1
|
Vold BS, Okamoto K, Murphy BJ, Green CJ. Transcriptional analysis of Bacillus subtilis rRNA-tRNA operons. I. The tRNA gene cluster of rrnB has an internal promoter. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68244-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
2
|
Kolman CJ, Snyder M, Söll D. Genomic organization of tRNA and aminoacyl-tRNA synthetase genes for two amino acids in Saccharomyces cerevisiae. Genomics 1988; 3:201-6. [PMID: 3066745 DOI: 10.1016/0888-7543(88)90080-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The genomic organization in Saccharomyces cerevisiae of the tRNA and aminoacyl-tRNA synthetase genes for two amino acids was investigated. Aspartic acid and serine were chosen for the study because of the number and diversity of their tRNA gene sequences and the availability of cloned tRNA and aminoacyl-tRNA synthetase genes. Chromosome assignments were determined by hybridization to DNA gel blots of chromosomal DNA resolved by contour-clamped homogeneous electric field gel electrophoresis. Our results show that the tRNA and the cognate synthetase genes in such a family are dispersed and, therefore, cannot be regulated via a mechanism dependent on close proximity of genes. In general, the genome of S. cerevisiae contains randomly dispersed tRNA genes that are transcribed individually. We have supported and expanded this view by applying the facile method of contour-clamped homogeneous electric field gel electrophoresis to the investigation of these small multigene families.
Collapse
Affiliation(s)
- C J Kolman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | | | | |
Collapse
|
3
|
Miller MJ. Sensitivity of RNA synthesis to actinomycin D inhibition is dependent on the frequency of transcription: a mathematical model. J Theor Biol 1987; 129:289-99. [PMID: 2458508 DOI: 10.1016/s0022-5193(87)80003-6] [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: 01/01/2023]
Abstract
The synthesis of ribosomal RNA is known to be up to 100-fold more sensitive to inhibition by actinomycin D than is messenger RNA. A model is presented here to explain the dose-response kinetics of this inhibition. The basic concept is that on very actively transcribed genes, such as ribosomal DNA, the first bound actinomycin D will sterically affect those densely packed polymerase molecules between it and the promoter, causing them to stack up into the promoter and interfere with the initiation of RNA synthesis. However, on less active genes, where the polymerases are widely spaced, the drug will inhibit individual polymerasas independently and only at the actinomycin blockade. Counteracting these inhibitory effects will be the tendency of genes bound with actinomycin to accumulate additional polymerases. A mathematical model is described which successfully explains previously reported dose-response kinetics of actinomycin inhibition in both frequently and infrequently transcribed genes. The analysis indicates that actinomycin inhibition is dependent on both polymerase packing and on gene size. The dose-response kinetics can be used to estimate both the size and transcriptional efficiency of individual genes. The model is also able to explain several other independent observations regarding the kinetics of inhibition of RNA synthesis by actinomycin.
Collapse
Affiliation(s)
- M J Miller
- Division of Cancer Etiology, National Cancer Institute, Bethesda 20892
| |
Collapse
|
4
|
|
5
|
von Meyenburg K, Nielsen LD, Johnsen K, Molin S, Svenningsen B, Miozzari G. Reevaluation of the mode of action of streptolydigin in Escherichia coli: induction of transcription termination in vivo. Antimicrob Agents Chemother 1978; 13:234-43. [PMID: 348095 PMCID: PMC352220 DOI: 10.1128/aac.13.2.234] [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
Growth of the permeable strain AS19 of Escherichia coli B is more sensitive to the antibiotic streptolydigin than is in vitro ribonucleic acid (RNA) synthesis. The in vivo chain elongation rates of lacZ messenger RNA and ribosomal RNA are not affected at 1.5 x 10(-6) M, a concentration that reduces the growth rate threefold. The synthesis of large proteins is inhibited preferentially, and a considerable fraction of the polypeptides synthesized is unstable. The synthesis of complete beta-galactosidase is inhibited relative to the synthesis of short, unstable polypeptides, which include the first 60 to 70 amino acids of beta-galactosidase. The expression of the following polycistronic transcription units is strongly biased against promoter-distal genes: trp, deo, rpoBC, and rrn. The extent of polarity is proportional to the distance transcribed and to the streptolydigin concentration. Streptolydigin appears to destabilize active transcription complexes irreversibly irrespective of the type of transcript (messenger RNA, ribosomal RNA) and of transcription intensity. We suggest that streptolydigin leads to premature termination of transcription, resulting in release of incomplete transcripts and, thus, a decrease in overall messenger RNA concentration, which becomes limiting for protein synthesis, i.e., for growth.
Collapse
|
6
|
Rungger D, Crippa M. The primary ribosomal DNA transcript in eukaryotes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978; 31:247-69. [PMID: 140416 DOI: 10.1016/0079-6107(78)90010-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
7
|
Gegenheimer P, Watson N, Apirion D. Multiple pathways for primary processing of ribosomal RNA in Escherichia coli. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40472-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
8
|
Zingales B, Colli W. Ribosomal RNA genes in Bacillus subtilis. Evidence for a cotranscription mechanism. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 474:562-77. [PMID: 402154 DOI: 10.1016/0005-2787(77)90076-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The analysis of the transcriptional mechanism of the ribosomal RNA genes in Bacillus subtilis was undertaken by a study of the rRNA chain elongation in the presence of rifampicin. The residual RNA synthesis after the addition of rifampicin and [3H] uridine to exponentially growing cells has shown that 56% of the radioactivity incorporated into total RNA belongs to the unstable fraction and 44% to the fraction containing mature rRNA and tRNA. Such study allowed an estimation of the half-life of messenger RNAs as being approximately 2 min. The analysis of the transcription pattern of the ribosomal RNA genes, as measured by the amount of radioactivity found in the ribosomal subunits, was complicated by a contamination of the 30 S subunits by 50 S subunits. A contamination of approximately 15% was estimated by polyacrylamide gel electrophoresis and competitive hybridization. The ratios of incorporated radioactivity at zero time when drug and label were concomitantly added ranged between 5.4-6.0, after correction for this contamination. The decay of the 23 S rRNA followed a straight line which became parabolic in its final portion. These results, and theoretical considerations on the lag of rifampicin action and on the variance of the specific activity of the nucleotide pool at the very early times of the experimental observation, favor the interpretation that the 16 and 23 S rRNA genes in B. subtilis belong to the same transcriptional unit, being cotranscribed, in that order, by the same molecule of RNA polymerase. The transcriptional times of the 16 and 23 S rRNA genes were estimated as being 30 and 60 s, respectively.
Collapse
|
9
|
Smith JD. Transcription and processing of transfer RNA precursors. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1976; 16:25-73. [PMID: 766079 DOI: 10.1016/s0079-6603(08)60755-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
10
|
Tang PW, Guha A. Determination of 5'-triphosphate terminus of 16S ribosomal RNA precursor. Nature 1975; 257:157-8. [PMID: 1099457 DOI: 10.1038/257157a0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
11
|
Gegenheimer P, Apirion D. Escherichia coli ribosomal ribonucleic acids are not cut from an intact precursor molecule. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41734-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
12
|
Hackett PB, Sauerbier W. Radiological mapping of the ribosomal RNA transcription unit in E. coli. Nature 1974; 251:639-41. [PMID: 4608761 DOI: 10.1038/251639a0] [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: 01/11/2023]
|
13
|
Pace NR. Structure and synthesis of the ribosomal ribonucleic acid of prokaryotes. BACTERIOLOGICAL REVIEWS 1973; 37:562-603. [PMID: 4203396 PMCID: PMC413834 DOI: 10.1128/br.37.4.562-603.1973] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
14
|
Nikolaev N, Silengo L, Schlessinger D. Synthesis of a large precursor to ribosomal RNA in a mutant of Escherichia coli. Proc Natl Acad Sci U S A 1973; 70:3361-5. [PMID: 4587249 PMCID: PMC427237 DOI: 10.1073/pnas.70.12.3361] [Citation(s) in RCA: 119] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A mutant of E. coli, isolated by Kindler and Hofschneider as a strain defective in RNase III activity, forms a 30S precursor of ribosomal RNA ("30S pre-rRNA"). The half-life of the 30S pre-rRNA in growing cells at 30 degrees , estimated by the rate of specific (3)[H]uridine incorporation, is about 1 min. In rifampicin-treated cells, the RNA is metabolized to mature rRNA with a half-life of about 2 min. The 30S pre-rRNA has been highly purified. DNA-RNA hybridization tests demonstrate that it contains both 16S and 23S rRNA sequences. Also, in cultures treated with rifampicin, the cleavage products of radioactive 30S pre-rRNA include 25S and 17.5S RNA species, destined to becomes 23S and 16S rRNA. Thus, each 30S chain probably contains one 16S and one 23S RNA sequence, as well as additional sequences. Two independent techniques indicate that the additional portions account for about 27% of the total lenght: (1) By comparison to the sedimentation rate and electrophoretic mobility of marker RNAs, the 30S pre-RNA has an apparent molecular weight of 2.3 x 10(6) +/- 5%, or 28% more than the sum of 16S and 23S rRNA; (2) 27% of the 30S pre-rRNA is not competed away from hybridization by mature 16S and 23S rRNA.Thus, bacteria appear to make a pre-rRNA similar in some respects to that observed in eukaryotes; though in normal E. coli cells, the pre-rRNA is ordinarily cleaved endonucleolytically during its formation.
Collapse
|
15
|
Stoof TJ, Planta RJ. On the biosynthesis of bacterial ribosomal RNA. Mol Biol Rep 1973; 1:243-9. [DOI: 10.1007/bf00357648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/1973] [Indexed: 10/26/2022]
|
16
|
Sogin ML, Woese CR, Pace B, Pace NR. The relationship between precursor and mature forms of the 23S ribosomal RNA. J Mol Evol 1973; 2:167-74. [PMID: 4219972 DOI: 10.1007/bf01653996] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
17
|
Juengst FW, Dworkin M. Ribonucleic acid and protein synthesis during germination of Myxococcus xanthus myxospores. J Bacteriol 1973; 113:786-97. [PMID: 4690965 PMCID: PMC285294 DOI: 10.1128/jb.113.2.786-797.1973] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Ribonucleic acid (RNA) and protein synthesis during myxospore germination were examined. When RNA synthesis was inhibited more than 90% by either actinomycin D (Act D) or rifampin, germination was prevented. The data were consistent with the interpretation that rifampin did not interfere with protein synthesis in any way other than by inhibition of messenger RNA formation. Act D concentrations as high as 20 mug/ml did not totally inhibit RNA synthesis. In the presence of 8 mug of Act D/ml, germinating myxospores synthesized transfer RNA, 16S RNA, and 23S RNA. Evidence was presented which indicated that messenger RNA was also synthesized early in the germination period both in the presence and absence of 8 mug of Act D/ml. One explanation for the escape synthesis of RNA in germinating myxospores is that Act D exerts a differential effect on the transcription of larger versus smaller cistrons, the latter having a lower probability of binding Act D. We have found that in the presence of 8 mug of Act D/ml, escape RNA synthesis in myxospores was 25% for 23S RNA, 55% for 16S RNA, and more than 90% for 4S RNA. We have shown that germination of myxospores requires both RNA and protein synthesis during the first 25 to 35 min in germination medium. This finding does not support the earlier suggestion by Ramsey and Dworkin that a stable germination messenger RNA is required for germination of the myxospores of Myxococcus xanthus.
Collapse
|
18
|
|
19
|
Gupta RS, Singh UN. Initiation of transcription and the sequential synthesis of 16-S and 23-S ribosomal RNA in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 277:567-75. [PMID: 4560815 DOI: 10.1016/0005-2787(72)90100-1] [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]
|
20
|
|
21
|
Webb KS, Bleyman MA. Collinearity of transcriptional and traditional genetic maps. NATURE: NEW BIOLOGY 1972; 237:79-81. [PMID: 4624457 DOI: 10.1038/newbio237079a0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
22
|
Surzycki SJ, Rochaix JD. Transcriptional mapping of ribosomal RNA genes of the chloroplast and nucleus of Chlamydomonas reinhardi. J Mol Biol 1971; 62:89-109. [PMID: 5157355 DOI: 10.1016/0022-2836(71)90133-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
23
|
Kossman CR, Stamato TD, Pettijohn DE. Tandem synthesis of the 16S and 23S ribosomal RNA sequences of Escherichia coli. NATURE: NEW BIOLOGY 1971; 234:102-4. [PMID: 4943519 DOI: 10.1038/newbio234102a0] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
24
|
Hayes F, Hayes DH. Biosynthesis of ribosomes in E. coli. I. Properties of ribosomal precursor particles and their RNA components. Biochimie 1971; 53:369-82. [PMID: 4935405 DOI: 10.1016/s0300-9084(71)80104-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
25
|
Quincey RV. The number and location of genes for 5S ribonucleic acid within the genome of Drosophila melanogaster. Biochem J 1971; 123:227-33. [PMID: 5127336 PMCID: PMC1176927 DOI: 10.1042/bj1230227] [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: 01/13/2023]
Abstract
DNA was prepared from wild-type and two mutant stocks of Drosophila melanogaster that differed in their dosage of the nucleolar organizer region. The relative amounts of DNA from the nucleolar organizer region in these preparations of DNA were determined by hybridization with (3)H-labelled 28S rRNA. As expected, the amount of (3)H-labelled 28S rRNA that hybridized was directly related to the dosage of nucleolar organizer region. No positive correlation was observed between the amount of (3)H-labelled 5S RNA that hybridized and the dosage of nucleolar organizer region. Thus genes for 5S RNA are located primarily, if not exclusively, outside the nucleolar organizer region. The haploid genome of the wild-type D. melanogaster used in this work has 106 genes for 28S rRNA and 96-105 genes for 5S RNA.
Collapse
|
26
|
van den Bos RC, Retèl J, Planta RJ. The size and the location of the ribosomal RNA segments in ribosomal precursor RNA of yeast. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 232:494-508. [PMID: 5572619 DOI: 10.1016/0005-2787(71)90603-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
27
|
Colli W, Smith I, Oishi M. Physical linkage between 5 s, 16 s and 23 s ribosomal RNA genes in Bacillus subtilis. J Mol Biol 1971; 56:117-27. [PMID: 4995655 DOI: 10.1016/0022-2836(71)90088-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
28
|
Lizardi PM, Luck DJ. Absence of a 5S RNA complnent in the mitochondrial ribosomes of Neurospora crassa. NATURE: NEW BIOLOGY 1971; 229:140-2. [PMID: 5280093 DOI: 10.1038/newbio229140a0] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
29
|
Pace B, Pace NR. Gene dosage for 5S ribosomal ribonucleic acid in Escherichia coli ad Bacillus megaterium. J Bacteriol 1971; 105:142-9. [PMID: 4993318 PMCID: PMC248333 DOI: 10.1128/jb.105.1.142-149.1971] [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: 01/13/2023] Open
Abstract
The number of gene copies for 5S ribosomal ribonucleic acid (rRNA), relative to that for 16 and 23S rRNA, has been determined by deoxyribonucleic acid (DNA)-RNA hybridization for Escherichia coli and Bacillus megaterium. In both cases, the number of 5S rRNA genes equals the number of 16 or 23S rRNA genes. Rapid procedures for preparing extremely highly purified DNA suitable for DNA-RNA hybridization experiments and chemically pure 5S rRNA are described.
Collapse
|
30
|
Pettijohn DE, Stonington OG, Kossman CR. Chain termination of ribosomal RNA synthesis in vitro. Nature 1970; 228:235-9. [PMID: 4920919 DOI: 10.1038/228235a0] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
31
|
Doolittle WF, Pace NR. Synthesis of 5S ribosomal RNA in Escherichia coli after rifampicin treatment. Nature 1970; 228:125-9. [PMID: 4918254 DOI: 10.1038/228125a0] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
32
|
Perry RP, Kelley DE. Inhibition of RNA synthesis by actinomycin D: characteristic dose-response of different RNA species. J Cell Physiol 1970; 76:127-39. [PMID: 5500970 DOI: 10.1002/jcp.1040760202] [Citation(s) in RCA: 429] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
33
|
|
34
|
Pace B, Peterson RL, Pace NR. Formation of all stable RNA species in Escherichia coli by posttranscriptional modification. Proc Natl Acad Sci U S A 1970; 65:1097-104. [PMID: 4909469 PMCID: PMC283028 DOI: 10.1073/pnas.65.4.1097] [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: 01/13/2023] Open
Abstract
The kinetics of accumulation of the known stable RNA species (23S, 16S, and 5S rRNA and tRNA) in Escherichia coli C122 were monitored by polyacrylamide gel electrophoresis of purified cellular RNA, following termination of brief pulse labeling with (32)P-orthophosphate. Isotopically labeled stable RNA species appear only after a time lag, while total cellular RNA and the ostensible precursors to the stable RNA classes accumulate from the earliest times examined. It is concluded that all the known stable RNA species in E. coli are the products of posttranscriptional modification.
Collapse
|