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Palumbo RJ, Belkevich AE, Pascual HG, Knutson BA. A clinically-relevant residue of POLR1D is required for Drosophila development. Dev Dyn 2022; 251:1780-1797. [PMID: 35656583 PMCID: PMC10723622 DOI: 10.1002/dvdy.505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND POLR1D is a subunit of RNA Polymerases I and III, which synthesize ribosomal RNAs. Dysregulation of these polymerases cause several types of diseases, including ribosomopathies. The craniofacial disorder Treacher Collins Syndrome (TCS) is a ribosomopathy caused by mutations in several subunits of RNA Polymerase I, including POLR1D. Here, we characterized the effect of a missense mutation in POLR1D and RNAi knockdown of POLR1D on Drosophila development. RESULTS We found that a missense mutation in Drosophila POLR1D (G30R) reduced larval rRNA levels, slowed larval growth, and arrested larval development. Remarkably, the G30R substitution is at an orthologous glycine in POLR1D that is mutated in a TCS patient (G52E). We showed that the G52E mutation in human POLR1D, and the comparable substitution (G30E) in Drosophila POLR1D, reduced their ability to heterodimerize with POLR1C in vitro. We also found that POLR1D is required early in the development of Drosophila neural cells. Furthermore, an RNAi screen revealed that POLR1D is also required for development of non-neural Drosophila cells, suggesting the possibility of defects in other cell types. CONCLUSIONS These results establish a role for POLR1D in Drosophila development, and present Drosophila as an attractive model to evaluate the molecular defects of TCS mutations in POLR1D.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Alana E Belkevich
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Haleigh G Pascual
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
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2
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Kurkela J, Fredman J, Salminen TA, Tyystjärvi T. Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase. Mol Microbiol 2021; 115:1-11. [PMID: 32920946 DOI: 10.1111/mmi.14603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
The conserved omega (ω) subunit of RNA polymerase (RNAP) is the only nonessential subunit of bacterial RNAP core. The small ω subunit (7 kDa-11.5 kDa) contains three conserved α helices, and helices α2 and α3 contain five fully conserved amino acids of ω. Four conserved amino acids stabilize the correct folding of the ω subunit and one is located in the vicinity of the β' subunit of RNAP. Otherwise ω shows high variation between bacterial taxa, and although the main interaction partner of ω is always β', many interactions are taxon-specific. ω-less strains show pleiotropic phenotypes, and based on in vivo and in vitro results, a few roles for the ω subunits have been described. Interactions of the ω subunit with the β' subunit are important for the RNAP core assembly and integrity. In addition, the ω subunit plays a role in promoter selection, as ω-less RNAP cores recruit fewer primary σ factors and more alternative σ factors than intact RNAP cores in many species. Furthermore, the promoter selection of an ω-less RNAP holoenzyme bearing the primary σ factor seems to differ from that of an intact RNAP holoenzyme.
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Affiliation(s)
- Juha Kurkela
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Julia Fredman
- Faculty of Science and Engineering/Biochemistry/Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, Finland
| | - Tiina A Salminen
- Faculty of Science and Engineering/Biochemistry/Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, Finland
| | - Taina Tyystjärvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
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3
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Zhou HR, Lin RN, Huang HW, Li L, Cai T, Zhu JK, Chen S, He XJ. The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production. Plant J 2020; 103:1503-1515. [PMID: 32412137 DOI: 10.1111/tpj.14818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 05/20/2023]
Abstract
Small interfering RNAs (siRNAs) are responsible for establishing and maintaining DNA methylation through the RNA-directed DNA methylation (RdDM) pathway in plants. Although siRNA biogenesis is well known, it is relatively unclear about how the process is regulated. By a forward genetic screen in Arabidopsis thaliana, we identified a mutant defective in NOT1 and demonstrated that NOT1 is required for transcriptional silencing at RdDM target genomic loci. We demonstrated that NOT1 is required for Pol IV-dependent siRNA accumulation and DNA methylation at a subset of RdDM target genomic loci. Furthermore, we revealed that NOT1 is a constituent of a multi-subunit CCR4-NOT deadenylase complex by immunoprecipitation combined with mass spectrometry and demonstrated that the CCR4-NOT components can function as a whole to mediate chromatin silencing. Therefore, our work establishes that the CCR4-NOT complex regulates the biogenesis of Pol IV-dependent siRNAs, and hence facilitates DNA methylation and transcriptional silencing in Arabidopsis.
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Affiliation(s)
- Hao-Ran Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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4
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Zhu Y, Mustafi M, Weisshaar JC. Biophysical Properties of Escherichia coli Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy. mBio 2020; 11:e00143-20. [PMID: 32546611 PMCID: PMC7298701 DOI: 10.1128/mbio.00143-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
In nature, bacteria must survive long periods of nutrient deprivation while maintaining the ability to recover and grow when conditions improve. This quiescent state is called stationary phase. The biochemistry of Escherichia coli in stationary phase is reasonably well understood. Much less is known about the biophysical state of the cytoplasm. Earlier studies of harvested nucleoids concluded that the stationary-phase nucleoid is "compacted" or "supercompacted," and there are suggestions that the cytoplasm is "glass-like." Nevertheless, stationary-phase bacteria support active transcription and translation. Here, we present results of a quantitative superresolution fluorescence study comparing the spatial distributions and diffusive properties of key components of the transcription-translation machinery in intact E. coli cells that were either maintained in 2-day stationary phase or undergoing moderately fast exponential growth. Stationary-phase cells are shorter and exhibit strong heterogeneity in cell length, nucleoid volume, and biopolymer diffusive properties. As in exponential growth, the nucleoid and ribosomes are strongly segregated. The chromosomal DNA is locally more rigid in stationary phase. The population-weighted average of diffusion coefficients estimated from mean-square displacement plots is 2-fold higher in stationary phase for both RNA polymerase (RNAP) and ribosomal species. The average DNA density is roughly twice as high as that in cells undergoing slow exponential growth. The data indicate that the stationary-phase nucleoid is permeable to RNAP and suggest that it is permeable to ribosomal subunits. There appears to be no need to postulate migration of actively transcribed genes to the nucleoid periphery.IMPORTANCE Bacteria in nature usually lack sufficient nutrients to enable growth and replication. Such starved bacteria adapt into a quiescent state known as the stationary phase. The chromosomal DNA is protected against oxidative damage, and ribosomes are stored in a dimeric structure impervious to digestion. Stationary-phase bacteria can recover and grow quickly when better nutrient conditions arise. The biochemistry of stationary-phase E. coli is reasonably well understood. Here, we present results from a study of the biophysical state of starved E. coli Superresolution fluorescence microscopy enables high-resolution location and tracking of a DNA locus and of single copies of RNA polymerase (the transcription machine) and ribosomes (the translation machine) in intact E. coli cells maintained in stationary phase. Evidently, the chromosomal DNA remains sufficiently permeable to enable transcription and translation to occur. This description contrasts with the usual picture of a rigid stationary-phase cytoplasm with highly condensed DNA.
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Affiliation(s)
- Yanyu Zhu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mainak Mustafi
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James C Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Hengge R. Linking bacterial growth, survival, and multicellularity - small signaling molecules as triggers and drivers. Curr Opin Microbiol 2020; 55:57-66. [PMID: 32244175 DOI: 10.1016/j.mib.2020.02.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 02/05/2023]
Abstract
An overarching theme of cellular regulation in bacteria arises from the trade-off between growth and stress resilience. In addition, the formation of biofilms contributes to stress survival, since these dense multicellular aggregates, in which cells are embedded in an extracellular matrix of self-produced polymers, represent a self-constructed protective and homeostatic 'niche'. As shown here for the model bacterium Escherichia coli, the inverse coordination of bacterial growth with survival and the transition to multicellularity is achieved by a highly integrated regulatory network with several sigma subunits of RNA polymerase and a small number of transcriptional hubs as central players. By conveying information about the actual (micro)environments, nucleotide second messengers such as cAMP, (p)ppGpp, and in particular c-di-GMP are the key triggers and drivers that promote either growth or stress resistance and organized multicellularity in a world of limited resources.
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Affiliation(s)
- Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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6
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Zhang QQ, Li Y, Fu ZY, Liu XB, Yuan K, Fang Y, Liu Y, Li G, Zhang XS, Chong K, Ge L. Intact Arabidopsis RPB1 functions in stem cell niches maintenance and cell cycling control. Plant J 2018; 95:150-167. [PMID: 29752751 DOI: 10.1111/tpj.13939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 02/07/2018] [Accepted: 03/27/2018] [Indexed: 05/14/2023]
Abstract
Plant meristem activity depends on accurate execution of transcriptional networks required for establishing optimum functioning of stem cell niches. An Arabidopsis mutant card1-1 (constitutive auxin response with DR5:GFP) that encodes a truncated RPB1 (RNA Polymerase II's largest subunit) with shortened C-terminal domain (CTD) was identified. Phosphorylation of the CTD repeats of RPB1 is coupled to transcription in eukaryotes. Here we uncover that the truncated CTD of RPB1 disturbed cell cycling and enlarged the size of shoot and root meristem. The defects in patterning of root stem cell niche in card1-1 indicates that intact CTD of RPB1 is necessary for fine-tuning the specific expression of genes responsible for cell-fate determination. The gene-edited plants with different CTD length of RPB1, created by CRISPR-CAS9 technology, confirmed that both the full length and the DK-rich tail of RPB1's CTD play roles in the accurate transcription of CYCB1;1 encoding a cell-cycle marker protein in root meristem and hence participate in maintaining root meristem size. Our experiment proves that the intact RPB1 CTD is necessary for stem cell niche maintenance, which is mediated by transcriptional regulation of cell cycling genes.
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Affiliation(s)
- Qian-Qian Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Ying Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhao-Ying Fu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xun-Biao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Kai Yuan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Ying Fang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Yan Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xian-Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lei Ge
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
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7
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Serna Martin I, Hengrung N, Renner M, Sharps J, Martínez-Alonso M, Masiulis S, Grimes JM, Fodor E. A Mechanism for the Activation of the Influenza Virus Transcriptase. Mol Cell 2018; 70:1101-1110.e4. [PMID: 29910112 PMCID: PMC6024077 DOI: 10.1016/j.molcel.2018.05.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/17/2018] [Accepted: 05/08/2018] [Indexed: 12/28/2022]
Abstract
Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For transcription, FluPol interacts with the C-terminal domain (CTD) of RNA polymerase II (Pol II), which enables FluPol to snatch capped RNA primers from nascent host RNAs. Here, we describe the co-crystal structure of influenza C virus polymerase (FluPolC) bound to a Ser5-phosphorylated CTD (pS5-CTD) peptide. The position of the CTD-binding site at the interface of PB1, P3, and the flexible PB2 C-terminal domains suggests that CTD binding stabilizes the transcription-competent conformation of FluPol. In agreement, both cap snatching and capped primer-dependent transcription initiation by FluPolC are enhanced in the presence of pS5-CTD. Mutations of amino acids in the CTD-binding site reduce viral mRNA synthesis. We propose a model for the activation of the influenza virus transcriptase through its association with pS5-CTD of Pol II.
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Affiliation(s)
- Itziar Serna Martin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Narin Hengrung
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Max Renner
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Jane Sharps
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Mónica Martínez-Alonso
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Simonas Masiulis
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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8
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Tarasenko VI, Katyshev AI, Yakovleva TV, Garnik EY, Chernikova VV, Konstantinov YM, Koulintchenko MV. RPOTmp, an Arabidopsis RNA polymerase with dual targeting, plays an important role in mitochondria, but not in chloroplasts. J Exp Bot 2016; 67:5657-5669. [PMID: 27591433 DOI: 10.1093/jxb/erw327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In a number of dicotyledonous plants, including Arabidopsis, the transcription of organellar genes is performed by three nuclear-encoded RNA polymerases, RPOTm, RPOTmp, and RPOTp. RPOTmp is a protein with a dual targeting, which is presumably involved in the control of gene expression in both mitochondria and chloroplasts. A previous study of the Arabidopsis insertion rpotmp mutant showed that it has retarded growth and development, altered leaf morphology, changed expression of mitochondrial and probably some chloroplast genes, and decreased activities of the mitochondrial respiratory complexes. To date, there is no clear evidence as to which of these disorders are associated with a lack of RPOTmp in each of the two organelles. The aim of this study was to elucidate the role that this RNA polymerase specifically plays in mitochondria and chloroplasts. Two sets of Arabidopsis transgenic lines with complementation of RPOTmp function in either mitochondria or chloroplasts were obtained. It was found that the recovery of RPOTmp RNA polymerase activity in chloroplasts, although restoring the transcription from the RPOTmp-specific PC promoter, did not lead to compensation of the mutant growth defects. In contrast, the rpotmp plants expressing RPOTmp with mitochondrial targeting restored the level of mitochondrial transcripts and exhibit a phenotype resembling that of the wild-type plants. We conclude that despite its localization in two cell compartments, Arabidopsis RPOTmp plays an important role in mitochondria, but not in chloroplasts.
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Affiliation(s)
- Vladislav I Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk, 664033, Russia
| | - Alexander I Katyshev
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk, 664033, Russia
| | - Tatiana V Yakovleva
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk, 664033, Russia
| | - Elena Y Garnik
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk, 664033, Russia
| | - Valentina V Chernikova
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk, 664033, Russia
| | - Yuri M Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk, 664033, Russia Irkutsk State University, 1 Karl Marx St, Irkutsk, 664003, Russia
| | - Milana V Koulintchenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk, 664033, Russia
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9
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Heberling T, Davis L, Gedeon J, Morgan C, Gedeon T. A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases. PLoS Comput Biol 2016; 12:e1005069. [PMID: 27517607 PMCID: PMC4982667 DOI: 10.1371/journal.pcbi.1005069] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/20/2016] [Indexed: 11/19/2022] Open
Abstract
In fast-transcribing prokaryotic genes, such as an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP motion on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases.
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Affiliation(s)
- Tamra Heberling
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Lisa Davis
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Jakub Gedeon
- Computer Science Department, Montana State University, Bozeman, Montana, United States of America
| | - Charles Morgan
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Tomáš Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
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10
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Cho EJ, Choi SH, Kim JH, Kim JE, Lee MH, Chung BY, Woo HR, Kim JH. A Mutation in Plant-Specific SWI2/SNF2-Like Chromatin-Remodeling Proteins, DRD1 and DDM1, Delays Leaf Senescence in Arabidopsis thaliana. PLoS One 2016; 11:e0146826. [PMID: 26752684 PMCID: PMC4709239 DOI: 10.1371/journal.pone.0146826] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/22/2015] [Indexed: 01/08/2023] Open
Abstract
Leaf senescence is a finely regulated complex process; however, evidence for the involvement of epigenetic processes in the regulation of leaf senescence is still fragmentary. Therefore, we chose to examine the functions of DRD1, a SWI2/SNF2 chromatin remodeling protein, in epigenetic regulation of leaf senescence, particularly because drd1-6 mutants exhibited a delayed leaf senescence phenotype. Photosynthetic parameters such as Fv/Fm and ETRmax were decreased in WT leaves compared to leaves of drd1-6 mutants after dark treatment. The WT leaves remarkably lost more chlorophyll and protein content during dark-induced senescence (DIS) than the drd1-6 leaves did. The induction of senescence-associated genes was noticeably inhibited in the drd1-6 mutant after 5-d of DIS. We compared changes in epigenetic regulation during DIS via quantitative expression analysis of 180-bp centromeric (CEN) and transcriptionally silent information (TSI) repeats. Their expression levels significantly increased in both the WT and the drd1-6 mutant, but did much less in the latter. Moreover, the delayed leaf senescence was observed in ddm1-2 mutants as well as the drd1-6, but not in drd1-p mutants. These data suggest that SWI2/SNF2 chromatin remodeling proteins such as DRD1 and DDM1 may influence leaf senescence possibly via epigenetic regulation.
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Affiliation(s)
- Eun Ju Cho
- Advanced Radiation Technology Institute, Korea Atomic Energy ResearchInstitute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Seung Hee Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy ResearchInstitute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Ji Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy ResearchInstitute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Ji Eun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy ResearchInstitute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Min Hee Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy ResearchInstitute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Byung Yeoup Chung
- Advanced Radiation Technology Institute, Korea Atomic Energy ResearchInstitute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy ResearchInstitute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
- Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- * E-mail:
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11
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Pfalz J, Holtzegel U, Barkan A, Weisheit W, Mittag M, Pfannschmidt T. ZmpTAC12 binds single-stranded nucleic acids and is essential for accumulation of the plastid-encoded polymerase complex in maize. New Phytol 2015; 206:1024-1037. [PMID: 25599833 PMCID: PMC6680207 DOI: 10.1111/nph.13248] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/19/2014] [Indexed: 05/04/2023]
Abstract
The plastid-encoded plastid RNA polymerase (PEP) represents the major transcription machinery in mature chloroplasts. Proteomic studies identified four plastome- and at least ten nuclear-encoded proteins making up this multimeric enzyme. Depletion of single subunits is known to result in strongly diminished PEP activity causing severe defects in chloroplast biogenesis. Here, we characterized one PEP subunit in maize, ZmpTAC12, and investigated the molecular basis underlying PEP-deficiency in Zmptac12 mutants. We show that the ZmpTAC12 gene encodes two different protein isoforms, both of which localize dually in chloroplasts and nuclei. Moreover, both variants assemble into the PEP-complex. Analysis of PEP-complex assembly in various maize mutants lacking different PEP-complex components demonstrates that ZmpTAC12, ZmpTAC2, ZmpTAC10 and ZmMurE are each required to accumulate a fully assembled PEP-complex. Antibodies to ZmpTAC12 coimmunoprecipitate a subset of plastid RNAs that are synthesized by PEP-dependent transcription. Gel mobility shift analyses with recombinant ZmpTAC12 revealed binding capabilities with ssRNA and ssDNA, but not dsDNA. Collectively these data demonstrate that ZmpTAC12 is required for the proper build-up of the PEP-complex and that it interacts with single-stranded nucleic acids.
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Affiliation(s)
- Jeannette Pfalz
- Department of Plant PhysiologyInstitute of General Botany and Plant PhysiologyFriedrich‐Schiller‐University JenaD‐07743JenaGermany
| | - Ute Holtzegel
- Department of Plant PhysiologyInstitute of General Botany and Plant PhysiologyFriedrich‐Schiller‐University JenaD‐07743JenaGermany
| | - Alice Barkan
- Institute of Molecular BiologyUniversity of OregonEugeneOR97403USA
| | - Wolfram Weisheit
- Department of General BotanyInstitute of General Botany and Plant PhysiologyFriedrich‐Schiller‐University JenaD‐07743JenaGermany
| | - Maria Mittag
- Department of General BotanyInstitute of General Botany and Plant PhysiologyFriedrich‐Schiller‐University JenaD‐07743JenaGermany
| | - Thomas Pfannschmidt
- Department of Plant PhysiologyInstitute of General Botany and Plant PhysiologyFriedrich‐Schiller‐University JenaD‐07743JenaGermany
- University Grenoble‐AlpesF‐38000GrenobleFrance
- CNRSUMR5168F‐38054GrenobleFrance
- CEAiRTSVLaboratoire de Physiologie Cellulaire & VégétaleF‐38054GrenobleFrance
- INRAUSC1359F‐38054GrenobleFrance
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12
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13
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Gunnelius L, Kurkela J, Hakkila K, Koskinen S, Parikainen M, Tyystjärvi T. The ω subunit of RNA polymerase is essential for thermal acclimation of the cyanobacterium Synechocystis sp. PCC 6803. PLoS One 2014; 9:e112599. [PMID: 25386944 PMCID: PMC4227741 DOI: 10.1371/journal.pone.0112599] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/09/2014] [Indexed: 01/26/2023] Open
Abstract
The rpoZ gene encodes the small ω subunit of RNA polymerase. A ΔrpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions (constant illumination at 40 µmol photons m−2 s−1; 32°C; ambient CO2) but was heat sensitive and died at 40°C. In the control strain, 71 genes were at least two-fold up-regulated and 91 genes down-regulated after a 24-h treatment at 40°C, while in ΔrpoZ 394 genes responded to heat. Only 62 of these heat-responsive genes were similarly regulated in both strains, and 80% of heat-responsive genes were unique for ΔrpoZ. The RNA polymerase core and the primary σ factor SigA were down-regulated in the control strain at 40°C but not in ΔrpoZ. In accordance with reduced RNA polymerase content, the total RNA content of mild-heat-stress-treated cells was lower in the control strain than in ΔrpoZ. Light-saturated photosynthetic activity decreased more in ΔrpoZ than in the control strain upon mild heat stress. The amounts of photosystem II and rubisco decreased at 40°C in both strains while PSI and the phycobilisome antenna protein allophycocyanin remained at the same level as in standard conditions. The phycobilisome rod proteins, phycocyanins, diminished during the heat treatment in ΔrpoZ but not in the control strain, and the nblA1 and nblA2 genes (encode NblA proteins required for phycobilisome degradation) were up-regulated only in ΔrpoZ. Our results show that the ω subunit of RNAP is essential in heat stress because it is required for heat acclimation of diverse cellular processes.
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Affiliation(s)
- Liisa Gunnelius
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Juha Kurkela
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Kaisa Hakkila
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Satu Koskinen
- Department of Biochemistry, University of Turku, Turku, Finland
| | | | - Taina Tyystjärvi
- Department of Biochemistry, University of Turku, Turku, Finland
- * E-mail:
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14
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Abstract
Gene expression is a fundamental cellular process by which proteins are synthesized based on the information coded in the genes. The two major steps of this process are the transcription of the DNA segment corresponding to a gene to mRNA molecules and the translation of the mRNA molecules to proteins by the ribosome. Thus, understanding, modeling and engineering the different stages of this process have both important biotechnological applications and contributions to basic life science. In previous studies we have introduced the Homogenous Ribosome Flow Model (HRFM) and demonstrated its advantages in analyses of the translation process. In this study we introduce the RNA Polymerase Flow Model (RPFM), a non trivial extension of the HRFM, which also includes a backward flow and can be used for modeling transcription and maybe other similar processes. We compare the HRFM and the RPFM in the three regimes of the transcription process: rate limiting initiation, rate limiting elongation and rate limiting termination via a simulative and analytical analysis. In addition, based on experimental data, we show that RPFM is a better choice for modeling transcription process.
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15
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Teng CY, Dang Y, Danne JC, Waller RF, Green BR. Mitochondrial Genes of Dinoflagellates Are Transcribed by a Nuclear-Encoded Single-Subunit RNA Polymerase. PLoS One 2013; 8:e65387. [PMID: 23840326 PMCID: PMC3686807 DOI: 10.1371/journal.pone.0065387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/27/2013] [Indexed: 11/18/2022] Open
Abstract
Dinoflagellates are a large group of algae that contribute significantly to marine productivity and are essential photosynthetic symbionts of corals. Although these algae have fully-functioning mitochondria and chloroplasts, both their organelle genomes have been highly reduced and the genes fragmented and rearranged, with many aberrant transcripts. However, nothing is known about their RNA polymerases. We cloned and sequenced the gene for the nuclear-encoded mitochondrial polymerase (RpoTm) of the dinoflagellate Heterocapsa triquetra and showed that the protein presequence targeted a GFP construct into yeast mitochondria. The gene belongs to a small gene family, which includes a variety of 3′-truncated copies that may have originated by retroposition. The catalytic C-terminal domain of the protein shares nine conserved sequence blocks with other single-subunit polymerases and is predicted to have the same fold as the human enzyme. However, the N-terminal (promoter binding/transcription initiation) domain is not well-conserved. In conjunction with the degenerate nature of the mitochondrial genome, this suggests a requirement for novel accessory factors to ensure the accurate production of functional mRNAs.
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Affiliation(s)
- Chang Ying Teng
- Botany Department, University of British Columbia, Vancouver, B.C., Canada
- Life Sciences Department, Ludong University, Yantai, Shandong, China
| | - Yunkun Dang
- Botany Department, University of British Columbia, Vancouver, B.C., Canada
| | - Jillian C. Danne
- School of Botany, University of Melbourne, Melbourne, Victoria, Australia
| | - Ross F. Waller
- School of Botany, University of Melbourne, Melbourne, Victoria, Australia
| | - Beverley R. Green
- Botany Department, University of British Columbia, Vancouver, B.C., Canada
- * E-mail:
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16
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Abstract
Mutations that directly affect transcription by RNA polymerases rank among the most central mediators of malignant transformation, but the frequency of new anticancer drugs that selectively target defective transcription apparatus entering the clinic has been limited. This is because targeting the large protein-protein and protein-DNA interfaces that control both generic and selective aspects of RNA polymerase transcription has proved extremely difficult. However, recent technological advances have led to a 'quantum leap' in our comprehension of the structure and function of the core RNA polymerase components, how they are dysregulated in a broad range of cancers and how they may be targeted for 'transcription therapy'.
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Affiliation(s)
- Megan J Bywater
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne 8006, Victoria, Australia
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17
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Abstract
Bio-polymerization processes like transcription and translation are central to proper function of a cell. The speed at which the bio-polymer grows is affected both by the number of pauses of elongation machinery, as well the number of bio-polymers due to crowding effects. In order to quantify these effects in fast transcribing ribosome genes, we rigorously show that a classical traffic flow model is the limit of a mean occupancy ODE model. We compare the simulation of this model to a stochastic model and evaluate the combined effect of the polymerase density and the existence of pauses on the instantaneous transcription rate of ribosomal genes.
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Affiliation(s)
- Lisa Davis
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717-2400, USA
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18
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Surovtseva YV, Shadel GS. Transcription-independent role for human mitochondrial RNA polymerase in mitochondrial ribosome biogenesis. Nucleic Acids Res 2013; 41:2479-88. [PMID: 23303773 PMCID: PMC3575816 DOI: 10.1093/nar/gks1447] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/07/2012] [Accepted: 12/12/2012] [Indexed: 12/05/2022] Open
Abstract
Human mitochondrial RNA polymerase, POLRMT, is required for mitochondrial DNA (mtDNA) transcription and forms initiation complexes with human mitochondrial transcription factor B2 (h-mtTFB2). However, POLRMT also interacts with the paralogue of h-mtTFB2, h-mtTFB1, which is a 12S ribosomal RNA methyltransferase required for small (28S) mitochondrial ribosome subunit assembly. Herein, we show that POLRMT associates with h-mtTFB1 in 28S mitochondrial ribosome complexes that are stable in the absence of mitochondrial transcription and distinct from transcription complexes containing POLRMT and h-mtTFB2. Overexpression of POLRMT in HeLa cells increases 12S rRNA methylation by h-mtTFB1 and reduces the steady-state levels of mtDNA-encoded proteins and respiration, apparently because of a decrease in fully assembled 55S mitochondrial ribosomes. We propose that POLRMT interacts directly with h-mtTFB1 in 28S mitochondrial ribosomes to augment its 12S rRNA methyltransferase activity, and that together they provide a checkpoint for proper 28S and 55S mitochondrial ribosome assembly. Thus, POLRMT is multi-functional, forming distinct protein complexes that regulate different steps in mitochondrial gene expression, at least one of which does not involve transcription per se. The significance of these results is discussed with regard to the mechanism and regulation of human mitochondrial gene expression and the potential multi-functionality of RNA polymerases in general.
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Affiliation(s)
- Yulia V. Surovtseva
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA and Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Gerald S. Shadel
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA and Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
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19
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Liang Y, Danzy S, Dao LD, Parslow TG, Liang Y. Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. PLoS One 2012; 7:e29485. [PMID: 22238617 PMCID: PMC3253111 DOI: 10.1371/journal.pone.0029485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 11/29/2011] [Indexed: 11/19/2022] Open
Abstract
Influenza A viral polymerase is a heterotrimeric complex that consists of PA, PB1, and PB2 subunits. We previously reported that a di-codon substitution mutation (G507A-R508A), denoted J10, in the C-terminal half of PA had no apparent effect on viral RNA synthesis but prevented infectious virus production, indicating that PA may have a novel role independent of its polymerase activity. To further examine the roles of PA in the viral life cycle, we have now generated and characterized additional mutations in regions flanking the J10 site from residues 497 to 518. All tested di-codon mutations completely abolished or significantly reduced viral infectivity, but they did so through disparate mechanisms. Several showed effects resembling those of J10, in that the mutant polymerase supported normal levels of viral RNA synthesis but nonetheless failed to generate infectious viral particles. Others eliminated polymerase activity, in most cases by perturbing the normal nuclear localization of PA protein in cells. We also engineered single-codon mutations that were predicted to pack near the J10 site in the crystal structure of PA, and found that altering residues K378 or D478 each produced a J10-like phenotype. In further studies of J10 itself, we found that this mutation does not affect the formation and release of virion-like particles per se, but instead impairs the ability of those particles to incorporate each of the eight essential RNA segments (vRNAs) that make up the viral genome. Taken together, our analysis identifies mutations in the C-terminal region of PA that differentially affect at least three distinct activities: protein nuclear localization, viral RNA synthesis, and a trans-acting function that is required for efficient packaging of all eight vRNAs.
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Affiliation(s)
- Yuhong Liang
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Shamika Danzy
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Luan Danh Dao
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Tristram G. Parslow
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Yuying Liang
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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20
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Abstract
Coronaviruses contain positive-stranded RNA with ca. 30 kb as a genome, which is wrapped by the envelope, and constitute Nidovirales together with Arteriviridae. The feature of viruses in Nidovirales is the unique structure of the mRNA set, called 3' co-terminal nested set. Coronaviruses have several to more than 10 different species of subgenomic mRNA and generally only the OFR located in the 5' end of each mRNA is translated. The 5' 20 kb of the coronavirus genome or mRNA-1 consists of two ORFs, 1a and 1b, between that there is a unique RNA structure called pseudoknot. From mRNA-1, 1a as well as 1a+1b are translated; the latter 1a+1b results from the translation due to ribosomal frame-shifting facilitated by the pseudoknot structure. From those two proteins, totally 16 proteins are produced as a result of auto-cleavage by the proteases included in la protein. Those proteins exhibit different functions, such as RNA-dependent RNA polymerase, helicase, proteases and proteins that regulate cellular functions, mRNAs smaller than mRNA-2 translate in general the structural proteins, nucleocapsid (N) protein, spike (S) protein, integrated membrane (M) protein and envelope (E) proteins. Those proteins assemble to the vesicles located from ER to Golgi (ER Golgi intermediate compartment) and virions bud into the vesicles. Those virions are released from infected cells via exocytosis.
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Affiliation(s)
- Fumihiro Taguchi
- Nippon Veterinary and Life Science University, Laboratory of Virology and Viral Infections.
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21
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Bai H, Zhou Y, Hou Z, Xue X, Meng J, Luo X. Targeting bacterial RNA polymerase: promises for future antisense antibiotics development. Infect Disord Drug Targets 2011; 11:175-187. [PMID: 21470098 DOI: 10.2174/187152611795589708] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 06/19/2010] [Indexed: 05/30/2023]
Abstract
The progress of transcription is synthesized by complex molecules, among which DNA-dependent RNA polymerase (RNAP) is the central enzyme. The prokaryotic RNAP is a large protein composed of core subunits (α2, β and β') and a σ factor that is required for specific recognition of the promoter site and the initiation of transcription. Despite its ubiquity, structural and functional similarities, bacterial RNAPs do not share extensive sequence homology with eukaryotic RNAPs. Bacterial RNAP an attractive target for the development of anti-bacterial drugs as its inactivation would lead to bacterial cell death. This review will present the state of knowledge on the assembly and function of RNAP subunits in bacteria with special focus on insights provided by structural analysis of a key component σ factor. Thorough retrospection has been provided for better understanding of progress and problems in targeting RNAP by traditional chemical compounds. Recent progress using innovative strategies including structural biology and phage based screening, especially the antisense technology, has shed light on developing the first set of macro-molecule RNAP inhibitors. In particular, exploration on targeting RNAP σ70 for realization of broad spectrum antisense bactericidal effect in gram negative bacteria presents the first successful example of PNA-peptide conjugate showing attractive potential as conventional broad-spectrum antibiotics, in which possible way the antisense antibiotics might develop into to meet the range and type of usage in future health care.
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Affiliation(s)
- Hui Bai
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, No. 17 Changle West Road, Xi'an, China
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22
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Bai H, Yan H, Hou Z. [Advances in the researches on bacterial RNA polymerase sigma subunit]. Sheng Li Ke Xue Jin Zhan 2011; 42:47-51. [PMID: 21595188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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23
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Tan XY, Liu XL, Wang W, Jia DJ, Chen LQ, Zhang XQ, Ye D. Mutations in the Arabidopsis nuclear-encoded mitochondrial phage-type RNA polymerase gene RPOTm led to defects in pollen tube growth, female gametogenesis and embryogenesis. Plant Cell Physiol 2010; 51:635-49. [PMID: 20231244 DOI: 10.1093/pcp/pcq029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The mitochondrial genes in Arabidopsis thaliana are transcribed by a small family of nuclear-encoded T3/T7 phage-type RNA polymerases (RPOTs). At least two nuclear-encoded RPOTs (RPOTm and RPOTmp) are located in mitochondria in A. thaliana. Their genetic roles are largely unknown. Here we report the characterization of novel mutations in the A. thaliana RPOTm gene. The mutations did not affect pollen formation, but significantly retarded the growth of the rpoTm mutant pollen tubes and had an impact on the fusion of the polar nuclei in the rpoTm mutant embryo sacs. Moreover, development of the rpoTm/- mutant embryo was arrested at the globular stage. The rpoTm rpoTmp double mutation could enhance the rpoTm mutant phenotype. Expression of RPOTmp under control of the RPOTm promoter could not complement the phenotype of the rpoTm mutations. All these data indicate that RPOTm is important for normal pollen tube growth, female gametogenesis and embryo development, and has distinct genetic and molecular roles in plant development, which cannot be replaced by RPOTmp.
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Affiliation(s)
- Xiao-Yun Tan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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24
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Fusté JM, Wanrooij S, Jemt E, Granycome CE, Cluett TJ, Shi Y, Atanassova N, Holt IJ, Gustafsson CM, Falkenberg M. Mitochondrial RNA polymerase is needed for activation of the origin of light-strand DNA replication. Mol Cell 2010; 37:67-78. [PMID: 20129056 DOI: 10.1016/j.molcel.2009.12.021] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 07/21/2009] [Accepted: 10/14/2009] [Indexed: 11/19/2022]
Abstract
Mitochondrial DNA is replicated by a unique enzymatic machinery, which is distinct from the replication apparatus used for copying the nuclear genome. We examine here the mechanisms of origin-specific initiation of lagging-strand DNA synthesis in human mitochondria. We demonstrate that the mitochondrial RNA polymerase (POLRMT) is the primase required for initiation of DNA synthesis from the light-strand origin of DNA replication (OriL). Using only purified POLRMT and DNA replication factors, we can faithfully reconstitute OriL-dependent initiation in vitro. Leading-strand DNA synthesis is initiated from the heavy-strand origin of DNA replication and passes OriL. The single-stranded OriL is exposed and adopts a stem-loop structure. At this stage, POLRMT initiates primer synthesis from a poly-dT stretch in the single-stranded loop region. After about 25 nt, POLRMT is replaced by DNA polymerase gamma, and DNA synthesis commences. Our findings demonstrate that POLRMT can function as an origin-specific primase in mammalian mitochondria.
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Affiliation(s)
- Javier Miralles Fusté
- Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
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25
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Kazerouninia A, Ngo B, Martinson HG. Poly(A) signal-dependent degradation of unprocessed nascent transcripts accompanies poly(A) signal-dependent transcriptional pausing in vitro. RNA 2010; 16:197-210. [PMID: 19926725 PMCID: PMC2802029 DOI: 10.1261/rna.1622010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Accepted: 09/22/2009] [Indexed: 05/28/2023]
Abstract
The poly(A) signal has long been known for its role in directing the cleavage and polyadenylation of eukaryotic mRNA. In recent years its additional coordinating role in multiple related aspects of gene expression has also become increasingly clear. Here we use HeLa nuclear extracts to study two of these activities, poly(A) signal-dependent transcriptional pausing, which was originally proposed as a surveillance checkpoint, and poly(A) signal-dependent degradation (PDD) of unprocessed transcripts from weak poly(A) signals. We confirm directly, by measuring the length of RNA within isolated transcription elongation complexes, that a newly transcribed poly(A) signal reduces the rate of elongation by RNA polymerase II and causes the accumulation of elongation complexes downstream from the poly(A) signal. We then show that if the RNA in these elongation complexes contains a functional but unprocessed poly(A) signal, degradation of the transcripts ensues. The degradation depends on the unprocessed poly(A) signal being functional, and does not occur if a mutant poly(A) signal is used. We suggest that during normal 3'-end processing the uncleaved poly(A) signal continuously samples competing reaction pathways for processing and for degradation, and that in the case of weak poly(A) signals, where poly(A) site cleavage is slow, the default pathway to degradation predominates.
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Affiliation(s)
- Amir Kazerouninia
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California 90095-1569, USA
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26
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Kato C. [Features of the enzymes produced by deep-sea microorganisms]. Seikagaku 2009; 81:1094-1100. [PMID: 20077853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Chiaki Kato
- Marine Biodiversity Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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27
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28
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Palmer AC, Ahlgren-Berg A, Egan JB, Dodd IB, Shearwin KE. Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter. Mol Cell 2009; 34:545-55. [PMID: 19524535 DOI: 10.1016/j.molcel.2009.04.018] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 02/24/2009] [Accepted: 04/14/2009] [Indexed: 01/01/2023]
Abstract
Elongating RNA polymerases (RNAPs) can interfere with transcription from downstream promoters by inhibiting DNA binding by RNAP and activators. However, combining quantitative measurement with mathematical modeling, we show that simple RNAP elongation cannot produce the strong asymmetric interference observed between a natural face-to-face promoter pair in bacteriophage lambda. Pausing of elongating polymerases over the RNAP-binding site of the downstream promoter is demonstrated in vivo and is shown by modeling to account for the increased interference. The model successfully predicts the effects on interference of treatments increasing or reducing pausing. Gene regulation by pausing-enhanced occlusion provides a general and potentially widespread mechanism by which even weak converging or tandem transcription, either coding or noncoding, can bring about strong in cis repression.
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Affiliation(s)
- Adam C Palmer
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
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29
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Pontes O, Costa-Nunes P, Vithayathil P, Pikaard CS. RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway. Mol Plant 2009; 2:700-710. [PMID: 19825650 PMCID: PMC2902898 DOI: 10.1093/mp/ssp006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Accepted: 01/16/2009] [Indexed: 05/19/2023]
Abstract
In Arabidopsis, pericentromeric repeats, retroelements, and silenced rRNA genes are assembled into heterochromatin within nuclear structures known as chromocenters. The mechanisms governing higher-order heterochromatin organization are poorly understood but 24-nt small interfering RNAs (siRNAs) are known to play key roles in heterochromatin formation. Nuclear RNA polymerase IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2), and DICER-LIKE 3 (DCL3) are required for biogenesis of 24-nt siRNAs that associate with ARGONAUTE 4 (AGO4). Nuclear RNA polymerase V (Pol V) collaborates with DRD1 (DEFICIENT IN RNA-DEPENDENT DNA METHYLATION 1) to generate transcripts at heterochromatic loci that are hypothesized to bind to siRNA-AGO4 complexes and subsequently recruit the de-novo DNA methylation and/or histone modifying machinery. Here, we report that decondensation of the major pericentromeric repeats and depletion of the heterochromatic mark histone H3 lysine 9 dimethylation at chromocenters occurs specifically in pol V and drd1 mutants. Disruption of pericentromeric repeats condensation is coincident with transcriptional reactivation of specific classes of pericentromeric 180-bp repeats. We further demonstrate that Pol V functions independently of Pol IV, RDR2, and DCL3-mediated siRNA production to affect interphase heterochromatin organization, possibly by involving RNAs that recruit structural or chromatin-modifying proteins.
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Affiliation(s)
- Olga Pontes
- Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA.
| | - Pedro Costa-Nunes
- Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA
| | - Paul Vithayathil
- Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA
| | - Craig S Pikaard
- Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA
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30
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Hirata A. [Archaeal transcriptional machinery]. Seikagaku 2009; 81:377-381. [PMID: 19522293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Akira Hirata
- Department of Material Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama 790-8577, Japan
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31
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Lahmy S, Pontier D, Cavel E, Vega D, El-Shami M, Kanno T, Lagrange T. PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Proc Natl Acad Sci U S A 2009; 106:941-6. [PMID: 19141635 PMCID: PMC2630096 DOI: 10.1073/pnas.0810310106] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Indexed: 01/22/2023] Open
Abstract
Two forms of a plant-specific RNA polymerase (Pol), PolIV(PolIVa) and PolV(PolIVb), currently defined by their respective largest subunits [NRPD1(NRPD1a) and NRPE1(NRPD1b)], have been implicated in the production and activity of 24-nt small RNAs (sRNAs) in RNA-directed DNA methylation (RdDM). Prevailing models support the view that PolIV(PolIVa) plays an upstream role in RdDM by producing the 24-nt sRNAs, whereas PolV(PolIVb) would act downstream at a structural rather than an enzymatic level to reinforce sRNA production by PolIV(PolIVa) and mediate DNA methylation. However, the composition and mechanism of action of PolIV(PolIVa)/PolV(PolIVb) remain unclear. In this work, we have identified a plant-specific PolV(PolIVb) subunit, NRPE5a, homologous to NRPB5a, a common subunit shared by PolI-III and shown here to be present in PolIV(PolIVa). Our results confirm the combinatorial diversity of PolIV(PolIVa)/PolV(PolIVb) subunit composition and indicate that these plant-specific Pols are eukaryotic-type polymerases. Moreover, we show that nrpe5a-1 mutation differentially impacts sRNAs accumulation at various PolIV(PolIVa)/PolV(PolIVb)-dependent loci, indicating a target-specific requirement for NRPE5a in the process of PolV(PolIVb)-dependent gene silencing. We then describe that the triad aspartate motif present in the catalytic center of PolV(PolIVb) is required for recapitulation of all activities associated with this Pol complex in RdDM, suggesting that RNA polymerization is important for PolV(PolIVb) to perform its regulatory functions.
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Affiliation(s)
- Sylvie Lahmy
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique/Institut de Recherche et Développement/Université de Perpignan, 66860 Perpignan Cedex, France; and
| | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique/Institut de Recherche et Développement/Université de Perpignan, 66860 Perpignan Cedex, France; and
| | - Emilie Cavel
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique/Institut de Recherche et Développement/Université de Perpignan, 66860 Perpignan Cedex, France; and
| | - Danielle Vega
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique/Institut de Recherche et Développement/Université de Perpignan, 66860 Perpignan Cedex, France; and
| | - Mahmoud El-Shami
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique/Institut de Recherche et Développement/Université de Perpignan, 66860 Perpignan Cedex, France; and
| | - Tatsuo Kanno
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, A-1030 Vienna, Austria
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique/Institut de Recherche et Développement/Université de Perpignan, 66860 Perpignan Cedex, France; and
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32
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Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X. Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription. Structure 2008; 16:1417-27. [PMID: 18786404 DOI: 10.1016/j.str.2008.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Revised: 06/11/2008] [Accepted: 06/30/2008] [Indexed: 11/30/2022]
Abstract
RapA, as abundant as sigma70 in the cell, is an RNA polymerase (RNAP)-associated Swi2/Snf2 protein with ATPase activity. It stimulates RNAP recycling during transcription. We report a structure of RapA that is also a full-length structure for the entire Swi2/Snf2 family. RapA contains seven domains, two of which exhibit novel protein folds. Our model of RapA in complex with ATP and double-stranded DNA (dsDNA) suggests that RapA may bind to and translocate on dsDNA. Our kinetic template-switching assay shows that RapA facilitates the release of sequestered RNAP from a posttranscrption/posttermination complex for transcription reinitiation. Our in vitro competition experiment indicates that RapA binds to core RNAP only but is readily displaceable by sigma70. RapA is likely another general transcription factor, the structure of which provides a framework for future studies of this bacterial Swi2/Snf2 protein and its important roles in RNAP recycling during transcription.
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Affiliation(s)
- Gary Shaw
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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33
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Toyoda T. [Influenza virus RNA polymerase]. Tanpakushitsu Kakusan Koso 2007; 52:1144-8. [PMID: 17824231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
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34
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Toulokhonov I, Zhang J, Palangat M, Landick R. A Central Role of the RNA Polymerase Trigger Loop in Active-Site Rearrangement during Transcriptional Pausing. Mol Cell 2007; 27:406-19. [PMID: 17679091 DOI: 10.1016/j.molcel.2007.06.008] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 05/10/2007] [Accepted: 06/06/2007] [Indexed: 11/15/2022]
Abstract
Transcriptional pausing by RNA polymerase is an underlying event in the regulation of transcript elongation, yet the physical changes in the transcribing complex that create the initially paused conformation remain poorly understood. We report that this nonbacktracked elemental pause results from an active-site rearrangement whose signature includes a trigger-loop conformation positioned near the RNA 3' nucleotide and a conformation of betaDloopII that allows fraying of the RNA 3' nucleotide away from the DNA template. During nucleotide addition, trigger-loop movements or folding appears to assist NTP-stimulated translocation and to be crucial for catalysis. At a pause, the trigger loop directly contributes to the paused conformation, apparently by restriction of its movement or folding, whereas a previously postulated unfolding of the bridge helix does not. This trigger-loop-centric model can explain many properties of transcriptional pausing.
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35
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Chao M. RNA recombination in hepatitis delta virus: Implications regarding the abilities of mammalian RNA polymerases. Virus Res 2007; 127:208-15. [PMID: 17296240 DOI: 10.1016/j.virusres.2007.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 10/02/2006] [Accepted: 01/08/2007] [Indexed: 12/18/2022]
Abstract
Hepatitis delta virus (HDV) requires the surface antigens of hepatitis B virus (HBV) for packaging and transmission, but replicates its RNA in an HBV-independent fashion. HDV contains a 1.7-kb circular RNA genome that is folded into an unbranched rod-like structure via intramolecular base-pairing, and possesses ribozyme activity. The HDV genome does not encode an RNA-dependent RNA polymerase (RdRp), but is instead replicated by host RNA polymerase(s) via a rolling-circle mechanism. As such, HDV is similar to the viroid plant pathogens. Recent findings suggest that HDV can also undergo template-switching recombination, a well-documented process that has been found in a large number of RdRp-encoding RNA viruses and is thought to affect viral evolution and pathogenesis. This mini-review examines HDV RNA recombination and how it may improve our understanding of the capacities of host RNA polymerases beyond typical DNA-directed transcription, and speculates on the role of host RNA polymerase-directed RNA template-switching in the origin of HDV.
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Affiliation(s)
- Mei Chao
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, 259, Wen-Hwa 1st Road, Kwei-Shan, Tao-yang 333, Taiwan.
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36
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Wang Q, Tullius TD, Levin JR. Effects of discontinuities in the DNA template on abortive initiation and promoter escape by Escherichia coli RNA polymerase. J Biol Chem 2007; 282:26917-26927. [PMID: 17650506 DOI: 10.1074/jbc.m702473200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using singly gapped or nicked templates containing the T7A1 promoter, we have measured several kinetic parameters related to the process of transcription initiation by Escherichia coli RNA polymerase, confirming and extending previous results using a population of randomly gapped templates. A reduced probability of transcript abortion at RNA lengths of 6 and 7 nucleotides and a lower ratio of abortive to productive initiation events was observed for some discontinuous templates, consistent with models attributing abortive initiation to the accumulation of strain in the initiating complex. The effect of DNA discontinuity on abortion of shorter RNA transcripts (2-3 nucleotides) was less pronounced; abortion at these short chain lengths may primarily be attributed to the low stability of the RNA-DNA hybrid. Certain discontinuities had significant effects on the intrinsic catalytic capacity of the open complex and also on the partitioning between productive and unproductive complexes, suggesting that subtle changes in the conformation of the open complex can profoundly affect its function. The rate and efficiency of promoter escape were not correlated with the stability of the open promoter complex despite previous suggestions to the contrary. We conclude that the stability of the open promoter complex is only one of several factors that contribute to the overall rate of promoter escape.
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Affiliation(s)
- Qun Wang
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215 and the
| | - Thomas D Tullius
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215 and the
| | - Judith R Levin
- Departments of Biological Sciences and Chemistry, Goucher College, Baltimore, Maryland 21204.
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37
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Ling F, Hori A, Yoshida M, Shibata T. [Rolling circle replication: a universal model for controlling mechanisms of mitochondrial DNA copy number]. Tanpakushitsu Kakusan Koso 2007; 52:886-92. [PMID: 17642272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
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38
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Abstract
DNA damage that blocks the transcription of genes is prioritized for repair by transcription-coupled DNA repair pathways. RNA polymerases stalled at DNA lesions obstruct repair enzymes, but this situation is turned to the advantage of the cell by transcription-repair coupling factors that remove the stalled RNA polymerase from DNA and increase the rate at which the lesion is repaired. Recent structural studies of the bacterial transcription-repair coupling factor, Mfd, have revealed a modular architecture in which an ATP-dependent DNA-based motor is coupled to protein-protein interaction domains that can attach the motor to RNA polymerase and the DNA repair protein UvrA. Here I review the key features of this multifunctional protein and discuss how recent mechanistic and structural findings have advanced our understanding of transcription-coupled DNA repair in bacteria.
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Affiliation(s)
- Nigel J Savery
- DNA-Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
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39
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Cook VM, Dehaseth PL. Strand opening-deficient Escherichia coli RNA polymerase facilitates investigation of closed complexes with promoter DNA: effects of DNA sequence and temperature. J Biol Chem 2007; 282:21319-26. [PMID: 17507375 DOI: 10.1074/jbc.m702232200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formation of the strand-separated, open complex between RNA polymerase and a promoter involves several intermediates, the first being the closed complex in which the DNA is fully base-paired. This normally short lived complex has been difficult to study. We have used a mutant Escherichia coli RNA polymerase, deficient in promoter DNA melting, and variants of the P(R) promoter of bacteriophage lambda to model the closed complex intermediate at physiologically relevant temperatures. Our results indicate that in the closed complex, RNA polymerase recognizes base pairs as double-stranded DNA even in the region that becomes single-stranded in the open complex. Additionally, a particular base pair in the -35 region engages in an important interaction with the RNA polymerase, and a DNase I-hypersensitive site, pronounced in the promoter DNA of the open complex, was not present. The effect of temperature on closed complex formation was found to be small over the temperature range from 15 to 37 degrees C. This suggests that low temperature complexes of wild type RNA polymerase and promoter DNA may adequately model the closed complex.
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Affiliation(s)
- Victoria M Cook
- Center for RNA Molecular Biology, Case Western Reserve University, Clevland, Ohio 44106, USA
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40
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Henry AA, Romesberg FE. The evolution of DNA polymerases with novel activities. Curr Opin Biotechnol 2007; 16:370-7. [PMID: 16006114 DOI: 10.1016/j.copbio.2005.06.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 06/01/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
DNA and RNA polymerases have evolved in nature to function in specific environments with specific substrates. Thus, although the commercial availability of these enzymes has revolutionized the biotechnology industry, their applications are limited. The availability of polymerases that have unnatural properties would be of even greater utility. Towards this goal, several activity-based screening and selection approaches have been developed. Using these techniques, polymerases that synthesize a variety of different polymers, including those containing 2'-O-methyl-modified nucleotides or unnatural base pairs, have been evolved. These results suggest that polymerases tailored for any specific application could soon be available.
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Affiliation(s)
- Allison A Henry
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, USA
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41
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Abstract
In addition to the three RNA polymerases (RNAP I-III) shared by all eukaryotic organisms, plant genomes encode a fourth RNAP (RNAP IV) that appears to be specialized in the production of siRNAs. Available data support a model in which dsRNAs are generated by RNAP IV and RNA-dependent RNAP 2 (RDR2) and processed by DICER (DCL) enzymes into 21- to 24-nt siRNAs, which are associated with different ARGONAUTE (AGO) proteins for transcriptional or posttranscriptional gene silencing. However, it is not yet clear what fraction of genomic siRNA production is RNAP IV-dependent, and to what extent these siRNAs are preferentially processed by certain DCL(s) or associated with specific AGOs for distinct downstream functions. To address these questions on a genome-wide scale, we sequenced approximately 335,000 siRNAs from wild-type and RNAP IV mutant Arabidopsis plants by using 454 technology. The results show that RNAP IV is required for the production of >90% of all siRNAs, which are faithfully produced from a discrete set of genomic loci. Comparisons of these siRNAs with those accumulated in rdr2 and dcl2 dcl3 dcl4 and those associated with AGO1 and AGO4 provide important information regarding the processing, channeling, and functions of plant siRNAs. We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Ian R. Henderson
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Cheng Lu
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711; and
| | - Pamela J. Green
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711; and
| | - Steven E. Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- To whom correspondence should be addressed. E-mail:
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42
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Arnoldi F, Campagna M, Eichwald C, Desselberger U, Burrone OR. Interaction of rotavirus polymerase VP1 with nonstructural protein NSP5 is stronger than that with NSP2. J Virol 2007; 81:2128-37. [PMID: 17182692 PMCID: PMC1865955 DOI: 10.1128/jvi.01494-06] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Accepted: 12/07/2006] [Indexed: 01/19/2023] Open
Abstract
Rotavirus morphogenesis starts in intracellular inclusion bodies called viroplasms. RNA replication and packaging are mediated by several viral proteins, of which VP1, the RNA-dependent RNA polymerase, and VP2, the core scaffolding protein, were shown to be sufficient to provide replicase activity in vitro. In vivo, however, viral replication complexes also contain the nonstructural proteins NSP2 and NSP5, which were shown to be essential for replication, to interact with each other, and to form viroplasm-like structures (VLS) when coexpressed in uninfected cells. In order to gain a better understanding of the intermediates formed during viral replication, this work focused on the interactions of NSP5 with VP1, VP2, and NSP2. We demonstrated a strong interaction of VP1 with NSP5 but only a weak one with NSP2 in cotransfected cells in the absence of other viral proteins or viral RNA. By contrast, we failed to coimmunoprecipitate VP2 with anti-NSP5 antibodies or NSP5 with anti-VP2 antibodies. We constructed a tagged form of VP1, which was found to colocalize in viroplasms and in VLS formed by NSP5 and NSP2. The tagged VP1 was able to replace VP1 structurally by being incorporated into progeny viral particles. When applying anti-tag-VP1 or anti-NSP5 antibodies, coimmunoprecipitation of tagged VP1 with NSP5 was found. Using deletion mutants of NSP5 or different fragments of NSP5 fused to enhanced green fluorescent protein, we identified the 48 C-terminal amino acids as the region essential for interaction with VP1.
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Affiliation(s)
- F Arnoldi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34012 Trieste, Italy
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43
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Smith AJ, Szczelkun MD, Savery NJ. Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase. Nucleic Acids Res 2007; 35:1802-11. [PMID: 17329375 PMCID: PMC1874598 DOI: 10.1093/nar/gkm019] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Motor proteins that couple ATP hydrolysis to movement along nucleic acids play a variety of essential roles in DNA metabolism. Often these enzymes function as components of macromolecular complexes, and DNA translocation by the motor protein drives movement of other components of the complex. In order to understand how the activity of motor proteins is regulated within multi-protein complexes we have studied the bacterial transcription-repair coupling factor, Mfd, which is a helicase superfamily 2 member that binds to RNA polymerase (RNAP) and removes stalled transcription complexes from DNA. Using an oligonucleotide displacement assay that monitors protein movement on double-stranded DNA we show that Mfd has little motor activity in isolation, but exhibits efficient oligonucleotide displacement activity when bound to a stalled transcription complex. Deletion of the C-terminal domain of Mfd increases the ATPase activity of the protein and allows efficient oligo-displacement in the absence of RNAP. Our results suggest that an autoinhibitory domain ensures the motor activity of Mfd is only functional within the correct macromolecular context: recruitment of Mfd to a stalled transcription complex relieves the autoinhibition and unmasks the motor activity.
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Affiliation(s)
| | | | - Nigel J. Savery
- *To whom correspondence should be addressed. +(44) 117 928 9708+(44) 117 928 8274
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44
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Vingadassalom D, Kolb A, Mayer C, Collatz E, Podglajen I. Probing the Importance of Selected Phylum-specific Amino Acids in σA of Bacteroides fragilis, a Primary σ Factor Naturally Devoid of an N-terminal Acidic Region 1.1. J Biol Chem 2007; 282:3442-9. [PMID: 17150963 DOI: 10.1074/jbc.m608855200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sigmaA factor of Bacteroides fragilis is the prototype of a novel subgroup of primary sigma factors that are essential for growth and ensure the initiation of transcription of the housekeeping genes. This subgroup is confined to the phyla Bacteroidetes and Chlorobi. Its members carry a specific amino acid signature and are notably characterized by a short, basic N-terminal segment instead of the typical acidic region 1.1. Using in vitro mutagenesis, we investigated the importance of this basic segment and of several residues of the signature for the function of sigmaA. We have shown that the conserved residues Phe-61 and Lys-265, located in the core binding and DNA binding subregions 2.1 and 4.2, respectively, are critical for full function of the B. fragilis holoenzyme. With respect to the unusual subregion composition of sigmaA, we have shown that truncation of the basic N-terminal segment, or reversion of its charge, strongly affects the overall transcriptional activity of B. fragilis RNA polymerase in vitro. Our results indicate that the presence of the intact basic segment is required for the formation of RNA polymerase (RNAP)-promoter open complexes, the correct architecture of the transcription bubble, and efficient promoter clearance.
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45
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Devaux S, Kelly S, Lecordier L, Wickstead B, Perez-Morga D, Pays E, Vanhamme L, Gull K. Diversification of function by different isoforms of conventionally shared RNA polymerase subunits. Mol Biol Cell 2007; 18:1293-301. [PMID: 17267688 PMCID: PMC1838988 DOI: 10.1091/mbc.e06-09-0841] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Eukaryotic nuclei contain three classes of multisubunit DNA-directed RNA polymerase. At the core of each complex is a set of 12 highly conserved subunits of which five--RPB5, RPB6, RPB8, RPB10, and RPB12--are thought to be common to all three polymerase classes. Here, we show that four distantly related eukaryotic lineages (the higher plant and three protistan) have independently expanded their repertoire of RPB5 and RPB6 subunits. Using the protozoan parasite Trypanosoma brucei as a model organism, we demonstrate that these distinct RPB5 and RPB6 subunits localize to discrete subnuclear compartments and form part of different polymerase complexes. We further show that RNA interference-mediated depletion of these discrete subunits abolishes class-specific transcription and hence demonstrates complex specialization and diversification of function by conventionally shared subunit groups.
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Affiliation(s)
- Sara Devaux
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Steven Kelly
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Laurence Lecordier
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - David Perez-Morga
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Etienne Pays
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Luc Vanhamme
- *Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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Yakhnin AV, Yakhnin H, Babitzke P. RNA polymerase pausing regulates translation initiation by providing additional time for TRAP-RNA interaction. Mol Cell 2007; 24:547-57. [PMID: 17114058 DOI: 10.1016/j.molcel.2006.09.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 08/10/2006] [Accepted: 09/22/2006] [Indexed: 11/22/2022]
Abstract
RNA polymerase (RNAP) pause sites have been identified in several prokaryotic genes. Although the presumed biological function of RNAP pausing is to allow synchronization of RNAP position with regulatory factor binding and/or RNA folding, a direct causal link between pausing and changes in gene expression has been difficult to establish. RNAP pauses at two sites in the Bacillus subtilis trpEDCFBA operon leader. Pausing at U107 and U144 participates in transcription attenuation and trpE translation control mechanisms, respectively. Substitution of U144 caused a substantial pausing defect in vitro and in vivo. These mutations led to increased trp operon expression that was suppressed by overproduction of TRAP, indicating that pausing at U144 provides additional time for TRAP to bind to the nascent transcript and promote formation of an RNA structure that blocks translation of trpE. These results establish that pausing is capable of playing a role in regulating translation in bacteria.
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Affiliation(s)
- Alexander V Yakhnin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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47
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Chan SWL, Henderson IR, Zhang X, Shah G, Chien JSC, Jacobsen SE. RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis. PLoS Genet 2007; 2:e83. [PMID: 16741558 PMCID: PMC1472700 DOI: 10.1371/journal.pgen.0020083] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Accepted: 04/18/2006] [Indexed: 11/25/2022] Open
Abstract
Cytosine DNA methylation protects eukaryotic genomes by silencing transposons and harmful DNAs, but also regulates gene expression during normal development. Loss of CG methylation in the Arabidopsis thaliana met1 and ddm1 mutants causes varied and stochastic developmental defects that are often inherited independently of the original met1 or ddm1 mutation. Loss of non-CG methylation in plants with combined mutations in the DRM and CMT3 genes also causes a suite of developmental defects. We show here that the pleiotropic developmental defects of drm1 drm2 cmt3 triple mutant plants are fully recessive, and unlike phenotypes caused by met1 and ddm1, are not inherited independently of the drm and cmt3 mutations. Developmental phenotypes are also reversed when drm1 drm2 cmt3 plants are transformed with DRM2 or CMT3, implying that non-CG DNA methylation is efficiently re-established by sequence-specific signals. We provide evidence that these signals include RNA silencing though the 24-nucleotide short interfering RNA (siRNA) pathway as well as histone H3K9 methylation, both of which converge on the putative chromatin-remodeling protein DRD1. These signals act in at least three partially intersecting pathways that control the locus-specific patterning of non-CG methylation by the DRM2 and CMT3 methyltransferases. Our results suggest that non-CG DNA methylation that is inherited via a network of persistent targeting signals has been co-opted to regulate developmentally important genes. The majority of DNA in large eukaryotic genomes (such as the human genome) consists of transposons, sequences that can reproduce at the expense of their host. Plants and animals mark transposon DNA with a chemical modification called DNA methylation. DNA methylation prevents the functional information in transposons from being copied into RNA and utilized—this process is termed “gene silencing.” Using a flowering plant called Arabidopsis, the authors created mutants lacking a particular type of DNA methylation, and found that these plants had defects in leaf shape, plant height, and fertility. This shows that a gene-silencing mechanism used to defend the genome from transposons is also important for normal plant development. When the mutated genes are restored, plant development returns to normal, showing that one type of DNA methylation can be efficiently re-established (other gene-silencing marks can be lost irreversibly). Small RNA molecules are important for targeting DNA methylation to transposons and harmful DNAs. Mutants in genes that are important for making small RNAs have similar developmental defects to those lacking DNA methylation. This implies that normal plant development requires DNA methylation that is targeted by small RNAs.
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Affiliation(s)
- Simon W.-L Chan
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ian R Henderson
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xiaoyu Zhang
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Govind Shah
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jason S.-C Chien
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Yao C, Luo J, Hsiao CHC, Donelson JE, Wilson ME. Leishmania chagasi: a tetracycline-inducible cell line driven by T7 RNA polymerase. Exp Parasitol 2007; 116:205-13. [PMID: 17320870 PMCID: PMC2231517 DOI: 10.1016/j.exppara.2007.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 12/22/2006] [Accepted: 01/02/2007] [Indexed: 11/24/2022]
Abstract
Trypanosomatid protozoa lack consensus promoters for RNA polymerase (RNAP) II. However, the artificial insertion of the T7 promoter (P(T7)) and the tetracycline repressor into Trypanosoma brucei cell lines expressing T7RNAP allows P(T7)-driven gene expression to be tetracycline-inducible. These cell lines provide a molecular tool to address protein function by several recombinant approaches. We describe here the development of an analogous Leishmania chagasi cell line bearing the genes for exogenous T7RNAP and the tetracycline repressor inserted in the multi-gene alpha-tubulin locus. A plasmid construct with P(T7) and the tetracycline operator upstream of a reporter gene, when introduced into this cell line as episomal plasmids or chromosomal insertion into the non-coding strand of an 18SrRNA gene, resulted in tetracycline-inducible expression of the reporter as much as 16- and 150-fold, respectively. The reporter was under a much tighter control when chromosomally inserted than extra-chromosomally born. Furthermore, P(T7) augmented the reporter's expression 2-fold more in comparison to P(T7)-less constructs. This cell line is the first Leishmania spp. that allows the exogenous T7RNAP-driven gene expression to be tetracycline-inducible; and may provide a useful tool for addressing protein function by manipulating expression levels of Leishmania endogenous genes.
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Affiliation(s)
- Chaoqun Yao
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.
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Klauck E, Typas A, Hengge R. The sigmaS subunit of RNA polymerase as a signal integrator and network master regulator in the general stress response in Escherichia coli. Sci Prog 2007; 90:103-27. [PMID: 17725229 PMCID: PMC10368345 DOI: 10.3184/003685007x215922] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The sigmaS (RpoS) subunit of RNA polymerase in Escherichia coli is a key master regulator which allows this bacterial model organism and important pathogen to adapt to and survive environmentally rough times. While hardly present in rapidly growing cells, sigmaS strongly accumulates in response to many different stress conditions, partly replaces the vegetative sigma subunit in RNA polymerase and thereby reprograms this enzyme to transcribe sigmaS-dependent genes (up to 10% of the E. coli genes). In this review, we summarize the extremely complex regulation of sigmaS itself and multiple signal input at the level of this master regulator, we describe the way in which sigmaS specifically recognizes "stress" promoters despite their similarity to vegetative promoters, and, while being far from comprehensive, we give a short overview of the far-reaching physiological impact of sigmaS. With sigmaS being a central and multiple signal integrator and master regulator of hundreds of genes organized in regulatory cascades and sub-networks or regulatory modules, this system also represents a key model system for analyzing complex cellular information processing and a starting point for understanding the complete regulatory network of an entire cell.
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Affiliation(s)
| | - Athanasios Typas
- Aristotle University of Thessaloniki in Greece, Freie Universität Berlin
| | - Regine Hengge
- University of Konstanz. University of Princeton (NJ, USA)
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50
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Santangelo TJ, Čuboňová L, James CL, Reeve JN. TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro. J Mol Biol 2006; 367:344-57. [PMID: 17275836 PMCID: PMC1855253 DOI: 10.1016/j.jmb.2006.12.069] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 12/22/2006] [Accepted: 12/27/2006] [Indexed: 11/18/2022]
Abstract
Archaeal RNA polymerases (RNAPs) are most similar to eukaryotic RNAP II (Pol II) but require the support of only two archaeal general transcription factors, TBP (TATA-box binding protein) and TFB (archaeal homologue of the eukaryotic general transcription factor TFIIB) to initiate basal transcription. However, many archaeal genomes encode more than one TFB and/or TBP leading to the hypothesis that different TFB/TBP combinations may be employed to direct initiation from different promoters in Archaea. As a first test of this hypothesis, we have determined the ability of RNAP purified from Thermococcus kodakaraensis (T.k.) to initiate transcription from a variety of T.k. promoters in vitro when provided with T.k. TBP and either TFB1 or TFB2, the two TFBs encoded in the T.k. genome. With every promoter active in vitro, transcription initiation occurred with either TFB1 or TFB2 although the optimum salt concentration for initiation was generally higher for TFB2 (approximately 250 mM K(+)) than for TFB1 (approximately 200 mM K(+)). Consistent with this functional redundancy in vitro, T.k. strains have been constructed with the TFB1- (tfb1; TK1280) or TFB2- (tfb2; TK2287) encoding gene deleted. These mutants exhibit no detectable growth defects under laboratory conditions. Domain swapping between TFB1 and TFB2 has identified a central region that contributes to the salt sensitivity of TFB activity, and deleting residues predicted to form the tip of the B-finger region of TFB2 had no detectable effects on promoter recognition or transcription initiation but did eliminate the production of very short (< or =5 nt) abortive transcripts.
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