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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Mol Cell 2023; 83:3921-3930.e7. [PMID: 37890482 PMCID: PMC10843261 DOI: 10.1016/j.molcel.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait B, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558837. [PMID: 37808858 PMCID: PMC10557602 DOI: 10.1101/2023.09.25.558837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N-terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5'-cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here we determine high-resolution cryo-electron microscopy structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Chemistry and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Present address: University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Lead contact:
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3
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Orbay S, Sanyal A. Molecularly Imprinted Polymeric Particles Created Using Droplet-Based Microfluidics: Preparation and Applications. MICROMACHINES 2023; 14:763. [PMID: 37420996 DOI: 10.3390/mi14040763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 07/09/2023]
Abstract
Recent years have witnessed increased attention to the use of droplet-based microfluidics as a tool for the fabrication of microparticles due to this method's ability to exploit fluid mechanics to create materials with a narrow range of sizes. In addition, this approach offers a controllable way to configure the composition of the resulting micro/nanomaterials. To date, molecularly imprinted polymers (MIPs) in particle form have been prepared using various polymerization methods for several applications in biology and chemistry. However, the traditional approach, that is, the production of microparticles through grinding and sieving, generally leads to poor control over particle size and distribution. Droplet-based microfluidics offers an attractive alternative for the fabrication of molecularly imprinted microparticles. This mini-review aims to present recent examples highlighting the application of droplet-based microfluidics to fabricate molecularly imprinted polymeric particles for applications in the chemical and biomedical sciences.
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Affiliation(s)
- Sinem Orbay
- Institute of Biomedical Engineering, Bogazici University, Istanbul 34684, Turkey
- Biomedical Engineering Department, Erzincan Binali Yildirim University, Erzincan 24002, Turkey
| | - Amitav Sanyal
- Department of Chemistry, Center for Life Sciences and Technologies, Bogazici University, Istanbul 34342, Turkey
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Vlachakis D. Genetic and structural analyses of ssRNA viruses pave the way for the discovery of novel antiviral pharmacological targets. Mol Omics 2021; 17:357-364. [PMID: 33725065 DOI: 10.1039/d0mo00173b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the era of big data and artificial intelligence, a lot of new discoveries have influenced the fields of antiviral drug design and pharmacophore identification. Viruses have always been a threat to society in terms of public health and economic stability. Viruses not only affect humans but also livestock and agriculture with a direct impact on food safety, economy and environmental imprint. Most recently, with the pandemic of COVID-19, it was made clear that a single virus can have a devastating impact on global well-being and economy. In this direction, there is an emerging need for the identification of promising pharmacological targets in viruses. Herein, an effort has been made to discuss the current knowledge, state-of-the-art applications and future implications for the main pharmacological targets of single-stranded RNA viruses.
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Affiliation(s)
- Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied BIology and Biotechnology, Agricultural University of Athens, Athens, Greece.
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Sutto-Ortiz P, Tcherniuk S, Ysebaert N, Abeywickrema P, Noël M, Decombe A, Debart F, Vasseur JJ, Canard B, Roymans D, Rigaux P, Eléouët JF, Decroly E. The methyltransferase domain of the Respiratory Syncytial Virus L protein catalyzes cap N7 and 2'-O-methylation. PLoS Pathog 2021; 17:e1009562. [PMID: 33956914 PMCID: PMC8130918 DOI: 10.1371/journal.ppat.1009562] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a negative sense single-stranded RNA virus and one of the main causes of severe lower respiratory tract infections in infants and young children. RSV RNA replication/transcription and capping are ensured by the viral Large (L) protein. The L protein contains a polymerase domain associated with a polyribonucleotidyl transferase domain in its N-terminus, and a methyltransferase (MTase) domain followed by the C-terminal domain (CTD) enriched in basic amino acids at its C-terminus. The MTase-CTD of Mononegavirales forms a clamp to accommodate RNA that is subsequently methylated on the cap structure and depending on the virus, on internal positions. These enzymatic activities are essential for efficient viral mRNA translation into proteins, and to prevent the recognition of uncapped viral RNA by innate immunity sensors. In this work, we demonstrated that the MTase-CTD of RSV, as well as the full-length L protein in complex with phosphoprotein (P), catalyzes the N7- and 2’-O-methylation of the cap structure of a short RNA sequence that corresponds to the 5’ end of viral mRNA. Using different experimental systems, we showed that the RSV MTase-CTD methylates the cap structure with a preference for N7-methylation as first reaction. However, we did not observe cap-independent internal methylation, as recently evidenced for the Ebola virus MTase. We also found that at μM concentrations, sinefungin, a S-adenosylmethionine analogue, inhibits the MTase activity of the RSV L protein and of the MTase-CTD domain. Altogether, these results suggest that the RSV MTase domain specifically recognizes viral RNA decorated by a cap structure and catalyzes its methylation, which is required for translation and innate immune system subversion. Respiratory syncytial virus (RSV) is responsible of infant bronchiolitis and severe lower respiratory tract infections in infants and young children, and the leading cause of hospitalization in children under one year of age. However, we still lack a vaccine and therapeutics against this important pathogen. The main enzymatic activities involved in RSV propagation are embedded in the Large (L) protein that contains the polymerase domain and also all the activities required for RNA cap structure synthesis and methylation. These post-transcriptional RNA modifications play a key role in virus replication because cap N7-methylation is required for viral RNA translation into proteins, and 2’-O-methylation hides viral RNA from innate immunity detection. Viral methyltransferase (MTase) activities are now considered potential antiviral targets because their inhibition might limit the virus production and strengthen early virus detection by innate immunity sensors. In this work, we compared the enzymatic activities of the MTase expressed as a single domain or in the context of the full-length L protein. We demonstrated that the MTase protein catalyzes the specific methylation of the cap structure at both N7- and 2’-O-positions, and we obtained the proof of concept that a S-adenosylmethionine analogue can inhibit the MTase activity of the L protein.
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Affiliation(s)
| | - Sergey Tcherniuk
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, Jouy en Josas, France
| | - Nina Ysebaert
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | | | - Mathieu Noël
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | - Alice Decombe
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Françoise Debart
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Bruno Canard
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Dirk Roymans
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, Jouy en Josas, France
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
- * E-mail:
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Asai A, Konno M, Ozaki M, Otsuka C, Vecchione A, Arai T, Kitagawa T, Ofusa K, Yabumoto M, Hirotsu T, Taniguchi M, Eguchi H, Doki Y, Ishii H. COVID-19 Drug Discovery Using Intensive Approaches. Int J Mol Sci 2020; 21:E2839. [PMID: 32325767 PMCID: PMC7215413 DOI: 10.3390/ijms21082839] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/20/2022] Open
Abstract
Since the infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China during December 2019, the coronavirus disease 2019 (COVID-19) has spread on a global scale, causing the World Health Organization (WHO) to issue a warning. While novel vaccines and drugs that target SARS-CoV-2 are under development, this review provides information on therapeutics which are under clinical trials or are proposed to antagonize SARS-CoV-2. Based on the information gained from the responses to other RNA coronaviruses, including the strains that cause severe acute respiratory syndrome (SARS)-coronaviruses and Middle East respiratory syndrome (MERS), drug repurposing might be a viable strategy. Since several antiviral therapies can inhibit viral replication cycles or relieve symptoms, mechanisms unique to RNA viruses will be important for the clinical development of antivirals against SARS-CoV-2. Given that several currently marketed drugs may be efficient therapeutic agents for severe COVID-19 cases, they may be beneficial for future viral pandemics and other infections caused by RNA viruses when standard treatments are unavailable.
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Affiliation(s)
- Ayumu Asai
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
- Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan;
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
- Artificial Intelligence Research Center, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Masamitsu Konno
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
| | - Miyuki Ozaki
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
| | - Chihiro Otsuka
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Rome “Sapienza”, Santo Andrea Hospital, via di Grottarossa, 1035-00189 Rome, Italy;
| | - Takahiro Arai
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
- Unitech Co., Ltd., Kashiwa 277-0005, Japan
| | - Toru Kitagawa
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
- Kyowa-kai Medical Corporation, Osaka 540-0008, Japan
| | - Ken Ofusa
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
- Prophoenix Division, Food and Life-Science Laboratory, Idea Consultants, Inc., Osaka-City, Osaka 559-8519, Japan
| | - Masami Yabumoto
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
- Kinshu-Kai Medical Corporation, Osaka 558-0041, Japan
| | - Takaaki Hirotsu
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
- Hirotsu Bio Science Inc., Tokyo 107-0062, Japan
| | - Masateru Taniguchi
- Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan;
| | - Hidetoshi Eguchi
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Yuichiro Doki
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Hideshi Ishii
- Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (A.A.); (M.K.); (M.O.); (C.O.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.); (H.E.); (Y.D.)
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Zhou Z, Liu T, Zhang J, Zhan P, Liu X. Influenza A virus polymerase: an attractive target for next-generation anti-influenza therapeutics. Drug Discov Today 2018; 23:503-518. [PMID: 29339107 DOI: 10.1016/j.drudis.2018.01.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/31/2017] [Accepted: 01/05/2018] [Indexed: 12/20/2022]
Abstract
The influenza RNA-dependent RNA polymerase (RdRP) is conserved among different types of influenza virus, playing an important part in transcription and replication. In this regard, influenza RdRP is an attractive target for novel anti-influenza drug discovery. Herein, we will introduce the structural and functional information of influenza polymerase; and an overview of inhibitors targeting the PA endonuclease and PB2 cap-binding site is provided, along with the approaches utilized for identification of these inhibitors. The protein-protein interactions (PPIs) of the three polymerase subunits: PA, PB1 and PB2, are described based on the published crystal structures, and inhibitors targeting the PA-PB1 interaction are introduced briefly.
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Affiliation(s)
- Zhongxia Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Tao Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China.
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Rice Stripe Tenuivirus Has a Greater Tendency To Use the Prime-and-Realign Mechanism in Transcription of Genomic than in Transcription of Antigenomic Template RNAs. J Virol 2017; 92:JVI.01414-17. [PMID: 29046442 DOI: 10.1128/jvi.01414-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/04/2017] [Indexed: 01/06/2023] Open
Abstract
Most segmented negative-sense RNA viruses employ a process termed cap snatching, during which they snatch capped RNA leaders from host cellular mRNAs and use the snatched leaders as primers for transcription, leading to the synthesis of viral mRNAs with 5' heterogeneous sequences (HSs). With traditional methods, only a few HSs can be determined, and identification of their donors is difficult. Here, the mRNA 5' ends of Rice stripe tenuivirus (RSV) and Rice grassy stunt tenuivirus (RGSV) and those of their host rice were determined by high-throughput sequencing. Millions of tenuiviral HSs were obtained, and a large number of them mapped to the 5' ends of corresponding host cellular mRNAs. Repeats of the dinucleotide AC, which are complementary to the U1G2 of the tenuiviral template 3'-U1G2U3G4UUUCG, were found to be prevalent at the 3' termini of tenuiviral HSs. Most of these ACs did not match host cellular mRNAs, supporting the idea that tenuiviruses use the prime-and-realign mechanism during cap snatching. We previously reported a greater tendency of RSV than RGSV to use the prime-and-realign mechanism in transcription with leaders cap snatched from a coinfecting reovirus. Besides confirming this observation in natural tenuiviral infections, the data here additionally reveal that RSV has a greater tendency to use this mechanism in transcribing genomic than in transcribing antigenomic templates. The data also suggest that tenuiviruses cap snatch host cellular mRNAs from translation- and photosynthesis-related genes, and capped RNA leaders snatched by tenuiviruses base pair with U1/U3 or G2/G4 of viral templates. These results provide unprecedented insights into the cap-snatching process of tenuiviruses.IMPORTANCE Many segmented negative-sense RNA viruses (segmented NSVs) are medically or agriculturally important pathogens. The cap-snatching process is a promising target for the development of antiviral strategies against this group of viruses. However, many details of this process remain poorly characterized. Tenuiviruses constitute a genus of agriculturally important segmented NSVs, several members of which are major viral pathogens of rice. Here, we for the first time adopted a high-throughput sequencing strategy to determine the 5' heterogeneous sequences (HSs) of tenuiviruses and mapped them to host cellular mRNAs. Besides providing deep insights into the cap snatching of tenuiviruses, the data obtained provide clear evidence to support several previously proposed models regarding cap snatching. Curiously and importantly, the data here reveal that not only different tenuiviruses but also the same tenuivirus synthesizing different mRNAs use the prime-and-realign mechanism with different tendencies during their cap snatching.
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9
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Mutagenesis of S-Adenosyl-l-Methionine-Binding Residues in Coronavirus nsp14 N7-Methyltransferase Demonstrates Differing Requirements for Genome Translation and Resistance to Innate Immunity. J Virol 2016; 90:7248-7256. [PMID: 27252528 PMCID: PMC4984653 DOI: 10.1128/jvi.00542-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/24/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Eukaryotic mRNAs possess a methylated 5'-guanosine cap that is required for RNA stability, efficient translation, and protection from cell-intrinsic defenses. Many viruses use 5' caps or other mechanisms to mimic a cap structure to limit detection of viral RNAs by intracellular innate sensors and to direct efficient translation of viral proteins. The coronavirus (CoV) nonstructural protein 14 (nsp14) is a multifunctional protein with N7-methyltransferase (N7-MTase) activity. The highly conserved S-adenosyl-l-methionine (SAM)-binding residues of the DxG motif are required for nsp14 N7-MTase activity in vitro However, the requirement for CoV N7-MTase activity and the importance of the SAM-binding residues during viral replication have not been determined. Here, we engineered mutations in murine hepatitis virus (MHV) nsp14 N7-MTase at residues D330 and G332 and determined the effects of these mutations on viral replication, sensitivity to mutagen, inhibition by type I interferon (IFN), and translation efficiency. Virus encoding a G332A substitution in nsp14 displayed delayed replication kinetics and decreased peak titers relative to wild-type (WT) MHV. In addition, replication of nsp14 G332A virus was diminished following treatment of cells with IFN-β, and nsp14 G332A genomes were translated less efficiently both in vitro and during viral infection. In contrast, substitution of alanine at MHV nsp14 D330 did not affect viral replication, sensitivity to mutagen, or inhibition by IFN-β compared to WT MHV. Our results demonstrate that the conserved MHV N7-MTase SAM-binding-site residues are not required for MHV viability and suggest that the determinants of CoV N7-MTase activity differ in vitro and during virus infection. IMPORTANCE Human coronaviruses, most notably severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV, cause severe and lethal human disease. Since specific antiviral therapies are not available for the treatment of human coronavirus infections, it is essential to understand the functions of conserved CoV proteins in viral replication. Here, we show that substitution of alanine at G332 in the N7-MTase domain of nsp14 impairs viral replication, enhances sensitivity to the innate immune response, and reduces viral RNA translation efficiency. Our data support the idea that coronavirus RNA capping could be targeted for development of antiviral therapeutics.
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10
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Liu X, Xiong G, Qiu P, Du Z, Kormelink R, Zheng L, Zhang J, Ding X, Yang L, Zhang S, Wu Z. Inherent properties not conserved in other tenuiviruses increase priming and realignment cycles during transcription of Rice stripe virus. Virology 2016; 496:287-298. [PMID: 27393974 DOI: 10.1016/j.virol.2016.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 11/29/2022]
Abstract
Two tenuiviruses Rice stripe virus (RSV) and Rice grassy stunt virus (RGSV) were found to co-infect rice with the same reovirus Rice ragged stunt virus (RRSV). During the co-infection, both tenuiviruses recruited 10-21 nucleotides sized capped-RNA leaders from the RRSV. A total of 245 and 102 RRSV-RGSV and RRSV-RSV chimeric mRNA clones, respectively, were sequenced. An analysis of the sequences suggested a scenario consistent with previously reported data on related viruses, in which capped leader RNAs having a 3' end complementary to the viral template are preferred and upon base pairing the leaders prime processive transcription directly or after one to several cycles of priming and realignment (repetitive prime-and-realign). Interestingly, RSV appeared to have a higher tendency to use repetitive prime-and-realign than RGSV even with the same leader derived from the same RRSV RNA. Combining with relevant data reported previously, this points towards an intrinsic feature of RSV.
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Affiliation(s)
- Xiaojuan Liu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Guihong Xiong
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ping Qiu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhenguo Du
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Luping Zheng
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jie Zhang
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xinlun Ding
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Liang Yang
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Songbai Zhang
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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11
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Chen Y, Guo D. Molecular mechanisms of coronavirus RNA capping and methylation. Virol Sin 2016; 31:3-11. [PMID: 26847650 PMCID: PMC7091378 DOI: 10.1007/s12250-016-3726-4] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 01/25/2016] [Indexed: 12/17/2022] Open
Abstract
The 5′-cap structures of eukaryotic mRNAs are important for RNA stability, pre-mRNA splicing, mRNA export, and protein translation. Many viruses have evolved mechanisms for generating their own cap structures with methylation at the N7 position of the capped guanine and the ribose 2′-Oposition of the first nucleotide, which help viral RNAs escape recognition by the host innate immune system. The RNA genomes of coronavirus were identified to have 5′-caps in the early 1980s. However, for decades the RNA capping mechanisms of coronaviruses remained unknown. Since 2003, the outbreak of severe acute respiratory syndrome coronavirus has drawn increased attention and stimulated numerous studies on the molecular virology of coronaviruses. Here, we review the current understanding of the mechanisms adopted by coronaviruses to produce the 5′-cap structure and methylation modification of viral genomic RNAs.![]()
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430070, China.
| | - Deyin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430070, China.
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12
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Sun Y, Wang Z, Tao J, Wang Y, Wu A, Yang Z, Wang K, Shi L, Chen Y, Guo D. Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase. Antiviral Res 2014; 104:156-64. [PMID: 24530452 PMCID: PMC7119097 DOI: 10.1016/j.antiviral.2014.02.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 01/29/2014] [Accepted: 02/03/2014] [Indexed: 12/17/2022]
Abstract
A yeast-based system for screening of coronavirus N7-MTases inhibitors was developed. Sinefungin is not an ideal antiviral inhibitor. Three natural extracts were observed to specifically inhibit the N7-MTases of coronavirus.
The 5′-cap structure is a distinct feature of eukaryotic mRNAs and is important for RNA stability and protein translation by providing a molecular signature for the distinction of self or non-self mRNA. Eukaryotic viruses generally modify the 5′-end of their RNAs to mimic the cellular mRNA structure, thereby facilitating viral replication in host cells. However, the molecular organization and biochemical mechanisms of the viral capping apparatus typically differ from its cellular counterpart, which makes viral capping enzymes attractive targets for drug discovery. Our previous work showed that SARS coronavirus (SARS-CoV) non-structural protein 14 represents a structurally novel and unique guanine-N7-methyltransferase (N7-MTase) that is able to functionally complement yeast cellular N7-MTase. In the present study, we developed a yeast-based system for identifying and screening inhibitors against coronavirus N7-MTase using both 96-well and 384-well microtiter plates. The MTase inhibitors previously identified by in vitro biochemical assays were tested, and some, such as sinefungin, effectively suppressed N7-MTase in the yeast system. However, other compounds, such as ATA and AdoHcy, did not exert an inhibitory effect within a cellular context. These results validated the yeast assay system for inhibitor screening yet also demonstrated the difference between cell-based and in vitro biochemical assays. The yeast system was applied to the screening of 3000 natural product extracts, and three were observed to more potently inhibit the activity of coronavirus than human N7-MTase.
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Affiliation(s)
- Ying Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zidao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Jiali Tao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yi Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Andong Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Ziwen Yang
- Biological Pesticide Engineering Research Center, Hubei Academy of Agricultural Science, Hubei 430072, PR China
| | - Kaimei Wang
- Biological Pesticide Engineering Research Center, Hubei Academy of Agricultural Science, Hubei 430072, PR China
| | - Liqiao Shi
- Biological Pesticide Engineering Research Center, Hubei Academy of Agricultural Science, Hubei 430072, PR China
| | - Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China.
| | - Deyin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China.
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13
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Narayanan K, Makino S. Interplay between viruses and host mRNA degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:732-41. [PMID: 23274304 PMCID: PMC3632658 DOI: 10.1016/j.bbagrm.2012.12.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/13/2012] [Accepted: 12/16/2012] [Indexed: 12/17/2022]
Abstract
Messenger RNA degradation is a fundamental cellular process that plays a critical role in regulating gene expression by controlling both the quality and the abundance of mRNAs in cells. Naturally, viruses must successfully interface with the robust cellular RNA degradation machinery to achieve an optimal balance between viral and cellular gene expression and establish a productive infection in the host. In the past several years, studies have discovered many elegant strategies that viruses have evolved to circumvent the cellular RNA degradation machinery, ranging from disarming the RNA decay pathways and co-opting the factors governing cellular mRNA stability to promoting host mRNA degradation that facilitates selective viral gene expression and alters the dynamics of host–pathogen interaction. This review summarizes the current knowledge of the multifaceted interaction between viruses and cellular mRNA degradation machinery to provide an insight into the regulatory mechanisms that influence gene expression in viral infections. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Krishna Narayanan
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA.
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14
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Ferron F, Decroly E, Selisko B, Canard B. The viral RNA capping machinery as a target for antiviral drugs. Antiviral Res 2012; 96:21-31. [PMID: 22841701 PMCID: PMC7114304 DOI: 10.1016/j.antiviral.2012.07.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/09/2012] [Accepted: 07/13/2012] [Indexed: 12/18/2022]
Abstract
Most viruses modify their genomic and mRNA 5′-ends with the addition of an RNA cap, allowing efficient mRNA translation, limiting degradation by cellular 5′–3′ exonucleases, and avoiding its recognition as foreign RNA by the host cell. Viral RNA caps can be synthesized or acquired through the use of a capping machinery which exhibits a significant diversity in organization, structure and mechanism relative to that of their cellular host. Therefore, viral RNA capping has emerged as an interesting field for antiviral drug design. Here, we review the different pathways and mechanisms used to produce viral mRNA 5′-caps, and present current structures, mechanisms, and inhibitors known to act on viral RNA capping.
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Affiliation(s)
- François Ferron
- Centre National de la Recherche Scientifique and Aix-Marseille Université, UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
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15
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Stachelska-Wierzchowska A, Wieczorek ZJ, Wierzchowski J. The hydrolysis of 5'-CAP dinucleotide analogs: catalysis by bi- and terpyridine complexes of Cu²⁺ and Zn²⁺ ions. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 31:61-71. [PMID: 22257211 DOI: 10.1080/15257770.2011.643847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The kinetics of the hydrolysis of P(1)-(7-methylguanosinyl-5') P(3)-(guanosinyl-5') triphosphate (m(7)GpppG), P(1)-(7-methylguanosinyl-5') P(4)-(guanosinyl-5') tetraphosphate (m(7)GppppG), and diadenosine 5', 5'( ')-P(1),P(3) -triphosphate (ApppA) in the presence of several Cu(2+) or Zn(2+) ions complexed with bi- or terpyridine has been studied at pH 8.0 and 60 °C. Time-dependent product distributions at various metal complex concentrations have been determined by capillary zone electrophoresis and reversed-phase high performance liquid chromatography. The results show that the predominant hydrolytic reaction is the cleavage of 5',5'-oligophosphate bridge, with Cu(2+) complexes being approximately 15-fold more efficient catalysts than Zn(2+) chelates. In addition, the effect of metal ions complexes at pH 7.0 and 8.0 on the imidazole ring opening in m(7)Gua mononucleotides has been studied. The influence of Cu(2+) complexes on imidazole ring cleavage of mononucleotides is modest, whereas Zn(2+) complexes are almost inactive.
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16
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Decroly E, Ferron F, Lescar J, Canard B. Conventional and unconventional mechanisms for capping viral mRNA. Nat Rev Microbiol 2011; 10:51-65. [PMID: 22138959 PMCID: PMC7097100 DOI: 10.1038/nrmicro2675] [Citation(s) in RCA: 328] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNAs are protected at their 5′ ends by a cap structure consisting of an N7-methylated GTP molecule linked to the first transcribed nucleotide by a 5′–5′ triphosphate bond. The cap structure is essential for RNA splicing, export and stability, and allows the ribosomal complex to recognize mRNAs and ensure their efficient translation. Uncapped RNA molecules are degraded in cytoplasmic granular compartments called processing bodies and may be detected as 'non-self' by the host cell, triggering antiviral innate immune responses through the production of interferons. Conventional RNA capping (that is, of mRNAs from the host cell and from DNA viruses) requires hydrolysis of the 5′ γ-phosphate of RNA by an RNA triphosphatase, transfer of a GMP molecule onto the 5′-end of RNA by a guanylyltransferase, and methylation of this guanosine by an (guanine-N7)-methyltransferase. Subsequent methylations on the first and second transcribed nucleotides by (nucleoside-2′-O)-methyltransferases form cap-1 and cap-2 structures. Viruses have evolved highly diverse capping mechanisms to acquire cap structures using their own or cellular capping machineries, or by stealing cap structures from cellular mRNAs. Virally encoded RNA-capping machineries are diverse in terms of their genetic components, protein domain organization, enzyme structures, and reaction mechanisms and pathways, making viral RNA capping an attractive target for antiviral-drug design.
Capping the 5′ end of eukaryotic mRNAs with a 7-methylguanosine moiety enables efficient splicing, nuclear export and translation of mRNAs, and also limits their degradation by cellular exonucleases. Here, Canard and colleagues describe how viruses synthesize their own mRNA cap structures or steal them from host mRNAs, allowing efficient synthesis of viral proteins and avoidance of host innate immune responses. In the eukaryotic cell, capping of mRNA 5′ ends is an essential structural modification that allows efficient mRNA translation, directs pre-mRNA splicing and mRNA export from the nucleus, limits mRNA degradation by cellular 5′–3′ exonucleases and allows recognition of foreign RNAs (including viral transcripts) as 'non-self'. However, viruses have evolved mechanisms to protect their RNA 5′ ends with either a covalently attached peptide or a cap moiety (7-methyl-Gppp, in which p is a phosphate group) that is indistinguishable from cellular mRNA cap structures. Viral RNA caps can be stolen from cellular mRNAs or synthesized using either a host- or virus-encoded capping apparatus, and these capping assemblies exhibit a wide diversity in organization, structure and mechanism. Here, we review the strategies used by viruses of eukaryotic cells to produce functional mRNA 5′-caps and escape innate immunity.
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Affiliation(s)
- Etienne Decroly
- Centre National de Recherche Scientifique and Aix-Marseille Université, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288 Marseille cedex 09, France
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17
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Abstract
Growing recognition that much of the evolutionary history of eukaryotic genomes reflects the operation of turnover processes involving repetitive DNA sequences has led to the recent formulation of models describing speciation as a consequence of such turnover. These models are of three general kinds: those attributing hybrid infertility to the process of transposition, those attributing hybrid infertility to mispairing between chromosomes of divergent repetitive DNA composition, and those assuming that change in repetitive DNA's can reset coordinated gene regulation. These models are discussed with respect to the kinds of evidence needed for their corroboration and to their significance for questions related to macroevolutionary punctuated equilibria and genetic revolutions.
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18
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Smith GE, Vlak JM, Summers MD. In Vitro Translation of Autographa californica Nuclear Polyhedrosis Virus Early and Late mRNAs. J Virol 2010; 44:199-208. [PMID: 16789231 PMCID: PMC256253 DOI: 10.1128/jvi.44.1.199-208.1982] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A preliminary translational map of the Autographa californica genome was constructed. Eighteen viral DNA restriction fragments were either purified from agarose gels or obtained from pBR322 recombinant DNA plasmids to locate specific gene products. The DNAs were immobilized on nitrocellulose filters and used to select viral mRNAs isolated from RNA obtained from the cytoplasm of infected Spodoptera frugiperda cells at 21 h postinfection. The fragment-specific mRNAs were translated in vitro in the presence of l-[(3)H]leucine by using a rabbit reticulocyte lysate system and analyzed on sodium dodecyl sulfate-polyacrylamide gels. The approximate locations of 19 A. californica nuclear polyhedrosis virus (AcMNPV) gene products were mapped. The genes for mRNAs present late in viral infection were mapped to DNA fragments that represent nearly the entire genome. The molecular weights of many of these proteins were similar to those present in purified AcMNPV extracellular virus and to proteins being made in infected cells at 18 to 21 h postinfection. Cytoplasmic RNA was isolated at 4 h postinfection from infected cells, a time early in the viral infection cycle, and hybridized to AcMNPV DNA immobilized on nitrocellulose filters. AcMNPV-specific early RNA was translated in vitro into at least six polypeptides, the most abundant having a molecular weight of 39,000. Viral polypeptides were detected in cells pulse-labeled with l-[(3)H]leucine at 3 to 6 h postinfection, with molecular weights similar to those of polypeptides made in vitro from early AcMNPV mRNA.
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Affiliation(s)
- G E Smith
- Department of Entomology, Texas A&M University, College Station, Texas 77843
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19
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Further evidence that the majority of primary nuclear RNA transcripts in mammalian cells do not contribute to mRNA. Mol Cell Biol 2003. [PMID: 14582165 DOI: 10.1128/mcb.2.6.701] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear RNA from Chinese hamster ovary cells was effectively separated into polyadenylic acid [poly(A)]-containing [poly (A)+] and non-poly(A)-containing [poly(A)-] fractions so that -90% of the poly(A) was present in the (A)+ fraction. Only 25% of the 5'-terminal caps of the large nuclear molecules were present in the (A)+ class, but about 70% of the specific mRNA sequences (assayed with cDNA clones) were in the (A)+ class. It appears that many long capped heterogeneous nuclear RNA molecules are of a different sequence category from those molecules that are successfully processed into mRNA.
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20
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Salditt-Georgieff M, Darnell JE. Further evidence that the majority of primary nuclear RNA transcripts in mammalian cells do not contribute to mRNA. Mol Cell Biol 2003; 2:701-7. [PMID: 14582165 PMCID: PMC369846 DOI: 10.1128/mcb.2.6.701-707.1982] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear RNA from Chinese hamster ovary cells was effectively separated into polyadenylic acid [poly(A)]-containing [poly (A)+] and non-poly(A)-containing [poly(A)-] fractions so that -90% of the poly(A) was present in the (A)+ fraction. Only 25% of the 5'-terminal caps of the large nuclear molecules were present in the (A)+ class, but about 70% of the specific mRNA sequences (assayed with cDNA clones) were in the (A)+ class. It appears that many long capped heterogeneous nuclear RNA molecules are of a different sequence category from those molecules that are successfully processed into mRNA.
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21
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22
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Wolffe AP, Meric F. Coupling transcription to translation: a novel site for the regulation of eukaryotic gene expression. Int J Biochem Cell Biol 1996; 28:247-57. [PMID: 8920634 DOI: 10.1016/1357-2725(95)00141-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Recent experiments using Xenopus oocytes demonstrate that the history of a particular mRNA in the nucleus can influence the efficiency with which that mRNA will be utilized by the translational machinery. Individual promoter elements, specific protein-RNA interactions and the splicing process within the nucleus can all influence translational fate within the cytoplasm. Central to the regulatory mechanisms influencing the translation process is the packaging of mRNA by a highly conserved family of Y-box proteins. These Y-box proteins are found in cytoplasmic messenger ribonucleoprotein particles where they have a causal role in restricting the recruitment of mRNA to the translational machinery. Nuclear processes influence the packaging of mRNA by the Y-box proteins in the cytoplasm and in consequence mRNA translation. This functional coupling provides a novel site for the regulation of eukaryotic gene expression.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892-2710, USA
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23
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Rosenfeld MG, Emeson RB, Yeakley JM, Merillat N, Hedjran F, Lenz J, Delsert C. Calcitonin gene-related peptide: a neuropeptide generated as a consequence of tissue-specific, developmentally regulated alternative RNA processing events. Ann N Y Acad Sci 1992; 657:1-17. [PMID: 1637077 DOI: 10.1111/j.1749-6632.1992.tb22754.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- M G Rosenfeld
- Howard Hughes Medical Institute, University of California, Department of Medicine, San Diego, La Jolla 92093-0648
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25
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Large heterogeneous nuclear ribonucleic acid has three times as many 5' caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol Cell Biol 1988. [PMID: 6152852 DOI: 10.1128/mcb.1.2.179] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rate of synthesis in Chinese hamster cells of 5' cap structures, m7 GpppNmp, in large (greater than 700 bases) heterogeneous nuclear ribonucleic acid (RNA) molecules is two to three times faster than the synthesis of 3'-terminal polyadenylic acid segments. As judged by presence of caps, newly synthesized polysomal messenger RNA, exclusive of messenger RNA the size of histone messenger RNA, is more than 90% in the polyadenylated category. It appears, therefore, that between half and two-thirds of the long capped heterogeneous nuclear RNA molecules do not contribute a capped polysomal derivative to the cytoplasm. There are capped, nonpolysomal, non-polyadenylated molecules with a rapid turnover rate that fractionate with the cytoplasm. These metabolically unstable molecules either could represent leakage into the cytoplasm during fractionation or could truly spend a brief time in the cytoplasm before decay.
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26
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Chinese hamster polyadenylated messenger ribonucleic acid: relationship to non-polyadenylated sequences and relative conservation during messenger ribonucleic acid processing. Mol Cell Biol 1988. [PMID: 6152853 DOI: 10.1128/mcb.1.2.188] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have further analyzed the metabolism of specific messenger ribonucleic acid (mRNA) sequences within the cytoplasmic and nuclear RNA of Chinese hamster ovary (CHO) cells by using a set of previously constructed complementary deoxyribonucleic acid (DNA) clones (Harpold et al., Cell 17:1025-1035, 1979) as specific molecular probes in a variety of RNA:DNA hybridization experiments. The majority of the labeled mRNA complementary to each of the nine clones was found in the polyribosomes, with some variation between individual sequences. The great majority of each specific mRNA labeled for 3 h or less was in the polyadenylated [poly(A)+] fraction. However, the amount of each sequence increased in the non-poly(A)+ [poly(A)-] fraction after very long label times, suggesting the derivation of the poly(A)- RNA from the poly(A)+ RNA. Eight of the nine mRNA's have cytoplasmic half-lives ranging from 8 to 14 h, whereas one of the mRNA's, the scarcest in the group, has a somewhat shorter half-life of approximately 3 h. The proportion of each of the specific long-lived mRNA's within the total labeled mRNA increased as a function of labeling time, indicating that a large fraction, probably greater than 50%, of the initially labeled poly(A)+ mRNA in CHO cells has a half-life of less than 3 h. A quantitative analysis of the kinetics of labeling of specific nuclear and cytoplasmic sequences indicated that a significant fraction of the mRNA sequences transcribed from genes containing these nine CHO sequences were successfully processed into mRNA. However, two of the CHO mRNA sequences were only partially conserved during nuclear processing to yield mRNA. These studies demonstrated that events at two post-transcriptional levels, differential nuclear processing efficiency of different primary transcripts and cytoplasmic stability of different mRNA's, can be involved in the determination of the cytoplasmic concentrations of different mRNA's.
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27
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Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol Cell Biol 1988. [PMID: 3683396 DOI: 10.1128/mcb.7.10.3602] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To analyze the specificity of RNA processing reactions, we constructed hybrid genes containing RNA polymerase III promoters fused to sequences that are normally transcribed by polymerase II and assessed their transcripts following transfection into human 293 cells. Transcripts derived from these chimeric constructs were analyzed by using a combined RNase H and S1 nuclease assay to test whether RNAs containing consensus 5' and 3' splicing signals could be efficiently spliced in intact cells, even though they were transcribed by RNA polymerase III. We found that polymerase III-derived RNAs are not substrates for splicing. Similarly, we were not able to detect poly(A)+ RNAs derived from genes that contained a polymerase III promoter linked to sequences that were necessary and sufficient to direct 3'-end cleavage and polyadenylation when transcribed by RNA polymerase II. Our findings are consistent with the view that in vivo splicing and polyadenylation pathways are obligatorily coupled to transcription by RNA polymerase II.
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28
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Sisodia SS, Sollner-Webb B, Cleveland DW. Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol Cell Biol 1987; 7:3602-12. [PMID: 3683396 PMCID: PMC368014 DOI: 10.1128/mcb.7.10.3602-3612.1987] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
To analyze the specificity of RNA processing reactions, we constructed hybrid genes containing RNA polymerase III promoters fused to sequences that are normally transcribed by polymerase II and assessed their transcripts following transfection into human 293 cells. Transcripts derived from these chimeric constructs were analyzed by using a combined RNase H and S1 nuclease assay to test whether RNAs containing consensus 5' and 3' splicing signals could be efficiently spliced in intact cells, even though they were transcribed by RNA polymerase III. We found that polymerase III-derived RNAs are not substrates for splicing. Similarly, we were not able to detect poly(A)+ RNAs derived from genes that contained a polymerase III promoter linked to sequences that were necessary and sufficient to direct 3'-end cleavage and polyadenylation when transcribed by RNA polymerase II. Our findings are consistent with the view that in vivo splicing and polyadenylation pathways are obligatorily coupled to transcription by RNA polymerase II.
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Affiliation(s)
- S S Sisodia
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
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29
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Abstract
We have previously isolated the region of the Drosophila melanogaster X chromosome which contains the dunce+ gene and mapped the dunce2 mutation by recombination to a 10- to 12-kilobase (kb) interval (R. L. Davis and N. Davidson, Mol. Cell. Biol. 4:358-367, 1984). Here, we examine the expression of the dunce+ chromosomal region and identify the dunce+ gene within that region. A region of ca. 25 kb which contains the 10- to 12-kb interval to which dunce2 was mapped codes for polyadenylated RNAs of 9.6, 7.4, 7.2, 7.0, 5.4, and 4.5 kb in adult flies. These transcripts are encoded by the same DNA strand and share sequences of some exons, indicating that the transcripts arise from the same gene. Some genome probes internal to the ca. 25-kb coding region show transcript-specific hybridization, demonstrating alternate usage of exonic sequence information in the formation of the mature transcripts. The basis for this internal heterogeneity in RNAs is most likely alternative splicing. Two dunce mutants examined show aberrant RNA expression from this coding region, confirming that this region is the dunce gene. The developmental expression of these transcripts has been examined. The 5.4-kb RNA is present at all developmental stages. The 9.6-, 7.4-, 7.2-, and 7.0-kb RNAs are not expressed at detectable levels in embryos, but are detected in late embryogenesis and in later developmental stages. The 4.5-kb species is found in early embryos and adults, but not in intermediate stages. We discuss the remarkable transcript heterogeneity and expression pattern with respect to the important function this gene performs in neurobiological and other physiological processes.
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Mizumoto K, Kaziro Y. Messenger RNA capping enzymes from eukaryotic cells. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1987; 34:1-28. [PMID: 3326038 DOI: 10.1016/s0079-6603(08)60491-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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31
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Tao TY, Towle HC. Coordinate regulation of rat liver genes by thyroid hormone and dietary carbohydrate. Ann N Y Acad Sci 1986; 478:20-30. [PMID: 3467640 DOI: 10.1111/j.1749-6632.1986.tb15518.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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32
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33
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Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing. Mol Cell Biol 1986. [PMID: 3016525 DOI: 10.1128/mcb.5.9.2298] [Citation(s) in RCA: 129] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N6-methyladenosine (m6A) residues are present as internal base modifications in most higher eucaryotic mRNAs; however, the biological function of this modification is not known. We describe a method for localizing and quantitating m6A within a large RNA molecule, the genomic RNA of Rous sarcoma virus. Specific fragments of 32P-labeled Rous sarcoma virus RNA were isolated by hybridization with complementary DNA restriction fragments spanning nucleotides 6185 to 8050. RNA was digested with RNase and finger-printed, and individual oligonucleotides were analyzed for the presence of m6A by paper electrophoresis and thin-layer chromatography. With this technique, seven sites of methylation in this region of the Rous sarcoma virus genome were localized at nucleotides 6394, 6447, 6507, 6718, 7414, 7424, and 8014. Further, m6A was observed at two additional sites whose nucleotide assignments remain ambiguous. A clustering of two or more m6A residues was seen at three positions within the RNA analyzed. Modification at certain sites was found to be heterogeneous, in that different molecules of RNA appeared to be methylated differently. Previous studies have determined that methylation occurs only in the sequences Gm6AC and Am6AC. We observed a high frequency of methylation at PuGm6ACU sequences. The possible involvement of m6A in RNA splicing events is discussed.
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34
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Abstract
The regulation of a thyroid hormone-responsive gene in rats, designated spot 14, was explored. The expression of this gene in liver is rapidly (less than 10 min) and markedly (greater than 10-fold) altered by the administration of 3,5,3'-triiodo-L-thyronine (T3) to hypothyroid rats (P. Narayan, C. W. Liaw, and H. C. Towle, Proc. Natl. Acad. Sci. USA 81:4687-4691, 1984). To investigate the cellular site at which T3 acts to induce this hepatic mRNA, we made parallel measurements of the relative levels of spot 14 mRNA and nuclear precursor RNA and of the rate of gene transcription after treatments designed to alter the thyroid status of rats. The relative levels of both the mRNA and nuclear precursor were elevated roughly 5- to 6-fold in euthyroid animals and 9- to 12-fold in hyperthyroid animals over those in hypothyroid controls. However, only a small difference of approximately 1.5-fold was detected in the rate of spot 14 gene transcription. After a single injection of T3 into hypothyroid animals, a small and transient rise in the transcription rate was detected at 30 min. However, the levels of spot 14 mRNA and nuclear precursor RNA increased much more dramatically throughout the first 4 h of treatment. In both cases, changes in the rate of gene transcription were not capable of accounting for the alterations observed in mRNA levels. Thus, the major site of spot 14 gene regulation by T3 is at a posttranscriptional level. The proportional changes observed in the nuclear precursor and mRNA levels suggest that the site of control is at the level of stability of the nuclear precursor RNA for spot 14 mRNA.
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35
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Davis RL, Davidson N. The memory gene dunce+ encodes a remarkable set of RNAs with internal heterogeneity. Mol Cell Biol 1986; 6:1464-70. [PMID: 2431279 PMCID: PMC367671 DOI: 10.1128/mcb.6.5.1464-1470.1986] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have previously isolated the region of the Drosophila melanogaster X chromosome which contains the dunce+ gene and mapped the dunce2 mutation by recombination to a 10- to 12-kilobase (kb) interval (R. L. Davis and N. Davidson, Mol. Cell. Biol. 4:358-367, 1984). Here, we examine the expression of the dunce+ chromosomal region and identify the dunce+ gene within that region. A region of ca. 25 kb which contains the 10- to 12-kb interval to which dunce2 was mapped codes for polyadenylated RNAs of 9.6, 7.4, 7.2, 7.0, 5.4, and 4.5 kb in adult flies. These transcripts are encoded by the same DNA strand and share sequences of some exons, indicating that the transcripts arise from the same gene. Some genome probes internal to the ca. 25-kb coding region show transcript-specific hybridization, demonstrating alternate usage of exonic sequence information in the formation of the mature transcripts. The basis for this internal heterogeneity in RNAs is most likely alternative splicing. Two dunce mutants examined show aberrant RNA expression from this coding region, confirming that this region is the dunce gene. The developmental expression of these transcripts has been examined. The 5.4-kb RNA is present at all developmental stages. The 9.6-, 7.4-, 7.2-, and 7.0-kb RNAs are not expressed at detectable levels in embryos, but are detected in late embryogenesis and in later developmental stages. The 4.5-kb species is found in early embryos and adults, but not in intermediate stages. We discuss the remarkable transcript heterogeneity and expression pattern with respect to the important function this gene performs in neurobiological and other physiological processes.
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36
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37
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Abstract
The regulation of a thyroid hormone-responsive gene in rats, designated spot 14, was explored. The expression of this gene in liver is rapidly (less than 10 min) and markedly (greater than 10-fold) altered by the administration of 3,5,3'-triiodo-L-thyronine (T3) to hypothyroid rats (P. Narayan, C. W. Liaw, and H. C. Towle, Proc. Natl. Acad. Sci. USA 81:4687-4691, 1984). To investigate the cellular site at which T3 acts to induce this hepatic mRNA, we made parallel measurements of the relative levels of spot 14 mRNA and nuclear precursor RNA and of the rate of gene transcription after treatments designed to alter the thyroid status of rats. The relative levels of both the mRNA and nuclear precursor were elevated roughly 5- to 6-fold in euthyroid animals and 9- to 12-fold in hyperthyroid animals over those in hypothyroid controls. However, only a small difference of approximately 1.5-fold was detected in the rate of spot 14 gene transcription. After a single injection of T3 into hypothyroid animals, a small and transient rise in the transcription rate was detected at 30 min. However, the levels of spot 14 mRNA and nuclear precursor RNA increased much more dramatically throughout the first 4 h of treatment. In both cases, changes in the rate of gene transcription were not capable of accounting for the alterations observed in mRNA levels. Thus, the major site of spot 14 gene regulation by T3 is at a posttranscriptional level. The proportional changes observed in the nuclear precursor and mRNA levels suggest that the site of control is at the level of stability of the nuclear precursor RNA for spot 14 mRNA.
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38
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Crosti N, Bajer J, Serra A, Rigo A, Scarpa M, Viglino P. Coordinate expression of MnSOD and CuZnSOD in human fibroblasts. Exp Cell Res 1985; 160:396-402. [PMID: 2931296 DOI: 10.1016/0014-4827(85)90186-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The amount of manganese superoxide dismutase (MnSOD) and the activity of copper-zinc superoxide dismutase (CuZnSOD) have been studied in five karyotypically normal human fibroblast strains, using nuclear magnetic resonance (NMR) and polarographic methods. A significant correlation between the two enzyme activities, and a linear increase of MnSOD with the increase of CuZnSOD have been demonstrated. Both enzymes are present in nuclei, mitochondria, lysosome-microsome fraction and cytosol. These findings suggest that the two enzymes dismutate the O-2 cooperatively and that a common genetic control maintains the relative amounts of the two enzymes constant.
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Kane SE, Beemon K. Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing. Mol Cell Biol 1985; 5:2298-306. [PMID: 3016525 PMCID: PMC366956 DOI: 10.1128/mcb.5.9.2298-2306.1985] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
N6-methyladenosine (m6A) residues are present as internal base modifications in most higher eucaryotic mRNAs; however, the biological function of this modification is not known. We describe a method for localizing and quantitating m6A within a large RNA molecule, the genomic RNA of Rous sarcoma virus. Specific fragments of 32P-labeled Rous sarcoma virus RNA were isolated by hybridization with complementary DNA restriction fragments spanning nucleotides 6185 to 8050. RNA was digested with RNase and finger-printed, and individual oligonucleotides were analyzed for the presence of m6A by paper electrophoresis and thin-layer chromatography. With this technique, seven sites of methylation in this region of the Rous sarcoma virus genome were localized at nucleotides 6394, 6447, 6507, 6718, 7414, 7424, and 8014. Further, m6A was observed at two additional sites whose nucleotide assignments remain ambiguous. A clustering of two or more m6A residues was seen at three positions within the RNA analyzed. Modification at certain sites was found to be heterogeneous, in that different molecules of RNA appeared to be methylated differently. Previous studies have determined that methylation occurs only in the sequences Gm6AC and Am6AC. We observed a high frequency of methylation at PuGm6ACU sequences. The possible involvement of m6A in RNA splicing events is discussed.
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40
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Rogers JH. The origin and evolution of retroposons. INTERNATIONAL REVIEW OF CYTOLOGY 1985; 93:187-279. [PMID: 2409043 DOI: 10.1016/s0074-7696(08)61375-3] [Citation(s) in RCA: 421] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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41
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Abstract
A method using restriction enzymes to locate the cap site in a cloned and sequenced 5' region of a gene is described. With a cDNA fragment (or synthetic oligonucleotide sequence), complementary to any portion of an mRNA, the position of the cap site nucleotide in a genomic clone can be precisely located. The steps include: (1) hybridization of a cDNA fragment to an mRNA sample, and reverse transcription from this primer to produce labeled, fully extended cDNA molecules, (2) hybridization of the extended cDNA to a genomic clone containing the region in which initiation occurs (previously sequenced), (3) restriction endonuclease digestion of the hybrid with two or more enzymes within the putative first exon, and (4) size analysis of the short labeled cDNA fragments produced. Multicut restriction enzymes are most useful in this technique. The sizes of the hybridized fragments correspond to the unique distances from the 5' end of the message to each of the different cleavage sites allowing the cap site to be positioned in the genomic sequence.
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42
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Krieg PA, Melton DA. Functional messenger RNAs are produced by SP6 in vitro transcription of cloned cDNAs. Nucleic Acids Res 1984; 12:7057-70. [PMID: 6207484 PMCID: PMC320142 DOI: 10.1093/nar/12.18.7057] [Citation(s) in RCA: 1293] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We describe a method for the synthesis of microgram quantities of eucaryotic messenger RNAs. Injection into the cytoplasm of frog oocytes and addition to wheat germ extracts show that these synthetic RNAs function efficiently as messenger RNAs. We confirm that a 5' cap on the mRNA is essential for translation in injected oocytes and show that most of the 3' flanking region, including the poly A tail, can be deleted without the abolition of protein synthesis. The method of mRNA synthesis involves in vitro transcription of cDNAs which have been cloned into SP6 vectors (described in the accompanying paper). This method enables one to produce large amounts of mRNA and consequently protein from any cDNA clone.
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43
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Abstract
Rat hippocampal slices were incubated with [3H]uridine in vitro to analyze the metabolism of nuclear RNA and the RNA precursor fractions. Labeling of total nuclear RNA was linear for 4 h of incubation and proportional to the concentration of labeled uridine in the incubation medium. Addition of 3.5 X 10(-8) M corticosterone to the incubation medium produced an enhancement of nuclear RNA labeling with no significant effect on the labeling of the RNA precursor fraction. Progesterone and dexamethasone, at the same concentration, had no effect on either variable. Labeling of RNA by cerebellar slices under the same conditions was approximately one-half the value obtained using hippocampal slices and the cerebellar RNA precursor fraction accumulated only 65% of the radioactivity from [3H]uridine found in the hippocampal pool. Corticosterone had no effect on the labeling of total nuclear RNA in cerebellar slices. Nuclear poly(A)-containing RNA constituted 19% of the total labeled nuclear RNA in these incubations, as estimated by oligo (dT)-cellulose chromatography. Cordycepin (3'-deoxyadenosine) at a concentration of 25 micrograms/ml inhibited to some extent the labeling of total nuclear RNA and the RNA precursor fraction, but preferentially diminished the amount of labeled RNA bound to oligo (dT)-cellulose. Corticosterone increased the amount of [3H]RNA which bound to oligo (dT)-cellulose, while progesterone had no effect. These results show that hippocampal slices maintained in vitro, can be used to analyze nuclear RNA metabolism, one positive regulator of which in the rat hippocampus is the adrenal steroid, corticosterone.
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44
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Leys EJ, Crouse GF, Kellems RE. Dihydrofolate reductase gene expression in cultured mouse cells is regulated by transcript stabilization in the nucleus. J Cell Biol 1984; 99:180-7. [PMID: 6736126 PMCID: PMC2275613 DOI: 10.1083/jcb.99.1.180] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Methotrexate-resistant cells, which contain a 500-fold amplification of dihydrofolate reductase (DHFR) genes, were used as a model system for studying the regulation of DHFR gene expression during growth stimulation. We have shown that a threefold increase in DHFR mRNA levels following growth stimulation results from a corresponding increase in DHFR mRNA production (i.e., delivery to the cytoplasm) and is not the result of a change in DHFR mRNA half-life. We previously showed that the increase in DHFR mRNA production during growth stimulation is not accompanied by an increase in the relative rate of transcription of the DHFR gene. This suggested that changes in DHFR mRNA production during growth stimulation are due to changes in the stability of DHFR transcripts in the nucleus. Using continuous labeling experiments in vivo comparing the stability of DHFR RNA with specific reference sequences, we show that in growing cells most DHFR transcripts were converted to mRNA, whereas in resting cells the majority of DHFR transcripts were rapidly degraded in the nucleus. There was no significant difference in the rate of processing and transport of stable DHFR transcripts. Therefore, changes in the stability of DHFR RNA in the nucleus control the amount of mRNA available for translation in the cytoplasm.
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45
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Abstract
Though vaccinia virus DNA and RNA replication take place predominantly in the cytoplasm of an infected cell, virus formation requires the presence of a functional nucleus in a yet undefined manner. When the nuclei from cells infected for 3 h are isolated and purified, they are found to synthesize five times more RNA in vitro than do corresponding nuclei from noninfected cells. Fifty percent of the RNA synthesized in vitro by nuclei from infected cells is vaccinia specific, and this vaccinia RNA synthesis is resistant to alpha-amanitin concentrations up to 100 micrograms/ml. Furthermore, when the RNA polymerase activities of these nuclei are separated on DEAE-Sephadex columns, 56% of the total nuclear enzyme activity is found to be the vaccinia-specific RNA polymerase known to be alpha-amanitin resistant. The nucleus associated vaccinia RNA polymerase represents 18% of the total cellular vaccinia RNA polymerase. This synthesis of vaccinia RNA in the nucleus may explain the nuclear requirement for vaccinia virus maturation.
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46
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Szego CM, Pietras RJ. Lysosomal functions in cellular activation: propagation of the actions of hormones and other effectors. INTERNATIONAL REVIEW OF CYTOLOGY 1984; 88:1-302. [PMID: 6145684 DOI: 10.1016/s0074-7696(08)62759-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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47
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48
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Different mRNAs have different nuclear transit times in Dictyostelium discoideum aggregates. Mol Cell Biol 1983. [PMID: 6621537 DOI: 10.1128/mcb.3.8.1511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear processing of mRNA precursors in differentiating multicellular Dictyostelium discoideum aggregates is markedly slower than in growing amoebae. Thus, we have been able to determine the time of nuclear processing of individual mRNA species in postaggregating cells by following the incorporation of 32PO4 into nuclear and cytoplasmic RNA complementary to cloned cDNAs. Precursors of mRNAs synthesized during both growth and differentiation remain in the nucleus for about 25 to 60 min. By contrast, typical mRNAs which are synthesized only by postaggregative cells have nuclear processing times between 50 and 100 min. Depending on the particular mRNA, between 20 and 60% of nuclear transcripts are converted into cytoplasmic mRNA. A third class of mRNAs are transcribed from a set of repetitive DNA segments and are expressed predominantly during differentiation. Nuclear precursors of these mRNAs are extensively degraded within the nucleus or very rapidly after transport to the cytoplasm. Those sequences that are stable in the cytoplasm exit from the nucleus only after a lag of over 2 h. Thus, mRNAs encoded by different genes that are subject to different types of developmental controls display different times of transit to the cytoplasm and different efficiencies of nuclear processing. Differential nuclear processing may contribute to the regulation of the level of individual cytoplasmic mRNAs.
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49
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A splice junction deletion deficient in the transport of RNA does not polyadenylate nuclear RNA. Mol Cell Biol 1983. [PMID: 6312290 DOI: 10.1128/mcb.3.8.1381] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A late region deletion mutant of simian virus 40 (dl5) was previously shown to be deficient in the transport of nuclear RNA. This is a splice junction deletion that has lost the 3' end of an RNA leader, an intervening sequence, and the 5' end of the splice acceptor site on the body of the mRNA. In this report, we analyzed the steady-state structure of the untransported nuclear RNA. The 5' ends of this RNA are heterogeneous but contain a prominent 5' end at the normal position (nucleotide 325) in addition to several other prominent 5' ends not seen in wild-type RNA. The 3' end of this RNA does not occur at the usual position (nucleotide 2674) of polyadenylation; instead, this RNA is non-polyadenylated, with the 3' end occurring either downstream or upstream of the normal position.
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50
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Amrani DL, Homandberg GA, Tooney NM, Wolfenstein-Todel C, Mosesson MW. Separation and analysis of the major forms of plasma fibronectin. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 748:308-20. [PMID: 6138099 DOI: 10.1016/0167-4838(83)90308-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Human plasma fibronectin exists in circulation in multiple molecular forms that are distinguishable by SDS-polyacrylamide gel electrophoresis (zone I, approx. 450 kDa dimers; zone II, 190-235 kDa; Zone III, 146-175 kDa). (Chen, A.B., Amrani, D.L. and Mosesson, M.W. (1977) Biochim. Biophys. Acta 493, 310-322). We report here on investigations of plasma fibronectin that had been purified from the 'heparin-precipitable fraction' of plasma by DEAE-cellulose chromatography using buffers containing a chaotropic salt (KSCN). Zone I fibronectin and zone II fibronectin were subsequently separated by Sepharose CL-6B chromatography in the presence of 0.3 M KSCN. Electrophoresis of reduced zone I fibronectin dimers showed the presence of three types of subunits (i.e., 220 kDa, 215 kDa, 207 kDa), evidently all having the same NH2-terminal sequence. Subunits of this size were also found in reduced zone II fibronectin, as well as another polypeptide of 190 kDa, the latter amounting to under 5% of the total. Unreduced zone I fibronectin was resolved by gel electrophoresis into a doublet. The upper component amounted to approx. 90% of the total and was comprised of 220 kDa and/or 215 kDa subunits; the lower component contained 207 kDa plus a 220 kDa or 215 kDa subunit. Scanning transmission electron microscopy indicated that under physiologic conditions zone II fibronectin molecules, like those in zone I, exist as pleiomorphic, loosely folded structures (approx. 16 X 8-12 nm) that are somewhat smaller than dimeric zone I molecules (approx. 24 X 16 nm). Circular dichroic spectral analyses suggests that both types have similarly folded local domains. Affinity chromatography experiments revealed a relative decrease in the binding of zone II fibronectin to gelatin but no difference from zone I fibronectin with respect to heparin or fibrin binding.
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