1
|
Purhonen J, Hofer A, Kallijärvi J. Quantification of all 12 canonical ribonucleotides by real-time fluorogenic in vitro transcription. Nucleic Acids Res 2024; 52:e6. [PMID: 38008466 PMCID: PMC10783517 DOI: 10.1093/nar/gkad1091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 11/28/2023] Open
Abstract
Enzymatic methods to quantify deoxyribonucleoside triphosphates have existed for decades. In contrast, no general enzymatic method to quantify ribonucleoside triphosphates (rNTPs), which drive almost all cellular processes and serve as precursors of RNA, exists to date. ATP can be measured with an enzymatic luminometric method employing firefly luciferase, but the quantification of other ribonucleoside mono-, di-, and triphosphates is still a challenge for a non-specialized laboratory and practically impossible without chromatography equipment. To allow feasible quantification of ribonucleoside phosphates in any laboratory with typical molecular biology and biochemistry tools, we developed a robust microplate assay based on real-time detection of the Broccoli RNA aptamer during in vitro transcription. The assay employs the bacteriophage T7 and SP6 RNA polymerases, two oligonucleotide templates encoding the 49-nucleotide Broccoli aptamer, and a high-affinity fluorogenic aptamer-binding dye to quantify each of the four canonical rNTPs. The inclusion of nucleoside mono- and diphosphate kinases in the assay reactions enabled the quantification of the mono- and diphosphate counterparts. The assay is inherently specific and tolerates concentrated tissue and cell extracts. In summary, we describe the first chromatography-free method to quantify ATP, ADP, AMP, GTP, GDP, GMP, UTP, UDP, UMP, CTP, CDP and CMP in biological samples.
Collapse
Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Helsinki 00290, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Helsinki 00290, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
2
|
McKinley LN, Kern RG, Assmann SM, Bevilacqua PC. Flanking Sequence Cotranscriptionally Regulates Twister Ribozyme Activity. Biochemistry 2024; 63:53-68. [PMID: 38134329 DOI: 10.1021/acs.biochem.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Small nucleolytic ribozymes are RNAs that cleave their own phosphodiester backbone. While proteinaceous enzymes are regulated by a variety of known mechanisms, methods of regulation for ribozymes remain unclear. Twister is one ribozyme class for which many structural and catalytic properties have been elucidated. However, few studies have analyzed the activity of twister ribozymes in the context of a native flanking sequence, even though ribozymes as transcribed in nature do not exist in isolation. Interactions between the ribozyme and its neighboring sequences can induce conformational changes that inhibit self-cleavage, providing a regulatory mechanism that could naturally determine ribozyme activity in vivo and in synthetic applications. To date, eight twister ribozymes have been identified within the staple crop rice (Oryza sativa). Herein, we select several twister ribozymes from rice and show that they are differentially regulated by their flanking sequence using published RNA-seq data sets, structure probing, and cotranscriptional cleavage assays. We found that the Osa 1-2 ribozyme does not interact with its flanking sequences. However, sequences flanking the Osa 1-3 and Osa 1-8 ribozymes form inactive conformations, referred to here as "ribozymogens", that attenuate ribozyme self-cleavage activity. For the Osa 1-3 ribozyme, we show that activity can be rescued upon addition of a complementary antisense oligonucleotide, suggesting ribozymogens can be controlled via external signals. In all, our data provide a plausible mechanism wherein flanking sequence differentially regulates ribozyme activity in vivo. More broadly, the ability to regulate ribozyme behavior locally has potential applications in control of gene expression and synthetic biology.
Collapse
Affiliation(s)
- Lauren N McKinley
- Depatment of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Reuben G Kern
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sarah M Assmann
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Depatment of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
3
|
Chen L, Liang J. A proximity ligation assay (PLA) based sensing platform for the ultrasensitive detection of P53 protein-specific SUMOylation. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
4
|
Passalacqua LFM, Dingilian AI, Lupták A. Single-pass transcription by T7 RNA polymerase. RNA (NEW YORK, N.Y.) 2020; 26:2062-2071. [PMID: 32958559 PMCID: PMC7668259 DOI: 10.1261/rna.076778.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
RNA molecules can be conveniently synthesized in vitro by the T7 RNA polymerase (T7 RNAP). In some experiments, such as cotranscriptional biochemical analyses, continuous synthesis of RNA is not desired. Here, we propose a method for a single-pass transcription that yields a single transcript per template DNA molecule using the T7 RNAP system. We hypothesized that stalling the polymerase downstream from the promoter region and subsequent cleavage of the promoter by a restriction enzyme (to prevent promoter binding by another polymerase) would allow synchronized production of a single transcript per template. The single-pass transcription was verified in two different scenarios: a short self-cleaving ribozyme and a long mRNA. The results show that a controlled single-pass transcription using T7 RNAP allows precise measurement of cotranscriptional ribozyme activity, and this approach will facilitate the study of other kinetic events.
Collapse
Affiliation(s)
- Luiz F M Passalacqua
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Armine I Dingilian
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
- Department of Chemistry, University of California, Irvine, California 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
| |
Collapse
|
5
|
Aufdembrink LM, Khan P, Gaut NJ, Adamala KP, Engelhart AE. Highly specific, multiplexed isothermal pathogen detection with fluorescent aptamer readout. RNA (NEW YORK, N.Y.) 2020; 26:1283-1290. [PMID: 32482894 PMCID: PMC7430665 DOI: 10.1261/rna.075192.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Isothermal, cell-free, synthetic biology-based approaches to pathogen detection leverage the power of tools available in biological systems, such as highly active polymerases compatible with lyophilization, without the complexity inherent to live-cell systems, of which nucleic acid sequence based amplification (NASBA) is well known. Despite the reduced complexity associated with cell-free systems, side reactions are a common characteristic of these systems. As a result, these systems often exhibit false positives from reactions lacking an amplicon. Here we show that the inclusion of a DNA duplex lacking a promoter and unassociated with the amplicon fully suppresses false positives, enabling a suite of fluorescent aptamers to be used as NASBA tags (Apta-NASBA). Apta-NASBA has a 1 pM detection limit and can provide multiplexed, multicolor fluorescent readout. Furthermore, Apta-NASBA can be performed using a variety of equipment, for example, a fluorescence microplate reader, a qPCR instrument, or an ultra-low-cost Raspberry Pi-based 3D-printed detection platform using a cell phone camera module, compatible with field detection.
Collapse
Affiliation(s)
- Lauren M Aufdembrink
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Pavana Khan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nathaniel J Gaut
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| |
Collapse
|
6
|
Huang Z, Lin CY, Jaremko W, Niu L. HPLC purification of RNA aptamers up to 59 nucleotides with single-nucleotide resolution. Methods Mol Biol 2015; 1297:83-93. [PMID: 25895997 DOI: 10.1007/978-1-4939-2562-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An RNA sample is usually heterogeneous. RNA heterogeneity refers to difference in length or size (i.e., number of nucleotides [nt]), sequence, or alternative but coexisting conformations. Separation and purification of RNA is generally required for investigating the structure and function of RNA, such as RNA catalysis and RNA structure determination by nuclear magnetic resonance or crystallography. Separation and purification of RNA is also required for using RNAs as functional probes and therapeutics as well as building blocks for RNA nanoparticles. Previously established protocols are limited in separating RNAs longer than 25 nt by single-nucleotide resolution. When the length of RNAs becomes longer, single-nucleotide separation of RNAs becomes more challenging. Here we describe protocols, by the use of ion-pair, reverse-phase high-performance liquid chromatography (HPLC), to extend our ability to separate regular RNAs up to 59 nt with single-nucleotide resolution. For chemically modified RNAs at 2' positions on the ribose, we can resolve RNAs of similar sizes even with a 26 Da difference. This is much less than 320 Da, an average single-nucleotide molecular weight difference.
Collapse
Affiliation(s)
- Zhen Huang
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), 1400 Washington Avenue, Albany, NY, 12222, USA
| | | | | | | |
Collapse
|
7
|
Jung HI, Yan J, Zhai Z, Vatamaniuk OK. Gene functional analysis using protoplast transient assays. Methods Mol Biol 2015; 1284:433-452. [PMID: 25757786 DOI: 10.1007/978-1-4939-2444-8_22] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The protoplast transient assay system has been widely used for rapid functional analyses of genes using cellular and biochemical approaches. This system has been increasingly employed for functional genetic studies using double-stranded (ds) RNA interference (RNAi). Here, we describe a modified procedure for the isolation of protoplasts from leaf mesophyll cells of 14-day-old Arabidopsis thaliana. This modification significantly simplifies and speeds up functional studies without compromising the yield and the viability of protoplasts. We also present the procedure for the isolation and transfection of protoplasts from mesophyll cells of an emerging model grass species, Brachypodium distachyon. Further, we detail procedures for RNAi-based functional studies of genes using transient expression of in vitro synthesized dsRNA in protoplasts.
Collapse
Affiliation(s)
- Ha-il Jung
- Department of Crop and Soil Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | | | | |
Collapse
|
8
|
Lin CY, Huang Z, Jaremko W, Niu L. High-performance liquid chromatography purification of chemically modified RNA aptamers. Anal Biochem 2013; 449:106-8. [PMID: 24373999 DOI: 10.1016/j.ab.2013.12.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/11/2013] [Accepted: 12/16/2013] [Indexed: 12/16/2022]
Abstract
2'-Fluoro modified RNAs are useful as potential therapeutics and as special substrates for studying RNA function. 2'-Fluoro modified RNAs generally need to be purified after they are prepared either enzymatically or by solid-phase synthesis. Here we introduce a protocol by which 2'-fluoro modified RNAs with 57 and 58 nucleotides can be resolved and purified using ion-pair, reverse-phase high-performance liquid chromatography (HPLC). Because the size of our RNA samples is in the range of many known RNA aptamers of therapeutic values, our protocol should be generally useful.
Collapse
Affiliation(s)
- Chi-Yen Lin
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA
| | - Zhen Huang
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA
| | - William Jaremko
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA
| | - Li Niu
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA.
| |
Collapse
|
9
|
Höfer K, Langejürgen LV, Jäschke A. Universal aptamer-based real-time monitoring of enzymatic RNA synthesis. J Am Chem Soc 2013; 135:13692-4. [PMID: 23991672 DOI: 10.1021/ja407142f] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In vitro transcription is an essential laboratory technique for enzymatic RNA synthesis. Unfortunately, no methods exist for analyzing quality and quantity of the synthesized RNA while the transcription proceeds. Here we describe a simple, robust, and universal system for monitoring and quantifying the synthesis of any RNA in real time without interference from abortive transcription byproducts. The distinguishing feature is a universal fluorescence module (UFM), consisting of the eGFP-like Spinach aptamer and a highly active hammerhead ribozyme, which is appended to the RNA of interest (ROI). In the transcription mixture, the primary transcript is cleaved rapidly behind the ROI, thereby releasing always the same UFM, independent of the ROI sequence, polymerase, or promoter used. The UFM binds to the target of the Spinach aptamer, the fluorogenic dye DFHBI, and thereby induces a strong fluorescence signal. This design allows real-time quantification, standardization, parallelization, and high-throughput screening.
Collapse
Affiliation(s)
- Katharina Höfer
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University , 69120 Heidelberg, Germany
| | | | | |
Collapse
|
10
|
Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate. Proc Natl Acad Sci U S A 2013; 110:11692-7. [PMID: 23818642 DOI: 10.1073/pnas.1222321110] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Liquid-liquid phase transitions in complex mixtures of proteins and other molecules produce crowded compartments supporting in vitro transcription and translation. We developed a method based on picoliter water-in-oil droplets to induce coacervation in Escherichia coli cell lysate and follow gene expression under crowded and noncrowded conditions. Coacervation creates an artificial cell-like environment in which the rate of mRNA production is increased significantly. Fits to the measured transcription rates show a two orders of magnitude larger binding constant between DNA and T7 RNA polymerase, and five to six times larger rate constant for transcription in crowded environments, strikingly similar to in vivo rates. The effect of crowding on interactions and kinetics of the fundamental machinery of gene expression has a direct impact on our understanding of biochemical networks in vivo. Moreover, our results show the intrinsic potential of cellular components to facilitate macromolecular organization into membrane-free compartments by phase separation.
Collapse
|
11
|
Calviello L, Stano P, Mavelli F, Luisi PL, Marangoni R. Quasi-cellular systems: stochastic simulation analysis at nanoscale range. BMC Bioinformatics 2013; 14 Suppl 7:S7. [PMID: 23815522 PMCID: PMC3633058 DOI: 10.1186/1471-2105-14-s7-s7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The wet-lab synthesis of the simplest forms of life (minimal cells) is a challenging aspect in modern synthetic biology. Quasi-cellular systems able to produce proteins directly from DNA can be obtained by encapsulating the cell-free transcription/translation system PURESYSTEM(PS) in liposomes. It is possible to detect the intra-vesicle protein production using DNA encoding for GFP and monitoring the fluorescence emission over time. The entrapment of solutes in small-volume liposomes is a fundamental open problem. Stochastic simulation is a valuable tool in the study of biochemical reaction at nanoscale range. QDC (Quick Direct-Method Controlled), a stochastic simulation software based on the well-known Gillespie's SSA algorithm, was used. A suitable model formally describing the PS reactions network was developed, to predict, from inner species concentrations (very difficult to measure in small-volumes), the resulting fluorescence signal (experimentally observable). RESULTS Thanks to suitable features specific of QDC, we successfully formalized the dynamical coupling between the transcription and translation processes that occurs in the real PS, thus bypassing the concurrent-only environment of Gillespie's algorithm. Simulations were firstly performed for large liposomes (2.67µm of diameter) entrapping the PS to synthetize GFP. By varying the initial concentrations of the three main classes of molecules involved in the PS (DNA, enzymes, consumables), we were able to stochastically simulate the time-course of GFP-production. The sigmoid fit of the GFP-production curves allowed us to extract three quantitative parameters which are significantly dependent on the various initial states. Then we extended this study for small-volume liposomes (575 nm of diameter), where it is more complex to infer the intra-vesicle composition, due to the expected anomalous entrapment phenomena. We identified almost two extreme states that are forecasted to give rise to significantly different experimental observables. CONCLUSIONS The present work is the first one describing in the detail the stochastic behavior of the PS. Thanks to our results, an experimental approach is now possible, aimed at recording the GFP production kinetics in very small micro-emulsion droplets or liposomes, and inferring, by using the simulation as a reverse-engineering procedure, the internal solutes distribution, and shed light on the still unknown forces driving the entrapment phenomenon.
Collapse
Affiliation(s)
- Lorenzo Calviello
- Dipartimento di Informatica, Università di Pisa, L.go B. Pontecorvo 3, 56127 Pisa, Italy
| | - Pasquale Stano
- Dipartimento di Biologia, Università di Roma III, Via G. Marconi 446, 00146 Roma, Italy
| | - Fabio Mavelli
- Dipartimento di Chimica, Università di Bari, Via E. Orabona 4, 70121 Bari, Italy
| | - Pier Luigi Luisi
- Dipartimento di Biologia, Università di Roma III, Via G. Marconi 446, 00146 Roma, Italy
| | - Roberto Marangoni
- Dipartimento di Informatica, Università di Pisa, L.go B. Pontecorvo 3, 56127 Pisa, Italy
- Istituto di Biofisica del CNR, Via G. Moruzzi 1, 56124 Pisa, Italy
| |
Collapse
|
12
|
Huang Z, Jayaseelan S, Hebert J, Seo H, Niu L. Single-nucleotide resolution of RNAs up to 59 nucleotides by high-performance liquid chromatography. Anal Biochem 2013; 435:35-43. [PMID: 23274387 PMCID: PMC5577504 DOI: 10.1016/j.ab.2012.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 12/27/2022]
Abstract
Ion-pair, reverse-phase high-performance liquid chromatography (HPLC) is a standard analytical platform for separating, purifying, and analyzing RNAs. However, a single-nucleotide resolution by using HPLC is currently limited to RNAs shorter than 25 nucleotides (nt). Here we describe a method of separating three RNA aptamers with 57, 58, and 59nt on an XBridge ion-pair, reverse-phase HPLC column by a single-nucleotide resolution. Under a similar condition, we also show the capability of our method to resolve two structurally different, yet sequence or mass identical, 59-nt aptamers. We establish that the optimal condition to achieve a single-nucleotide resolution correlates to 50°C and zero magnesium concentration in mobile phases. The ion-pairing agent, the buffer, and the solvent we use are also compatible for post-HPLC analysis such as mass spectrometry. Therefore, our method provides a new way of detecting, analyzing, and separating RNAs by conformation or structure and extends the ability to separate RNAs that are longer than 25nt by single-nucleotide resolution.
Collapse
Affiliation(s)
- Zhen Huang
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, New York 12222, USA
| | - Sabarinath Jayaseelan
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, New York 12222, USA
| | - Jeffrey Hebert
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, New York 12222, USA
| | - Hyojung Seo
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, New York 12222, USA
| | - Li Niu
- Department of Chemistry, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, New York 12222, USA
| |
Collapse
|
13
|
Pardi N, Muramatsu H, Weissman D, Karikó K. In vitro transcription of long RNA containing modified nucleosides. Methods Mol Biol 2013; 969:29-42. [PMID: 23296925 DOI: 10.1007/978-1-62703-260-5_2] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The in vitro synthesis of long RNA can be accomplished using phage RNA polymerase and template DNA. However, the in vitro synthesized RNA, unlike those transcribed in vivo in cells, lacks nucleoside modifications. Introducing modified nucleosides into in vitro transcripts is important because they reduce the potential of RNA to activate RNA sensors and translation of such nucleoside-modified RNA is increased in cell lines, primary cells, and after in vivo delivery. Here, we describe the in vitro synthesis of nucleoside-modified RNA with enhanced translational capacity and reduced ability to activate immune sensors.
Collapse
Affiliation(s)
- Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | |
Collapse
|
14
|
Finan K, Torella JP, Kapanidis AN, Cook PR. T7 RNA polymerase functions in vitro without clustering. PLoS One 2012; 7:e40207. [PMID: 22768341 PMCID: PMC3388079 DOI: 10.1371/journal.pone.0040207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 06/06/2012] [Indexed: 11/18/2022] Open
Abstract
Many nucleic acid polymerases function in clusters known as factories. We investigate whether the RNA polymerase (RNAP) of phage T7 also clusters when active. Using ‘pulldowns’ and fluorescence correlation spectroscopy we find that elongation complexes do not interact in vitro with a Kd<1 µM. Chromosome conformation capture also reveals that genes located 100 kb apart on the E. coli chromosome do not associate more frequently when transcribed by T7 RNAP. We conclude that if clustering does occur in vivo, it must be driven by weak interactions, or mediated by a phage-encoded protein.
Collapse
Affiliation(s)
- Kieran Finan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Joseph P. Torella
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Achillefs N. Kapanidis
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Peter R. Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|
15
|
Stögbauer T, Windhager L, Zimmer R, Rädler JO. Experiment and mathematical modeling of gene expression dynamics in a cell-free system. Integr Biol (Camb) 2012; 4:494-501. [PMID: 22481223 DOI: 10.1039/c2ib00102k] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cell-free in vitro expression is increasingly important for high-throughput expression screening, high yield protein production and synthetic biology applications. Yet its potential for quantitative investigation of gene expression and regulatory circuits is limited by the availability of data on composition, kinetic rate constants and standardized computational tools for modeling. Here we report on calibration measurements and mathematical modeling of a reconstituted in vitro expression system. We measured a series of GFP expression and mRNA transcription time courses under various initial conditions and established the translation step as the bottle neck of in vitro protein synthesis. Cell-free translation was observed to expire after 3 h independent of initial template DNA concentration. We developed a minimalistic rate equation model and optimized its parameters by performing a concurrent fit to measured time courses. The model predicts the dependence of protein yield not only on template DNA concentration, but also on experimental timing and hence is a valuable tool to optimize yield strategies.
Collapse
Affiliation(s)
- Tobias Stögbauer
- Fakultät für Physik, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, D-80539 München, Germany
| | | | | | | |
Collapse
|
16
|
Retraction for Lipardi and Paterson, "Identification of an RNA-dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression". Proc Natl Acad Sci U S A 2011. [PMID: 21821790 DOI: 10.1073/pnas.1111383108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
17
|
Jung HI, Zhai Z, Vatamaniuk OK. Direct transfer of synthetic double-stranded RNA into protoplasts of Arabidopsis thaliana. Methods Mol Biol 2011; 744:109-27. [PMID: 21533689 DOI: 10.1007/978-1-61779-123-9_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Double-stranded (ds) RNA interference (RNAi) is widely used as a reverse genetic approach for functional analysis of plant genes. Constitutive or transient RNAi effects in plants have been achieved via generating stable transformants expressing dsRNAs or artificial microRNAs (amiRNAs) in planta or by viral-induced gene silencing (VIGS). Although these tools provide outstanding resources for functional genomics, they require generation of vectors expressing dsRNAs or amiRNAs against targeted genes, transformation and propagation of transformed plants, or maintenance of multiple VIGS lines and thus impose time, labor, and space requirements. As we showed recently, these limitations can be circumvented by inducing RNAi effects in protoplasts via transfecting them with in vitro-synthesized dsRNAs. In this chapter we detail the procedure for transient gene silencing in protoplasts using synthetic dsRNAs and provide examples of approaches for subsequent functional analyses.
Collapse
Affiliation(s)
- Ha-Il Jung
- Department of Crop and Soil Sciences, Cornell University, Ithaca, NY 14853, USA
| | | | | |
Collapse
|
18
|
Park C, Kwon EY, Shin NY, Choi SM, Kim SH, Park SH, Lee DG, Choi JH, Yoo JH. Evaluation of nucleic acid sequence based amplification using fluorescence resonance energy transfer (FRET-NASBA) in quantitative detection of Aspergillus 18S rRNA. Med Mycol 2010; 49:73-9. [PMID: 20718604 DOI: 10.3109/13693786.2010.507604] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We attempted to apply fluorescence resonance energy transfer technology to nucleic acid sequence-based amplification (FRET-NASBA) on the platform of the LightCycler system to detect Aspergillus species. Primers and probes for the Aspergillus 18S rRNA were newly designed to avoid overlapping with homologous sequences of human 18s rRNA. NASBA using molecular beacon (MB) showed non-specific results which have been frequently observed from controls, although it showed higher sensitivity (10(-2) amol) than the FRET. FRET-NASBA showed a sensitivity of 10(-1) amol and a high fidelity of reproducibility from controls. As FRET technology was successfully applied to the NASBA assay, it could contribute to diverse development of the NASBA assay. These results suggest that FRET-NASBA could replace previous NASBA techniques in the detection of Aspergillus.
Collapse
Affiliation(s)
- Chulmin Park
- Catholic Research Institutes of Medical Science, The Catholic University of Korea, College of Medicine, Seoul, South Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Yang YM, Barankiewicz TJ, He M, Taussig MJ, Chen SS. Selection of antigenic markers on a GFP-Cκ fusion scaffold with high sensitivity by eukaryotic ribosome display. Biochem Biophys Res Commun 2007; 359:251-7. [PMID: 17537405 DOI: 10.1016/j.bbrc.2007.05.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Accepted: 05/10/2007] [Indexed: 11/22/2022]
Abstract
Ribosome display is a cell-free system permitting gene selection through the physical association of genetic material (mRNA) and its phenotypic (protein) product. While often used to select single-chain antibodies from large libraries by panning against immobilized antigens, we have adapted ribosome display for use in the 'reverse' format in order to select high affinity antigenic determinants against solid-phase antibody. To create an antigenic scaffold, DNA encoding green fluorescent protein (GFP) was fused to a light chain constant domain (Ckappa) with stop codon deleted, and with 5' signals (T7 promoter, Kozak) enabling coupled transcription/translation in a eukaryotic cell-free system. Epitopes on either GFP (5') or Ckappa (3') were selected by anti-GFP or anti-Ckappa antibodies, respectively, coupled to magnetic beads. After selection, mRNA was amplified directly from protein-ribosome-mRNA (PRM) complexes by in situ PCR followed by internal amplification and reassembly PCR. As little as 10fg of the 1kb DNA construct, i.e. approximately 7500 molecules, could be recovered following a single round of interaction with solid-phase anti-GFP antibody. This platform is highly specific and sensitive for the antigen-antibody interaction and may permit selection and reshaping of high affinity antigenic variants of scaffold proteins.
Collapse
Affiliation(s)
- Yong-Min Yang
- The Institute of Genetics, San Diego, CA 92121-2233, USA
| | | | | | | | | |
Collapse
|
20
|
Ma C, Lyons-Weiler M, Liang W, LaFramboise W, Gilbertson JR, Becich MJ, Monzon FA. In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays. J Mol Diagn 2006; 8:183-92. [PMID: 16645204 PMCID: PMC1867595 DOI: 10.2353/jmoldx.2006.050077] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of different amplification and labeling methods on DNA microarray expression results has not been previously delineated. To analyze the variation associated with widely accepted T7-based RNA amplificationand labeling methods, aliquots of the Stratagene Human Universal Reference RNA were labeled using three eukaryotic target preparation methods followed by uniform replicate array hybridization (Affymetrix U95Av2). Method-dependent variability was observed in the yield and size distribution of labeled products, as well as in the gene expression results. A significant increase in short transcripts, when compared to unamplified mRNA, was observed in methods with long in vitro transcription reactions. Intramethod reproducibility showed correlation coefficients >0.99, whereas intermethod comparisons showed coefficients ranging from 0.94 to 0.98 and a nearly twofold increase in coefficient of variation. Fold amplification for each method positively correlated with the number of genes present. Our experiments uncovered two factors that introduced significant bias in gene expression data: the number of labeled nucleotides, which introduces sequence-dependent bias, and the length of the in vitro transcription reaction, which introduces transcript size-dependent bias. This study provides evidence that variability in expression data may be caused, in part, by differences in amplification and labeling protocols.
Collapse
Affiliation(s)
- Changqing Ma
- Department of Pathology, Center for Pathology Informatics, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15237, USA.
| | | | | | | | | | | | | |
Collapse
|
21
|
Poole AM, Logan DT. Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol Biol Evol 2005; 22:1444-55. [PMID: 15774424 PMCID: PMC7107533 DOI: 10.1093/molbev/msi132] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
RNA repair has now been demonstrated to be a genuine biological process and appears to be present in all three domains of life. In this article, we consider what this might mean for the transition from an early RNA-dominated world to modern cells possessing genetically encoded proteins and DNA. There are significant gaps in our understanding of how the modern protein-DNA world could have evolved from a simpler system, and it is currently uncertain whether DNA genomes evolved once or twice. Against this backdrop, the discovery of RNA repair in modern cells is timely food for thought and brings us conceptually one step closer to understanding how RNA genomes were replaced by DNA genomes. We have examined the available literature on multisubunit RNA polymerase structure and function and conclude that a strong case can be made that the Last Universal Common Ancestor (LUCA) possessed a repair-competent RNA polymerase, which would have been capable of acting on an RNA genome. However, while this lends credibility to the proposal that the LUCA had an RNA genome, the alternative, that LUCA had a DNA genome, cannot be completely ruled out.
Collapse
Affiliation(s)
- Anthony M Poole
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden.
| | | |
Collapse
|
22
|
Abstract
Telomerase is a reverse transcriptase that uses an integral RNA molecule to add de novo G-rich repeats onto telomeric DNA, or onto nontelomeric DNA generated during chromosome fragmentation and breakage events. A telomerase-mediated DNA substrate cleavage activity has been reported in ciliates and yeasts. Nucleolytic cleavage may serve a proofreading function, enhance processivity or ensure that nontemplate telomerase RNA sequences are not copied into DNA. We identified and characterized a human telomerase-mediated nucleolytic cleavage activity using enzyme reconstituted in a rabbit reticulocyte lysate in vitro transcription/translation system and native enzyme extracted from cells. We found that telomerase catalyzed the removal of nucleotides from DNA substrates including those that can form a mismatch with the RNA template or that contain nontelomeric sequences located 3' to a telomeric sequence. Unlike Tetrahymena telomerase, human telomerase catalyzed the removal of more than one nucleotide (up to 13) from telomeric primers. DNA substrates predicted to align at the 3'-end of the RNA template were not cleaved, consistent with cleavage being dictated by the template 5'-end. We also found some differences in the nuclease activity between RRL-reconstituted human telomerase and native enzyme.
Collapse
Affiliation(s)
- Sylvain Huard
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec H3A 2B4, Canada
| | | |
Collapse
|
23
|
Spiess AN, Mueller N, Ivell R. Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. BMC Genomics 2003; 4:44. [PMID: 14606961 PMCID: PMC280674 DOI: 10.1186/1471-2164-4-44] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Accepted: 11/10/2003] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The amplification of RNA with the T7-System is a widely used technique for obtaining increased amounts of RNA starting from limited material. The amplified RNA (aRNA) can subsequently be used for microarray hybridizations, warranting sufficient signal for image analysis. We describe here an amplification-time dependent degradation of aRNA in prolonged standard T7 amplification protocols, that results in lower average size aRNA and decreased yields. RESULTS A time-dependent degradation of amplified RNA (aRNA) could be observed when using the classical "Eberwine" T7-Amplification method. When the amplification was conducted for more than 4 hours, the resulting aRNA showed a significantly smaller size distribution on gel electrophoresis and a concomitant reduction of aRNA yield. The degradation of aRNA could be correlated to the presence of the T7 RNA Polymerase in the amplification cocktail. The aRNA degradation resulted in a strong bias in microarray hybridizations with a high coefficient of variation and a significant reduction of signals of certain transcripts, that seem to be susceptible to this RNA degrading activity. The time-dependent degradation of these transcripts was verified by a real-time PCR approach. CONCLUSIONS It is important to perform amplifications not longer than 4 hours as there is a characteristic 'quality vs. yield' situation for longer amplification times. When conducting microarray hybridizations it is important not to compare results obtained with aRNA from different amplification times.
Collapse
Affiliation(s)
- Andrej-Nikolai Spiess
- Institute for Hormone and Fertility Research, Centre of Innovative Medicine, Falkenried 88, 20251 Hamburg, Germany
| | - Nadine Mueller
- Institute for Hormone and Fertility Research, Centre of Innovative Medicine, Falkenried 88, 20251 Hamburg, Germany
| | - Richard Ivell
- Institute for Hormone and Fertility Research, Centre of Innovative Medicine, Falkenried 88, 20251 Hamburg, Germany
| |
Collapse
|
24
|
Jung Y, Lippard SJ. Multiple states of stalled T7 RNA polymerase at DNA lesions generated by platinum anticancer agents. J Biol Chem 2003; 278:52084-92. [PMID: 14534300 DOI: 10.1074/jbc.m310120200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Transcription inhibition by DNA adducts of cisplatin is considered to be one of the major routes by which this anticancer drug kills cancer cells. Stalled RNA polymerases at platinum-DNA lesions evoke various cellular responses such as nucleotide excision repair, polymerase degradation, and apoptosis. T7 RNA polymerase and site-specifically platinated DNA templates immobilized on a solid support were used to study stalled transcription elongation complexes. In vitro transcription studies were performed in both a promoter-dependent and -independent manner. An elongation complex is strongly blocked by cisplatin 1,2-intrastrand d(GpG) and 1,3-intrastrand d(GpTpG) cross-links located on the template strand. Polymerase action is inhibited at multiple sites in the vicinity of the platinum lesion, the nature of which can be altered by the choice and concentration of NTPs. The [(1R,2R-diaminocyclohexane)Pt]2+ DNA adducts formed by oxaliplatin, which carries a stereochemically more demanding spectator ligand than the ammine groups in cisplatin, also strongly block the polymerase with measurable differences compared with cis-[(NH3)2Pt]2+ lesions. Elongation complexes stopped at sites of platinum damage were isolated and characterized. The stalled polymerase can be dissociated from the DNA by subsequent polymerases initiated from the same template. We also discovered that a polymerase stalled at the platinum-DNA lesion can resume transcription after the platinum adduct is chemically removed from the template.
Collapse
Affiliation(s)
- Yongwon Jung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | | |
Collapse
|
25
|
Fish RN, Kane CM. Promoting elongation with transcript cleavage stimulatory factors. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1577:287-307. [PMID: 12213659 DOI: 10.1016/s0167-4781(02)00459-1] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Transcript elongation by RNA polymerase is a dynamic process, capable of responding to a number of intrinsic and extrinsic signals. A number of elongation factors have been identified that enhance the rate or efficiency of transcription. One such class of factors facilitates RNA polymerase transcription through blocks to elongation by stimulating the polymerase to cleave the nascent RNA transcript within the elongation complex. These cleavage factors are represented by the Gre factors from prokaryotes, and TFIIS and TFIIS-like factors found in archaea and eukaryotes. High-resolution structures of RNA polymerases and the cleavage factors in conjunction with biochemical investigations and genetic analyses have provided insights into the mechanism of action of these elongation factors. However, there are yet many unanswered questions regarding the regulation of these factors and their effects on target genes.
Collapse
Affiliation(s)
- Rachel N Fish
- Department of Molecular and Cell Biology, University of California-Berkeley, 401 Barker Hall, Berkeley, CA 94720-3202, USA
| | | |
Collapse
|
26
|
Song H, Kang C. Sequence-specific termination by T7 RNA polymerase requires formation of paused conformation prior to the point of RNA release. Genes Cells 2001; 6:291-301. [PMID: 11318872 DOI: 10.1046/j.1365-2443.2001.00420.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The sequence-specific, hairpin-independent termination signal for the bacteriophage RNA polymerases in Escherichia coli rrnB t1 terminator consists of two modules. The upstream module includes the conserved sequence and the downstream one is U-rich. RESULTS Elongation complexes of T7 RNA polymerase paused 2 bp before reaching the termination site at a 500 microM concentration of NTP. At 5-50 microM NTP, however, they paused and terminated there or resumed elongation beyond the termination site. Only at higher concentrations of NTP (500 microM), the pause complex proceeded slowly to and became incompetent at the termination site. At 4 bp or more before the termination site, the unprotected single-stranded region of transcription bubble shrank at the trailing edge to 4-5 bp from approximately 10 bp, resulting from duplex formation of the conserved sequence. The pause and bubble collapse were not observed with an inactive mutant of the termination signal. CONCLUSION Sequence-specific termination requires the slow elongation mode of paused conformation, working only at high concentrations of NTP for a few bp prior to the RNA release site. The collapse of bubble that was observed several base pairs before the termination site and/or the resulting duplex might subsequently lead to the paused conformation of T7 elongation complexes.
Collapse
Affiliation(s)
- H Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Kusong-dong, Yusong-gu, Taejon 305-701
| | | |
Collapse
|
27
|
Toulmé F, Mosrin-Huaman C, Sparkowski J, Das A, Leng M, Rahmouni AR. GreA and GreB proteins revive backtracked RNA polymerase in vivo by promoting transcript trimming. EMBO J 2000; 19:6853-9. [PMID: 11118220 PMCID: PMC305891 DOI: 10.1093/emboj/19.24.6853] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The GreA and GreB proteins of Escherichia coli show a multitude of effects on transcription elongation in vitro, yet their physiological functions are poorly understood. Here, we investigated whether and how these factors influence lateral oscillations of RNA polymerase (RNAP) in vivo, observed at a protein readblock. When RNAP is stalled within an (ATC/TAG)(n) sequence, it appears to oscillate between an upstream and a downstream position on the template, 3 bp apart, with concomitant trimming of the transcript 3' terminus and its re-synthesis. Using a set of mutant E.coli strains, we show that the presence of GreA or GreB in the cell is essential to induce this trimming. We show further that in contrast to a ternary complex that is stabilized at the downstream position, the oscillating complex relies heavily on the GreA/GreB-induced 'cleavage-and-restart' process to become catalytically competent. Clearly, by promoting transcript shortening and re-alignment of the catalytic register, the Gre factors function in vivo to rescue RNAP from being arrested at template positions where the lateral stability of the ternary complex is impaired.
Collapse
Affiliation(s)
- F Toulmé
- Centre de Biophysique Moléculaire, CNRS, rue Charles Sadron, 45071 Orléans cédex 2, France
| | | | | | | | | | | |
Collapse
|
28
|
Bhargava P, Kassavetis GA. Abortive initiation by Saccharomyces cerevisiae RNA polymerase III. J Biol Chem 1999; 274:26550-6. [PMID: 10473618 DOI: 10.1074/jbc.274.37.26550] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Promoter escape can be rate-limiting for transcription by bacterial RNA polymerases and RNA polymerase II of higher eukaryotes. Formation of a productive elongation complex requires disengagement of RNA polymerase from promoter-bound eukaryotic transcription factors or bacterial sigma factors. RNA polymerase III (pol III) stably associates with the TFIIIB-DNA complex even in the absence of localized DNA unwinding associated with the open promoter complex. To explore the role that release of pol III from the TFIIIB-DNA complex plays in limiting the overall rate of transcription, we have examined the early steps of RNA synthesis. We find that, on average, only three rounds of abortive initiation precede the formation of each elongation complex and that nearly all pol III molecules escape the abortive initiation phase of transcription without significant pausing or arrest. However, when elongation is limited to 5 nucleotides, the intrinsic exoribonuclease activity of pol III cleaves 5-mer RNA at a rate considerably faster than product release or reinitiation. This cleavage also occurs in the normal process of forming a productive elongation complex. The possible role of nucleolytic retraction in disengaging pol III from TFIIIB is discussed.
Collapse
Affiliation(s)
- P Bhargava
- Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634, USA.
| | | |
Collapse
|
29
|
Mote J, Reines D. Recognition of a human arrest site is conserved between RNA polymerase II and prokaryotic RNA polymerases. J Biol Chem 1998; 273:16843-52. [PMID: 9642244 PMCID: PMC3371603 DOI: 10.1074/jbc.273.27.16843] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA sequences that arrest transcription by either eukaryotic RNA polymerase II or Escherichia coli RNA polymerase have been identified previously. Elongation factors SII and GreB are RNA polymerase-binding proteins that enable readthrough of arrest sites by these enzymes, respectively. This functional similarity has led to general models of elongation applicable to both eukaryotic and prokaryotic enzymes. Here we have transcribed with phage and bacterial RNA polymerases, a human DNA sequence previously defined as an arrest site for RNA polymerase II. The phage and bacterial enzymes both respond efficiently to the arrest signal in vitro at limiting levels of nucleoside triphosphates. The E. coli polymerase remains in a template-engaged complex for many hours, can be isolated, and is potentially active. The enzyme displays a relatively slow first-order loss of elongation competence as it dwells at the arrest site. Bacterial RNA polymerase arrested at the human site is reactivated by GreB in the same way that RNA polymerase II arrested at this site is stimulated by SII. Very efficient readthrough can be achieved by phage, bacterial, and eukaryotic RNA polymerases in the absence of elongation factors if 5-Br-UTP is substituted for UTP. These findings provide additional and direct evidence for functional similarity between prokaryotic and eukaryotic transcription elongation and readthrough mechanisms.
Collapse
Affiliation(s)
| | - Daniel Reines
- To whom correspondence should be addressed. Tel.: 404-727-3361; Fax: 404-727-3452;
| |
Collapse
|
30
|
Koulich D, Nikiforov V, Borukhov S. Distinct functions of N and C-terminal domains of GreA, an Escherichia coli transcript cleavage factor. J Mol Biol 1998; 276:379-89. [PMID: 9512710 DOI: 10.1006/jmbi.1997.1545] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The prokaryotic transcription factors GreA and GreB are involved in the regulation of transcript elongation by RNA polymerase (RNAP). Their known activities include suppression of transcription arrest, enhancement of transcription fidelity, and facilitation of the transition from abortive initiation to productive elongation. Presumably, Gre proteins exert their functions by altering the conformation of the enzyme in ternary elongation complexes (TEC) and inducing the cleavage of nascent RNA. GreA and GreB have a similar structural organization and consist of two domains: a C-terminal globular and an extended N-terminal coiled-coil domain. To investigate the functional roles of Gre domains, we expressed separately the N and C-terminal domains of GreA (NTD and CTD, respectively) and characterized their activities with in vitro assays. We demonstrate that the NTD possesses the residual transcript cleavage activity of the wild-type GreA. The CTD does not display any nucleolytic activity; however, it substantially increases the cleavage activity of the NTD. In contrast to NTD, the CTD competes with GreA and GreB for binding to RNAP and inhibits their transcript cleavage and antiarrest activities. Both domains individually and together inhibit transcription elongation. From these results we conclude that the NTD is responsible for the GreA induction of nucleolytic activity while the CTD determines the binding of GreA to RNAP. Both domains are required for full functional activity of GreA.
Collapse
Affiliation(s)
- D Koulich
- Department of Microbiology and Immunology, State University of New York Health Science Center at Brooklyn 11203, USA
| | | | | |
Collapse
|