1
|
Abstract
In two Escherichia coli genomes, laboratory strain K-12 and pathological strain O157:H7, tandem termination codons as a group are slightly over-represented as termination signals. Individually however, they span the range of representations, over, as expected, or under, in one or both of the strains. In vivo, tandem termination codons do not make more efficient signals. The second codon can act as a backstop where readthrough of the first has occurred, but not at the expected efficiency. UGAUGA remains an enigma, highly over-represented, but with the second UGA a relatively inefficient back up stop codon.
Collapse
Affiliation(s)
- Louise L Major
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | | | | | | | | |
Collapse
|
2
|
FLAVELL R, SABO D, BANDLE E, WEISSMANN C. Site-directed Mutagenesis : Generation of an Extracistronic Mutation in Bacteriophage Qβ RNA. Mol Biol 1989. [DOI: 10.1016/b978-0-12-131200-8.50038-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
3
|
Abstract
The addition of Ser AGC AGU tRNA to an E. coli cell-free protein synthesizing system which contains the endogenous tRNA levels results in up to 100% of the ribosomes translating the MS2 coat gene shifting into the -1 reading frame. An analogous phenomenon is seen at a much lower level without the tRNA addition, where a shift into the +1 frame can also be detected. Thus translation with the endogenous tRNA levels yields proteins which have the amino terminus of the coat protein but which are substantially larger than the coat protein and comprise about 5% of the coat translation. Since the lysis gene overlaps the 3' end of the coat gene in the +1 frame, we conclude that the reading frame shift into the +1 frame yields a hybrid protein. Also, we present evidence that ribosomes translating the synthetase gene shift into the -1 frame near the distal end of the gene. This frameshifting is promoted by thrACU ACC tRNA. Specific competitor tRNAs for both Thr and Ser tRNA-promoted frameshifting have been characterized. The generality of this new mechanism for producing additional proteins is unclear, but it investigation should increase understanding of the coding mechanism and its origin.
Collapse
|
4
|
Goldman E, Holmes WM, Hatfield GW. Specificity of codon recognition by Escherichia coli tRNALeu isoaccepting species determined by protein synthesis in vitro directed by phage RNA. J Mol Biol 1979; 129:567-85. [PMID: 383997 DOI: 10.1016/0022-2836(79)90469-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
5
|
|
6
|
Sabo DL, Domingo E, Bandle EF, Flavell RA, Weissmann C. A guanosine to adenosine transition in the 3' terminal extracistronic region of bacteriophage Q beta RNA leading to loss of infectivity. J Mol Biol 1977; 112:235-52. [PMID: 875018 DOI: 10.1016/s0022-2836(77)80141-1] [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]
|
7
|
Jou WM, Fiers W. Studies on the bacteriophages MS2. XXXIII. Comparison of the nucleotide sequences in related bacteriophage RNAs. J Mol Biol 1976; 106:1047-60. [PMID: 978743 DOI: 10.1016/0022-2836(76)90352-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
8
|
Domingo E, Flavell RA, Weissmann C. In vitro site-directed mutagenesis: generation and properties of an infectious extracistronic mutant of bacteriophage Qbeta. Gene 1976; 1:3-25. [PMID: 1052322 DOI: 10.1016/0378-1119(76)90003-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An infectious extracistronic mutant of phage Qbeta has been prepared by site-directed mutagenesis. Qbeta RNA minus strands containing the mutagenic base analog N4-hydroxy-CMP instead of UMP at position 39 from the 5' end were synthesized in vitro and used as template for Qbeta replicase to synthesize one generation of plus strands. E. coli spheroplasts were infected with the newly synthesized plus strands and phage recovered from single plaques. RNA sequence analysis revealed that four out of the eighteen phage clones analyzed contained RNA with an A leads to G transition at position 40 from the 3' end (which corresponds to position 39 of the minus strand). Thus, the viability of phage Qbeta does not depend on a unique nucleotide sequence in the 3'-extracistronic RNA segment. Upon in vivo propagation of mutant 40, spontaneous true revertants arose with high frequency and overgrew the parental clone within about 10 passages, indicating a selective disadvantage of the extracistronic mutant. Replication of mixtures of wild type and mutant RNA in vitro resulted in a decrease of the proportion of mutated RNA in the progeny plus strands. The fact that Qbeta RNA containing an A leads to G transition in nucleotide--40 of Qbeta RNA is less efficiently replicated in vitro may explain the selective disadvantage of the mutant phage in vivo. The preparation of an infectious mutated RNA by site-directed mutagenesis shows that the method is suitable to produce specific nucleotide exchanges without impairing the biological competence of the RNA.
Collapse
|
9
|
Engelberg H, Brudo I, Israeli-Reches M. Discriminative effect of rifampin of RNA replication of various RNA bacteriophages. J Virol 1975; 16:340-7. [PMID: 1097734 PMCID: PMC354673 DOI: 10.1128/jvi.16.2.340-347.1975] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rifampin interferes exclusively with RNA replication in vivo of the group I phages MS2, f2, and R17, whereas QbetaRNA replication is unaffected by the drug. In addition, rifampin has a discriminative effect of group I phage RNA replication. In the experimental system employed by us the antibiotic differentially interferes with the synthesis of minus RNA strands in f2, whereas it has almost no effect on the synthesis of progeny plus strands. In MS2, the drug differentially arrests the synthesis of progeny plus strands and almost fails to affect the synthesis of minus RNA strands. In R17 both steps of its RNA replication are affected by rifampin, although each step is only partially (approximately 50%) inhibited. The relation of the present results to the possible role of bacterial proteins and tertiary structure of phage RNA in the process of template recognition is discussed.
Collapse
|
10
|
|
11
|
Robertson HD, Hunter T. Sensitive methods for the detection and characterization of double helical ribonucleic acid. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41915-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
12
|
Hunter T, Hunt T, Jackson RJ, Robertson HD. The characteristics of inhibition of protein synthesis by double-stranded ribonucleic acid in reticulocyte lysates. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41914-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
13
|
Flavell RA, Sabo DL, Bandle EF, Weissmann C. Site-directed mutagenesis: generation of an extracistronic mutation in bacteriophage Q beta RNA. J Mol Biol 1974; 89:255-72. [PMID: 4444051 DOI: 10.1016/0022-2836(74)90517-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
14
|
Baptist JN, Tevethia MJ, Mandel M, Shaw CR. Altered proteins with triosephosphate isomerase activity in suppressor-containing strains of Bacillus subtilis. J Bacteriol 1974; 119:976-85. [PMID: 4211788 PMCID: PMC245705 DOI: 10.1128/jb.119.3.976-985.1974] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Suppressor mutations in Bacillus subtilis cause the synthesis of a new protein with the enzymatic activity of l-leucine dehydrogenase and two groups of new proteins with the activity of triosephosphate isomerase. The new isoenzymes of triosephosphate isomerase are separable by zone electrophoresis and differ among themselves in elution behavior upon gel permeation chromatography. One group has an apparent average molecular weight of 120,000 to 135,000, which is more than twice that of the wild-type enzyme. Another group appears to be even higher in molecular weight. These data are consistent with the working hypothesis that the new isoenzymes are produced by extension of growing polypeptide chains through one or more chain-terminating triplets, although other mechanisms resulting in alteration of shapes, charges, or associations of the enzymes are not excluded.
Collapse
|
15
|
Rensing UF, Coulson A, Schoenmakers JG. A sequence of 54 nucleotides from the A-protein cistron of coliphage-R17 RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 41:431-8. [PMID: 4361645 DOI: 10.1111/j.1432-1033.1974.tb03284.x] [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]
|
16
|
3. Polypeptide Chain Termination. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s1874-6047(08)60135-3] [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]
|
17
|
Rensing UF, Coulson A, Thompson EO. Nucleotide sequences of similar size from the coliphage R17 genome. Biochem J 1973; 131:605-10. [PMID: 4720715 PMCID: PMC1177508 DOI: 10.1042/bj1310605] [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: 01/12/2023]
Abstract
A sequence of 33 nucleotides from the coliphage R17 RNA genome was determined. It constitutes the main component of a mixture of fragments that migrate together on electrophoresis in a separation according to molecular weight. Fragments of comparable chain length from 3' end of RNA from coliphage R17, from a region preceding and overlapping the coat-protein cistron ribosome binding site and from the beginning of the A-protein cistron, were also found and characterized. ;Hairpin'-like secondary structures are proposed for the longer fragments, one of which appears to have a tetranucleotide excised in the loop region.
Collapse
|
18
|
Abstract
1. A sequence of 73 nucleotides of the RNA genome from coliphage R17 was determined. It can be read through in only one translational frame. The fragment is not part of the coatprotein cistron (Min Jou et al., 1972), nor does it come from the untranslated sequences described previously (Steitz, 1969; Nichols, 1970; Cory et al., 1970; de Wachter et al., 1971; Contreras et al., 1971; Cory et al., 1972). It contains two sequences of 23 and 24 nucleotides, 22 of which are identical. This kind of reiteration is the first one found in bacteriophage nucleic acid. 2. Improved conditions were found and tested for blocking oligonucleotides with carbodi-imide and cleaving by ribonuclease A at cytidylate residues. 3. A synthetic medium is described which allows labelling in vivo with (32)P to give specific radioactivities higher than those obtained in the procedures used previously.
Collapse
|
19
|
Rensing UF, Schoenmakers GG. A sequence of 50 nucleotides from coliphage R17 RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 33:8-18. [PMID: 4347963 DOI: 10.1111/j.1432-1033.1973.tb02648.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
20
|
MESH Headings
- Cell-Free System
- Centrifugation, Density Gradient
- Chromosome Mapping
- Coliphages/enzymology
- DNA, Viral/isolation & purification
- Dipeptides/biosynthesis
- Electrophoresis, Paper
- Formates/metabolism
- Methionine/metabolism
- Molecular Biology
- Muramidase/biosynthesis
- Mutation
- Peptide Chain Initiation, Translational
- RNA, Messenger/biosynthesis
- RNA, Messenger/isolation & purification
- RNA, Messenger/metabolism
- RNA, Viral/biosynthesis
- RNA, Viral/isolation & purification
- RNA, Viral/metabolism
- Spectrophotometry, Ultraviolet
- Sulfur Isotopes
- Time Factors
- Tritium
Collapse
|
21
|
Remaut E, Fiers W. Studies on the bacteriophage MS2. XVI. The termination signal of the A protein cistron. J Mol Biol 1972; 71:243-61. [PMID: 4564480 DOI: 10.1016/0022-2836(72)90349-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
22
|
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.
Collapse
|
23
|
COOH-terminal Amino Acid Sequence of Histidinol Dehydrogenase from a Salmonella typhimurium Mutant. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)44744-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
24
|
Rechler MM, Bruni CB, Martin RG, Terry W. An intercistronic region in the histidine operon of Salmonella typhimurium. J Mol Biol 1972; 69:427-52. [PMID: 4562711 DOI: 10.1016/0022-2836(72)90256-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
25
|
Contreras R, Vandenberghe A, Volckaert G, Min Jou W, Fiers W. Studies on the bacteriophage MS2. Some nucleotide sequences from the RNA-polymerase gene. FEBS Lett 1972; 24:339-342. [PMID: 11946702 DOI: 10.1016/0014-5793(72)80386-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- R Contreras
- Laboratory of Molecular Biology and Laboratory of Physiological Chemistry University of Ghent, 9000, Ghent, Belgium
| | | | | | | | | |
Collapse
|
26
|
|
27
|
Fitch WM. Considerations regarding the regulation of gene transcription and messenger translation. J Mol Evol 1972; 1:185-207. [DOI: 10.1007/bf01659164] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/1972] [Indexed: 11/29/2022]
|
28
|
Min Jou W, Haegeman G, Ysebaert M, Fiers W. Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein. Nature 1972; 237:82-8. [PMID: 4555447 DOI: 10.1038/237082a0] [Citation(s) in RCA: 340] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
29
|
Steitz JA. Oligonucleotide sequence of replicase initiation site in Q RNA. NATURE: NEW BIOLOGY 1972; 236:71-5. [PMID: 4502455 DOI: 10.1038/newbio236071a0] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
30
|
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]
|
31
|
Nichols JL, Hay AJ, Joklik WK. 5'-terminal nucleotide sequence of reovirus mRNA synthesized in vitro. NATURE: NEW BIOLOGY 1972; 235:105-7. [PMID: 4501191 DOI: 10.1038/newbio235105a0] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
32
|
Cory S, Adams JM, Spahr PF, Rensing U. Sequence of 51 nucleotides at the 3'-end of R17 bacteriophage RNA. J Mol Biol 1972; 63:41-56. [PMID: 5016970 DOI: 10.1016/0022-2836(72)90520-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
33
|
Sanger F. Nucleotide sequences in bacteriophage ribonucleic acid. The eighth hopkins memorial lecture. Biochem J 1971; 124:833-43. [PMID: 5131010 PMCID: PMC1177270 DOI: 10.1042/bj1240833a] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
34
|
|
35
|
Jeppesen PG. The nucleotide sequences of some large ribonuclease T 1 products from bacteriophage R17 ribonucleic acid. Biochem J 1971; 124:357-66. [PMID: 5158505 PMCID: PMC1177150 DOI: 10.1042/bj1240357] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A method of ;fingerprinting' high-molecular-weight (32)P-labelled RNA species, using a two-dimensional thin-layer-chromatographic separation of ribonuclease T(1) digestion products, has been applied to RNA from the Escherichia coli bacteriophage R17. The ;fingerprinting' technique, besides giving a unique pattern that can be used as a characterization of the RNA, has made it possible to isolate a number of the larger oligonucleotides and to determine their nucleotide sequences.
Collapse
|
36
|
|