, Farias RN, Salomon R, Severinov K. Mutations of bacterial RNA polymerase leading to resistance to microcin j25. J Biol Chem 2002; 277:50867-75. [PMID: 12401787 DOI: 10.1074/jbc.m209425200] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A mutation in the conserved segment of the rpoC gene, which codes for the largest RNA polymerase (RNAP) subunit, beta', was found to make Escherichia coli cells resistant to microcin J25 (MccJ25), a bactericidal 21-amino acid peptide active against Gram-negative bacteria (Delgado, M. A., Rintoul, M. R., Farias, R. N., and Salomon, R. A. (2001) J. Bacteriol. 183, 4543-4550). Here, we report that mutant RNAP prepared from MccJ25-resistant cells, but not the wild-type RNAP, is resistant to MccJ25 in vitro, thus establishing that RNAP is a true cellular target of MccJ25. We also report the isolation of additional rpoC mutations that lead to MccJ25 resistance in vivo and in vitro. The new mutations affect beta' amino acids in evolutionarily conserved segments G, G', and F and are exposed into the RNAP secondary channel, a narrow opening that connects the enzyme surface with the catalytic center. We also report that previously known rpoB (RNAP beta subunit) mutations that lead to streptolydigin resistance cause resistance to MccJ25. We hypothesize that MccJ25 inhibits transcription by binding in RNAP secondary channel and blocking substrate access to the catalytic center.
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Affiliation(s)
- Julia Yuzenkova
- Department of Genetics, Waksman Institute, Piscataway, New Jersey 08854, USA
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26
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Epshtein V, Mustaev A, Markovtsov V, Bereshchenko O, Nikiforov V, Goldfarb A. Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol Cell 2002; 10:623-34. [PMID: 12408829 DOI: 10.1016/s1097-2765(02)00640-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Each elementary step of transcription involves translocation of the 3' terminus of RNA in the RNA polymerase active center, followed by the entry of a nucleoside triphosphate. The structural basis of these transitions was studied using RNA-protein crosslinks. The contacts were mapped and projected onto the crystal structure, in which the "F bridge" helix in the beta' subunit is either bent or relaxed. Bending/relaxation of the F bridge correlates with lateral movements of the RNA 3' terminus. The bent conformation is sterically incompatable with the occupancy of the nucleotide site, suggesting that the switch regulates both the entry of substrates and the translocation of the transcript. The switch occurs as part of a cooperative transition of a larger structural domain that consists of the F helix and the supporting G loop.
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27
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Delgado MA, Rintoul MR, Farías RN, Salomón RA. Escherichia coli RNA polymerase is the target of the cyclopeptide antibiotic microcin J25. J Bacteriol 2001; 183:4543-50. [PMID: 11443089 PMCID: PMC95349 DOI: 10.1128/jb.183.15.4543-4550.2001] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli microcin J25 (MccJ25) is a plasmid-encoded, cyclic peptide antibiotic consisting of 21 unmodified amino acid residues. It is primarily active on gram-negative bacteria related to the producer strain, inducing cell filamentation in an SOS-independent way. A mutation causing resistance to MccJ25 was isolated. Genetic analysis indicated that it resided in the rpoC gene, encoding the beta' subunit of RNA polymerase, at 90 min on the E. coli genetic map. The mutation was genetically crossed on to a plasmid containing the wild-type rpoC gene. The presence of the recombinant plasmid conferred complete resistance to otherwise sensitive strains. Nucleotide sequencing of the plasmid-borne, mutant rpoC gene revealed a ACC (Thr)-to-ATC (Ile) change at codon 931, within homology block G, an evolutionarily conserved region in the large subunits of all RNA polymerases. MccJ25 decreased RNA synthesis both in vivo and in vitro. These results point to the RNA polymerase as the target of microcin action. We favor the possibility that the filamentous phenotype induced by MccJ25 results from impaired transcription of genes coding for cell division proteins. As far as we know, MccJ25 is the first peptide antibiotic shown to affect RNA polymerase.
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Affiliation(s)
- M A Delgado
- Departamento de Bioquímica de la Nutrición, Instituto Superior de Investigaciones Biológicas (Consejo Nacional de Investigaciones Cientificas y Técnicas-Universidad Nacional de Tucumán), Chacabuco 461, 4000 San Miguel de Tucumán, Tucumán, Argentina
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28
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Hamada M, Sakulich AL, Koduru SB, Maraia RJ. Transcription termination by RNA polymerase III in fission yeast. A genetic and biochemically tractable model system. J Biol Chem 2000; 275:29076-81. [PMID: 10843998 DOI: 10.1074/jbc.m003980200] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In order for RNA polymerase (pol) III to produce a sufficient quantity of RNAs of appropriate structure, initiation, termination, and reinitiation must be accurate and efficient. Termination-associated factors have been shown to facilitate reinitiation and regulate transcription in some species. Suppressor tRNA genes that differ in the dT(n) termination signal were examined for function in Schizosaccharomyces pombe. We also developed an S. pombe extract that is active for tRNA transcription that is described here for the first time. The ability of this tRNA gene to be transcribed in extracts from different species allowed us to compare termination in three model systems. Although human pol III terminates efficiently at 4 dTs and S. pombe at 5 dTs, Saccharomyces cerevisiae pol III requires 6 dTs to direct comparable but lower termination efficiency and also appears qualitatively distinct. Interestingly, this pattern of sensitivity to a minimal dT(n) termination signal was found to correlate with the sensitivity to alpha-amanitin, as S. pombe was intermediate between human and S. cerevisiae pols III. The results establish that the pols III of S. cerevisiae, S. pombe, and human exhibit distinctive properties and that termination occurs in S. pombe in a manner that is functionally more similar to human than is S. cerevisiae.
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Affiliation(s)
- M Hamada
- Laboratory of Molecular Growth Regulation, NICHHD, National Institutes of Health, Bethesda, Maryland 20892-2753, USA
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29
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Katayama A, Fujita N, Ishihama A. Mapping of subunit-subunit contact surfaces on the beta' subunit of Escherichia coli RNA polymerase. J Biol Chem 2000; 275:3583-92. [PMID: 10652354 DOI: 10.1074/jbc.275.5.3583] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA polymerase core enzyme of Escherichia coli with the catalytic activity of RNA polymerization is assembled sequentially under the order: 2alpha --> alpha(2) --> alpha(2)beta --> alpha(2)betabeta'. The core enzyme gains the activities of promoter recognition and transcription initiation after binding the sigma subunit. The subunit-subunit contact surfaces of beta' subunit (1407 residues) were analyzed by testing complex formation between various beta' fragments and either the alpha(2)beta complex or the sigma(70) subunit. Results indicate that two regions, one central region between residues 515 and 842 and the other COOH-terminal proximal region downstream from residue 1141, are involved in binding the alpha(2)beta complex; and the NH(2)-terminal proximal region between residues 201 and 345 plays a major role in binding the sigma(70) subunit. However, both alpha(2)beta binding sites have weak activity of the sigma(70) subunit; likewise, the sigma(70) subunit-contact surface has weak binding activity of the alpha(2)beta complex. The sites involved in the catalytic function of RNA polymerization are all located within two spacer regions sandwiched between these three subunit-subunit contact surfaces.
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Affiliation(s)
- A Katayama
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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30
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Opalka N, Mooney RA, Richter C, Severinov K, Landick R, Darst SA. Direct localization of a beta-subunit domain on the three-dimensional structure of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 2000; 97:617-22. [PMID: 10639128 PMCID: PMC15379 DOI: 10.1073/pnas.97.2.617] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To identify the location of a domain of the beta-subunit of Escherichia coli RNA polymerase (RNAP) on the three-dimensional structure, we developed a method to tag a nonessential surface of the multisubunit enzyme with a protein density easily detectable by electron microscopy and image processing. Four repeats of the IgG-binding domain of Staphylococcus aureus protein A were inserted at position 998 of the E. coli RNAP beta-subunit. The mutant RNAP supported E. coli growth and showed no apparent functional defects in vitro. The structure of the mutant RNAP was determined by cryoelectron microscopy and image processing of frozen-hydrated helical crystals. Comparison of the mutant RNAP structure with the previously determined wild-type RNAP structure by Fourier difference analysis at 20-A resolution directly revealed the location of the inserted protein domain, thereby locating the region around position 998 of the beta-subunit within the RNAP three-dimensional structure and refining a model for the subunit locations within the enzyme.
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Affiliation(s)
- N Opalka
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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31
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Markov D, Naryshkina T, Mustaev A, Severinov K. A zinc-binding site in the largest subunit of DNA-dependent RNA polymerase is involved in enzyme assembly. Genes Dev 1999; 13:2439-48. [PMID: 10500100 PMCID: PMC317019 DOI: 10.1101/gad.13.18.2439] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
All multisubunit DNA-dependent RNA polymerases (RNAP) are zinc metalloenzymes, and at least two zinc atoms are present per enzyme molecule. RNAP residues involved in zinc binding and the functional role of zinc ions in the transcription mechanism or RNAP structure are unknown. Here, we locate four cysteine residues in the Escherichia coli RNAP largest subunit, beta', that coordinate one of the two zinc ions tightly associated with the enzyme. In the absence of zinc, or when zinc binding is prevented by mutation, the in vitro-assembled RNAP retains the proper subunit stoichiometry but is not functional. We demonstrate that zinc acts as a molecular chaperone, converting denatured beta' into a compact conformation that productively associates with other RNAP subunits. The beta' residues coordinating zinc are conserved throughout eubacteria and chloroplasts, but are absent from homologs from eukaryotes and archaea. Thus, the involvement of zinc in the RNAP assembly may be a unique feature of eubacterial-type enzymes.
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Affiliation(s)
- D Markov
- Waksman Institute and Department of Genetics, Rutgers, The State University, Piscataway, New Jersey 08854 USA
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32
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Abstract
A ternary complex composed of RNA polymerase (RNAP), DNA template, and RNA transcript is the central intermediate in the transcription cycle responsible for the elongation of the RNA chain. Although the basic biochemistry of RNAP functioning is well understood, little is known about the underlying structural determinants. The absence of high- resolution structural data has hampered our understanding of RNAP mechanism. However, recent work suggests a structure-function model of the ternary elongation complex, if not at a defined structural level, then at least as a conceptual view, such that key components of RNAP are defined operationally on the basis of compelling biochemical, protein chemical, and genetic data. The model has important implications for mechanisms of transcription elongation and also for initiation and termination.
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Affiliation(s)
- E Nudler
- Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA.
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33
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Nussbaum-Shochat A, Amster-Choder O. BglG, the transcriptional antiterminator of the bgl system, interacts with the beta' subunit of the Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 1999; 96:4336-41. [PMID: 10200263 PMCID: PMC16333 DOI: 10.1073/pnas.96.8.4336] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Escherichia coli BglG protein antiterminates transcription at two terminator sites within the bgl operon in response to the presence of beta-glucosides in the growth medium. BglG was previously shown to be an RNA-binding protein that recognizes a specific sequence located just upstream of each of the terminators and partially overlapping with them. We show here that BglG also binds to the E. coli RNA polymerase, both in vivo and in vitro. By using several techniques, we identified the beta' subunit of RNA polymerase as the target for BglG binding. The region that contains the binding site for BglG was mapped to the N-terminal region of beta'. The beta' subunit, produced in excess, prevented BglG activity as a transcriptional antiterminator. Possible roles of the interaction between BglG and the polymerase beta' subunit are discussed.
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Affiliation(s)
- A Nussbaum-Shochat
- Department of Molecular Biology, Hebrew University-Hadassah Medical School, P.O.Box 12272, Jerusalem 91120, Israel
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34
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Zakharova N, Bass I, Arsenieva E, Nikiforov V, Severinov K. Mutations in and monoclonal antibody binding to evolutionary hypervariable region of Escherichia coli RNA polymerase beta' subunit inhibit transcript cleavage and transcript elongation. J Biol Chem 1998; 273:24912-20. [PMID: 9733798 DOI: 10.1074/jbc.273.38.24912] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A 190 amino acid-long region centered around position 1050 of the 1407-amino acid-long beta' subunit of Escherichia coli RNA polymerase (RNAP) is absent from homologues in eukaryotes, archaea and many bacteria. In chloroplasts, the corresponding region can be more than 900 amino acids long. The role of this hypervariable region was studied by deletion mutagenesis of the cloned E. coli rpoC, encoding beta'. Long deletions mimicking beta' from Gram-positive bacteria failed to assemble into RNAP. Mutants with short, 40-60-amino acid-long deletions spanning beta' residues 941-1130 assembled into active RNAP in vitro. These mutant enzymes were defective in the transcript cleavage reaction and had dramatically reduced transcription elongation rates at subsaturating substrate concentrations due to prolonged pausing at sites of transcriptional arrest. Binding of a monoclonal antibody, Pyn1, to the hypervariable region inhibited transcription elongation and intrinsic transcript cleavage and, to a lesser degree, GreB-induced transcript cleavage, but did not interfere with GreB binding to RNAP. We propose that mutations in and antibody binding to the hypervariable, functionally dispensable region of beta' inhibit transcript cleavage and elongation by distorting the flanking conserved segment G in the active center.
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Affiliation(s)
- N Zakharova
- Waksman Institute, Piscataway, New Jersey 08854, USA
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35
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Mooney RA, Artsimovitch I, Landick R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J Bacteriol 1998; 180:3265-75. [PMID: 9642176 PMCID: PMC107278 DOI: 10.1128/jb.180.13.3265-3275.1998] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- R A Mooney
- Department of Bacteriology, University of Wisconsin, Madison 53706-1567, USA
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36
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Archambault J, Jansma DB, Kawasoe JH, Arndt KT, Greenblatt J, Friesen JD. Stimulation of transcription by mutations affecting conserved regions of RNA polymerase II. J Bacteriol 1998; 180:2590-8. [PMID: 9573141 PMCID: PMC107208 DOI: 10.1128/jb.180.10.2590-2598.1998] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mutations that increase the low-level transcription of the Saccharomyces cerevisiae HIS4 gene, which results from deletion of the genes encoding transcription factors BAS1, BAS2, and GCN4, were isolated previously in SIT1 (also known as RPO21, RPB1, and SUA8), the gene encoding the largest subunit of RNA polymerase II (RNAPII). Here we show that sit1 substitutions cluster in two conserved regions of the enzyme which form part of the active site. Six sit1 mutations, affect region F, a region that is involved in transcriptional elongation and in resistance to alpha-aminatin. Four sit1 substitutions lie in another region involved in transcriptional elongation, region D, which binds Mg2+ ions essential for RNA catalysis. One region D substitution is lethal unless suppressed by a substitution in region G and interacts genetically with PPR2, the gene encoding transcription elongation factor IIS. Some sit1 substitutions affect the selection of transcriptional start sites at the CYC1 promoter in a manner reminiscent of that of sua8 (sua stands for suppression of upstream ATG) mutations. Together with previous findings which indicate that regions D and G are in close proximity to the 3' end of the nascent transcript and that region F is involved in the translocation process, our results suggest that transcriptional activation by the sit1 mutations results from alteration of the RNAPII active center.
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Affiliation(s)
- J Archambault
- Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada.
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37
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Mustaev A, Kozlov M, Markovtsov V, Zaychikov E, Denissova L, Goldfarb A. Modular organization of the catalytic center of RNA polymerase. Proc Natl Acad Sci U S A 1997; 94:6641-5. [PMID: 9192618 PMCID: PMC21211 DOI: 10.1073/pnas.94.13.6641] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Fe2+ ion that specifically replaces Mg2+ in the active center of RNA polymerase generates reactive hydroxyl radicals that cause highly localized cleavage of polypeptide chains. Mapping of the cleavage sites revealed the overall architecture of the active center. Nine distinct sites, five in the beta subunit and four in the beta' subunit of Escherichia coli RNA polymerase, all at or near highly conserved sequence motifs, are brought together in the enzyme's ternary structure within the distance of approximately 1 nm from the active center Me2+. These sites are located in at least six different domains of the subunits, reflecting modular organization of the active center.
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Affiliation(s)
- A Mustaev
- Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA
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38
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Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. J Biol Chem 1996; 271:27969-74. [PMID: 8910400 DOI: 10.1074/jbc.271.44.27969] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The beta and beta' subunits of Escherichia coli DNA-dependent RNA polymerase are highly conserved throughout eubacterial and eukaryotic kingdoms. However, in some archaebacteria and chloroplasts, the corresponding sequences are "split" into smaller polypeptides that are encoded by separate genes. To test if such split sites can be accommodated into E. coli RNA polymerase, subunit fragments encoded by the segments of E. coli rpoB and rpoC genes corresponding to archaebacterial and chloroplast split subunits were individually overexpressed. The purified fragments, when mixed in vitro with complementing intact RNA polymerase subunits, yielded an active enzyme capable of catalyzing the phosphodiester bond formation. Thus, the large subunits of eubacteria and eukaryotes are composed of independent structural modules corresponding to the smaller subunits of archaebacteria and chloroplasts.
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Affiliation(s)
- K Severinov
- The Rockefeller University, New York, New York 10021, USA
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39
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Tavormina PL, Landick R, Gross CA. Isolation, purification, and in vitro characterization of recessive-lethal-mutant RNA polymerases from Escherichia coli. J Bacteriol 1996; 178:5263-71. [PMID: 8752347 PMCID: PMC178326 DOI: 10.1128/jb.178.17.5263-5271.1996] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The beta subunit of prokaryotic RNA polymerase shares significant sequence similarity with its eukaryotic and archaeal counterparts across most of the protein. Nine segments of particularly high similarity have been identified and are termed segments A through I. We have isolated severely defective Escherichia coli RNA polymerase mutants, most of which are unable to support bacterial growth. The majority of the substitutions affect residues in one of the conserved segments of beta, including invariant residues in segments D (amino acids 548 to 577), E (amino acids 660 to 678), and I (amino acids 1198 to 1296). In addition, recessive-lethal mutations that affect residues highly conserved only among prokaryotes were identified. They include a substitution in the extreme amino terminus of beta, a region in which no substitutions have previously been identified, and one rpoB mutation that truncates the polypeptide without abolishing minimal polymerase function in vitro. To examine the recessive-lethal alleles in vitro, we devised a novel method to remove nonmutant enzyme from RNA polymerase preparations by affinity tagging the chromosomal rpoB gene. In vitro examination of a subset of purified recessive-lethal RNA polymerases revealed that several substitutions, including all of those altering conserved residues in segment I, severely decrease transcript elongation and increase termination. We discuss the insights these mutants lend to a structure-function analysis of RNA polymerase.
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Affiliation(s)
- P L Tavormina
- Department of Bacteriology, University of Wisconsin--Madison 53706, USA
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40
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Rudd MD, Luse DS. Amanitin greatly reduces the rate of transcription by RNA polymerase II ternary complexes but fails to inhibit some transcript cleavage modes. J Biol Chem 1996; 271:21549-58. [PMID: 8702941 DOI: 10.1074/jbc.271.35.21549] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The toxin alpha-amanitin is frequently employed to completely block RNA synthesis by RNA polymerase II. However, we find that polymerase II ternary transcription complexes stalled by the absence of NTPs resume RNA synthesis when NTPs and amanitin are added. Chain elongation with amanitin can continue for hours at approximately 1% of the normal rate. Amanitin also greatly slows pyrophosphorolysis by elongation-competent complexes. Complexes which are arrested (that is, which have paused in transcription for long periods in the presence of excess NTPs) are essentially incapable of resuming transcription in the presence of alpha-amanitin. Complexes traversing sequences that can provoke arrest are much more likely to stop transcription in the presence of the toxin. The substitution of IMP for GMP at the 3' end of the nascent RNA greatly increases the sensitivity of stalled transcription complexes to amanitin. Neither arrested nor stalled complexes display detectable SII-mediated transcript cleavage following amanitin treatment. However, arrested complexes possess a low level, intrinsic transcript cleavage activity which is completely amanitin-resistant; furthermore, pyrophosphorolytic transcript cleavage in arrested complexes is not affected by amanitin.
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Affiliation(s)
- M D Rudd
- Department of Molecular Biology, Cleveland Clinic Foundation Research Institute, Cleveland, Ohio 44195, USA
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41
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Heisler LM, Feng G, Jin DJ, Gross CA, Landick R. Amino acid substitutions in the two largest subunits of Escherichia coli RNA polymerase that suppress a defective Rho termination factor affect different parts of the transcription complex. J Biol Chem 1996; 271:14572-83. [PMID: 8662850 DOI: 10.1074/jbc.271.24.14572] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Among the earliest rpoBC mutations identified are three suppressors of the conditional lethal rho allele, rho201. These three mutations are of particular interest because, unlike rpoB8, they do not increase termination at all rho-dependent and rho-independent terminators. rpoB211 and rpoB212 both change Asn-1072 to His in conserved region H of rpoB (betaN1072H), whereas rpoC214 changes Arg-352 to Cys in conserved region C of rpoC (beta'R352C). Both substitutions significantly reduce the overall rate of transcript elongation in vitro relative to wild-type RNA polymerase; however, they probably slow elongation for different reasons. The nucleotide triphosphate concentrations required at the T7 A1 promoter for both abortive trinucleotide synthesis and for promoter escape are much greater for betaN1072H. In contrast, beta'R352C and two adjacent substitutions (beta'G351S and beta'S350F), but not betaN1072H, formed open complexes of greatly reduced stability. The sequence in this region of beta' modestly resembles a region of Escherichia coli DNA polymerase I that contacts the phosphate backbone of DNA in co-crystals. Core determinants affecting open complex formation do not reside exclusively in beta', however, since the Rifr mutation rpoB2 in beta also dramatically destabilized open complexes. We suggest that the principal defects of the two Rho-suppressing substitutions may differ, perhaps reflecting a greater role of beta region H in nucleoside triphosphate-binding and nucleotide addition and of beta' region C in contacts to the DNA strands that could be important for translocation. Although both probably suppress rho201 by slowing RNA chain elongation, these differences may lead to terminator specificity that depends on the rate-limiting step at different sites.
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Affiliation(s)
- L M Heisler
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
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42
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Jin DJ, Zhou YN. Mutational analysis of structure-function relationship of RNA polymerase in Escherichia coli. Methods Enzymol 1996; 273:300-19. [PMID: 8791620 DOI: 10.1016/s0076-6879(96)73027-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- D J Jin
- Laboratory of Molecular Biology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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43
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Yang X, Price CW. Streptolydigin resistance can be conferred by alterations to either the beta or beta' subunits of Bacillus subtilis RNA polymerase. J Biol Chem 1995; 270:23930-3. [PMID: 7592585 DOI: 10.1074/jbc.270.41.23930] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Rifampicin and streptolydigin are antibiotics which inhibit prokaryotic RNA polymerase at the initiation and elongation steps, respectively. In Escherichia coli, resistance to each antibiotic results from alterations in the beta subunit of the core enzyme. However, in Bacillus subtilis, reconstitution studies found rifampicin resistance (RifR) associated with the beta subunit and streptolydigin resistance (StlR) with beta'. To understand the basis of bacterial StlR, we isolated the B. subtilis rpoC gene, which encodes a 1,199-residue product that is 53% identical to E. coli beta'. Two spontaneous StlR mutants carried the same D796G substitution in rpoC, and this substitution alone was sufficient to confer StlR in vivo. D796 falls within Region F, which is conserved among the largest subunits of prokaryotic and eukaryotic RNA polymerases. Among eukaryotes, alterations in Region F promote resistance to alpha-amanitin, a toxin which inhibits transcription elongation; among prokaryotes, alterations in Region F cause aberrant termination. To determine whether alterations in the beta subunit of B. subtilis could also confer StlR, we made three StlR substitutions (A499V, G500R, and E502V) in the rif region of rpoB. Together these results suggest that beta and beta' interact to form an Stl binding site, and that this site is important for transcription elongation.
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Affiliation(s)
- X Yang
- Department of Food Science and Technology, University of California, Davis 95616, USA
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