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Hyde JL, Diamond MS. Innate immune restriction and antagonism of viral RNA lacking 2׳-O methylation. Virology 2015; 479-480:66-74. [PMID: 25682435 PMCID: PMC4424151 DOI: 10.1016/j.virol.2015.01.019] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/22/2015] [Indexed: 01/31/2023]
Abstract
N-7 and 2′-O methylation of host cell mRNA occurs in the nucleus and results in the generation of cap structures (cap 0, m7GpppN; cap 1, m7GpppNm) that control gene expression by modulating nuclear export, splicing, turnover, and protein synthesis. Remarkably, RNA cap modification also contributes to mammalian cell host defense as viral RNA lacking 2′-O methylation is sensed and inhibited by IFIT1, an interferon (IFN) stimulated gene (ISG). Accordingly, pathogenic viruses that replicate in the cytoplasm have evolved mechanisms to circumvent IFIT1 restriction and facilitate infection of mammalian cells. These include: (a) generating cap 1 structures on their RNA through cap-snatching or virally-encoded 2′-O methyltransferases, (b) using cap-independent means of translation, or (c) using RNA secondary structural motifs to antagonize IFIT1 binding. This review will discuss new insights as to how specific modifications at the 5′-end of viral RNA modulate host pathogen recognition responses to promote infection and disease.
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Affiliation(s)
- Jennifer L Hyde
- Departments of Medicine, Washington University School of Medicine, St Louis., MO 63110, USA
| | - Michael S Diamond
- Departments of Medicine, Washington University School of Medicine, St Louis., MO 63110, USA; Molecular Microbiology, Washington University School of Medicine, St Louis., MO 63110 USA; Pathology & Immunology, Washington University School of Medicine, St Louis., MO 63110, USA; The Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis., MO 63110, USA.
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Wang Q, Zhang S, Jiang H, Wang J, Weng L, Mao Y, Sekiguchi S, Yasui F, Kohara M, Buchy P, Deubel V, Xu K, Sun B, Toyoda T. PA from an H5N1 highly pathogenic avian influenza virus activates viral transcription and replication and induces apoptosis and interferon expression at an early stage of infection. Virol J 2012; 9:106. [PMID: 22681768 PMCID: PMC3507744 DOI: 10.1186/1743-422x-9-106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 05/21/2012] [Indexed: 12/28/2022] Open
Abstract
Background Although gene exchange is not likely to occur freely, reassortment between the H5N1 highly pathogenic avian influenza virus (HPAIV) and currently circulating human viruses is a serious concern. The PA polymerase subunit of H5N1 HPAIV was recently reported to activate the influenza replicon activity. Methods The replicon activities of PR8 and WSN strains (H1N1) of influenza containing PA from HPAIV A/Cambodia/P0322095/2005 (H5N1) and the activity of the chimeric RNA polymerase were analyzed. A reassortant WSN virus containing the H5N1 Cambodia PA (C-PA) was then reconstituted and its growth in cells and pathogenicity in mice examined. The interferon promoter, TUNEL, and caspase 3, 8, and 9 activities of C-PA-infected cells were compared with those of WSN-infected cells. Results The activity of the chimeric RNA polymerase was slightly higher than that of WSN, and C-PA replicated better than WSN in cells. However, the multi-step growth of C-PA and its pathogenicity in mice were lower than those of WSN. The interferon promoter, TUNEL, and caspase 3, 8, and 9 activities were strongly induced in early infection in C-PA-infected cells but not in WSN-infected cells. Conclusions Apoptosis and interferon were strongly induced early in C-PA infection, which protected the uninfected cells from expansion of viral infection. In this case, these classical host-virus interactions contributed to the attenuation of this strongly replicating virus.
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Affiliation(s)
- Qiang Wang
- Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 411 Hefei Road, 200025, Shanghai, P. R. China
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3
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Molecular mechanisms of transcription and replication of the influenza A virus genome. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11515-011-1151-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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4
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Abstract
Influenza virus RNA polymerase is composed of three virus-coded proteins, and is involved in both transcription and replication of the negative-strand genome RNA. Subunit PB1 plays key roles in both the RNA polymerase assembly and the catalytic function of RNA polymerization. Using yeast two-hybrid screening, a HeLa cell protein with the molecular mass of 45 kDa was identified. After cloning and sequencing, this protein was identified to be Ebp1, ErbB3-binding protein. Epb1 specifically interacts with PB1 both in vitro and in vivo, and Epb1 contact site on PB1 was mapped at its binding site of transcription primers. Ebp1 was found to interfere with in vitro RNA synthesis by influenza virus RNA polymerase (3P complex), but no inhibition was observed for capped RNA endonuclease and RNA-cap binding, the intrinsic activities of RNA polymerase. Since inhibition was not observed against other nucleic acid polymerases tested, we propose that Ebp1 is a selective inhibitor of influenza viral RNA polymerase. Accordingly over-expression of Ebp1 interfered with virus production. The PB1-contact site on Ebp1 overlaps with the interaction site with ErbB3 (epidermal receptor tyrosine kinase), androgen receptor (AR) and retinoblastoma gene product (Rb), which are involved in controlling cell proliferation and differentiation.
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Affiliation(s)
- Ayae Honda
- Department of Frontier Bioscience and Micro-Nano-Technology Research Center, Hosei University, Koganei, Tokyo 184-8584, Japan.
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5
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Ohtsu Y, Honda Y, Sakata Y, Kato H, Toyoda T. Fine mapping of the subunit binding sites of influenza virus RNA polymerase. Microbiol Immunol 2002; 46:167-75. [PMID: 12008925 DOI: 10.1111/j.1348-0421.2002.tb02682.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Influenza virus RNA polymerase consists of three subunits, PB1, PB2 and PA, and catalyzes both transcription and replication of the RNA genome. PB1 is a catalytic subunit of RNA polymerization and a core of the subunit assembly. The subunit binding sites were mapped at about several hundred amino-acid size. Fine mapping of the subunit binding sites was determined. The PB1-PA binding regions were mapped within in the N-terminal 25 amino acids of PB1 and 668-692 of PA. PB1 and PB2 interacted within wider regions, 600-757 of PB1 and 51-259 of PB2. In these amino-acid spans, 206-259 of PB2 may be the most important region of PB1 binding and 718-732 of PB1 may be the most important region of PB2 binding because the binding activity was lost when the regions were lost in the subunits. The additional regions contributed to strong binding of these subunits.
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Affiliation(s)
- Yasushi Ohtsu
- Department of Virology, Kurume University School of Medicine, Fukuoka, Japan
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6
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Honda A, Mizumoto K, Ishihama A. Minimum molecular architectures for transcription and replication of the influenza virus. Proc Natl Acad Sci U S A 2002; 99:13166-71. [PMID: 12271117 PMCID: PMC130604 DOI: 10.1073/pnas.152456799] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RNA-dependent RNA polymerase of influenza virus is composed of three viral P proteins (PB1, PB2, and PA) and involved in both transcription and replication of the RNA genome. The PB1 subunit plays a key role in both the assembly of three P protein subunits and the catalytic function of RNA polymerization. We have established a simultaneous expression system of three P proteins in various combinations using recombinant baculoviruses, and isolated the PA-PB1-PB2 ternary (3P) complex and two kinds of the binary (2P) complex, PA-PB1 and PB1-PB2. The affinity-purified 3P complex showed all of the catalytic properties characteristic of the transcriptase, including capped RNA-binding, capped RNA cleavage, model viral RNA binding, model viral RNA-directed RNA synthesis, and polyadenylation of newly synthesized RNA. The PB1-PB2 binary complex showed essentially the same catalytic properties as does the 3P complex, whereas the PA-PB1 complex catalyzed de novo initiation of RNA synthesis in the absence of primers. Taken together we propose that the catalytic specificity of PB1 subunit is modulated to the transcriptase by binding PB2 or the replicase by interaction with PA.
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Affiliation(s)
- Ayae Honda
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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7
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Abstract
The influenza virus polymerase complex contains two associated enzymatic activities, an endoribonuclease and a RNA-dependent RNA polymerase activity. Both activities have so far been observed only with the complete polymerase complex consisting of three subunits, PB1, PB2, and PA. This chapter describes a robust and optimized procedure for the purification of active influenza virus polymerase in complex with genomic RNA and the single-stranded RNA-binding protein nucleoprotein from influenza virus particles. It also explains the synthesis of capped RNA molecules as substrates of the influenza virus endonuclease. The enzymatic properties of influenza virus-derived endoribonuclease activity have been characterized with a model RNA substrate of 20-nucleotide length, termed G20 RNA. The rate of RNA cleavage under steady state conditions appears to be limited by product dissociation. Therefore conditions have been optimized to study the chemical step of RNA cleavage under single turnover conditions. The enzyme requires divalent metal ions for activity and can use Mn(II), Co(II), and Fe(II) efficiently at pH 7, Mg(II) with intermediate efficiency, and Ni(II) and Zn(II) with lower efficiency. The reaction progress curves show slow binding of Zn(II) and Ni(II) to the protein, suggesting a conformational change of the active site as a prerequisite for endonuclease activity in the presence of these two metal ions. Low concentrations of the detergent DOC inhibit the activity and also disrupt the trimeric polymerase complex, whereas other detergents do not have a significant effect on the activity.
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Affiliation(s)
- K Klumpp
- Roche Products Ltd., Welwyn Garden City, Hertfordshire AL7 3AY, United Kingdom
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Tado M, Abe T, Hatta T, Ishikawa M, Nakada S, Yokota T, Takaku H. Inhibitory effect of modified 5'-capped short RNA fragments on influenza virus RNA polymerase gene expression. Antivir Chem Chemother 2001; 12:353-8. [PMID: 12018680 DOI: 10.1177/095632020101200605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We have shown previously that the 5'-capped short phosphodiester RNA fragments, Cap decoy, (Gm 12 nt) are potent inhibitors of influenza virus RNA polymerase gene expression. Here we investigate the modified capped RNA derivative containing phosphorothioate oligonucleotides (Cap decoy) as a potential influenza virus RNA polymerase inhibitor. The modified 5'-capped short phosphorothioate RNA fragments (Gms 12-15 nt) with the 5'-capped structure (m7GpppGm) were synthesized by T7 RNA polymerase. The 5'-capped short RNA fragments (Gms 12-15 nt) were encapsulated in liposome particulates and tested for their inhibitory effects on influenza virus RNA polymerase gene expression in the clone 76 cells. The 12-15 nt long Gms RNA fragments showed highly inhibitory effects. By contrast, the inhibitory effects of the 13 nt long short RNA fragments (Gm 13 nt) were considerably less in comparison with the 5'-capped short phosphorothioate RNA fragments (Gms 12-15 nt). In particular, the various Gms RNA chain lengths showed no significant differences in the inhibition of influenza virus RNA polymerase gene expression. Furthermore, the capped RNA with a phosphorothioate backbone was resistant to nuclease activity. These phosphorothioate RNA fragments exhibited higher inhibitory activity than the 5'-capped short RNA fragments (Gm 12 nt). These decoys may prove to be useful in anti-influenza virus therapeutics.
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Affiliation(s)
- M Tado
- Department of Industrial Chemistry, Chiba Institute of Technology, Tsudanuma, Narashino, Japan
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9
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Ohtsu Y, Honda Y, Toyoda T. Fine mapping of the subunit binding sites of influenza virus RNA polymerase. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0531-5131(01)00395-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Honda A, Endo A, Mizumoto K, Ishihama A. Differential roles of viral RNA and cRNA in functional modulation of the influenza virus RNA polymerase. J Biol Chem 2001; 276:31179-85. [PMID: 11373286 DOI: 10.1074/jbc.m102856200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA-dependent RNA polymerase of influenza virus is composed of three viral P proteins (PB1, PB2, and PA) and involved in both transcription and replication of the RNA genome. For the molecular anatomy of this multifunctional enzyme, we have established a simultaneous expression of three P proteins in cultured insect cells using recombinant baculoviruses. For purification of P protein complexes, the PA protein was expressed as a fusion with a histidine tag added at its N terminus. By using affinity chromatography, a complex consisting of the three P proteins was isolated from nuclear extracts of virus-infected cells. The affinity-purified 3P complex showed the activities of capped RNA binding, capped RNA cleavage, viral model RNA binding, model RNA-directed RNA synthesis, and polyadenylation of newly synthesized RNA. We conclude that a functional form of the viral RNA polymerase with the catalytic specificity of transcriptase is formed in recombinant baculovirus-infected insect cells. Using the viral RNA-free 3P complex, we found that the capped RNA cleavage takes place in the presence of vRNA but not of cRNA, indicating that the vRNA functions as a regulatory factor for the specificity control of viral RNA polymerase as well as a template for transcription. The structural elements of RNA directing the expression of RNA polymerase functions were analyzed using variant forms of the model RNA templates.
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Affiliation(s)
- A Honda
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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Hara K, Shiota M, Kido H, Ohtsu Y, Kashiwagi T, Iwahashi J, Hamada N, Mizoue K, Tsumura N, Kato H, Toyoda T. Influenza virus RNA polymerase PA subunit is a novel serine protease with Ser624 at the active site. Genes Cells 2001; 6:87-97. [PMID: 11260254 DOI: 10.1046/j.1365-2443.2001.00399.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Influenza virus RNA polymerase is a multifunctional enzyme that catalyses both transcription and replication of the RNA genome. The function of the influenza virus RNA polymerase PA subunit in viral replication is poorly understood, although the enzyme is known to be required for cRNA --> vRNA synthesis. The protease related activity of PA has been discussed ever since protease-inducing activity was demonstrated in transfection experiments. RESULTS PA protein was highly purified from insect cells infected with the recombinant baculovirus carrying PA cDNA, and a novel chymotrypsin-type serine protease activity was identified with the synthetic peptide, Suc-LLVY-MCA, in the PA protein. [3H]DFP was crosslinked with PA and a mutational analysis revealed that serine624 was as an active site for the protease activity. CONCLUSIONS These results constitute the demonstration of protease activity in PA subunit of the influenza virus RNA polymerase complexes.
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Affiliation(s)
- K Hara
- Departments of Virology, Kurume University School of Medicine, Kurume 830-0011, Japan
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Klumpp K, Doan L, Roberts NA, Handa B. RNA and DNA hydrolysis are catalyzed by the influenza virus endonuclease. J Biol Chem 2000; 275:6181-8. [PMID: 10692410 DOI: 10.1074/jbc.275.9.6181] [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: 11/06/2022] Open
Abstract
The influenza virus polymerase complex contains a metal ion-dependent endonuclease activity, which generates short capped RNA primer molecules from capped RNA precursors. Previous studies have provided evidence for a two-metal ion mechanism of RNA cleavage, and the data are consistent with a direct interaction of a divalent metal ion with the catalytic water molecule. To refine the model of this active site, we have generated a series of DNA, RNA, and DNA-RNA chimeric molecules to study the role of the 2'-hydroxy groups on nucleic acid substrates of the endonuclease. We could observe specific cleavage of nucleic acid substrates devoid of any 2'-hydroxy groups if they contained a cap structure (m7GpppG) at the 5'-end. The capped DNA endonuclease products were functional as primers for transcription initiation by the influenza virus polymerase. The apparent cleavage rates were about 5 times lower with capped DNA substrates as compared with capped RNA substrates. Cleavage rates with DNA substrates could be increased to RNA levels by substituting the deoxyribosyl moieties immediately 5' and 3' of the cleavage site with ribosyl moieties. Similarly, cleavage rates of RNA substrates could be lowered to DNA levels by exchanging the same two ribosyl groups with deoxyribosyl groups at the cleavage site. These results demonstrate that the 2'-hydroxy groups are not essential for binding and cleavage of nucleic acids by the influenza virus endonuclease, but small differences of the nucleic acid conformation in the endonuclease active site can influence the overall rate of hydrolysis. The observed relative cleavage rates with DNA and RNA substrates argue against a direct interaction of a catalytic metal ion with a 2'-hydroxy group in the endonuclease active site.
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Affiliation(s)
- K Klumpp
- Roche Discovery Welwyn, 40 Broadwater Road, Welwyn Garden City, Herts AL7 3AY, United Kingdom.
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13
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Honda A, Mizumoto K, Ishihama A. Two separate sequences of PB2 subunit constitute the RNA cap-binding site of influenza virus RNA polymerase. Genes Cells 1999; 4:475-85. [PMID: 10526235 DOI: 10.1046/j.1365-2443.1999.00275.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Influenza virus RNA polymerase with the subunit composition of PB1-PB2-PA is a unique multifunctional enzyme with the activities of both synthesis and cleavage of RNA, and is involved in both transcription and replication of the RNA genome. Transcription is initiated by using capped RNA fragments, which are generated after cleavage of host cell mRNA by the RNA polymerase-associated capped RNA endonuclease. To identify the RNA cap 1-binding site on the RNA polymerase, viral ribonucleoprotein (RNP) cores were subjected to UV-crosslinking with RNA which was labelled with 32P only at the cap-1 structure. RESULTS After SDS-PAGE of UV-crosslinked cores, 32P was found to be associated only with the PB2 subunit (759 amino acid residues). The labelled PB2 was subjected, together with PB2 expressed in E. coli, to limited digestion with V8 protease. Analysis of the amino terminal sequences of some isolated fragments with the crosslinked cap-1 indicated that two separate sequences within the PB2 were involved in RNA cap-1 binding, one (N-site) at the N-terminal proximal region approximately between amino acid residues 242-282 downstream from the PB1 subunit-binding site and the other (C-site) between residues 538-577 including the cap-binding motifs. Two lines of evidence support the prediction of the involvement of two separate PB2 sequences on the RNA cap-binding: (i) cross-linking of the capped RNA on to expressed and isolated PB2 fragments, each containing either the N-site or the C-site; and (ii) competition of capped RNA-binding to PB2 by both of the N- and C-terminal PB2 fragments. Taking together, we propose that two separate sequences within PB2 constitute the capped RNA-binding site of the RNA polymerase. CONCLUSION Two separate sequences, one N-(242-282) and the other C-terminal (538-577) proximal segments of PB2 subunit, constitute the RNA cap-binding site of the influenza virus RNA polymerase.
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Affiliation(s)
- A Honda
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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14
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Masunaga K, Mizumoto K, Kato H, Ishihama A, Toyoda T. Molecular mapping of influenza virus RNA polymerase by site-specific antibodies. Virology 1999; 256:130-41. [PMID: 10087233 DOI: 10.1006/viro.1999.9625] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Influenza virus RNA polymerase with the subunit structure PB1-PB2-PA is involved in both transcription and replication of the RNA genome, including the unique cap-I-dependent RNase activity. To map the important domains for RNA polymerization, cap-I-dependent RNase, and cap-I-binding activity, we generated site-specific antibodies against overlapping 150-amino-acid peptides that cover each entire subunit. Monospecific antibodies against each subunit inhibited RNA synthesis in vitro. Those against PB1 and PB2 inhibited the cap-I-dependent RNase activity, but those against PB2 alone slightly inhibited the cap-I-binding activity. Antibodies against the N-terminal amino acids 1-159 of PB2 that overlap the PB1-binding site on PB2 and the C-terminal amino acids 501-617 of PA that overlap the putative nucleotide-binding site and PB1-binding site on PA inhibited RNA polymerizing activity as well as monospecific antibodies. Those against the N-terminal (amino acids 1-159); the central region (amino acids 305-559) of PB2, where a part of the cap-binding domain predicted previously is localized; the N-terminal (amino acids 1-222) of PB1; and amino acids 301-517 and 601-716 of PA inhibited the cap-I-dependent RNase activity. The cap-binding domain on PB2 could be mapped in amino acids 402-559, where one of the cap-binding domains mapped previously overlapped.
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Affiliation(s)
- K Masunaga
- Department of Virology, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
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Hatta T, Ishikawa M, Takai K, Nakada S, Yokota T, Hata T, Miura K, Takaku H. Inhibition of influenza virus RNA polymerase by 5'-capped short RNA fragments. Biochem Biophys Res Commun 1998; 249:103-6. [PMID: 9705839 DOI: 10.1006/bbrc.1998.9085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have demonstrated that 5'-capped short RNA fragments inhibit the expression of chloramphenicol acetyltransferase (CAT) in the murine 76 cell line, derived which expresses the genes for the RNA polymerases (PB1, PB2, and PA) and the nucleoprotein (NP) of influenza virus in response to treatment with dexamethasone. We have synthesized 5'-capped short RNA fragments (8-13 ntds long) with a 5'-capped structure (m7GpppGm) using T7 RNA polymerase. The 5'-capped short RNA fragments (8-13 ntds long) were encapsulated in liposomes and were tested for their inhibitory effect by a CAT-ELISA assay using the clone 76 cells. The RNA fragments that were 9-12 ntds long showed inhibitory effects. In particular, the 9 ntds long RNA fragment, was highly inhibitory. On the other hand, the inhibitory effect of the 13 ntds long RNA fragment was considerably decreased in comparison with the other short RNA fragments. The minimal RNA chain length required for priming activity was found to be 12 ntds long. Furthermore, the 5'-capped RNA fragments exhibited higher inhibitory activities than the antisense phosphorothioate oligonucleotide (PB2-AUG-as, 20 ntds long) complementary to the site of the PB2-AUG initiation codon. Liposome encapsulation protected the RNA fragments in serum-containing medium and substantially improved their cellular accumulation.
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Affiliation(s)
- T Hatta
- Department of Industrial Chemistry, Chiba Institute of Technology, Japan
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16
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Weber F, Haller O, Kochs G. Nucleoprotein viral RNA and mRNA of Thogoto virus: a novel "cap-stealing" mechanism in tick-borne orthomyxoviruses? J Virol 1996; 70:8361-7. [PMID: 8970956 PMCID: PMC190924 DOI: 10.1128/jvi.70.12.8361-8367.1996] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Tick-borne Thogoto virus (THOV) represents the prototype virus of a new genus in the Orthomyxoviridae family. Its genome consists of six segments of negative-sense, single-stranded RNA. We have cloned and sequenced the fifth genomic segment, which codes for the viral nucleoprotein (NP). The deduced amino acid sequence shows 43% similarity to the NP of Dhori virus, a related tick-transmitted orthomyxovirus, and about 14% sequence similarity to those of the influenza viruses. To reveal the mechanism by which THOV initiates mRNA synthesis, we characterized the 5' ends of the NP mRNAs. Transcripts were recognized by a cap-specific monoclonal antibody, indicating that THOV mRNAs are capped. Surprisingly, no large heterogeneous extensions were found at the 5' end, as would have been expected if THOV were using a classical "cap-stealing" mechanism. We therefore propose that THOV is stealing only the cap structure with one or two additional nucleotides from cellular mRNAs to generate appropriate primers for initiation of viral mRNA transcription.
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Affiliation(s)
- F Weber
- Abteilung Virologie, Institut für Medizinische Mikrobiologie und Hygiene, Universität Freiburg, Germany
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Shi L, Galarza JM, Summers DF. Recombinant-baculovirus-expressed PB2 subunit of the influenza A virus RNA polymerase binds cap groups as an isolated subunit. Virus Res 1996; 42:1-9. [PMID: 8806170 DOI: 10.1016/0168-1702(96)01289-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The influenza A virus RNA-dependent RNA polymerase catalyzes several reactions in transcription and replication of the genome RNA. The first step in viral mRNA synthesis is the recognition of the 5' end cap structure of host cell hnRNA and the cleavage of the RNA substrate between 10 and 14 nucleotides from the 5' end to generate capped primers for initiation of transcription of virus-specific mRNAs. This report describes the use of an in vitro UV crosslinking and protein renaturation assay to identify the polymerase subunits which interact with the 5' end cap structure of an artificial RNA substrate. Our results showed, for the first time, that purified polymerase subunit PB2 expressed by recombinant baculovirus in insect cells possessed cap-binding activity by itself after renaturation by Escherichia coli thioredoxin, whereas cleavage of the artificial capped substrate required the holoenzyme expressed in insect cells triply-infected with baculovirus containing all three polypeptide components, PB1, PB2, and PA. Purified polyclonal anti-PB2 IgG inhibited the binding activity; anti-PB1 and anti-PA IgGs did not.
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Affiliation(s)
- L Shi
- Department of Microbiology and Molecular Genetics, University of California, Irvine 92717-4025, USA
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Toyoda T, Kobayashi M, Nakada S, Ishihama A. Molecular dissection of influenza virus RNA polymerase: PB1 subunit alone is able to catalyze RNA synthesis. Virus Genes 1996; 12:155-63. [PMID: 8879132 DOI: 10.1007/bf00572954] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Influenza virus RNA polymerase with the subunit structure PB1-PB2-PA is involved in both transcription and replication of the RNA genome. Enzyme reconstitution experiments indicated that all three P proteins are required for RNA synthesis in vitro (Kobayashi, et al. Virus Res 22, 235-245, 1992). Nuclear extracts of HeLa cells infected with three kinds of the recombinant vaccinia virus, each carrying one of the three P protein cDNAs, exhibited the activity of complete replication, that is, vRNA-sense RNA-directed and cRNA-sense RNA-directed RNA synthesis in the absence of primers. The nuclear extract from cells singly infected with the virus carrying PB1 cDNA exhibited a significant level of model v-sense RNA-directed RNA synthesis activity. Thus we conclude that PB1 is the catalytic subunit of influenza virus RNA polymerase and that under certain conditions, PB1 alone is able to catalyze RNA synthesis in vitro.
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Affiliation(s)
- T Toyoda
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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19
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Ishihama A. A multi-functional enzyme with RNA polymerase and RNase activities: molecular anatomy of influenza virus RNA polymerase. Biochimie 1996; 78:1097-102. [PMID: 9150890 DOI: 10.1016/s0300-9084(97)86735-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Influenza virus-associated RNA polymerase is composed of one molecule each of three viral P proteins and carries the complete activity of capped RNA-primed vRNA-directed transcription. The RNA polymerase holoenzyme also carries capped RNA endonuclease to generate capped oligonucleotide primers for transcription and 3'-to-5' exonuclease to remove erroneously polymerized nucleotides at nascent RNA 3' termini prior to the addition of correct substrates. PB1 is the core subunit for not only RNA synthesis but also the assembly of PB2 and PA into the holoenzyme complex, while PB2 plays a key role in capped RNA cleavage. The transcriptase is converted into the RNA replicase with the full activity of replication, ie vRNA-directed cRNA synthesis and cRNA-directed vRNA synthesis, after interaction with an as yet unidentified host factor(s).
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Affiliation(s)
- A Ishihama
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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Cianci C, Tiley L, Krystal M. Differential activation of the influenza virus polymerase via template RNA binding. J Virol 1995; 69:3995-9. [PMID: 7769657 PMCID: PMC189131 DOI: 10.1128/jvi.69.7.3995-3999.1995] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Primary transcripts synthesized by the influenza virus polymerase contain the capped 5' ends of eukaryotic mRNAs. These sequences are derived from host mRNA and scavenged by the viral polymerase as a prerequisite to transcription. The first step in this reaction is the specific binding of the viral polymerase to the cap structure of the host RNA. The role that template RNA plays in this RNA binding reaction was examined in quantitative capped mRNA binding and endonuclease assays. Capped RNA binding was shown to be a template-dependent property of the influenza virus polymerase. Addition of only the 5' end of viral RNA stimulates capped mRNA binding by the viral polymerase, but endonuclease activity requires the addition of the 3' end. The addition of template RNA corresponding to the positive-sense complementary RNA replicative intermediate was also able to stimulate capped mRNA binding but was not able to efficiently activate the viral endonuclease. Thus, regulation of endonuclease activity by the influenza virus polymerase can be dependent on template RNA binding.
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Affiliation(s)
- C Cianci
- Department of Virology, Bristol-Myers Squibb Pharmaceutical Research Institute, Wallingford, Connecticut 06492, USA
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Bárcena J, Ochoa M, de la Luna S, Melero JA, Nieto A, Ortín J, Portela A. Monoclonal antibodies against influenza virus PB2 and NP polypeptides interfere with the initiation step of viral mRNA synthesis in vitro. J Virol 1994; 68:6900-9. [PMID: 7933070 PMCID: PMC237125 DOI: 10.1128/jvi.68.11.6900-6909.1994] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two panels of monoclonal antibodies (MAbs) specific for the influenza A virus PA and PB2 polypeptides have been obtained from mice immunized with denatured proteins produced in Escherichia coli. All MAbs (13 specific for the PA polypeptide and 8 specific for the PB2 protein) reacted to the corresponding influenza virus protein in Western blotting (immunoblotting), immunoprecipitation, and immunofluorescence assays. To gain information about the roles of the nucleoprotein (NP) and PB2 and PA proteins during viral mRNA synthesis, the 21 anti-P antibodies and 3 anti-NP antibodies (J. A. López, M. Guillen, A. Sánchez-Fauquier, and J. A. Melero, J. Virol. Methods 13:255-264, 1986) were purified and tested for their ability to inhibit the transcriptase activity associated with viral cores purified from virions. Four of the antibodies (one anti-PB2 and the three anti-NP MAbs) inhibited transcription by more than 50% compared with unrelated control antibodies. The inhibitory effect was not due to a nonspecific effect of the antibody preparations, because these MAbs did not inhibit transcription when tested on influenza B virus nucleocapsids, which are not recognized by the antibodies. To determine whether the antibodies were acting on an early transcription step, transcription reactions were carried out in the presence of globin mRNA (a mixture of alpha- and beta-globin chains) and only one labeled nucleoside triphosphate (either GTP or CTP). The results obtained showed that MAbs to the PB2 and NP polypeptides interfered with the initiation step of mRNA-primed transcription. The implications of these results regarding initiation of viral mRNA synthesis are discussed.
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Affiliation(s)
- J Bárcena
- Centro Nacional de Microbiología Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Madrid, Spain
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Toyoda T, Kobayashi M, Ishihama A. Replication in vitro of the influenza virus genome: selective dissociation of RNA replicase from virus-infected cell ribonucleoprotein complexes. Arch Virol 1994; 136:269-86. [PMID: 8031233 DOI: 10.1007/bf01321057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Replication of the influenza virus genome involves two discrete step reactions: vRNA-directed primer-independent (unprimed) synthesis of cRNA; and cRNA-directed unprimed synthesis of vRNA. Nuclear extracts from both MDCK and HeLa cells infected with influenza virus A/PR8/34 exhibited unprimed synthesis of both cRNA and vRNA strands (a parameter of RNA replication). Ribonucleoprotein (RNP) complexes with the replication activity were isolated from these nuclear extracts by glycerol gradient centrifugation in the presence of 0.1 M KCl. At 0.5 M KCl, however, these complexes were dissociated into stripped RNP and soluble protein fractions. The soluble fraction contained the activity of exogenous template-dependent unprimed RNA synthesis, indicating that the RNA replicase is dissociated from RNP upon exposure to high salt concentrations. On the other hand, the high salt-treated RNP catalyzed only primer-dependent RNA synthesis, but regained a low level activity of exogenous template-dependent unprimed RNA synthesis by adding nuclear extracts from uninfected cells, suggesting that host factor(s) is involved in the functional interconversion of influenza virus RNA polymerase.
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Affiliation(s)
- T Toyoda
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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Chung TD, Cianci C, Hagen M, Terry B, Matthews JT, Krystal M, Colonno RJ. Biochemical studies on capped RNA primers identify a class of oligonucleotide inhibitors of the influenza virus RNA polymerase. Proc Natl Acad Sci U S A 1994; 91:2372-6. [PMID: 7510890 PMCID: PMC43373 DOI: 10.1073/pnas.91.6.2372] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A synthetic 67-nt RNA substrate, containing a 32P-labeled cap-1 structure (m7G32pppGm) was specifically cleaved by the influenza virus RNA polymerase (EC 2.7.7.48) to yield a single capped 11-nt fragment capable of directly priming transcription. An analysis of systematic truncations of this RNA substrate demonstrated that an additional nucleotide beyond this cleavage site was required for cleavage. The minimal RNA chain length required for priming activity was found to be 9 nt, while in contrast an RNA chain length of at least 4 nt was required for efficient binding to the viral polymerase. On the basis of these chain length requirements we show that a pool of capped oligonucleotides too short to prime transcription, but long enough to bind with high affinity to the viral polymerase, are potent inhibitors of cap-dependent transcription in vitro.
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Affiliation(s)
- T D Chung
- Department of Virology, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000
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Hankins RW, Nagata K, Kato A, Ishihama A. Mechanism of influenza virus transcription inhibition by matrix (M1) protein. RESEARCH IN VIROLOGY 1990; 141:305-14. [PMID: 2392615 DOI: 10.1016/0923-2516(90)90002-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mechanism by which influenza virus matrix (M1) protein inhibits viral RNA (vRNA) transcription was investigated. Evidence has been generated that M1 protein inhibits the steps of vRNA transcription initiation and reinitiation more effectively than that of RNA chain elongation. The vRNA-associated nucleocapsid protein (NP) appears to be critical for this inhibition, implying that M1 protein binds to the ribonucleoprotein complex (RNP) through NP.
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Affiliation(s)
- R W Hankins
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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Abstract
Recent progress in molecular biological techniques revealed that genomes of animal viruses are complex in structure, for example, with respect to the chemical nature (DNA or RNA), strandedness (double or single), genetic sense (positive or negative), circularity (circle or linear), and so on. In agreement with this complexity in the genome structure, the modes of transcription and replication are various among virus families. The purpose of this article is to review and bring up to date the literature on viral RNA polymerases involved in transcription of animal DNA viruses and in both transcription and replication of RNA viruses. This review shows that the viral RNA polymerases are complex in both structure and function, being composed of multiple subunits and carrying multiple functions. The functions exposed seem to be controlled through structural interconversion.
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Affiliation(s)
- A Ishihama
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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Proofreading function associated with the RNA-dependent RNA polymerase from influenza virus. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67540-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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RNA polymerase of influenza virus. Dinucleotide-primed initiation of transcription at specific positions on viral RNA. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)38482-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Kato A, Mizumoto K, Ishihama A. Purification and enzymatic properties of an RNA polymerase-RNA complex from influenza virus. Virus Res 1985; 3:115-27. [PMID: 3840635 DOI: 10.1016/0168-1702(85)90002-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An RNA polymerase-viral RNA complex was purified from influenza A/PR/8 virions by combination of cesium trifluoroacetate centrifugation and phosphocellulose column chromatography. Surface proteins were removed from the detergent-treated virions by the centrifugation. Starting from the M protein-free ribonucleoprotein (RNP) fraction, an RNA polymerase-RNA complex lacking NP protein was isolated by repeated chromatography on phosphocellulose columns. The isolated RNA polymerase-RNA complex, which is composed of PB1, PB2, PA and vRNA, cleaved capped poly(A) endonucleolytically at 10-12 nucleotides from the 5' end and incorporated GMP into the 3' end of the resulting capped fragments. In the presence of all four ribonucleotide triphosphate substrates, the cleaved fragments were elongated to polynucleotides in the absence of exogenous vRNA. The RNA synthesis was primed not only by capped polynucleotides but also dinucleotide ApG. These results indicate that the purified RNA polymerase-RNA complex is as active in viral mRNAs synthesis as native RNP and that NP protein is not required for the catalytic function.
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