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Geiduschek EP, Kassavetis GA. Transcription of the T4 late genes. Virol J 2010; 7:288. [PMID: 21029432 PMCID: PMC2988020 DOI: 10.1186/1743-422x-7-288] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/28/2010] [Indexed: 11/16/2022] Open
Abstract
This article reviews the current state of understanding of the regulated transcription of the bacteriophage T4 late genes, with a focus on the underlying biochemical mechanisms, which turn out to be unique to the T4-related family of phages or significantly different from other bacterial systems. The activator of T4 late transcription is the gene 45 protein (gp45), the sliding clamp of the T4 replisome. Gp45 becomes topologically linked to DNA through the action of its clamp-loader, but it is not site-specifically DNA-bound, as other transcriptional activators are. Gp45 facilitates RNA polymerase recruitment to late promoters by interacting with two phage-encoded polymerase subunits: gp33, the co-activator of T4 late transcription; and gp55, the T4 late promoter recognition protein. The emphasis of this account is on the sites and mechanisms of actions of these three proteins, and on their roles in the formation of transcription-ready open T4 late promoter complexes.
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Affiliation(s)
- E Peter Geiduschek
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0634, USA.
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Affiliation(s)
- E Peter Geiduschek
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, California 92093, USA.
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Activation of MDA5 requires higher-order RNA structures generated during virus infection. J Virol 2009; 83:10761-9. [PMID: 19656871 DOI: 10.1128/jvi.00770-09] [Citation(s) in RCA: 346] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Recognition of virus presence via RIG-I (retinoic acid inducible gene I) and/or MDA5 (melanoma differentiation-associated protein 5) initiates a signaling cascade that culminates in transcription of innate response genes such as those encoding the alpha/beta interferon (IFN-alpha/beta) cytokines. It is generally assumed that MDA5 is activated by long molecules of double-stranded RNA (dsRNA) produced by annealing of complementary RNAs generated during viral infection. Here, we used an antibody to dsRNA to show that the presence of immunoreactivity in virus-infected cells does indeed correlate with the ability of RNA extracted from these cells to activate MDA5. Furthermore, RNA from cells infected with encephalomyocarditis virus or with vaccinia virus and precipitated with the anti-dsRNA antibody can bind to MDA5 and induce MDA5-dependent IFN-alpha/beta production upon transfection into indicator cells. However, a prominent band of dsRNA apparent in cells infected with either virus does not stimulate IFN-alpha/beta production. Instead, stimulatory activity resides in higher-order structured RNA that contains single-stranded RNA and dsRNA. These results suggest that MDA5 activation requires an RNA web rather than simply long molecules of dsRNA.
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Kolesky S, Ouhammouch M, Brody EN, Geiduschek EP. Sigma competition: the contest between bacteriophage T4 middle and late transcription. J Mol Biol 1999; 291:267-81. [PMID: 10438620 DOI: 10.1006/jmbi.1999.2953] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In bacterial transcription, diverse sigma-family promoter recognition proteins compete for a common RNA polymerase core. Bacteriophage T4 infection ultimately reduces this competition to a duel between activated viral middle and enhanced late transcription, involving two sigma proteins, two phage-encoded activator proteins and two phage-specific co-activators. This competition has been analyzed in vitro, and the relative abundances in T4-infected Escherichia coli of the participating proteins have been measured. Activated late transcription holds an advantage over activated middle transcription, especially at higher ionic strength. This advantage is further compounded by ADP-ribosylation of the RNA polymerase alpha subunits, and by the phage-specific, RNA polymerase core-bound RpbA subunit. The largest contribution to the middle-late competition is made by gp55, the late sigma factor, but not enough of gp55 is produced during T4 infection to shut off middle transcription by direct competition with sigma(70). AsiA, the originally identified anti-sigma protein is not a major determinant of middle-late competition.
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Affiliation(s)
- S Kolesky
- Department of Biology and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0634, USA.
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Geiduschek EP. Two prokaryotic transcriptional enhancer systems. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1992; 43:109-33. [PMID: 1410444 DOI: 10.1016/s0079-6603(08)61046-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- E P Geiduschek
- Department of Biology, University of California, San Diego, La Jolla 92093
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Westin G, Djurhuus R, Skreslett U. In vitro transcription of phage T4 late genes on purified DNA by partially purified RNA polymerase from T4-infected Escherichia coli b cells. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 699:28-39. [PMID: 6756478 DOI: 10.1016/0167-4781(82)90168-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNA polymerase was purified from 'late' phage T4-infected Escherichia coli B cells by DNA-cellulose affinity chromatography and high salt agarose filtration. The DNA-cellulose-purified RNA polymerase preparation contained T4-coded DNA endonuclease activity and several proteins, some with sizes comparable with the known T4 maturation factors, essential for late RNA synthesis. Some of these proteins, and the DNA endonuclease utilizing native, parental T4 DNA and supercoiled phi X 174 DNA as substrates, were partially separated from the RNA polymerase as a complex during agarose filtration. In vitro RNA was made by the DNA-cellulose-purified RNA polymerase using native, parental T4 DNA as template. About 26% of the in vitro RNA was transcribed from the DNA r-strand; 75% from the same r-strand region as in vivo late after infection. Both the abundancy and specificity of the in vitro r-strand transcription were markedly reduced after agarose filtration of the enzyme. Addition of the proteins separated from the RNA polymerase during agarose filtration caused a restoration of in vitro r-strand transcription abundance, but not its specificity. These results show that partially purified RNA polymerase from T4-infected E. coli B cells was able to transcribe late T4 genes in vitro with some abundancy and specificity on purified, parental T4 DNA, but further purification of the enzyme caused an irreversible reduction of this ability.
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Bacteriophage T4 infection mechanisms. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/b978-0-444-80400-6.50013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Sogo JM, Inciarte MR, Corral J, Viñuela E, Salas M. RNA polymerase binding sites and transcription map of the DNA of Bacillus subtilis phage phi29. J Mol Biol 1979; 127:411-36. [PMID: 107317 DOI: 10.1016/0022-2836(79)90230-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Frederick RJ, Snyder L. [Regulation of anti-late RNA synthesis in bacteriophage T4: a delayed early control]. J Mol Biol 1977; 114:461-76. [PMID: 335074 DOI: 10.1016/0022-2836(77)90172-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Mittelstaedt R, Oppermann H, Koch G. Poliovirus-induced infectious double-stranded RNA: Effect of RNA-degrading enzymes. Arch Virol 1975; 47:381-92. [PMID: 166628 DOI: 10.1007/bf01347980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The infectivity of replicative form RNA (RF-RNA) isolated from poliovirus-infected HeLa cells is completely resistant to the action of T-1 RNase but decreases after exposure to RNase A in the presence of 0.3 M NaCl. Under these conditions neither enzyme produces single-stranded nicks in RF-RNA. Three endonuclease-free exonuleases (RNase II, polynucleotide phosphorylase and spleen phosphodiesterase) rapidly destroy the infectivity of single-stranded RNA, but do not alter the infectivity of RF-RNA. It is concluded that RF-RNA does not contain single-stranded ends essential for infectivity. Indirect evidence suggests that all or most of the poly A region at the 3' end of the plus strand of infectious RF-RNA is base-paired to a poly U region at the 5 end of the minus strand.
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Desai LS, Foley GE. Human leukemic cells: properties of an RNA synthesized in the presence of actinomycin D. Exp Cell Res 1974; 86:143-51. [PMID: 4524709 DOI: 10.1016/0014-4827(74)90659-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Yoshida M. Lack of discrimination between early and late T4 mRNA by host initiation factors. NATURE: NEW BIOLOGY 1972; 239:178-80. [PMID: 4573695 DOI: 10.1038/newbio239178a0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Lucas JJ, Ginsberg HS. Identification of double-stranded virus-specific ribonucleic acid in KB cells infected with type 2 adenovirus. Biochem Biophys Res Commun 1972; 49:39-44. [PMID: 5077859 DOI: 10.1016/0006-291x(72)90006-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Black DR, Eckstein F, Hobbs JB, Sternbach H, Merigan TC. The antiviral activity of certain thiophosphate and 2'-chloro substituted polynucleotide homopolymer duplexes. Virology 1972; 48:537-45. [PMID: 4337034 DOI: 10.1016/0042-6822(72)90064-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Chao J, Chao L, Speyer J. The inhibition of f2 RNA directed E. coli protein synthesis by poly rI-rC in vitro. Biochem Biophys Res Commun 1971; 45:1096-102. [PMID: 4940604 DOI: 10.1016/0006-291x(71)90450-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Guha A, Szybalski W, Salser W, Geiduschek EP, Pulitzer JF, Bolle A. Controls and polarity of transcription during bacteriophage T4 development. J Mol Biol 1971; 59:329-49. [PMID: 5566419 DOI: 10.1016/0022-2836(71)90054-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Robertson HD. Enzymatic synthesis of bacteriophage fl DNA: RNA hybrid and double stranded RNA. NATURE: NEW BIOLOGY 1971; 229:169-72. [PMID: 5280103 DOI: 10.1038/newbio229169a0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Colby C. The induction of interferon by natural and synthetic polynucleotides.hs. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1971; 11:1-32. [PMID: 5004307 DOI: 10.1016/s0079-6603(08)60324-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Colby C, Jurale C, Kates JR. Mechanism of synthesis of vaccinia virus double-stranded ribonucleic acid in vivo and in vitro. J Virol 1971; 7:71-6. [PMID: 5543434 PMCID: PMC356079 DOI: 10.1128/jvi.7.1.71-76.1971] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The synthesis of vaccinia virus double-stranded ribonucleic acid (RNA) in infected HeLa cells was sensitive to actinomycin D, suggesting that a deoxyribonucleic acid dependent reaction is involved. Some double-stranded RNA was made in the presence of cytosine arabinoside in infected cells. Double-stranded and complementary RNA were synthesized in vitro by using vaccinia cores. These two observations indicate that some of the double-stranded RNA is read from "early" genes. The double-stranded RNA synthesized in vitro had the same properties as that made in vivo. At least 70% of the double-stranded RNA made in vivo was in ribonuclease-resistant form prior to sodium dodecyl sulfate-phenol extraction. In addition, there was a complementary RNA in infected cells which could be converted to double-stranded RNA by annealing.
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