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Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum-A Novel Lineage of Lactobacillus Phages Comprising Five New Members. Viruses 2019; 11:v11070611. [PMID: 31277436 PMCID: PMC6669764 DOI: 10.3390/v11070611] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/07/2019] [Accepted: 07/02/2019] [Indexed: 01/01/2023] Open
Abstract
Lactobacillus plantarum is a bacterium with probiotic properties and promising applications in the food industry and agriculture. So far, bacteriophages of this bacterium have been moderately addressed. We examined the diversity of five new L. plantarum phages via whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. These analyses revealed a high degree of similarity among the five phages, which extended to the vast majority of predicted virion-associated proteins. Based on these, we selected one of the phages as a representative and performed transmission electron microscopy and structural protein sequencing tests. Overall, the results suggested that the five phages belong to the family Myoviridae, they have a long genome of 137,973-141,344 bp, a G/C content of 36.3-36.6% that is quite distinct from their host's, and surprisingly, 7 to 15 tRNAs. Only an average 41/174 of their predicted genes were assigned a function. The comparative analyses unraveled considerable genetic diversity for the five L. plantarum phages in this study. Hence, the new genus "Semelevirus" was proposed, comprising exclusively of the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp. The five new Lactobacillus phages have potential value for the development of more robust starters through, for example, the selection of mutants insensitive to phage infections. The five phages could also form part of phage cocktails, which producers would apply in different stages of L. plantarum fermentations in order to create a range of organoleptic outputs.
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Genome sequence of Ostreococcus tauri virus OtV-2 throws light on the role of picoeukaryote niche separation in the ocean. J Virol 2011; 85:4520-9. [PMID: 21289127 DOI: 10.1128/jvi.02131-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ostreococcus tauri, a unicellular marine green alga, is the smallest known free-living eukaryote and is ubiquitous in the surface oceans. The ecological success of this organism has been attributed to distinct low- and high-light-adapted ecotypes existing in different niches at a range of depths in the ocean. Viruses have already been characterized that infect the high-light-adapted strains. Ostreococcus tauri virus (OtV) isolate OtV-2 is a large double-stranded DNA algal virus that infects a low-light-adapted strain of O. tauri and was assigned to the algal virus family Phycodnaviridae, genus Prasinovirus. Our working hypothesis for this study was that different viruses infecting high- versus low-light-adapted O. tauri strains would provide clues to propagation strategies that would give them selective advantages within their particular light niche. Sequence analysis of the 184,409-bp linear OtV-2 genome revealed a range of core functional genes exclusive to this low-light genotype and included a variety of unexpected genes, such as those encoding an RNA polymerase sigma factor, at least four DNA methyltransferases, a cytochrome b(5), and a high-affinity phosphate transporter. It is clear that OtV-2 has acquired a range of potentially functional genes from its host, other eukaryotes, and even bacteria over evolutionary time. Such piecemeal accretion of genes is a trademark of large double-stranded DNA viruses that has allowed them to adapt their propagation strategies to keep up with host niche separation in the sunlit layers of the oceanic environment.
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Wu JR, Yeh YC. New Late Gene, dar, Involved in DNA Replication of Bacteriophage T4 I. Isolation, Characterization, and Genetic Location. J Virol 2010; 15:1096-106. [PMID: 16789147 PMCID: PMC354564 DOI: 10.1128/jvi.15.5.1096-1106.1975] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Suppressors of gene 59-defective mutants were isolated by screening spontaneous, temperature-sensitive (ts) revertants of the amber mutant, amC5, in gene 59. Six ts revertants were isolated. No gene 59-defective ts recombinant was obtained by crossing each ts revertant with the wild type, T4D. However, suppressors of gene 59-defective mutants were obtained from two of these ts revertants. These suppressor mutants are referred to as dar (DNA arrested restoration). dar mutants specifically restored the abnormalities, both in DNA synthesis and burst size, caused by gene 59-defective mutants to normal levels. It is unlikely that dar mutants are nonsense suppressors since theý failed to suppress amber mutations in 11 other genes investigated. The genetic expression of dar is controlled by gene 55; therefore, dar is a late gene. The genetic location of dar has been mapped between genes 24 and 25, a region contiguous to late genes. dar appears to be another nonessential gene of T4 since burst sizes of dar were almost identical to those of the wild type. Mutations in dar did not affect genetic recombination and repair of UV-damaged DNA, but caused a sensitivity to hydroxyurea in progeny formation. The effect of the dar mutation on host DNA degradation cannot account for its hydroxyurea sensitivity. dar mutant alleles were recessive to the wild-type allele as judged by restoration of arrested DNA synthesis. The possible mechanisms for the suppression of defects in gene 59 are discussed.
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Affiliation(s)
- J R Wu
- Department of Biochemistry, School of Medicine, University of Arkansas, Little Rock, Arkansas 72201
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Losick R, Pero J. Bacillus subtilis RNA polymerase and its modification in sporulating and phage-infected bacteria. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 44:165-85. [PMID: 58549 DOI: 10.1002/9780470122891.ch5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillus subtilis RNA polymerase holoenzyme consists of the subunits beta', beta, sigma, alpha, delta, and omega. In sporulating bacteria and in bacteria infected with phages SP01 and SP82, this enzyme undergoes changes in subunit composition and transcriptional specificity that could play a regulatory role in gene transcription. Sporulating bacteria may contain a specific component that inhibits the activity of the sigma subunit of polymerase probably by interfering with the binding of sigma-polypeptide to core enzyme. The hypothetical inhibitor may be metabolically unstable, since its activity is rapidly depleted from sporulating cells in the presence of chloramphenicol. Inhibition of sigma-polypeptide activity may restrict the transcription of phage DNA an infected sporulating cells. Although lacking the sigma-subunit, RNA polymerase purified from sporulating cells contains sporulation-specific subunits of 85,000 and 27,000 daltons. In SP01-infected bacteria, the sigma-subunit is replaced by phage-induced subunits. Purified enzyme containing the protein product of SP01 regulatory gene 28 directs the transcription of phage middle genes in vitro, while enzyme containing phage-induced polypeptides V and VI preferentially copies late genes. Accurate transcription of middle and late genes in vitro requires the host delta-subunit of polymerase (or high ionic strength) but not sigma-subunit. Phage PBS2 induces an entirely new multisubunit RNA polymerase that specifically transcribes PBS2 DNA in vitro. This enzyme is synthesized de novo after infection and does not arise by modification of the B. subtilis holoenzyme.
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Anthony LC, Burgess RR. Conformational flexibility in sigma70 region 2 during transcription initiation. J Biol Chem 2002; 277:46433-41. [PMID: 12359719 DOI: 10.1074/jbc.m208205200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prokaryotic RNA polymerase holoenzyme is composed of core subunits (alpha(2)betabeta'omega) plus a sigma factor that confers promoter specificity allowing for regulation of gene expression. Holoenzyme is known to undergo several conformational changes during the multiple steps of transcription initiation. However, the effects of these changes on the functions of specific regions have not been well characterized. In this work, we addressed the role of possible conformational change in region 2 of Escherichia coli sigma(70) by engineering disulfide bonds that "lock" region 2.1 with region 2.2 and region 2.2 with region 2.3. When these mutant holoenzymes were characterized for gross defects in multiple-round transcription, we found that insertion of either disulfide bond did not result in a fundamental block, indicating that the disulfide-containing holoenzymes are active. However, both disulfide-containing holoenzymes exhibited defects in formation and stability of the open complex. Our results suggest that conformational flexibility within sigma(70) region 2 facilitates open complex formation and transcription initiation.
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Affiliation(s)
- Larry C Anthony
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin 53706
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Bowser CA, Hanna MM. Sigma subunit of Escherichia coli RNA polymerase loses contacts with the 3' end of the nascent RNA after synthesis of a tetranucleotide. J Mol Biol 1991; 220:227-39. [PMID: 1713273 DOI: 10.1016/0022-2836(91)90009-u] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have used photocrosslinking to analyze the contacts between the 3' end of the RNA and Escherichia coli RNA polymerase during the early steps of RNA synthesis using the nucleotide analog 8-azido-ATP (8-N3-ATP). The crosslinking group on 8-N3-ATP contacts the beta, beta' and sigma subunits when the analog is bound to the holoenzyme. We show here that 8-N3-ATP is a substrate for E. coli RNA polymerase and acts as an RNA chain terminator when incorporated into the 3' end of nascent RNA. 8-N3-AMP was incorporated uniquely at the 3' end of tri-, tetra- and pentanucleotides synthesized from a poly[d(A-T)] template and at the 3' end of pentanucleotides from two promoters (lambda PR' and E. coli rrnB P1). The oligonucleotides were covalently attached to the RNA polymerase by irradiation of transcription complexes with ultraviolet light. All RNAs labeled the beta and beta' subunits, but sigma was contacted only by the trinucleotide and tetranucleotide on poly[d(A-T)]. Sigma is still present in transcription complexes containing the pentanucleotide on poly[d(A-T)], despite the lack of labeling. Neither pentanucleotide from the authentic promoters contacted sigma. We conclude that as holoenzyme moves downstream, either two separate conformational changes occur, after synthesis of the trinucleotide and tetranucleotide, which result in movement of sigma away from the nucleotide binding site or, alternatively, sigma remains fixed relative to the DNA while the domain on core polymerase forming the nucleotide binding site moves downstream.
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Affiliation(s)
- C A Bowser
- Department of Biological Chemistry, University of California, Irvine 92717
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A Backward Glance. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/b978-0-444-80702-1.50011-x] [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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10
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Costanzo M, Brzustowicz L, Hannett N, Pero J. Bacteriophage SPO1 genes 33 and 34. Location and primary structure of genes encoding regulatory subunits of Bacillus subtilis RNA polymerase. J Mol Biol 1984; 180:533-47. [PMID: 6441846 DOI: 10.1016/0022-2836(84)90026-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bacteriophage SPO1 gene 33 and 34 products are required for SPO1 late gene transcription. Both proteins bind to the core RNA polymerase of the Bacillus subtilis host to direct the recognition of SPO1 late gene promoters, whose sequences differ from those of SPO1 early and middle gene promoters. We have located and cloned the genes for these two regulatory proteins, and have engineered their expression in Escherichia coli by placing them under the control of the bacteriophage lambda PL promoter. Nucleotide sequence analysis indicated that genes 33 and 34 overlap by 4 base-pairs and encode highly charged, slightly basic proteins of molecular weight 11,902 and 23,677, respectively.
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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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13
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Mattson T, Van Houwe G, Epstein RH. Isolation and characterization of conditional lethal mutations in the mot gene of bacteriophage T4. J Mol Biol 1978; 126:551-70. [PMID: 745239 DOI: 10.1016/0022-2836(78)90058-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Willis DB, Goorha R, Miles M, Granoff A. Macromolecular synthesis in cells infected by frog virus 3. VII. Transcriptional and post-transcriptional regulation of virus gene expression. J Virol 1977; 24:326-42. [PMID: 561861 PMCID: PMC515934 DOI: 10.1128/jvi.24.1.326-342.1977] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We have used improved techniques for separating individual species of RNA and protein to study the mechanisms that control gene expression by frog virus 3, a eucaryotic DNA virus. Forty-seven species of viral RNA and 35 viral polypeptide species were resolved by polyacrylamide gel electrophoresis. The relative molar ratios of virus-specific polypeptides synthesized at various times after infection were determined by computer planimetry and were compared with the molar ratios of appropriate-sized viral RNAs to code for each polypeptide. Viral polypeptides were classified according to the time during the growth cycle at which their maximal rate of synthesis occurred - early, 2 to 2.5 h; intermediate, 4 to 4.5 h; and late, 6 to 6.5 h. The viral RNAs, which were assumed to be mRNA's, could not be classified according to time of maximum synthesis; once their synthesis had begun, most of the RNAs continued to be synthesized at the same or higher rates. However, only 10 of the 47 viral RNA bands were plainly visible after electrophoresis of extracts from cells labeled from 1 to 1.5 h after infection; these 10 RNAs were designated "early" RNA. The early pattern of both RNA and polypeptide synthesis was maintained for at least 6 h in the presence of the amino acid analog fluorophenylalanine, which indicates that a functional viral polypeptide was required for "late" transcription and translation. The presumptive mRNA's for late polypeptides did not appear until 2 h after infection, but two of these "late" RNAs became the major products of transcription by 4 h into the infectious cycle. In contrast to the declining rate of synthesis of the early proteins, corresponding early RNA species continued to be synthesized at the same or higher rates throughout the replicative cycle. Although the synthesis of late virus-specific proteins appeared to be regulated at the level of transcription, our results suggest that the synthesis of both early and intermediate proteins was regulated at the post-transcriptional level.
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Müller UR, Marchin GL. Purification and properties of a T4 bacteriophage factor that modifies valyl-tRNA synthetase of Escherichia coli. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)39895-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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16
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Thermes C, Daegelen P, De Franciscis V, Brody E. In vitro system for induction of delayed early RNA of bacteriophage T4. Proc Natl Acad Sci U S A 1976; 73:2569-73. [PMID: 785471 PMCID: PMC430689 DOI: 10.1073/pnas.73.8.2569] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Concentrated lysates of Escherichia coli that had been infected with bacteriophage T4 in the presence of chloramphenicol show the same restriction of transcription in vitro as is found in vivo. Restricted lysates can be complemented with lysates from infected cells to induce production of delayed early RNA. Complementation takes place between the RNA polymerase of the restricted lysate and the DNA of the unrestricted lysate. We present evidence that delayed early RNA in these lysates is initiated at quasi-late (middle) promoters, and that such recognition is related to changes in the state of the template DNA.
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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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18
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Pero J, Tjian R, Nelson J, Losick R. In vitro transcription of a late class of phage SP01 genes. Nature 1975; 257:248-51. [PMID: 808738 DOI: 10.1038/257248a0] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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19
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Young ET. Analysis of bacteriophage T4 chloramphenicol RNA by DNA-RNA hybridization and by cell-free protein synthesis, and the effect of Escherichia coli polarity-suppressing alleles on its synthesis. J Mol Biol 1975; 96:393-424. [PMID: 1100847 DOI: 10.1016/0022-2836(75)90168-0] [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: 12/25/2022]
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21
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Duffy JJ, Geiduschek EP. RNA polymerase from phage SP01-infected and uninfected Bacillus subtilis. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41334-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Pitale MP, Jayaraman R. Transcription of bacteriophage T4 genome in vitro. Heterogeneity of RNA polymerase in crude extracts of normal and T4-infected Escherichia coli B. Biochemistry 1975; 14:1265-71. [PMID: 1091288 DOI: 10.1021/bi00677a027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In order to obtain RNA polymerase preparations carrying the necessary specificity determinants to transcribe the delayed-early genes of bacteriophage T4, crude extracts of uninfected and T4-infected Escherichia coli were fractionated in glycerol gradients of low ionic strength. In contrast to the reported sedimentation behavior of the purified enzyme, the RNA polymerase activity in crude extracts of normal and infected cells sedimented heterogeneously over a wide range of sedimentation coefficients. When the "heavy" (24-33 S) and "light" (14-20 S) regions of the gradient were precipitated with ammonium sulfate and recentrifuged, the former split into two subfractions, one again sedimenting heavy and the other sedimenting light. The latter did not split under the same conditions. The resulting subfractions from uninfected cell extracts had different thermal thermal stabilities at 50 degrees (half-lives ranging from 2-3 to 25 min) while those from T4-infected cell extracts were very thermolabile (half-life of 1-2 min). All the subfractions were more active on T4 DNA than on calf-thymus DNA. They also formed rifampicin-resistant, RNA chain initiation complexes with T4 DNA. Based on the kinetics of heat inactivation with T4 and calf thymus DNAs as templates and preferential transcription of T4 DNA, it is proposed that the T4-infected cell enzymes prepared as described here harbor heat-labile initiation factor(s). During infection the heavy sedimenting RNA polymerase activity disappears after 2.5 min at 37 degrees. This appears to require phage-specific protein synthesis because (a) it does not happen in the presence of chloramphenicol and (b) it does not happen in T4 ghost-infected cells.
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Purification and characterization of bacteriophage gh-I-induced deoxyribonucleic acid-dependent ribonucleic acid polymerase from Pseudomonas putida. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41754-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Ratner D. Letter to the editor: Bacteriophage T4 transcriptional control gene 55 codes for a protein bound to Escherichia coli RNA polymerase. J Mol Biol 1974; 89:803-7. [PMID: 4615168 DOI: 10.1016/0022-2836(74)90054-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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25
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Snyder LR, Montgomery DL. Inhibition of T4 growth by an RNA polymerase mutation of Escherichia coli: physiological and genetic analysis of the effects during phage development. Virology 1974; 62:184-96. [PMID: 4278501 DOI: 10.1016/0042-6822(74)90314-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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26
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Bogdanova ES, Gorlenko ZM, Khourgess EM. On the effect of bacteriophage infection on host RNA polymerase. MOLECULAR & GENERAL GENETICS : MGG 1974; 133:261-72. [PMID: 4614071 DOI: 10.1007/bf00267675] [Citation(s) in RCA: 3] [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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Spiegelman GB, Whiteley H. In Vivo and in Vitro Transcription by Ribonucleic Acid Polymerase from SP82-infected Bacillus subtilis. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42908-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Spiegelman GB, Whiteley H. Purification of Ribonucleic Acid Polymerase from SP82-infected Bacillus subtilis. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42907-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Crouch RJ. Ribonuclease III Does Not Degrade Deoxyribonucleic Acid-Ribonucleic Acid Hybrids. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42977-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Natale PJ, Buchanan JM. Initiation characteristics for the synthesis of five T4 phage-specific messenger RNAs in vitro. Proc Natl Acad Sci U S A 1974; 71:422-6. [PMID: 4360943 PMCID: PMC388018 DOI: 10.1073/pnas.71.2.422] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The involvement of the nucleoside triphosphates in the initiation of the synthesis of the messenger ribonucleic acid of five T4 specific enzymes has been studied. Only one of these, the messenger RNA for deoxynucleosidemonophosphate kinase, can be initiated in the presence of one nucleoside triphosphate, namely ATP. All of the remaining four require the presence of at least two nucleoside triphosphates during the initiation period. The combination of ATP and UTP was best for the initiation of messenger RNA for dihydrofolate reductase, ATP and CTP for deoxycytidylate hydroxymethyltransferase and beta-glucosyltransferase, and ATP and GTP for alpha-glucosyltransferase. We have concluded that there is a great variation in the nucleotide composition and sequence of the initiation sites in T4 DNA. No correlation in the requirements of nucleoside triphosphates during the initiation period could be observed among the five systems studied according to their classification as one type or another of "early" T4 messenger RNA.
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Stevens A. Deoxyribonucleic acid dependent ribonucleic acid polymerases from two T4 phage-infected systems. Biochemistry 1974; 13:493-503. [PMID: 4589313 DOI: 10.1021/bi00700a015] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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32
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Brown A, Cohen SN. Effects of λ development on template specificity of Escherichia coli RNA polymerase. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/0005-2787(74)90218-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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33
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Abstract
We have investigated the possibility of assigning genes of T4 bacteriophage to their units of transcription (scriptons) by studying gene expression from UV-irradiated DNA templates. Since RNA chains are prematurely terminated on UV-irradiated DNA templates and since the promotor distal part of the RNA chain is deleted, the expression of any gene is inversely proportional to the distance between the promotor and the promotor distal end of the gene. We find that the early genes, 43, 45 and rIIB, are promotor proximal. Since at least genes 43 and rIIB are classified as delayed early genes, these results suggest that their synthesis may require the recognition of new promotors. Additional early genes (44, 62, 42, 46, 47, 55, and rIIA) and some late genes (34, 37, and 38) have also been assigned positions relative to their promotors.
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34
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Stevens A. An inhibitor of host sigma-stimulated core enzyme activity that purifies with DNA-dependent RNA polymerase of E. coli following T4 phage infection. Biochem Biophys Res Commun 1973; 54:488-93. [PMID: 4585685 DOI: 10.1016/0006-291x(73)91447-2] [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: 01/11/2023]
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35
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36
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Horvitz HR. Polypeptide bound to the host RNA polymerase is specified by T4 control gene 33. NATURE: NEW BIOLOGY 1973; 244:137-40. [PMID: 4579464 DOI: 10.1038/newbio244137a0] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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37
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Babcock DF, Rich MA. Deoxyribonucleic acid-dependent ribonucleic acid polymerases from murine spleen cells. Increased amounts of the nucleolar species in leukaemic tissue. Biochem J 1973; 133:797-804. [PMID: 4795941 PMCID: PMC1177770 DOI: 10.1042/bj1330797] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
1. In the spleens of infected mice, the Friend leukaemia virus induces a sharp increase in the ability of subsequently isolated nuclei to incorporate exogenous UTP into an acid-insoluble product. Inhibitor studies indicate that the incremental RNA synthesis proceeds from a DNA template and that both nucleolar and nucleoplasmic activities are involved. 2. The partially purified DNA-dependent RNA polymerases from control and virus-infected tissue are indistinguishable with respect to chromatographic mobility, dependence on bivalent cations, ionic strength, pH and their susceptibility to alpha-amanitin. The RNA polymerases of the murine spleen resemble the enzymes of other mammalian tissue in these properties. 3. A comparison of the amount of polymerase solubilized from normal and infected tissue correlates with the activity observed in assays of the respective nuclei. These experiments indicated that the increase in nucleolar RNA synthesis after infection is mediated by increased extractable polymerase I activity whereas the change in nucleoplasmic RNA synthesis results from an alteration of chromatin or a chromatin-associated factor.
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38
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Dausse JP, Sentenac A, Fromageot P. Interaction of RNA polymerase from Escherichia coli with DNA. Influence of DNA scissions on RNA-polymerase binding and chain initiation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 31:394-404. [PMID: 4567123 DOI: 10.1111/j.1432-1033.1972.tb02546.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Jayaraman R. Transcription of bacteriophage T4 DNA by Escherichia coli RNA polymerase in vitro: identification of some immediate-early and delayed-early genes. J Mol Biol 1972; 70:253-63. [PMID: 4562318 DOI: 10.1016/0022-2836(72)90537-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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