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Wu XX, Mu WH, Li F, Sun SY, Cui CJ, Kim C, Zhou F, Zhang Y. Cryo-EM structures of the plant plastid-encoded RNA polymerase. Cell 2024; 187:1127-1144.e21. [PMID: 38428393 DOI: 10.1016/j.cell.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024]
Abstract
Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. Here, we determined the cryo-EM structures of Nicotiana tabacum (tobacco) PEP-PAP apoenzyme and PEP-PAP transcription elongation complexes at near-atomic resolutions. Our data show the PEP core adopts a typical fold as bacterial RNAP. Fifteen PAPs bind at the periphery of the PEP core, facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and likely couple gene transcription with RNA processing. Our results report the high-resolution architecture of the chloroplast transcription apparatus and provide the structural basis for the mechanistic and functional study of transcription regulation in chloroplasts.
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Affiliation(s)
- Xiao-Xian Wu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen-Hui Mu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Fan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shu-Yi Sun
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao-Jun Cui
- University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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2
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Stephanie F, Tambunan USF, Siahaan TJ. M. tuberculosis Transcription Machinery: A Review on the Mycobacterial RNA Polymerase and Drug Discovery Efforts. Life (Basel) 2022; 12:1774. [PMID: 36362929 PMCID: PMC9695777 DOI: 10.3390/life12111774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 09/08/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is the main source of tuberculosis (TB), one of the oldest known diseases in the human population. Despite the drug discovery efforts of past decades, TB is still one of the leading causes of mortality and claimed more than 1.5 million lives worldwide in 2020. Due to the emergence of drug-resistant strains and patient non-compliance during treatments, there is a pressing need to find alternative therapeutic agents for TB. One of the important areas for developing new treatments is in the inhibition of the transcription step of gene expression; it is the first step to synthesize a copy of the genetic material in the form of mRNA. This further translates to functional protein synthesis, which is crucial for the bacteria living processes. MTB contains a bacterial DNA-dependent RNA polymerase (RNAP), which is the key enzyme for the transcription process. MTB RNAP has been targeted for designing and developing antitubercular agents because gene transcription is essential for the mycobacteria survival. Initiation, elongation, and termination are the three important sequential steps in the transcription process. Each step is complex and highly regulated, involving multiple transcription factors. This review is focused on the MTB transcription machinery, especially in the nature of MTB RNAP as the main enzyme that is regulated by transcription factors. The mechanism and conformational dynamics that occur during transcription are discussed and summarized. Finally, the current progress on MTB transcription inhibition and possible drug target in mycobacterial RNAP are also described to provide insight for future antitubercular drug design and development.
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Affiliation(s)
- Filia Stephanie
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Usman Sumo Friend Tambunan
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Teruna J. Siahaan
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, KS 66045, USA
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3
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Garrido-Godino AI, Gutiérrez-Santiago F, Navarro F. Biogenesis of RNA Polymerases in Yeast. Front Mol Biosci 2021; 8:669300. [PMID: 34026841 PMCID: PMC8136413 DOI: 10.3389/fmolb.2021.669300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/31/2021] [Indexed: 01/25/2023] Open
Abstract
Eukaryotic RNA polymerases (RNA pols) transcriptional processes have been extensively investigated, and the structural analysis of eukaryotic RNA pols has been explored. However, the global assembly and biogenesis of these heteromultimeric complexes have been narrowly studied. Despite nuclear transcription being carried out by three RNA polymerases in eukaryotes (five in plants) with specificity in the synthesis of different RNA types, the biogenesis process has been proposed to be similar, at least for RNA pol II, to that of bacteria, which contains only one RNA pol. The formation of three different interacting subassembly complexes to conform the complete enzyme in the cytoplasm, prior to its nuclear import, has been assumed. In Saccharomyces cerevisiae, recent studies have examined in depth the biogenesis of RNA polymerases by characterizing some elements involved in the assembly of these multisubunit complexes, some of which are conserved in humans. This study reviews the latest studies governing the mechanisms and proteins described as being involved in the biogenesis of RNA polymerases in yeast.
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Affiliation(s)
- Ana I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain
| | | | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
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An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase. EcoSal Plus 2019; 8. [PMID: 30109846 DOI: 10.1128/ecosalplus.esp-0004-2018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA polymerase (RNAP) is the essential enzyme responsible for transcribing genetic information stored in DNA to RNA. Understanding the structure and function of RNAP is important for those who study basic principles in gene expression, such as the mechanism of transcription and its regulation, as well as translational sciences such as antibiotic development. With over a half-century of investigations, there is a wealth of information available on the structure and function of Escherichia coli RNAP. This review introduces the structural features of E. coli RNAP, organized by subunit, giving information on the function, location, and conservation of these features to early stage investigators who have just started their research of E. coli RNAP.
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Murayama S, Ishikawa S, Chumsakul O, Ogasawara N, Oshima T. The Role of α-CTD in the Genome-Wide Transcriptional Regulation of the Bacillus subtilis Cells. PLoS One 2015; 10:e0131588. [PMID: 26154296 PMCID: PMC4495994 DOI: 10.1371/journal.pone.0131588] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 06/02/2015] [Indexed: 11/22/2022] Open
Abstract
The amino acid sequence of the RNA polymerase (RNAP) α-subunit is well conserved throughout the Eubacteria. Its C-terminal domain (α-CTD) is important for the transcriptional regulation of specific promoters in both Escherichia coli and Bacillus subtilis, through interactions with transcription factors and/or a DNA element called the "UP element". However, there is only limited information regarding the α-CTD regulated genes in B. subtilis and the importance of this subunit in the transcriptional regulation of B. subtilis. Here, we established strains and the growth conditions in which the α-subunit of RNAP was replaced with a C-terminally truncated version. Transcriptomic and ChAP-chip analyses revealed that α-CTD deficiency reduced the transcription and RNAP binding of genes related to the utilization of secondary carbon sources, transition state responses, and ribosome synthesis. In E. coli, it is known that α-CTD also contributes to the expression of genes related to the utilization of secondary carbon sources and ribosome synthesis. Our results suggest that the biological importance of α-CTD is conserved in B. subtilis and E. coli, but that its specific roles have diversified between these two bacteria.
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Affiliation(s)
- Satohiko Murayama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Shu Ishikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Onuma Chumsakul
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Taku Oshima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
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Dhieb A, Elleuch A, Kriaa W, Masmoudi F, Drira N. Molecular characterization and in silico analysis of RNA polymerase alpha subunit gene (rpoA) in Date Palm (Phoenix dactylifera L.) cv. Deglet Nour. Genes Genomics 2012. [DOI: 10.1007/s13258-012-0027-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mukhamedyarov D, Makarova KS, Severinov K, Kuznedelov K. Francisella RNA polymerase contains a heterodimer of non-identical α subunits. BMC Mol Biol 2011; 12:50. [PMID: 22108176 PMCID: PMC3294249 DOI: 10.1186/1471-2199-12-50] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 11/22/2011] [Indexed: 11/11/2022] Open
Abstract
Background All sequenced genomes of representatives of the Francisella genus contain two rpoA genes, which encode non-identical RNA polymerase (RNAP) subunits, α1 and α2. In all other bacteria studied to date, a dimer of identical α subunits initiates the assembly of the catalytically proficient RNAP core (subunit composition α2ββ'). Based on an observation that both α1 and α2 are incorporated into Francisella RNAP, Charity et al. (2007) previously suggested that up to four different species of RNAP core enzyme might form in the same Francisella cell. Results By in vitro assembly from fully denatured state, we determined that both Francisella α subunits are required for efficient dimerization; no homodimer formation was detected. Bacterial two-hybrid system analysis likewise indicated strong interactions between the α1 and α2 N-terminal domains (NTDs, responsible for dimerization). NTDs of α2 did not interact detectably, while weak interaction between α1 NTDs was observed. This weak homotypic interaction may explain low-level transcription activity observed in in vitro RNAP reconstitution reactions containing Francisella large subunits (β', β) and α1. No activity was observed with RNAP reconstitution reactions containing α2, while robust transcription activity was detected in reactions containing α1 and α2. Phylogenetic analysis based on RpoA resulted in a tree compatible with standard bacterial taxonomy with both Francisella RpoA branches positioned within γ-proteobacteria. The observed phylogeny and analysis of constrained trees are compatible with Francisella lineage-specific rpoA duplication followed by acceleration of evolutionary rate and subfunctionalization. Conclusions The results strongly suggest that most Francisella RNAP contains α heterodimer with a minor subfraction possibly containing α1 homodimer. Comparative sequence analysis suggests that this heterodimer is oriented, in a sense that only one monomer, α1, interacts with the β subunit during the α2β RNAP subassembly formation. Most likely the two rpoA copies in Francisella have emerged through a lineage-specific duplication followed by subfunctionalization of interacting paralogs.
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Affiliation(s)
- Damir Mukhamedyarov
- Department of Biochemistry and Molecular Biology and Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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The E. coli anti-sigma factor Rsd: studies on the specificity and regulation of its expression. PLoS One 2011; 6:e19235. [PMID: 21573101 PMCID: PMC3089606 DOI: 10.1371/journal.pone.0019235] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 03/23/2011] [Indexed: 12/31/2022] Open
Abstract
Background Among the seven different sigma factors in E. coli σ70 has the highest concentration and affinity for the core RNA polymerase. The E. coli protein Rsd is regarded as an anti-sigma factor, inhibiting σ70-dependent transcription at the onset of stationary growth. Although binding of Rsd to σ70 has been shown and numerous structural studies on Rsd have been performed the detailed mechanism of action is still unknown. Methodology/Principal Findings We have performed studies to unravel the function and regulation of Rsd expression in vitro and in vivo. Cross-linking and affinity binding revealed that Rsd is able to interact with σ70, with the core enzyme of RNA polymerase and is able to form dimers in solution. Unexpectedly, we find that Rsd does also interact with σ38, the stationary phase-specific sigma factor. This interaction was further corroborated by gel retardation and footprinting studies with different promoter fragments and σ38- or σ70-containing RNA polymerase in presence of Rsd. Under competitive in vitro transcription conditions, in presence of both sigma factors, a selective inhibition of σ70-dependent transcription was prevailing, however. Analysis of rsd expression revealed that the nucleoid-associated proteins H-NS and FIS, StpA and LRP bind to the regulatory region of the rsd promoters. Furthermore, the major promoter P2 was shown to be down-regulated in vivo by RpoS, the stationary phase-specific sigma factor and the transcription factor DksA, while induction of the stringent control enhanced rsd promoter activity. Most notably, the dam-dependent methylation of a cluster of GATC sites turned out to be important for efficient rsd transcription. Conclusions/Significance The results contribute to a better understanding of the intricate mechanism of Rsd-mediated sigma factor specificity changes during stationary phase.
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Twist KA, Husnain SI, Franke JD, Jain D, Campbell EA, Nickels BE, Thomas MS, Darst SA, Westblade LF. A novel method for the production of in vivo-assembled, recombinant Escherichia coli RNA polymerase lacking the α C-terminal domain. Protein Sci 2011; 20:986-95. [PMID: 21416542 DOI: 10.1002/pro.622] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 02/22/2011] [Accepted: 03/02/2011] [Indexed: 11/08/2022]
Abstract
The biochemical characterization of the bacterial transcription cycle has been greatly facilitated by the production and characterization of targeted RNA polymerase (RNAP) mutants. Traditionally, RNAP preparations containing mutant subunits have been produced by reconstitution of denatured RNAP subunits, a process that is undesirable for biophysical and structural studies. Although schemes that afford the production of in vivo-assembled, recombinant RNAP containing amino acid substitutions, insertions, or deletions in either the monomeric β or β' subunits have been developed, there is no such system for the production of in vivo-assembled, recombinant RNAP with mutations in the homodimeric α-subunits. Here, we demonstrate a strategy to generate in vivo-assembled, recombinant RNAP preparations free of the α C-terminal domain. Furthermore, we describe a modification of this approach that would permit the purification of in vivo-assembled, recombinant RNAP containing any α-subunit variant, including those variants that are lethal. Finally, we propose that these related approaches can be extended to generate in vivo-assembled, recombinant variants of other protein complexes containing homomultimers for biochemical, biophysical, and structural analyses.
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Affiliation(s)
- Kelly-Anne Twist
- The Rockefeller University, Laboratory of Molecular Biophysics, 1230 York Avenue, New York, New York 10065, USA
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Ganguly A, Chatterji D. Sequential assembly of an active RNA polymerase molecule at the air-water interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:3808-3814. [PMID: 21395266 DOI: 10.1021/la200225t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
At the heart of understanding cellular processes lies our ability to explore the specific nature of communication between sequential information carrying biopolymers. However, the data extracted from conventional solution phase studies may not reflect the dynamics of communication between recognized partners as they occur in the crowded cellular milieu. We use the principle of immobilization of histidine-tagged biopolymers at a Ni(II)-encoded Langmuir monolayer to study sequence-specific protein-protein interactions in an artificially crowded environment. The advantage of this technique lies in increasing the surface density of one of the interacting partners that allows us to study macromolecular interactions in a controlled crowded environment, but without compromising the speed of the reactions. We have taken advantage of this technique to follow the sequential assembly process of the multiprotein complex Escherichia coli RNA polymerase at the interface and also deciphered the role of one of the proteins, omega (ω), in the assembly pathway. Our reconstitution studies indicate that in the absence of molecular chaperones or other cofactors, omega (ω) plays a decisive role in refolding the largest protein beta prime (β') and its recruitment into the multimeric assembly to reconstitute an active RNA polymerase. It was also observed that the monolayer had the ability to distinguish between sequence-specific and -nonspecific interactions despite the immobilization of one of the biomacromolecules. The technique provides a universal two-dimensional template for studying protein-ligand interactions while mimicking molecular crowding.
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Affiliation(s)
- Abantika Ganguly
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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11
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Wurm R, Neußer T, Wagner R. 6S RNA-dependent inhibition of RNA polymerase is released by RNA-dependent synthesis of small de novo products. Biol Chem 2010; 391:187-196. [PMID: 20030589 DOI: 10.1515/bc.2010.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
6S RNA from Escherichia coli is known to bind to RNA polymerase, preventing interaction with many promoters during stationary growth. The resulting repression is released under conditions of nutritional upshift, when the growth situation improves. 6S RNA, which binds to the active site of RNA polymerase, has the particularly interesting feature to act as a template, causing the transcription of defined de novo RNAs (dnRNA) that are complementary to a specific sequence region of the 6S RNA. We analyzed the conditions of dnRNA synthesis and determined their effect on the 6S RNA-mediated inhibition of RNA polymerase in vitro and in vivo. Upon nutritional upshift the RNA polymerase/6S RNA complex induces the rapid synthesis of dnRNAs, which form stable hybrids with the 6S RNA template. The resulting structural change destabilizes the inactivated RNA polymerase complex, causing sigma subunit release. Both dnRNA and 6S RNA are rapidly degraded after complex disintegration. Experiments using the transcriptional inhibitor rifampicin demonstrate that active transcription is required for the disintegration of the RNA polymerase/6S RNA complex. Our results support the conclusion that 6S RNA not only inhibits transcription during stationary growth but also enables cells to resume rapid growth after starvation and help to escape from stationary phase.
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Affiliation(s)
- Reinhild Wurm
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Thomas Neußer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Rolf Wagner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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Lamour V, Westblade LF, Campbell EA, Darst SA. Crystal structure of the in vivo-assembled Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex. J Struct Biol 2009; 168:352-6. [PMID: 19580872 DOI: 10.1016/j.jsb.2009.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 06/30/2009] [Accepted: 07/01/2009] [Indexed: 11/30/2022]
Abstract
The Bacillus subtilis Spx protein is a global transcription factor that interacts with the C-terminal domain of the RNA polymerase alpha subunit (alphaCTD) and regulates transcription of genes involved in thiol-oxidative stress, sporulation, competence, and organosulfur metabolism. Here we determined the X-ray crystal structure of the Spx/alphaCTD complex from an entirely new crystal form than previously reported [Newberry, K.J., Nakano, S., Zuber, P., Brennan, R.G., 2005. Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase. Proc. Natl. Acad. Sci. USA 102, 15839-15844]. Comparison of the previously reported sulfate-bound complex and our sulfate-free complex reveals subtle conformational changes that may be important for the role of Spx in regulating organosulfur metabolism.
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Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes. Appl Environ Microbiol 2009; 75:2705-11. [PMID: 19251886 DOI: 10.1128/aem.01888-08] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Combinatorial or random methods for strain engineering have been extensively used for the improvement of multigenic phenotypes and other traits for which the underlying mechanism is not fully understood. Although the preferred method has traditionally been mutagenesis and selection, our laboratory has successfully used mutant transcription factors, which direct the RNA polymerase (RNAP) during transcription, to engineer complex phenotypes in microbial cells. Here, we show that it is also possible to impart new phenotypes by altering the RNAP core enzyme itself, in particular through mutagenesis of the alpha subunit of the bacterial polymerase. We present the use of this tool for improving tolerance of Escherichia coli to butanol and other solvents and for increasing the titers of two commercially relevant products, L-tyrosine and hyaluronic acid. In addition, we explore the underlying physiological changes that give rise to the solvent-tolerant mutant.
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Neußer T, Gildehaus N, Wurm R, Wagner R. Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation. Biol Chem 2008; 389:285-97. [DOI: 10.1515/bc.2008.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe small bacterial 6S RNA has been recognized as a transcriptional regulator, facilitating the transition from exponential to stationary growth phase by preferentially inhibiting Eσ70RNA polymerase holoenzyme transcription. Consistent with this function, the cellular concentration of 6S RNA increases with stationary phase. We have studied the underlying mechanisms responsible for the growth phase-dependent differences in 6S RNA concentration. To this aim, we have analyzed the effects of the typical bacterial growth phase and stress regulators FIS, H-NS, LRP and StpA on 6S RNA expression. Measurements of 6S RNA accumulation in strains deficient in each one of these proteins support their contribution as potential regulators. Specific binding of the four proteins to DNA fragments containing 6S RNA promoters was demonstrated by gel retardation and DNase I footprinting. Moreover,in vitrotranscription analysis with both RNA polymerase holoenzymes, Eσ70and Eσ38, demonstrated a direct inhibition of 6S RNA transcription by H-NS, StpA and LRP, while FIS seems to act as a dual regulator.In vitrotranscription in the presence of ppGpp indicates that 6S RNA promoters are not stringently regulated. Our results underline that regulation of 6S RNA transcription depends on a complex network, involving a set of bacterial regulators with general importance in the adaptation to changing growth conditions.
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15
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Gildehaus N, Neußer T, Wurm R, Wagner R. Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts. Nucleic Acids Res 2007; 35:1885-96. [PMID: 17332013 PMCID: PMC1874619 DOI: 10.1093/nar/gkm085] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/30/2007] [Accepted: 01/30/2007] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli 6S RNA represents a non-coding RNA (ncRNA), which, based on the conserved secondary structure and previous functional studies, had been suggested to interfere with transcription. Selective inhibition of sigma-70 holoenzymes, preferentially at extended -10 promoters, but not stationary-phase-specific transcription was described, suggesting a direct role of 6S RNA in the transition from exponential to stationary phase. To elucidate the underlying mechanism, we have analysed 6S RNA interactions with different forms of RNA polymerase by gel retardation and crosslinking. Preferred binding of 6S RNA to Esigma(70) was confirmed, however weaker binding to Esigma(38) was also observed. The crosslinking analysis revealed direct contact between a central 6S RNA sequence element and the beta/beta' and sigma subunits. Promoter complex formation and in vitro transcription analysis with exponential- and stationary-phase-specific promoters and the corresponding holoenzymes demonstrated that 6S RNA interferes with transcription initiation but does not generally distinguish between exponential- and stationary-phase-specific promoters. Moreover, we show for the first time that 6S RNA acts as a template for the transcription of defined RNA molecules in the absence of DNA. In conclusion, this study reveals new aspects of 6S RNA function.
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MESH Headings
- Binding Sites
- DNA-Directed RNA Polymerases/metabolism
- Escherichia coli/genetics
- Gene Expression Regulation, Bacterial
- Promoter Regions, Genetic
- RNA/biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Bacterial/physiology
- RNA, Untranslated/chemistry
- RNA, Untranslated/metabolism
- RNA, Untranslated/physiology
- Sigma Factor/metabolism
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
| | | | | | - Rolf Wagner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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Conclusions. Proteomics 2005. [DOI: 10.1007/0-306-46895-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Imamura S, Asayama M, Shirai M. In vitro transcription analysis by reconstituted cyanobacterial RNA polymerase: roles of group 1 and 2 sigma factors and a core subunit, RpoC2. Genes Cells 2005; 9:1175-87. [PMID: 15569150 DOI: 10.1111/j.1365-2443.2004.00808.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RNA polymerase (RNAP) core enzyme of cyanobacterium Synechocystis sp. strain PCC 6803 was reconstituted with overproduced recombinant subunits and purified with C-terminal histidine-tagged RpoA. The core enzyme with purified a sigma factor, SigA/SigD or SigB, allowed specific in vitro transcription from the light-inducible psbA2 or the dark-/heat-inducible lrtA/hspA promoters, respectively. Further analysis using a mutant psbA2 promoter revealed that the -35 hexamer of the promoter was essential for SigA but not SigD. Similar but distinct patterns of psbA2 transcription were found for two types of RNAP, cyanobacterial (alpha2betabeta'gamma) and E. coli (alpha2betabeta') core enzymes. Specific binding of PCC 6803 RpoC2 (beta') to E. coli core enzyme and its contribution to efficient psbA2 transcription by RNAP-SigA/D suggest that this subunit could confer an important role on the cyanobactrial RNAP. Differences in affinity and specificity among cyanobacterial sigma factors for the core enzyme and promoters were discussed.
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Affiliation(s)
- Sousuke Imamura
- Laboratory of Molecular Genetics, College of Agriculture, Ibaraki University, Ami, Inashiki, Ibaraki 300-0393, Japan
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18
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Suzuki JY, Ytterberg AJ, Beardslee TA, Allison LA, Wijk KJ, Maliga P. Affinity purification of the tobacco plastid RNA polymerase and in vitro reconstitution of the holoenzyme. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 40:164-72. [PMID: 15361150 DOI: 10.1111/j.1365-313x.2004.02195.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We affinity-purified the tobacco plastid-encoded plastid RNA polymerase (PEP) complex by the alpha subunit containing a C-terminal 12 x histidine tag using heparin and Ni(2+) chromatography. The composition of the complex was determined by mass spectrometry after separating the proteins of the >900 kDa complex in blue native and SDS polyacrylamide gels. The purified PEP contained the core alpha, beta, beta', beta" subunits and five major associated proteins of unknown function, but lacked sigma factors required for promoter recognition. The holoenzyme efficiently recognized a plastid psbA promoter when it was reconstituted from the purified PEP and recombinant plastid sigma factors. Reconstitution of a plastid holoenzyme with individual sigma factors will facilitate identification of sigma factor-specific promoter elements.
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Affiliation(s)
- Jon Y Suzuki
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
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19
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Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W. Bacteriophage T4 genome. Microbiol Mol Biol Rev 2003; 67:86-156, table of contents. [PMID: 12626685 PMCID: PMC150520 DOI: 10.1128/mmbr.67.1.86-156.2003] [Citation(s) in RCA: 558] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.
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Affiliation(s)
- Eric S Miller
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA.
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20
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Ruiz R, Ramos JL, Egan SM. Interactions of the XylS regulators with the C-terminal domain of the RNA polymerase alpha subunit influence the expression level from the cognate Pm promoter. FEBS Lett 2001; 491:207-11. [PMID: 11240128 DOI: 10.1016/s0014-5793(01)02192-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Pseudomonas putida meta-cleavage operon encodes the enzymes for the catabolism of alkylbenzoates. Activation of meta-operon transcription is mediated by the XylS protein which, upon activation by effectors, binds two sites between -70 and -35 with respect to the main transcription initiation point at the Pm promoter. Two naturally occurring regulators, XylS and XylS1, that differ by only five amino acids, have been analyzed with regard to potential interactions of these positive regulators with the C-terminal domain of the alpha subunit of RNA polymerase (alpha-CTD). For these studies we expressed a derivative of alpha deprived of the entire C-terminal domain (alpha-Delta235) and found that expression from Pm with XylS or XylS1 was significantly decreased. To discern whether alpha-CTD activation depended on interactions with DNA and/or XylS proteins we tested a large collection of alanine substitutions within alpha-CTD. Most substitutions that had an effect on XylS and XylS1-dependent transcription were located in or adjacent to helix 1 and 4, which are known to be involved in alpha-CTD interactions with DNA. Two alanine substitutions in helix 3 (residues 287 and 291) identified a putative region of alpha-CTD/XylS regulator interactions.
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Affiliation(s)
- R Ruiz
- Consejo Superior de Investigaciones Cientificas, Estación Experimental del Zaidín, Department of Plant Biochemistry, Albareda, Granada, Spain
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21
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Sommer N, Salniene V, Gineikiene E, Nivinskas R, Rüger W. T4 early promoter strength probed in vivo with unribosylated and ADP-ribosylated Escherichia coli RNA polymerase: a mutation analysis. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 10):2643-2653. [PMID: 11021939 DOI: 10.1099/00221287-146-10-2643] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The consensus sequence of T4 early promoters differs in length, sequence and degree of conservation from that of Escherichia coli sigma(70) promoters. The enzyme interacting with these promoters, and transcribing the T4 genome, is native host RNA polymerase, which is increasingly modified by the phage-encoded ADP-ribosyltransferase, Alt. T4 early transcription is a very active process, possibly out-competing host transcription. The much stronger T4 promoters enhance viral transcription by a factor of at least two and the Alt-catalysed ADP-ribosylation of the host enzyme triggers an additional enhancement, again by a factor of about two. To address the question of which promoter elements contribute to the increasing transcriptional activity directed towards phage genes, the very strong E. coli promoter, Ptac, was sequentially mutated towards the sequence of the T4 early promoter consensus. Second, mutations were introduced into the highly conserved regions of the T4 early promoter, P8.1. The co-occurrence of the promoter-encoding plasmid pKWIII and vector pTKRI, which expresses Alt in E. coli, constitutes a test system that allows comparison of the transcriptional activities of phage and bacterial promoters, in the presence of native, or alternatively ADP-ribosylated RNA polymerase. Results reveal that T4 early promoters exhibit a bipartite structure, capable of strong interaction with both types of RNA polymerase. The -10, -16, -42 and -52 regions are important for transcript initiation with the native polymerase. To facilitate acceleration of transcription, the ADP-ribosylated enzyme requires not only the integrity of the -10, -16 and -35 regions, but also that of position -33, and even more importantly, maintenance of the upstream promoter element at position -42. The latter positions introduced into the E. coli Ptac promoter render this mutant promoter responsive to Alt-ADP-ribosylated RNA polymerase, like T4 early promoters.
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Affiliation(s)
- Nicole Sommer
- Arbeitsgruppe Molekulare Genetik, Fakultät für Biologie, Ruhr-Universität Bochum, D-44780 Bochum, Germany1
| | - Vida Salniene
- Institute of Biochemistry, Laboratory of Gene Engineering, Vilnius 2600, Lithuania2
| | - Egle Gineikiene
- Institute of Biochemistry, Laboratory of Gene Engineering, Vilnius 2600, Lithuania2
| | - Rimas Nivinskas
- Institute of Biochemistry, Laboratory of Gene Engineering, Vilnius 2600, Lithuania2
| | - Wolfgang Rüger
- Arbeitsgruppe Molekulare Genetik, Fakultät für Biologie, Ruhr-Universität Bochum, D-44780 Bochum, Germany1
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22
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Fujita N, Endo S, Ishihama A. Structural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase. Biochemistry 2000; 39:6243-9. [PMID: 10821700 DOI: 10.1021/bi000020d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The carboxy-terminal domain of the alpha subunit of Escherichia coli RNA polymerase, which is connected with the core part of RNA polymerase through a long flexible linker, plays decisive roles in transcription activation by directly interacting with a large number of transcription factors and upstream (UP) element DNA. Here we constructed a set of mutant RNA polymerases, each containing a mutant alpha subunit with an altered interdomain linker. Deletion of three amino acids from the linker exhibited 50% inhibition of cAMP receptor protein- (CRP-) dependent lac P1 transcription. Deletion of six amino acids completely knocked out the activity. Insertion of three amino acids did not affect the activity, whereas 40-60% inhibition was observed after insertion of one, two, or four amino acids. Substitution of 10 consecutive glycine residues resulted in nearly 90% reduction of the CRP-dependent activity, whereas 50% activity was retained after substitution of 10 proline residues or a sequence expected to form a strong alpha-helix. Essentially the same results were obtained with UP element-dependent rrnB P1 transcription. These observations altogether suggest that (i) sufficient length of the interdomain linker is required for transcription activation mediated by the alpha carboxy-terminal domain, (ii) the linker is not totally unstructured but has structural and torsional preferences to facilitate positioning of the carboxy-terminal domain to a proper location for the interaction with CRP and UP element, and (iii) CRP-dependent activation and UP element-dependent activation share a common intermediary state in which the positioning of the alpha carboxy-terminal domain is of primary importance.
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Affiliation(s)
- N Fujita
- Department of Molecular Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
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23
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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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24
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Nomura T, Fujita N, Ishihama A. Mapping of subunit-subunit contact surfaces on the beta subunit of Escherichia coli RNA polymerase. Biochemistry 1999; 38:1346-55. [PMID: 9930997 DOI: 10.1021/bi982381n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The RNA polymerase core enzyme of Escherichia coli is composed of 2alpha, 1beta, and 1beta' subunits. Previously we mapped the alpha-alpha, alpha-beta, and alpha-beta' contact sites on the alpha subunit. Here we analyzed the alpha subunit contact sites on the beta subunit by using various experimental approaches: (i) comparison of the proteolytic cleavage map between the unassembled free beta subunit and the alpha2 beta complex; (ii) analysis of the binary complex formation between His6-tagged intact alpha subunit and various truncated beta fragments; and (iii) analysis of the complex formation between the alpha subunit and various His6-tagged beta fragments. The results altogether indicate that two regions of the beta subunit are involved in the full activity of alpha binding, that is, the primary contact site between residues 737 and 904 and the secondary region with assembly control activity downstream from residue 1138. All of the alpha subunit-beta fragment binary complexes identified in this study were found to bind beta' subunit and form pseudo-core complexes, indicating that the regions of beta involved in alpha subunit contact also participate in interaction with the beta' subunit.
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Affiliation(s)
- T Nomura
- Department of Molecular Genetics, National Institute of Genetics, and School of Life Science, Graduate University for Advances Studies, Mishima, Shizuoka 411-8540, Japan
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25
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Darst SA, Polyakov A, Richter C, Zhang G. Insights into Escherichia coli RNA polymerase structure from a combination of x-ray and electron crystallography. J Struct Biol 1998; 124:115-22. [PMID: 10049799 DOI: 10.1006/jsbi.1998.4057] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Our goal is to understand the mechanism of transcription and its regulation. Determining structures of RNA polymerase and transcription complexes is an essential step. Because of their large size and complexity, determination of these structures will require a combination of electron microscopy, biophysical methods, and biochemical methods to identify functionally and structurally relevant subassemblies and domains and x-ray crystallography to determine high-resolution structures of RNA polymerase components and accessory factors. We recently solved the 2.5-A crystal structure of the Escherichia coli RNA polymerase alpha subunit N-terminal domain, which is the first high-resolution structure of a core component required for RNA polymerase assembly and basal transcription. This structure, combined with a new 19-A resolution structure determined by cryo-electron microscopy of helical crystals of E. coli core RNAP embedded in vitreous ice, leads to a model for the organization of the RNAP subunits.
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Affiliation(s)
- S A Darst
- The Rockefeller University, New York, New York, 10021, USA.
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26
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Rojo F, Mencía M, Monsalve M, Salas M. Transcription activation and repression by interaction of a regulator with the alpha subunit of RNA polymerase: the model of phage phi 29 protein p4. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1998; 60:29-46. [PMID: 9594570 DOI: 10.1016/s0079-6603(08)60888-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Regulatory protein p4, encoded by Bacillus subtilis phage phi 29, has proved to be a very useful model to analyze the molecular mechanisms of transcription regulation. Protein p4 modulates the transcription of phage phi 29 genome by activating the late A3 promoter (PA3) and simultaneously repressing the two main early promoters, A2b and A2c (or PA2b and PA2c). This review describes in detail the regulatory mechanism leading to activation or repression, and discusses them in the context of the recent findings on the role of the RNA polymerase alpha subunit in transcription regulation. Activation of PA3 implies the p4-mediated stabilization of RNA polymerase at the promoter as a closed complex. Repression of the early A2b promoter occurs by binding of protein p4 to a site that partially overlaps the -35 consensus region of the promoter, therefore preventing the binding of RNA polymerase to the promoter. Repression of the A2c promoter, located 96 bp downstream from PA2b, occurs by a different mechanism that implies the simultaneous binding of protein p4 and RNA polymerase to the promoter in such a way that promoter clearance is inhibited. Interestingly, activation of PA3 and repression of PA2c require an interaction between protein p4 and RNA polymerase, and in both cases this interaction occurs between the same surface of protein p4 and the C-terminal domain of the alpha subunit of RNA polymerase, which provides new insights into how a protein can activate or repress transcription by subtle variations in the protein-DNA complexes formed at promoters.
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Affiliation(s)
- F Rojo
- Centro Nacional de Biotecnología (CSIC), Universidad Autónoma, Madrid, Spain
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27
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Miyake R, Murakami K, Owens JT, Greiner DP, Ozoline ON, Ishihama A, Meares CF. Dimeric association of Escherichia coli RNA polymerase alpha subunits, studied by cleavage of single-cysteine alpha subunits conjugated to iron-(S)-1-[p-(bromoacetamido)benzyl]ethylenediaminetetraacetate. Biochemistry 1998; 37:1344-9. [PMID: 9477962 DOI: 10.1021/bi9723313] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Proximity relationships between the two associated monomers of the Escherichia coli RNA polymerase alpha subunit were studied using a set of four mutant alpha subunits, each with a single Cys residue at one of the naturally occurring positions (54, 131, 176, and 269). These mutant alpha subunits were conjugated with the cutting reagent iron-(S)-1-[p-(bromoacetamido)benzyl]ethylenediaminetetraacetate (Fe-BABE), and the peptide backbone was cleaved at locations near the modified Cys. Analysis of the cleavage sites identified segments within approximately 12 A of the conjugation site. These results show that, for intermolecular cutting, segments of the subunit assembly domain (N-terminal domain) of one subunit and the linker region between N- and C-terminal domains of the other subunit are near each other, and the N-terminal domains of both subunits are in close proximity to one another. Intramolecular cutting however, was observed only within an individual N- or C-terminal domain.
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Affiliation(s)
- R Miyake
- Department of Chemistry, University of California, Davis 95616, USA
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28
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Ozoline ON, Murakami K, Negishi T, Fujita N, Ishihama A. Specific fluorescent labeling of two functional domains in RNA polymerase α subunit. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(19980201)30:2<183::aid-prot8>3.0.co;2-o] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Mencía M, Monsalve M, Rojo F, Salas M. Substitution of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit by that from Bacillus subtilis makes the enzyme responsive to a Bacillus subtilis transcriptional activator. J Mol Biol 1998; 275:177-85. [PMID: 9466901 DOI: 10.1006/jmbi.1997.1463] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Regulatory protein p4 of Bacillus subtilis phage phi 29 activates transcription from the viral late A3 promoter by interacting with the C-terminal domain (CTD) of the B. subtilis RNA polymerase alpha subunit, thereby stabilizing the holoenzyme at the promoter. Protein p4 does not interact with the Escherichia coli RNA polymerase and cannot activate transcription with this enzyme. We have constructed a chimerical alpha subunit containing the N-terminal domain of the E. coli alpha subunit and the CTD of the B. subtilis alpha subunit. Reconstitution of RNA polymerases containing this chimerical alpha subunit, the E. coli beta and beta' subunits, and the vegetative sigma factor from either E. coli (sigma 70) or B. subtilis (sigma A), generated hybrid enzymes that were responsive to protein p4 and efficiently supported activation at the A3 promoter. Protein p4 activated transcription with the chimerical enzymes through the same activation surface used with B. subtilis RNA polymerase. Therefore, the B. subtilis alpha-CTD allowed activation by p4 even when the rest of the RNA polymerase subunits belonged to E. coli, a distantly related bacterium. These results strongly suggest that protein p4 works essentially by serving as an anchor that stabilizes RNA polymerase at the promoter.
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Affiliation(s)
- M Mencía
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
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30
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Wang Y, Severinov K, Loizos N, Fenyö D, Heyduk E, Heyduk T, Chait BT, Darst SA. Determinants for Escherichia coli RNA polymerase assembly within the beta subunit. J Mol Biol 1997; 270:648-62. [PMID: 9245594 DOI: 10.1006/jmbi.1997.1139] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We used binding assays and other approaches to identify fragments of the Escherichia coli RNAP beta subunit involved in the obligatory interaction with the alpha subunit to form the stable assembly intermediate alpha2beta as well as in the interaction to recruit the beta' subunit into the alpha2beta sub-assembly. We show that two regions of evolutionarily conserved sequence near the C terminus of beta (conserved regions H and I) are central to the assembly of RNAP and likely make subunit-subunit contacts with both alpha and beta'.
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Affiliation(s)
- Y Wang
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
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31
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Larkin RM, Guilfoyle TJ. Reconstitution of yeast and Arabidopsis RNA polymerase alpha-like subunit heterodimers. J Biol Chem 1997; 272:12824-30. [PMID: 9139743 DOI: 10.1074/jbc.272.19.12824] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Two subunits of about 36-44 kDa and 13-19 kDa in the eukaryotic nuclear RNA polymerases share limited amino acid sequence similarity to the alpha subunit in Escherichia coli RNA polymerase. The alpha subunit in the prokaryotic enzyme has a stoichiometry of 2, but the stoichiometry of the alpha-like subunits in the eukaryotic enzymes is not entirely clear. To gain insight into the subunit stoichiometry and assembly pathway for eukaryotic RNA polymerases, in vitro reconstitution experiments have been carried out with recombinant alpha-like subunits from yeast and plant RNA polymerase II. The large and small alpha-like subunits from each species formed stable heterodimers in vitro, but neither the large or small alpha-like subunits formed stable homodimers. Furthermore, mixed heterodimers were formed between corresponding subunits of yeast and plants, but were not formed between corresponding subunits in different RNA polymerases from the same species. Our results suggest that RNA polymerase II alpha-like heterodimers may be the equivalent of alpha homodimers found in E. coli RNA polymerase.
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Affiliation(s)
- R M Larkin
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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32
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Murakami K, Kimura M, Owens JT, Meares CF, Ishihama A. The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Proc Natl Acad Sci U S A 1997; 94:1709-14. [PMID: 9050843 PMCID: PMC19981 DOI: 10.1073/pnas.94.5.1709] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
RNA polymerase core enzyme of Escherichia coli is composed of two alpha subunits and one each of the beta and beta' subunits. The C-terminal domain of the RNA polymerase alpha subunit plays a key role in molecular communications with class I transcription factors and upstream (UP) elements of promoter DNA, using the same protein surface. To identify possible differences in the functional roles of the two alpha subunits, we have developed a reconstitution method for hybrid RNA polymerases containing two distinct alpha subunit derivatives in a defined orientation ("oriented alpha-heterodimer"). The binding sites of two alpha C-terminal domains on the UP element DNA were determined by hydroxyl radical-based DNA cleavage mediated by (p-bromoacetamidobenzyl)-EDTA x Fe, which was bound at Cys-269 on the UP recognition surface of one or both alpha subunits. The results clearly indicated that the two alpha subunits bind in tandem to two helix turns of the rrnBP1 UP element, and that the beta'-associated alpha subunit is bound to the promoter-distal region.
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Affiliation(s)
- K Murakami
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
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33
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Wilkens K, Tiemann B, Bazan F, Rüger W. ADP-ribosylation and early transcription regulation by bacteriophage T4. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1997; 419:71-82. [PMID: 9193638 DOI: 10.1007/978-1-4419-8632-0_8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bacteriophage T4 codes at least for two ADP-ribosylating activities, the 76 kDa Alt and the 24 kDa Mod gene products. The main target for both enzymes is the host RNA polymerase. We cloned and sequenced the alt gene and overexpressed the corresponding enzyme. The recombinant protein shows ADP-ribosylating activities in vitro, as had been described earlier for the native enzyme isolated from phage heads. The native as well as the recombinant protein ADP-ribosylate the alpha-subunit of RNA polymerase, but also subunits beta, beta' and sigma 70 and perform an autoribosylation reaction. Taking advantage of the pKWIII test system, constructed to measure promoter strengths in vivo, it was found that ADP-ribosylation of RNA polymerase leads to an increase of transcription from T4 early promoters up to a factor of two. In an infected host cell this should cause an enhanced expression of T4 genes. Depending on whether RNA polymerase was ADP-ribosylated or not, it initiated transcription at T4 promoters with different sequence characteristics: unribosylated RNA polymerase recognizes the early T4 promoters by an extended -10 region, whereas the ribosylated enzyme selects for T4 early promoters with an extended T4-specific and highly conserved -35 region. These results may reflect how the virus, step by step imposes its genetic program on the host cell, and in part they give a rationale for the extension of the consensus sequence observed with these promoters. We also sequenced the genomic region of the T4 mod gene and found two open reading frames coding both for proteins of approximately 24 kDa. Up to now none of the reading frames could be cloned into E. coli in an active form, making it highly probable that the ADP-ribosylation pattern inflicted by gene product Mod on host RNA polymerase is deleterious to these bacteria. Comparisons of the amino acid sequences showed significant homologies among the two reading frames. Computer analysis reveals that both Mod sequences and also the sequence of the Alt protein exhibit a structural concordance with the catalytic domains of other prokaryotic ADP-mono-ribosyltransferases such as the Pseudomonas aeruginosa exotoxin A, the cholera labile enterotoxin, the diphteria toxin, the heat labile enterotoxin A of E. coli, and pertussis toxin. We present a detailed model for T4 transcription regulation.
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Affiliation(s)
- K Wilkens
- Lehrstuhl für Biologie der Mikoorganismen, Ruhr-Universität Bochum, Germany
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34
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35
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Jafri S, Urbanowski ML, Stauffer GV. The glutamic acid residue at amino acid 261 of the alpha subunit is a determinant of the intrinsic efficiency of RNA polymerase at the metE core promoter in Escherichia coli. J Bacteriol 1996; 178:6810-6. [PMID: 8955301 PMCID: PMC178580 DOI: 10.1128/jb.178.23.6810-6816.1996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A mutation in the rpoA gene (which encodes the alpha subunit of RNA polymerase) that changed the glutamic acid codon at position 261 to a lysine codon decreased the level of expression of a metE-lacZ fusion 10-fold; this decrease was independent of the MetR-mediated activation of metE-lacZ. Glutamine and alanine substitutions at this position are also metE-lacZ down mutations, suggesting that the glutamic acid residue at position 261 is essential for metE expression. In vitro transcription assays with RNA polymerase carrying the lysine residue at codon 261 indicated that the decreased level of metE-lacZ expression was not due to a failure of the mutant polymerase to respond to any other trans-acting factors, and a deletion analysis using a lambda metE-lacZ gene fusion suggested that there is no specific cis-acting sequence upstream of the -35 region of the metE promoter that interacts with the alpha subunit. Our data indicate that the glutamic acid at position 261 in the alpha subunit of RNA polymerase influences the intrinsic ability of the enzyme to transcribe the metE core promoter.
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Affiliation(s)
- S Jafri
- Department of Microbiology, University of Iowa, Iowa City 52242, USA
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36
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Nakasone K, Kato C, Horikoshi K. Molecular cloning of the gene encoding RNA polymerase alpha subunit from deep-sea barophilic bacterium. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1308:107-10. [PMID: 8764826 DOI: 10.1016/0167-4781(96)00105-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have cloned the gene encoding RNA polymerase alpha subunit from a gene library of deep-sea barophilic bacterium strain DB6705. The clone contains the genes for ribosomal protein S4, RNA polymerase subunit alpha and ribosomal protein L17 in this order. The alpha gene has 328 amino acids and a molecular mass of 36 100 Da with 86.9% identity to Escherichia coli alpha gene. Differences between the two sequences were mainly in the N-terminal portion of the alpha subunit, which is involved in the assembly of the core RNA polymerase; while the 87 C-terminal residues, which form a region involved in contact with some positive regulators and rrnB P1 promoter region called UP-element, were identical in the both strain. Plasmid encoding the alpha subunit with an N-terminal hexahistidine tag was constructed. Using the plasmid, the recombinant fusion alpha subunit was overexpressed and successfully purified to near homogeneity.
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Affiliation(s)
- K Nakasone
- DEEP STAR group, Japan Marine Science and Technology Center, Kanagawa, Japan.
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37
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Larkin RM, Guilfoyle TJ. A 14-kDa Arabidopsis thaliana RNA polymerase III subunit contains two alpha-motifs flanked by a highly charged C terminus. Gene 1996; 172:211-5. [PMID: 8682305 DOI: 10.1016/0378-1119(96)00030-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have sequenced a cDNA and a gene, AtRPC14, from Arabidopsis thaliana (At) (ecotype Columbia) that encode a protein related to the yeast RNA polymerases (Pol) I and III subunits, yAC19. Polyclonal antibodies raised against the recombinant At polypeptide (AtC14) bind to the Pol I and/or III subunits of about 13-15 kDa, but do not bind to any Pol II subunit in Pol purified from cauliflower, wheat or At. The amino acid (aa) sequence derived from the AtRPC14 cDNA and genomic clones consists of 122 aa, as compared to the 142 aa in the yeast yAC19 subunit and 143 aa in a putative Caenorhabditis elegans CeAC16 subunit. AtC14, yAC19 and CeAC16 contain a conserved sequence of about 85 aa which is related to two motifs in the alpha subunit of Escherichia coli (Ec) Pol. AtC14 lacks a highly charged N terminus of about 50 aa found in both yAC19 and CeAC16, but has a highly charged C terminus of about 30 aa not found in yAC19 and CeAC16.
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Affiliation(s)
- R M Larkin
- Department of Biochemistry, University of Missouri, Columbia 65211, USA
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38
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Ulmasov T, Larkin RM, Guilfoyle TJ. Association between 36- and 13.6-kDa alpha-like subunits of Arabidopsis thaliana RNA polymerase II. J Biol Chem 1996; 271:5085-94. [PMID: 8617787 DOI: 10.1074/jbc.271.9.5085] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Two subunits in RNA polymerase II (e.g. RPB3 and RPB11 in yeast) and two subunits common to RNA polymerases I and III (e.g. AC40 and AC19 in yeast) contain one or two motifs related to the alpha subunit in prokaryotic RNA polymerases. We have sequenced two different cDNAs (AtRPB36a and AtRPB36b), the two corresponding genes from Arabidopsis thaliana that are homologs of yeast RPB3, and an Arabidopsis cDNA (AtRPB13.6) that is a homolog of yeast RPB11. The B36a subunit is the predominant B36 subunit associated with RNA polymerase II purified from Arabidopsis suspension culture cells, and this subunit has a stoichiometry of about 1. Results from protein association assays showed that the B36a and B36b subunits did not associate, but each of these subunits did associate with the B13.6 subunit in vivo and in vitro. Two motifs in the B36b subunit related to the prokaryotic alpha subunit were shown to be required for the in vitro interactions with the B13.6 subunit. Our results suggest that the B36 and B13.6 subunits associate to form heterodimers in Arabidopsis RNA polymerase II like the AC40 and AC19 heterodimers reported for yeast RNA polymerases I and III but unlike the B44 homodimers reported for yeast RNA polymerase II.
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Affiliation(s)
- T Ulmasov
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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39
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Sharif KA, Luo J, Krakow JS. Epitope mapping of monoclonal antibodies directed against subunits of RNA polymerase of Escherichia coli. Methods Enzymol 1996; 274:503-13. [PMID: 8902828 DOI: 10.1016/s0076-6879(96)74040-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- K A Sharif
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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40
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Ulmasov T, Larkin RM, Guilfoyle TJ. Arabidopsis expresses two genes that encode polypeptides similar to the yeast RNA polymerase I and III AC40 subunit. Gene X 1995; 167:203-7. [PMID: 8566778 DOI: 10.1016/0378-1119(95)00643-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A 40-kDa subunit in eukaryotic RNA polymerases (Pol) I and III (e.g., yeast yAC40) is related in a part of its aa sequence to the alpha subunit of prokaryotic Pol and to a 35-44-kDa subunit in Pol II (e.g., yeast yB44). We have cloned two cDNAs, AtRPAC42 and AtRPAC43, from an Arabidopsis thaliana (At) (ecotype Columbia) lambda Yes expression library that encode Pol I and III subunits related to yAC40. The aa sequences derived from the cDNA clones were found to be 72% identical to each other and 40% identical to yeast Pol I and III subunits yAC40, but only 30% identical to yeast Pol II subunit yB44. While most other nuclear Pol genes identified to date are single-copy genes, two genes encode 42 and 43-kDa subunits of At Pol I and/or III. A 42-kDa subunit with identical mobility in SDS-PAGE to the aAC42 in vitro translated subunit is found in Pol III purified from At suspension culture cells.
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Affiliation(s)
- T Ulmasov
- Department of Biochemistry, University of Missouri, Columbia 65211, USA
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41
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Liu X, Fujita N, Ishihama A, Matsumura P. The C-terminal region of the alpha subunit of Escherichia coli RNA polymerase is required for transcriptional activation of the flagellar level II operons by the FlhD/FlhC complex. J Bacteriol 1995; 177:5186-8. [PMID: 7665504 PMCID: PMC177305 DOI: 10.1128/jb.177.17.5186-5188.1995] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A number of transcription activators have been found to activate transcription via protein-protein contact between RNA polymerase alpha subunits and transcription factors; they are classified as class I factors. In this report, we demonstrate that the FlhD/FlhC complex, a transcription activator of the Escherichia coli flagellar regulon, requires the C-terminal domain of the RNA polymerase alpha subunit for transcription activation. We conclude that FlhD/FlhC is a class I transcription factor.
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Affiliation(s)
- X Liu
- Department of Microbiology and Immunology, University of Illinois at Chicago 60612-7344, USA
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42
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Jafri S, Urbanowski ML, Stauffer GV. A mutation in the rpoA gene encoding the alpha subunit of RNA polymerase that affects metE-metR transcription in Escherichia coli. J Bacteriol 1995; 177:524-9. [PMID: 7836282 PMCID: PMC176623 DOI: 10.1128/jb.177.3.524-529.1995] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The DNA-binding protein MetR belongs to the LysR family of transcriptional activators and is required for expression of the metE and metH promoters in Escherichia coli. However, it is not known if this activation is mediated by a direct interaction of MetR with RNA polymerase. In a search for RNA polymerase mutants defective in MetR-mediated activation of the metE gene, we isolated a mutation in the alpha subunit of RNA polymerase that decreases metE expression independently of the MetR protein. The mutation does not affect expression from the metH promoter, suggesting that the alpha subunit of RNA polymerase interacts differently at these two promoters. The mutation was mapped to codon 261 of the rpoA gene, resulting in a change from a glutamic acid residue to a lysine residue. Growth of the mutant is severely impaired in minimal medium even when supplemented with methionine and related amino acids, indicating a pleiotropic effect on gene expression. This rpoA mutation may identify either a site of contact with an as yet unidentified activator protein for metE expression or a site of involvement by the alpha subunit in sequence-specific recognition of the metE promoter.
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Affiliation(s)
- S Jafri
- Department of Microbiology, University of Iowa, Iowa City 52242
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43
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Tang H, Severinov K, Goldfarb A, Fenyo D, Chait B, Ebright RH. Location, structure, and function of the target of a transcriptional activator protein. Genes Dev 1994; 8:3058-67. [PMID: 8001824 DOI: 10.1101/gad.8.24.3058] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have isolated and characterized single-amino-acid substitution mutants of RNA polymerase alpha subunit defective in CAP-dependent transcription at the lac promoter but not defective in CAP-independent transcription. Our results establish that (1) amino acids 258-265 of alpha constitute an "activation target" essential for CAP-dependent transcription at the lac promoter but not essential for CAP-independent transcription, (2) amino acid 261 is the most critical amino acid of the activation target, (3) amino acid 261 is distinct from the determinants for alpha-DNA interaction, and (4) the activation target may fold as a surface amphipathic alpha-helix. We propose a model for transcriptional activation at the lac promoter that integrates these and other recent results regarding transcriptional activation and RNA polymerase structure and function.
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Affiliation(s)
- H Tang
- Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08855
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44
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Ayers DJ, Sunshine MG, Six EW, Christie GE. Mutations affecting two adjacent amino acid residues in the alpha subunit of RNA polymerase block transcriptional activation by the bacteriophage P2 Ogr protein. J Bacteriol 1994; 176:7430-8. [PMID: 8002564 PMCID: PMC197197 DOI: 10.1128/jb.176.24.7430-7438.1994] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The bacteriophage P2 ogr gene product is a positive regulator of transcription from P2 late promoters. The ogr gene was originally defined by compensatory mutations that overcame the block to P2 growth imposed by a host mutation, rpoA109, in the gene encoding the alpha subunit of RNA polymerase. DNA sequence analysis has confirmed that this mutation affects the C-terminal region of the alpha subunit, changing a leucine residue at position 290 to a histidine (rpoAL290H). We have employed a reporter plasmid system to screen other, previously described, rpoA mutants for effects on activation of a P2 late promoter and have identified a second allele, rpoA155, that blocks P2 late transcription. This mutation lies just upstream of rpoAL290H, changing the leucine residue at position 289 to a phenylalanine (rpoAL289F). The effect of the rpoAL289F mutation is not suppressed by the rpoAL290H-compensatory P2 ogr mutation. P2 ogr mutants that overcome the block imposed by rpoAL289F were isolated and characterized. Our results are consistent with a direct interaction between Ogr and the alpha subunit of RNA polymerase and support a model in which transcription factor contact sites within the C terminus of alpha are discrete and tightly clustered.
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Affiliation(s)
- D J Ayers
- Department of Microbiology, Virginia Commonwealth University, Richmond
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45
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Shi X, Bennett GN. Effects of rpoA and cysB mutations on acid induction of biodegradative arginine decarboxylase in Escherichia coli. J Bacteriol 1994; 176:7017-23. [PMID: 7961466 PMCID: PMC197075 DOI: 10.1128/jb.176.22.7017-7023.1994] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
For Escherichia coli, there have been more and more examples illustrating that the alpha subunit of RNA polymerase is directly involved in the activation of gene transcription by interaction with activator proteins. Because of the vital function of the alpha subunit in cell growth, only a limited number of mutations in its structural gene, rpoA, have been isolated. We obtained a number of these mutants and examined the effects of these mutations on the acid induction of adi and cad gene expression. Several mutations caused a small reduction in adi promoter activity at inducing pH. One mutation, rpoA341, essentially eliminated adi promoter activity, while it had little effect on the cad promoter. During the course of a separate study, we isolated a plasmid that enhanced adi expression. Further characterization of this plasmid showed that it contained cysB, the structural gene for the positive regulator for most cys operon genes. Introduction of a cysB mutation into an adi::lac fusion strain and beta-galactosidase assay studies of the resultant adi::lac cysB mutant established that a wild-type cysB gene was required for efficient acid induction of adi expression. These results suggest that a possible interaction between CysB and the alpha subunit of RNA polymerase is involved in activation of adi transcription.
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Affiliation(s)
- X Shi
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251
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46
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Blatter EE, Ross W, Tang H, Gourse RL, Ebright RH. Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 1994; 78:889-96. [PMID: 8087855 DOI: 10.1016/s0092-8674(94)90682-3] [Citation(s) in RCA: 194] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using limited proteolysis, we show that the Escherichia coli RNA polymerase alpha subunit consists of an N-terminal domain comprised of amino acids 8-241, a C-terminal domain comprised of amino acids 249-329, and an unstructured and/or flexible interdomain linker. We have carried out a detailed structural and functional analysis of an 85 amino acid proteolytic fragment corresponding to the C-terminal domain (alpha CTD-2). Our results establish that alpha CTD-2 has a defined secondary structure (approximately 40% alpha helix, approximately 0% beta sheet). Our results further establish that alpha CTD-2 is a dimer and that alpha CTD-2 exhibits sequence-specific DNA binding activity. Our results suggest a model for the mechanism of involvement of alpha in transcription activation by promoter upstream elements and upstream-binding activator proteins.
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Affiliation(s)
- E E Blatter
- Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08855
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47
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Pati UK. Human RNA polymerase II subunit hRPB14 is homologous to yeast RNA polymerase I, II, and III subunits (AC19 and RPB11) and is similar to a portion of the bacterial RNA polymerase alpha subunit. Gene 1994; 145:289-92. [PMID: 8056345 DOI: 10.1016/0378-1119(94)90022-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The cDNA cloning of the human polII 14-kDa subunit, hRPB14, and the comparison of its aa sequence with those of other pol subunits are described. The aa sequence of hRPB14 has homology to yeast poIII subunit RPB11 (44%), to a common subunit of yeast polI and polIII AC19 (24%) and to a Caenorhabditis elegans sequence (33%). hRPB14 contains a 19-aa motif, located in its N terminus, which was also found in human polII 33-kDa subunit hRPB33, yeast pol subunits (AC40, AC19, RPB3 and RPB11), and in the bacterial pol alpha subunit, which was involved in subunit assembly. This motif was also conserved in the conjugation-specific gene products of Tetrahymena (CnjC), Merchantia polymorpha chloroplast DNA (RNLVA) and C. elegans DNA (CEF58A4; deduced from the nucleotide sequence and of unknown function). The evolutionary emergence of a probable eukaryotic heterodimer, hRPB14/hRPB33, from a prokaryotic homodimer, alpha 2, is hypothesized.
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Affiliation(s)
- U K Pati
- Department of Medicine, Medical College of Georgia, Augusta 30912-3100
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48
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Zou C, Fujita N, Ishihama A. Asymmetric arrangement of two alpha subunits within Escherichia coli RNA polymerase. Involvement of one alpha subunit in contact with cAMP receptor protein. J Mol Biol 1994; 236:1283-8. [PMID: 8126719 DOI: 10.1016/0022-2836(94)90057-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Class I transcription factors of Escherichia coli have been proposed to make contact with contact site I on the alpha subunit, C-terminal region of RNA polymerase with the subunit composition of alpha 2 beta beta ' sigma. Both a reconstituted mutant holoenzyme containing two C-terminally truncated alpha-235 subunits and a hybrid enzyme containing one wild-type alpha (alpha-329) and one C-terminal truncated alpha (alpha-235) subunit were found to be as active in transcription from factor-independent simple promoters as the wild-type holoenzyme. The mutant enzyme was, however, inactive in cAMP receptor protein (CRP)-dependent transcription from lacP1 promoter, but the hybrid enzyme was about 50% as active in lacP1 transcription as the wild-type enzyme. The results indicate that only one specific alpha subunit makes contact with CRP.
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Affiliation(s)
- C Zou
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
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49
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Kabata H, Kurosawa O, Arai I, Washizu M, Margarson SA, Glass RE, Shimamoto N. Visualization of single molecules of RNA polymerase sliding along DNA. Science 1993; 262:1561-3. [PMID: 8248804 DOI: 10.1126/science.8248804] [Citation(s) in RCA: 239] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Transcription requires that RNA polymerase binds to promoters buried in nonspecific sites on DNA. The search for promoters may be facilitated if the polymerase slides along the molecule of DNA. Single molecules of Escherichia coli RNA polymerase were visualized, and their movements on immobilized bacteriophage lambda and T7 DNAs were examined. Deviating from drifts by bulk flow, about 40 percent of the enzyme molecules moved along the extended DNA. The results provide direct evidence for sliding as a mechanism for relocation of the enzyme on DNA.
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Affiliation(s)
- H Kabata
- DNA Research Center, National Institute of Genetics, Mishima, Japan
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50
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Sharif TR, Igo MM. Mutations in the alpha subunit of RNA polymerase that affect the regulation of porin gene transcription in Escherichia coli K-12. J Bacteriol 1993; 175:5460-8. [PMID: 8396118 PMCID: PMC206602 DOI: 10.1128/jb.175.17.5460-5468.1993] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The two-component regulatory system consisting of OmpR and EnvZ controls the differential expression of major outer membrane porin proteins OmpF and OmpC of Escherichia coli K-12. We have isolated and characterized two mutations in rpoA, the gene encoding the alpha subunit of RNA polymerase, that decrease the expression of OmpF. These mutations have a number of properties that distinguish them from previously isolated rpoA mutations that affect porin expression. The rpoA203 mutation decreases the expression of porin genes ompF and ompC and also decreases the expression of the malE and phoA genes. In contrast, rpoA207 decreases the expression of ompF but does not affect ompC, malE, or phoA transcription. Our results suggest that mutations at various positions in the alpha subunit may affect the OmpR-dependent transcription of ompF and ompC differently and may be useful for analyzing the mechanism underlying their differential expression in response to medium osmolarity.
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Affiliation(s)
- T R Sharif
- Department of Microbiology, University of California, Davis 95616
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