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Gorzelnik KV, Zhang J. Cryo-EM reveals infection steps of single-stranded RNA bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:79-86. [PMID: 32841651 DOI: 10.1016/j.pbiomolbio.2020.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/23/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Single-stranded RNA bacteriophages (ssRNA phages) are small spherical RNA viruses that infect bacteria with retractile pili. The single positive-sense genomic RNA of ssRNA phages, which is protected by a capsid shell, is delivered into the host via the retraction of the host pili. Structures involved in ssRNA phage infection cycle are essential for understanding the underlying mechanisms that can be used to engineer them for therapeutic applications. This review summarizes the recent breakthroughs in high-resolution structural studies of two ssRNA phages, MS2 and Qβ, and their interaction with the host, E. coli, by cryo-electron microscopy (cryo-EM). These studies revealed new cryo-EM structures, which provide insights into how MS2 and Qβ package the RNA, lyse E. coli, and adsorb to the receptor F-pili, responsible for conjugation. Methodologies described here can be expanded to study other ssRNA phages that target pathogenic bacteria.
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Affiliation(s)
- Karl Victor Gorzelnik
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA.
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2
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Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP, Hill C. RNA Phage Biology in a Metagenomic Era. Viruses 2018; 10:E386. [PMID: 30037084 PMCID: PMC6071253 DOI: 10.3390/v10070386] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022] Open
Abstract
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies.
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Affiliation(s)
- Julie Callanan
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
| | - Stephen R Stockdale
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland.
| | - Andrey Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland.
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
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3
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Grumet R, Sanford JC, Johnston SA. Pathogen-derived resistance to viral infection using a negative regulatory molecule. Virology 1987; 161:561-9. [PMID: 3318096 DOI: 10.1016/0042-6822(87)90152-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The principle of pathogen-derived resistance (the use of pathogen-derived genes to interfere with the pathogenic process and thereby confer disease resistance to the host) has been put forward as a broadly applicable conceptual tool for use in the genetic engineering of resistance to pathogens and parasites. It was previously predicted that four mechanisms of pathogen-derived resistance could be established using the bacteriophage QB and its host, Escherichia coli, as a model system. This paper demonstrates and helps ellucidate the first of these mechanisms by using a viral regulatory protein, the QB coat protein, to block viral replication. The QB coat protein gene was transferred to susceptible E. coli. Expression of this gene had no obvious detrimental effect on the host. Low-level, constitutive expression of the coat protein conditions very high levels of resistance to QB infection. The resulting resistance is not associated with RNA interference or loss of pili as attachment sites, and does not appear to be associated with premature encapsidation. This low-level expression of the QB coat protein also produces an intermediate level of resistance to the closely related phage SP, but fails to protect against the unrelated phage f2. Thus the resistance does not result from a generalized antiviral host response induced by the presence of the coat protein. We conclude that the QB coat protein blocks viral infection, as was predicted, due to its action as a negative regulatory molecule. The use of negative regulatory molecules may provide an effective mechanism for use in the genetic engineering of pathogen-derived resistance.
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Affiliation(s)
- R Grumet
- Botany Department, Duke University, Durham, North Carolina 27706
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4
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Berkhout B, van Duin J. Mechanism of translational coupling between coat protein and replicase genes of RNA bacteriophage MS2. Nucleic Acids Res 1985; 13:6955-67. [PMID: 3840590 PMCID: PMC322015 DOI: 10.1093/nar/13.19.6955] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have analyzed the molecular mechanism that makes translation of the MS2 replicase cistron dependent on the translation of the upstream coat cistron. Deletion mapping on cloned cDNA of the phage shows that the ribosomal binding site of the replicase cistron is masked by a long distance basepairing to an internal coat cistron region. Removal of the internal coat cistron region leads to uncoupled replicase synthesis. Our results confirm the model as originally proposed by Min Jou et al. (1). Activation of the replicase start is sensitive to the frequency of upstream translation, but never reaches the level of uncoupled replicase synthesis.
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Abstract
We have isolated a conditional lethal mutant of bacteriophage 12 which makes plaques only on E. coli strains carrying a UGA suppressor. It grows normally in nonsuppressing hosts but does not lyse such strains. The mutation complements with amber mutations in each of the three known phage cistrons. These observations lead us to postulate the existence of a fourth gene in the RNA phage.
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6
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Goldberger RF, Deeley RG, Mullinix KP. Regulation of gene expression in prokaryotic organisms. ADVANCES IN GENETICS 1976; 18:1-67. [PMID: 181963 DOI: 10.1016/s0065-2660(08)60436-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Atkins JF, Gesteland RF. The synthetase gene of the RNA phages R17, MS2 and f2 has a single UAG terminator codon. MOLECULAR & GENERAL GENETICS : MGG 1975; 139:19-31. [PMID: 1177864 DOI: 10.1007/bf00267992] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Translation of the RNA from the wild-type bacteriophages R17, MS2, and f2 in bacterial cell-free extracts containing an amber suppressor yields 30-40% of the synthetase with an approximate molecular weight of 63 500, slightly larger than the major synthetase product (63 000 daltons). The occurrence of the 63 500 dalton in vitro product is dependent on the presence of an amber suppressor, and we predict that it is due to read-through of a UAG termination codon at the end of the synthetase gene. Previous results of Capecchi and Klein (Nature, 226, 1029-1033, 1070) showed that antibodies to both release factors RF1 and RF2 are required to block release of synthetase, suggesting that synthetase is released at a UAA codon. If the interpretations of both experiments are correct, the termination and release may not be synonomous and may be spatially separated. In addition there is the unexplained fact that 7% of the synthetase made in vitro in both su+ and su- extracts with either R17, MS2 or f2 as template has an apparent molecular weight of 66 000.
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9
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Ochoa S, Mazumder R. 1. Polypeptide Chain Initiation. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s1874-6047(08)60133-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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10
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Thach SS, Thach RE. Mechanism of viral replication. I. Structure of replication complexes of R17 bacteriophage. J Mol Biol 1973; 81:367-80. [PMID: 4588279 DOI: 10.1016/0022-2836(73)90147-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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11
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Chroboczek J, Pietrzak M, Zagórski W. Specificity of formation of complexes between coat protein and bacteriophage f2 RNA. J Virol 1973; 12:230-40. [PMID: 4201187 PMCID: PMC356617 DOI: 10.1128/jvi.12.2.230-240.1973] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The specificity of formation of phage f2 RNA-protein complexes was studied. Complex I contains up to 8 mol of coat protein per 1 mol of RNA. Its formation proceeds equally well in medium (i) without magnesium ions, (ii) containing magnesium ions, (iii) containing 4 mM EDTA, and (iv) at temperatures from 0 to 45 C. Complex II contains up to 200 mol of coat protein per 1 mol of RNA. Its formation is inhibited by the presence of magnesium ions in medium. Formaldehyde- or methoxyamine-treated f2 RNA in which only exposed bases were modified showed a normal pattern of complex II formation, whereas formation of complex I was inhibited or abolished. We conclude that complex I formation involves the interaction between coat protein and specific region of exposed bases in RNA. A possible site of attachment of coat protein is discussed.
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12
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Weissmann C, Billeter MA, Weber H, Goodman HM, Hindley J. Structure and function of phage RNA: a summary of current knowledge. BASIC LIFE SCIENCES 1973; 1:13-28. [PMID: 4589675 DOI: 10.1007/978-1-4684-0877-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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13
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Hindley J. Structure and strategy in phage RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1973; 26:269-321. [PMID: 4575322 DOI: 10.1016/0079-6107(73)90021-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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14
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Bernardi A, Spahr PF. Nucleotide sequence at the binding site for coat protein on RNA of bacteriophage R17. Proc Natl Acad Sci U S A 1972; 69:3033-7. [PMID: 4507620 PMCID: PMC389701 DOI: 10.1073/pnas.69.10.3033] [Citation(s) in RCA: 100] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The binding of a few molecules [1-6] of RNA bacteriophage coat protein to 1 molecule of RNA represses in vitro translation of the RNA synthetase cistron. Digestion of the complex, R17 coat protein-R17 RNA, by T1 RNase yields an RNA fragment bound to the coat protein. The nucleotide sequence of this fragment (59 residues) reveals that it contains the punctuation signal between the coat protein and RNA synthetase cistrons, suggesting that this is the site on the RNA where the coat protein acts as a translational repressor.
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15
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16
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Abstract
A chromatographic procedure is described which can discriminate among single-stranded ribonucleic acid (RNA) molecules in solution on the basis of the extent of their secondary structure. The assay is effected through chromatography at different temperatures with columns of cellulose CF-11. When Sindbis virus RNA is chromatographed in this system, the ratio of the amounts of RNA eluting in the single-stranded peak to those eluting in the double-stranded peak increases at higher temperatures, presumably a measure of the relative amounts of Sindbis virus RNA secondary structure at different temperatures. With this assay, Sindbis virus RNA, phage f2 RNA, and polyuridylate have been found to have different amounts of secondary structure.
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17
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Kozak M, Nathans D. Translation of the genome of a ribonucleic acid bacteriophage. BACTERIOLOGICAL REVIEWS 1972; 36:109-34. [PMID: 4555183 PMCID: PMC378432 DOI: 10.1128/br.36.1.109-134.1972] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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18
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Kamen R. A new method for the purification of Q RNA-dependent RNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 262:88-100. [PMID: 4552904 DOI: 10.1016/0005-2787(72)90221-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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Skogerson L, Roufa D, Leder P. Characterization of the initial peptide of Q-beta RNA polymerase and control of its synthesis. Proc Natl Acad Sci U S A 1971; 68:276-9. [PMID: 5277068 PMCID: PMC388916 DOI: 10.1073/pnas.68.2.276] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bacteriophage Qbeta RNA directs the cell-free synthesis of two fMet-containing dipeptides prior to the first round of ribosomal translocation. One of these, fMet-Ala, corresponds to the initial segment of the Qbeta coat protein. In the present work we take advantage of the fact that translation of the Qbeta RNA polymerase cistron is repressed by its coat protein to correlate the other peptide, fMet-Ser, with the Qbeta RNA polymerase gene. Our experiments show that repression affects translation of the first two codons of the polymerase cistron, thereby isolating the effect of Qbeta coat repressor. Further studies, using single rounds of translocation of the Qbeta mRNA and codon-specific tRNAs, allow us to predict the first three amino acids of the Qbeta RNA polymerase protein, fMet-Ser-Lys, and to suggest that the initiation region of the Qbeta RNA polymerase cistron has the sequence ...AUG.UC[unk].AA[unk]...
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20
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Ward R, Konings RN, Hofschneider PH. Coat protein repression of bacteriophage M12 RNA directed polysome formation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 17:106-15. [PMID: 5486574 DOI: 10.1111/j.1432-1033.1970.tb01142.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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21
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Robertson HD, Lodish HF. Messenger characteristics of nascent bacteriophage RNA. Proc Natl Acad Sci U S A 1970; 67:710-6. [PMID: 5289017 PMCID: PMC283263 DOI: 10.1073/pnas.67.2.710] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The proteins initiated in vitro by nascent bacteriophage f2 RNA strands attached to isolated replicating structures have been analyzed. The observations confirm that coat protein is the major product initiated and completed. Nascent strands direct the initiation of viral maturation protein in amounts similar to the maximum levels observed in vivo; this synthesis is independent of translation of the coat protein gene. However, only a fraction of these maturation protein molecules initiated in vitro is completed. Nascent RNA molecules also direct the initiation of appreciable amounts of viral RNA polymerase protein, very little of which is completed. Certain constraints on the in vitro translation of the polymerase gene from single-stranded RNA appear to be relaxed in the nascent strands, as indicated by the reduced effect of a polar amber mutation in the coat cistron upon polymerase protein initiation from nascent RNA.
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22
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23
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Knolle P, Hohn T. R17 coat protein interaction with multi-stranded R17 RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 16:19-24. [PMID: 5456128 DOI: 10.1111/j.1432-1033.1970.tb01048.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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Atabekov JG, Novikov VK, Vishnichenko VK, Kaftanova AS. Some properties of hybrid viruses reassembled in vitro. Virology 1970; 41:519-32. [PMID: 4193211 DOI: 10.1016/0042-6822(70)90172-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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25
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Zebovitz E, Brown A. Altered viral ribonucleic acid synthesis by a temperature-sensitive mutant of Eastern equine encephalitis virus. J Mol Biol 1970; 50:185-98. [PMID: 5466757 DOI: 10.1016/0022-2836(70)90114-2] [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: 01/15/2023]
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26
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Sugiyama T, Nakada D. Translational control of bacteriophage MS2 RNA cistrons by MS2 coat protein: affinity and specificity of the interaction of MS2 coat protein with MS2 RNA. J Mol Biol 1970; 48:349-55. [PMID: 5448594 DOI: 10.1016/0022-2836(70)90166-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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27
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28
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Hung PP, Ling CM, Overby LR. Self-assembly of Q-beta and MS2 phage particles: possible function of initiation complexes. Science 1969; 166:1638-40. [PMID: 5360586 DOI: 10.1126/science.166.3913.1638] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Four kinds of particles were reconstituted with RNA and protein from the genetically unrelated bacteriophages Qbeta and MS2, namely, two homologous and two heterologous, with respect to RNA and protein. However, once Qbeta RNA (or MS2 RNA) reacted with a few molecules of either Qbeta or MS2 protein to form a nucleoprotein complex (initiation complex), it formed a phagelike particle only with subsequent addition of the same protein.
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29
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32
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Sugiyama T, Stone HO. Protein synthesis directed by an amber coat-protein mutant of the RNA phage MS2. J Mol Biol 1969; 42:97-115. [PMID: 5808552 DOI: 10.1016/0022-2836(69)90489-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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33
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The Lack of Messenger Activity of Ribonucleic Acid Complementary to the Viral Ribonucleic Acid of Bacteriophage R17. J Biol Chem 1969. [DOI: 10.1016/s0021-9258(18)94414-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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34
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35
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Nathans D, Oeschger MP, Polmar SK, Eggen K. Regulation of protein synthesis directed by coliphage MS2 RNA. I. Phage protein and RNA synthesis in cells infected with suppressible mutants. J Mol Biol 1969; 39:279-92. [PMID: 4188558 DOI: 10.1016/0022-2836(69)90317-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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36
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Eggen K, Nathans D. Regulation of protein synthesis directed by coliphage MS2 RNA. II. In vitro repression by phage coat protein. J Mol Biol 1969; 39:293-305. [PMID: 4903176 DOI: 10.1016/0022-2836(69)90318-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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37
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38
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39
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Hotham-Iglewski B, Phillips LA, Franklin RM. Viral RNA transcription--translation complex in Escherichia coli infected with bacteriophage R17. Nature 1968; 219:700-3. [PMID: 4875343 DOI: 10.1038/219700a0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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