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Pourseif MM, Masoudi-Sobhanzadeh Y, Azari E, Parvizpour S, Barar J, Ansari R, Omidi Y. Self-amplifying mRNA vaccines: Mode of action, design, development and optimization. Drug Discov Today 2022; 27:103341. [PMID: 35988718 DOI: 10.1016/j.drudis.2022.103341] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 07/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
The mRNA-based vaccines are quality-by-design (QbD) immunotherapies that provide safe, tunable, scalable, streamlined and potent treatment possibilities against different types of diseases. The self-amplifying mRNA (saRNA) vaccines, as a highly advantageous class of mRNA vaccines, are inspired by the intracellular self-multiplication nature of some positive-sense RNA viruses. Such vaccine platforms provide a relatively increased expression level of vaccine antigen(s) together with self-adjuvanticity properties. Lined with the QbD saRNA vaccines, essential optimizations improve the stability, safety, and immunogenicity of the vaccine constructs. Here, we elaborate on the concepts and mode-of-action of mRNA and saRNA vaccines, articulate the potential limitations or technical bottlenecks, and explain possible solutions or optimization methods in the process of their design and development.
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Affiliation(s)
- Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yosef Masoudi-Sobhanzadeh
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Erfan Azari
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rais Ansari
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, Florida, USA
| | - Yadollah Omidi
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, Florida, USA.
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Nishio T, Sugino K, Yoshikawa Y, Matsumoto M, Oe Y, Sadakane K, Yoshikawa K. K+ promotes the favorable effect of polyamine on gene expression better than Na. PLoS One 2020; 15:e0238447. [PMID: 32881909 PMCID: PMC7470421 DOI: 10.1371/journal.pone.0238447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/10/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Polyamines are involved in a wide variety of biological processes including a marked effect on the structure and function of DNA. During our study on the interaction of polyamines with DNA, we found that K+ enhanced in vitro gene expression in the presence of polyamine more strongly than Na+. Thus, we sought to clarify the physico-chemical mechanism underlying this marked difference between the effects of K+ and Na+. PRINCIPAL FINDINGS It was found that K+ enhanced gene expression in the presence of spermidine, SPD(3+), much more strongly than Na+, through in vitro experiments with a Luciferase assay on cell extracts. Single-DNA observation by fluorescence microscopy showed that Na+ prevents the folding transition of DNA into a compact state more strongly than K+. 1H NMR measurement revealed that Na+ inhibits the binding of SPD to DNA more strongly than K+. Thus, SPD binds to DNA more favorably in K+-rich medium than in Na+-rich medium, which leads to favorable conditions for RNA polymerase to access DNA by decreasing the negative charge. CONCLUSION AND SIGNIFICANCE We found that Na+ and K+ exhibit markedly different effects through competitive binding with a cationic polyamine, SPD, to DNA, which causes a large difference in the higher-order structure of genomic DNA. It is concluded that the larger favorable effect of Na+ than K+ on in vitro gene expression observed in this study is well attributable to the significant difference between Na+ and K+ on the competitive binding inducing conformational transition of DNA.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kaito Sugino
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | | | - Yohei Oe
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Japan
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Gottesman ME, Chudaev M, Mustaev A. Key features of magnesium that underpin its role as the major ion for electrophilic biocatalysis. FEBS J 2020; 287:5439-5463. [DOI: 10.1111/febs.15318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 02/06/2020] [Accepted: 03/30/2020] [Indexed: 01/05/2023]
Affiliation(s)
- Max E. Gottesman
- Department of Microbiology & Immunology Columbia University Medical Center New York NY USA
| | - Maxim Chudaev
- Public Health Research Institute & Department of Microbiology and Molecular Genetics New Jersey Medical School Rutgers Biomedical and Health Sciences Newark NJ USA
| | - Arkady Mustaev
- Public Health Research Institute & Department of Microbiology and Molecular Genetics New Jersey Medical School Rutgers Biomedical and Health Sciences Newark NJ USA
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Tabor H, Tabor CW. Biosynthesis and metabolism of 1,4-diaminobutane, spermidine, spermine, and related amines. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 36:203-68. [PMID: 4628436 DOI: 10.1002/9780470122815.ch7] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Action of intact AP (apurinic/apyrimidinic) sites and AP sites associated with breaks on the transcription of T7 coliphage DNA by Escherichia coli RNA polymerase. Biochem J 1985; 229:173-81. [PMID: 2412545 PMCID: PMC1145164 DOI: 10.1042/bj2290173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effect of apurinic/apyrimidinic (AP) sites in DNA on RNA and protein synthesis was studied in vitro using T7 coliphage DNA. Initiation of RNA synthesis by Escherichia coli RNA polymerase was synchronized and heparin was used to prevent reinitiation. When the T7 DNA contained AP sites, the rate of RNA synthesis was decreased but it remained higher than the values calculated on the assumption that an AP site in the transcribed strand is a complete block to the enzyme progression. Moreover, after the time taken by an unimpeded enzyme to go from promoter to terminator, the rate of RNA synthesis remained elevated and the number of complete RNA molecules (7000 nucleotides) continued to increase for some time. These results suggest that, if the E. coli RNA polymerase is stopped by an AP site, most often, after a pause, the enzyme resumes elongation of the RNA chain which is continuous over the AP site. Sometimes however, RNA synthesis is definitively interrupted during the pause; the probability of interruption has been estimated to be 0.3 in our experimental conditions. When a nick is placed 5' to the AP site by an AP endonuclease, the results are similar: most often, the RNA chain is synthesized without interruption past the nick in the template strand. The pause of the E. coli RNA polymerase at this combined lesion appears to be shorter than when the AP site is intact. To investigate whether a nucleotide is placed in the RNA chain in front of the AP site in the template strand by E. coli RNA polymerase, RNA synthesis was taken to completion before using this RNA for protein synthesis and measuring the activity of gene-1 product, T7 RNA polymerase. The result suggests that, after pausing, the E. coli RNA polymerase places a nucleotide in the RNA chain when passing over an AP site. The mechanism of the delayed lethality of T7 coliphages treated with monofunctional alkylating agents, which is due to the appearance of AP sites, is discussed.
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Russell DH. Ornithine decarboxylase: a key regulatory enzyme in normal and neoplastic growth. Drug Metab Rev 1985; 16:1-88. [PMID: 3905315 DOI: 10.3109/03602538508991430] [Citation(s) in RCA: 178] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Wu CW, Tweedy N. Mechanistic aspects of promoter binding and chain initiation by RNA polymerase. Mol Cell Biochem 1982; 47:129-49. [PMID: 6755217 DOI: 10.1007/bf00229597] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Niyogi SK, Feldman RP. Effect of several metal ions on misincorporation during transcription. Nucleic Acids Res 1981; 9:2615-27. [PMID: 7024904 PMCID: PMC326876 DOI: 10.1093/nar/9.11.2615] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
By use of poly(dA-dT) as template and Escherichia coli RNA polymerase, several metal ions were tested for their effect on the efficiency of transcription and on the misincorporation of CMP into the poly(rA-rU) product. In the presence of 10 mM MgCl2, Mn2+ has a stimulatory effect on the transcription, Co2+ has very little effect on the reaction, Cu2+ and Zn2+ are strongly inhibitory, and Cd2+ and Ni2+ are less inhibitory. The background misincorporation of CMP in the presence of MgCl2 is about 1 nucleotide per 2000 correct nucleotides incorporated and is independent of Mg2+ concentration. Zn2+, Ca2+, Sr2+, Li+, Na+, and K+--all nonmutagenic and noncarcinogenic--do not increase misincorporation. Mn2+ causes a concentration-dependent threefold increase in the misincorporation that can be slightly reversed at higher MgCl2 concentrations. Cd2+ causes a dramatic increase in the misincorporation with increasing CdCl2 concentration that can be substantially overcome by higher concentrations of Mg2+. Cu2+ also increases the misincorporation, Ni2+ slightly increases it, and Co2+ does not increase it at all. Several control experiments indicate that the misincorporation of CMP is dependent on the template-directed synthesis of poly(rA-rU). Nearest-neighbor analysis indicates that CMP is incorporated in place of UMP into the poly(rA-rU) product. The increase in misincorporation appears to be related both to the "hard-soft" character of the metal ions and to their carcinogenic potential.
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Hoffman DJ, Niyogi SK. Metal mutagens and carcinogens affect RNA synthesis rates in a distinct manner. Science 1977; 198:513-4. [PMID: 910143 DOI: 10.1126/science.910143] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Five metal salts (lead, cadmium, cobalt, copper, and manganese),which are mutagenic or carcinogenic, decreasing the fidelity of DNA synthesis in vitro, stimulated chain initiation of RNA synthesis at concentrations that inhibited overall RNA synthesis. In contrast, other metal salts (zinc, magnesium, lithium, sodium,and potassium) not in this category inhibited chain initiation of RNA synthesis at concentrations that inhibited overall RNA synthesis.
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12
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Karpetsky TP, Hieter PA, Frank JJ, Levy CC. Polyamines, ribonucleases, and the stability of RNA. Mol Cell Biochem 1977; 17:89-99. [PMID: 333273 DOI: 10.1007/bf01743432] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Raaphorst GP, Frey HE, Kruuv J. Effect of salt solutions on radiosensitivity of mammalian cells. III. Treatment with hypertonic solutions. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1977; 32:109-26. [PMID: 302244 DOI: 10.1080/09553007714550791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
V79 Chinese hamster cells were treated with hypertonic solutions of NaCl or KCl and irradiated rat various times before, during, or after exposure to the solution. In solutions of molarities between 0-2 and 0-5 M, the cellular radiosensitivity increases with the molarity of the bathing solution. At these molarities, the hypertonic solution need not be present during irradiation to sensitize cells. Furthermore, radiosensitivity of cells could be increased by exposing cells for longer times to the hypertonic solution before irradiation. At higher salt concentrations (at 1-5 to 1-8 M), significant radioprotection is observed. Survival curve data showed that this protection was characterized by an increase in DO and a decrease in n, while the survival curves of cells sensitized with 0-465 M NaCl or with lower concentrations exhibited mainly changes in DO. The 1-55 M NaCl solution must be present during radiation to give a protective effect. Prolonged exposure to the salt before irradiation reduced the amount of radioprotection afforded by the salt. The results are discussed in terms of the effects of ions on histones, cellular water structure and the cell-aging cycle.
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McMillian R, Kumar BV, Medoff G, Schlessinger D, Kobayashi GS. Inhibition of Histoplasma capsulatum ribonucleic acid polymerases by homologous and heterologous ribonucleic acid. J Bacteriol 1977; 130:1387-9. [PMID: 324986 PMCID: PMC235367 DOI: 10.1128/jb.130.3.1387-1389.1977] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ribonucleic acid (RNA) polymerases from the yeast phase of Histoplasma capsulatum are differentially sensitive to RNA isolated from the yeast and mycelial phases of this fungus and from Escherichia coli. Low-molecular-weight RNA from H. capsulatum was the most effective inhibitor.
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15
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Ranade SS. The effect of U.V.-irradiation on lambda DNA transcription. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1977; 31:451-8. [PMID: 326709 DOI: 10.1080/09553007714550541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effect of U.V.-irradiation of template DNA has been studied in vitro in the E. coli RNA polymerase system with native and U.V.-treated lambda DNA. Lambda DNA is more susceptible to U.V. than is calf-thymus DNA, yet a residual activity is observed at a U.V. dose of 0-5+10(4) erg/mm2. From the kinetic analysis of the reaction and the incorporation of lambda 32P-labelled nucleoside triphosphates, it seems reasonable to conclude that U.V.-irradiation probably does not affect the DNA initiation sites, recognizable by RNA polymerase. The transcription products made with U.V.-irradiated lambda DNA are assymmetrical, and hybridized to the right half (R) and the left half (L) of lambda DNA with the ratio of R/L = 4/1, and they show a lower hybridizability than the transcripts with native lambda DNA. The initiation sites recognizable by RNA polymerase seem to be the same on both native and U.V.-irradiated lambda DNA though the transcription of U.V.-treated lambda DNA appears to terminate with rather short RNA chains.
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16
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Chetsanga CJ, Novetsky JI, Dimino MJ. Some properties of rat liver mitochondrial RNA polymerase. Mol Cell Biochem 1976; 13:147-56. [PMID: 1004501 DOI: 10.1007/bf01731777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A rapid method suitable for purifying large amounts of mitochondria from rat liver using isopycnic zonal centrifugation is described. The RNA polymerase isolated from the purified mitochrondria was found associated with one peak when resolved by DEAE Sephadex chromatography. The enzyme was next fractionated on a phosphocellulose column followed by glycerol gradient centrifugation. A 600-fold purification was achieved when the enzyme was finally filtered through agarose gel. This final enzyme fraction consisted of one polypeptide chain as shown by polyacrylamide gel electrophoresis profiles. The enzyme has a greater preference for poly [d(A-T)] templates than for rat liver mitochondrial DNA. Inhibition of the enzyme activity required high concentrations of the inhibitors. The resistance of the enzyme to alpha-amanitin indicated that there was no contamination from nuclear RNA polymerase II. The conclusion is drawn that the mitochondrial RAN polymerase activity is associated with a single polypeptide.
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17
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Heller JS, Fong WF, Canellakis ES. Induction of a protein inhibitor to ornithine decarboxylase by the end products of its reaction. Proc Natl Acad Sci U S A 1976; 73:1858-62. [PMID: 1064859 PMCID: PMC430406 DOI: 10.1073/pnas.73.6.1858] [Citation(s) in RCA: 274] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Putrescine, the end-product of ornithine decarboxylase (ODC: L-ornithine carboxylyase, EC; 4.1.1.17) action, induces the synthesis of a protein(s), in L1210, neuroblastoma, and H-35 cells as well as in rat liver, which inhibits ODC activity. Spermidine and spermine, distal products of ODC activity, also induce the synthesis of a similar protein in H-35 cells. These ODC-inhibitors are heat-labile, trypsin-sensitive, and their induction is dependent upon protein synthesis. They have short half-lives which range from 18 to 66 min; these half-lives are similar to those of the ODC derived from the same source. They are noncompetitive inhibitors of ODC activity with an apparent molecular weight of 26,500. Each inhibitor crossreacts with the ODC's of the other cells and forms an enzyme-inhibitor complex which is stable during Sephadex chromatography; however, after treatment with ammonium sulfate, enzyme and inhibitor activities can be dissociated and recovered intact from the same column. We propose the name antizyme for proteins whose synthesis is induced by the proximal or distal products of the enzyme they inhibit.
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18
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Kleppe RK, Kleppe K. Preparations and properties of ribonucleic acid polymerase from Acinetobacter calcoaceticus. J Bacteriol 1976; 125:435-43. [PMID: 1380 PMCID: PMC236101 DOI: 10.1128/jb.125.2.435-443.1976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Deoxyribonucleic acid (DNA)-dependent ribonucleic acid (RNA) polymerase (EC 2.7.7.6) from Acinetobacter calcoaceticus was purified to apparent homogeneity and its properties were compared with those of the Escherichia coli B enzyme. The molecular weights of the two native active enzymes as well as their alpha and beta subunits appeared to be similar. No subunit corresponding to that of sigma from E. coli was found, and furthermore no separation between the beta subunits could be detected by gel electrophoresis. A number of different DNAs were transcribed by the enzyme from A. calcoaceticus. Maximal RNA synthesis occurred at pH 8.7, 10 mM Mg2+, or 0.3 mM Mn2+ and at a total ionic strength of 0.1. Higher ionic strengths led to increasing inhibition of transcription and at mu = 0.4 complete inhibition was observed. The mechanism of inhibition of salt was not related to the initiation event as observed with T4 core RNA polymerase (R.Kleppe, 1975). In an attempt to understand the mechanism of inhibition by salt, the effect of ionic strength on the sedimentation properties of the enzyme was investigated. At low ionic strength, enzyme species with sedimentation coefficients, s20,w, of 5.8S, 12.4S, and 19.3S were present. In buffers with higher ionic strengths the relative amounts of the 12.4S species decreased. It is suggested, therefore, that the inhibition of activity at higher salt concentrations is caused by a decrease in concentration of the active enzyme species.
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de Pomerai DI, Chesterton CJ, Butterworth PH. Preparation of chromatin. Variation in the template properties of chromatin dependent on the method of perparation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 46:461-71. [PMID: 4853746 DOI: 10.1111/j.1432-1033.1974.tb03639.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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21
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Studies of Ribonucleic Acid Chain Initiation by Escherichia coli Ribonucleic Acid Polymerase Bound to T7 Deoxyribonucleic Acid. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42628-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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22
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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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23
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Mandel JL, Chambon P. Animal DNA-dependent RNA polymerases. Analysis of the RNAs synthesized on Simian virus 40 superhelical DNA by mammalian RNA polymerases AI and B. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 41:379-95. [PMID: 4361418 DOI: 10.1111/j.1432-1033.1974.tb03280.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Sobieski RJ, Olsen RH. Cold-sensitive Pseudomonas RNA polymerase. II. Cold-promoted restriction of bacteriophage CB3 and the lack of host-dependent bacteriophage-specific RNA transcription. J Virol 1973; 12:1384-94. [PMID: 4202618 PMCID: PMC356779 DOI: 10.1128/jvi.12.6.1384-1394.1973] [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: 01/09/2023] Open
Abstract
Cold-sensitive restriction of Pseudomonas phage CB3 by Pseudomonas aeruginosa strain PAT2 involves some aspect of CB3 specific RNA synthesis at 20 C. Experiments using chloramphenicol treatment and RNA-DNA hybridization establish that the amount of CB3 RNA present at 20 C is consistent with the known percentage of phage yielder cells at 20 C. Thus, it appears that nonyielder cells of PAT2 synthesize little or no phage-specific mRNA. Burgess technique extracted PAT2 RNA polymerase (RNAP) is cold sensitive when assayed in vitro with CB3 DNA at 20 C. However, it is not cold sensitive when either calf thymus or PAT2 DNA are the templates for transcription. Low ionic strength assay conditions eliminate the cold sensitivity of PAT2 RNAP. The effect of low ionic environments on transcription initiation along with the in vivo and in vitro suppression of cold sensitivity by host rifampin resistance suggests that the inability of CB3 to reproduce in PAT2 at 20 C is a cold-sensitive step in host RNAP initiation. Our modified RNAP extraction procedure for PAT2 and PAO1C also results in the recovery of cold-sensitive PAT2 RNAP with respect to CB3 DNA templates and points to basic enzymological differences between the two hosts. A model is presented for the unusual influence of temperature on the initiation process of both PAT2 and PAO1C on RNAP transcription.
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Morris DR, Hansen MT. Influence of polyamine limitation on the chain growth rates of beta-galactosidase and of its messenger ribonucleic acid. J Bacteriol 1973; 116:588-92. [PMID: 4583242 PMCID: PMC285422 DOI: 10.1128/jb.116.2.588-592.1973] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The rates of elongation of beta-galactosidase and its messenger ribonucleic acid (RNA) were estimated in a polyamine-deficient mutant of Escherichia coli through an analysis of the kinetics of enzyme induction. The chain growth of beta-galactosidase was calculated from the time required after the appearance of an amino terminal fragment of 60 amino acids (auto-alpha) until completed enzyme began to accumulate. The elongation rate of beta-galactosidase messenger RNA was estimated from the time after induction at which streptolydigen-resistant, enzyme-forming capacity first appeared. Upon polyamine starvation, the rate of polypeptide elongation slowed from 17 to 10 amino acids per s and the messenger RNA elongation rate decreased from 47 to 30 nucleotides per s. These reductions in polymerization rates were proportional to the decrease in cellular growth rate produced by polyamine starvation. It was concluded that, although it is quite unlikely that polyamine levels are involved in regulation of cell growth, they may be acting as cofactors in the synthesis of RNA or protein, or both.
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Pannekoek H, Pouwels PH. The specificity of transcription in vitro of the trp operon of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1973; 123:159-72. [PMID: 4579984 DOI: 10.1007/bf00267332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Dezélée S, Sentenac A. Role of DNA-RNA hybrids in eukaryotes. Purification and properties of yeast RNA polymerase B. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 34:41-52. [PMID: 4573680 DOI: 10.1111/j.1432-1033.1973.tb02726.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Schäfer R, Zillig W. The effects of ionic strength on termination of transcription of DNAs from bacteriophages T4, T5 and T7 by DNA-dependent RNA polymerase from Escherichia coli and the nature of termination by factor rho. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 33:215-26. [PMID: 4571594 DOI: 10.1111/j.1432-1033.1973.tb02672.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
Exogenous polyribonucleotides stimulated the ribonucleic acid (RNA) transcriptase in Sendai virions. Added yeast RNA, polyadenylic acid, or polycytidylic acid increased incorporation of (3)H-guanosine monophosphate as much as fivefold. The products of stimulated reactions were virus-specific as determined by hybridization with Sendai virion RNA, but they sedimented more slowly (13s) than the product of an unstimulated reaction (16s). The stimulating activity was nondialyzable and heat stable, but was abolished by alkaline hydrolysis. Nucleoside monophosphates, individually or in combination, were ineffective, confirming the requirement for a polymer. Among other substances tested for effects on Sendai virion transcriptase, polyaspartic acid and polyglutamic acid stimulated the enzyme; polyinosinic acid, polyuridylic acid, and polyamines had no effect; and dextran sulfate and polyvinyl sulfate were inhibitory.
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De Robertis EM, Ezcurra PM, Judewicz ND, Pucci PR, Torres HN. Inhibition of E. coli RNA polymerase by polyadenylic acid. FEBS Lett 1972; 25:175-178. [PMID: 11946746 DOI: 10.1016/0014-5793(72)80479-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- E M. De Robertis
- Instituto de Investigaciones Bioquímicas "Fundación Campomar" and Facultad de Ciencias Exactay y Naturales, Obligado 2490, Buenos Aires, Argentina
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Lazarus LH, Popescu M, Barzilai R, Goldblum N. Spermidine stimulation of foot-and-mouth disease virus RNA-dependent RNA polymerase activity. ARCHIV FUR DIE GESAMTE VIRUSFORSCHUNG 1972; 36:311-6. [PMID: 4336494 DOI: 10.1007/bf01249861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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33
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34
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Murooka Y, Lazzarini RA. Stimulation of RNA synthesis by two protein factors in extracts of Escherichia coli. Proc Natl Acad Sci U S A 1972; 69:2336-40. [PMID: 4559601 PMCID: PMC426929 DOI: 10.1073/pnas.69.8.2336] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Two separate protein factors that markedly stimulate DNA-dependent RNA polymerase have been partially purified from ribosome-free extracts of E. coli Q13 cells. These proteins appear to differ from sigma, M, H, psi, and the factor described by Mahadik and Srinivasan. The stimulation by either factor requires the presence of the sigma protein. Using RNA-DNA hybridization competition analyses, we also demonstrate that neither of the new factors preferentially stimulates the synthesis of ribosomal RNA. The purification, properties, and mechanism of action of these new factors are examined.
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35
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Gibbins AM, Gregory KF. Relatedness among Rhizobium and Agrobacterium species determined by three methods of nucleic acid hybridization. J Bacteriol 1972; 111:129-41. [PMID: 4591471 PMCID: PMC251249 DOI: 10.1128/jb.111.1.129-141.1972] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Deoxyribonucleic acid (DNA) was isolated from 20 strains of Rhizobium and Agrobacterium and from one strain of Serratia marcescens; the guanine plus cytosine content of each DNA sample was determined by thermal denaturation. Radioactive DNA was isolated from three reference strains following the uptake of [2-(14)C]thymidine in the presence of deoxyadenosine. Ribonucleic acid (RNA) polymerase was used to synthesize radioactive RNA on DNA templates from the three reference strains. Radioactive DNA and RNA from the three reference strains were each hybridized with filter-bound DNA from all of the 21 test strains in 6 x SSC (standard saline citrate) and 50% formamide at 43 C for 40 hr. DNA/DNA relatedness was also determined by spectrophotometric measurement of the rates of association of single-stranded DNA. The order of relatedness between strains was similar by each method. Overall standard deviations for the DNA/DNA and DNA/RNA membrane filter techniques were +/-0.87 and +/-1.03%, respectively; that for the spectrophotometric technique was +/-4.11%. The DNA/DNA membrane technique gave higher absolute values of hybridization than did the DNA/RNA technique. R. leguminosarum and R. trifolii could not be distinguished from each other by these techniques. These results also indicated close relationships between R. lupini and R. japonicum, and (with less certainty) between R. meliloti and R. phaseoli. Of all the rhizobia tested against the A. tumefaciens 371 reference strain, the R. japonicum strains were the most unrelated. The three Agrobacterium strains used were as related to the R. lupini and R. leguminosarum references as were several rhizobium strains.
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36
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Lazarus LH, Itin A, Popescu M, Goldblum N. Mono- and divalent cationic parameters of foot-and-mouth disease virus replicase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 27:335-40. [PMID: 4340565 DOI: 10.1111/j.1432-1033.1972.tb01843.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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37
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Sarov I, Becker Y. Deoxyribonucleic acid-dependent ribonucleic acid polymerase activity in purified trachoma elementary bodies: effect of sodium chloride on ribonucleic acid transcription. J Bacteriol 1971; 107:593-8. [PMID: 5095283 PMCID: PMC246976 DOI: 10.1128/jb.107.3.593-598.1971] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Highly purified trachoma elementary bodies (T'ang strain), incubated in the presence of the four nucleoside triphosphates [Mg(2+), Mn(2+), 2-mercaptoethanol, tris(hydroxymethyl)aminomethane buffer (pH 7.5)] were found to incorporate (3)H-uridine triphosphate (UTP) into ribonucleic acid (RNA) molecules. Eighty-seven per cent of the labeled molecules were sensitive to ribonuclease treatment. In vitro RNA synthesis was almost completely inhibited by actinomycin D. Rifampin was also inhibitory, but allowed some initial RNA synthesis before complete inhibition occurred. When the reaction mixture lacked Mn(2+), trachoma elementary bodies synthesized, for a limited period, high-molecular-weight RNA species (23 to 24S, 16 to 17S, and 10 to 11S). Addition of 0.2 m NaCl to the same reaction mixture stimulated and prolonged (3)H-UTP incorporation into the same radioactive RNA species. Addition of 0.001 m Mn(2+) instead of NaCl also stimulated (3)H-UTP incorporation but prevented the synthesis of the high-molecular-weight RNA species.
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38
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Avila J, Hermoso JM, Vinuela E, Salas M. Purification and properties of DNA-dependent RNA polymerase from Bacillus subtilis vegetative cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 21:526-35. [PMID: 4999759 DOI: 10.1111/j.1432-1033.1971.tb01498.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Austin SJ, Tittawella IP, Hayward RS, Scaife JG. Amber mutations of Escherichia coli RNA polymerase. NATURE: NEW BIOLOGY 1971; 232:133-6. [PMID: 4937090 DOI: 10.1038/newbio232133a0] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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40
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Morris ME, Gould H. Reinitiation of RNA synthesis on transcription of chromatin DNA by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 1971; 68:481-5. [PMID: 5277105 PMCID: PMC388965 DOI: 10.1073/pnas.68.2.481] [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: 01/14/2023] Open
Abstract
The transcription of DNA in chromatin by Escherichia coli RNA polymerase resembles that of isolated DNA in two important respects: the release of nascent RNA and reinitiation of RNA synthesis is dependent on the salt concentration, and RNA synthesis is markedly stimulated by the addition of ribosomes.
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41
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Doerfler W. Integration of the deoxyribonucleic acid of adenovirus type 12 into the deoxyribonucleic acid of baby hamster kidney cells. J Virol 1970; 6:652-66. [PMID: 5530012 PMCID: PMC376171 DOI: 10.1128/jvi.6.5.652-666.1970] [Citation(s) in RCA: 101] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In a previous report, evidence was presented that the deoxyribonucleic acid (DNA) of adenovirus type 12 (Ad12) is integrated by covalent linkage into the DNA of baby hamster kidney cells (BHK-21 cells). These studies have been extended. The DNA of Ad12 and that of BHK-21 cells grown in medium containing 5-bromodeoxyuridine could be separated by equilibrium centrifugation in alkaline CsCl density gradients. BHK-21 cells were infected with (3)H-labeled Ad12, and the total intracellular DNA was analyzed at various times after infection in alkaline CsCl density gradients. The (3)H label in the position of cellular DNA hybridized predominantly with viral DNA and to a lesser extent also with cellular DNA. Replication of viral DNA could not be detected in BHK-21 cells. The appearance of viral (3)H label in the density stratum of cellular DNA was not significantly affected when DNA synthesis in Ad12-infected BHK-21 cells was inhibited >96% by cytosine arabinoside. These findings provided additional evidence for integration of Ad12 DNA into the DNA of BHK-21 cells. It could be calculated that 5 to 55 Ad12 DNA equivalents per cell are integrated. Replication of viral or cellular DNA was not required for integration. Inhibition of protein or ribonucleic acid synthesis interfered with integration only slightly.
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Stirpe F, Novello F. Factors affecting the activity of ribonucleic acid polymerase solubilized from rat liver nuclei. Effect on ionic strength, spermine and divalent ions with native and denatured deoxyribonucleic acid. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 15:505-12. [PMID: 5455663 DOI: 10.1111/j.1432-1033.1970.tb01033.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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44
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Gillis E, De Boever JG, Fiers W. The effect of salt concentration on the polyribonucleotide synthesizing activities in extracts of uninfected and RNA-bacteriophage infected "Escherichia coli". ARCHIVES INTERNATIONALES DE PHYSIOLOGIE ET DE BIOCHIMIE 1970; 78:519-30. [PMID: 4098002 DOI: 10.3109/13813457009075203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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45
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Banerjee AK, Shatkin AJ. Transcription in vitro by reovirus-associated ribonucleic acid-dependent polymerase. J Virol 1970; 6:1-11. [PMID: 5529847 PMCID: PMC376083 DOI: 10.1128/jvi.6.1.1-11.1970] [Citation(s) in RCA: 94] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Digestion of purified reovirus type 3 with chymotrypsin degrades 70% of the viral protein and converts the virions to subviral particles (SVP). The SVP contain 3 of the 6 viral structural proteins and all 10 double-stranded ribonucleic acid (RNA) genome segments but not adenine-rich, single-stranded RNA. An RNA polymerase which is structurally associated with SVP transcribes one strand of each genome segment by a conservative mechanism in vitro. The single-stranded products include large (1.2 x 10(6) daltons), medium (0.7 x 10(6) daltons), and small (0.4 x 10(6) daltons) molecules which hybridize exclusively with the corresponding genome segments. The enzyme obtained by heating virions at 60 C synthesizes similar products. Kinetic and pulse-chase studies indicate that the different-sized products are synthesized simultaneously but at rates which are in the order: small > medium > large.
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Schäfer KP, Cramer F. Action of RNA polymerase from Escherichia coli. Homopolymerization with ATP and -or UTP as substrates in the absence of template. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 15:103-10. [PMID: 4924738 DOI: 10.1111/j.1432-1033.1970.tb00982.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Costanzo F, Fiume L, La Placa M, Mannini-Palenzona A, Novello F, Stirpe F. Ribonucleic acid polymerase induced by vaccinia virus: lack of inhibition by rifampicin and alpha-amanitin. J Virol 1970; 5:266-9. [PMID: 5464578 PMCID: PMC375998 DOI: 10.1128/jvi.5.2.266-269.1970] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The RNA polymerase activity present in the cytoplasm of BHK cells infected with vaccinia virus is not affected by rifampicin or by alpha-amanitin.
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49
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Su S, Weinberg F, So AG, Davie EW. RNA polymerase and the shut-off of host RNA and protein synthesis in T4 phage infection. Nature 1970; 225:62-3. [PMID: 5410196 DOI: 10.1038/225062a0] [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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50
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Lezzi M. Differential gene activation in isolated chromosomes. INTERNATIONAL REVIEW OF CYTOLOGY 1970; 29:127-68. [PMID: 4930417 DOI: 10.1016/s0074-7696(08)60034-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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