1
|
Anacker ML, Drecktrah D, LeCoultre RD, Lybecker M, Samuels DS. RNase III Processing of rRNA in the Lyme Disease Spirochete Borrelia burgdorferi. J Bacteriol 2018; 200:e00035-18. [PMID: 29632096 PMCID: PMC5996687 DOI: 10.1128/jb.00035-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/04/2018] [Indexed: 02/08/2023] Open
Abstract
The rRNA genes of Borrelia (Borreliella) burgdorferi are unusually organized; the spirochete has a single 16S rRNA gene that is more than 3 kb from a tandem pair of 23S-5S rRNA operons. We generated an rnc null mutant in B. burgdorferi that exhibits a pleiotropic phenotype, including decreased growth rate and increased cell length. Here, we demonstrate that endoribonuclease III (RNase III) is, as expected, involved in processing the 23S rRNA in B. burgdorferi The 5' and 3' ends of the three rRNAs were determined in the wild type and rncBb mutants; the results suggest that RNase III in B. burgdorferi is required for the full maturation of the 23S rRNA but not for the 5S rRNA nor, curiously, for the 16S rRNA.IMPORTANCE Lyme disease, the most common tick-borne zoonosis in the Northern Hemisphere, is caused by the bacterium Borrelia (Borreliella) burgdorferi, a member of the deeply branching spirochete phylum. B. burgdorferi carries a limited suite of ribonucleases, enzymes that cleave RNA during processing and degradation. Several ribonucleases, including RNase III, are involved in the production of ribosomes, which catalyze translation and are a major target of antibiotics. This is the first study to dissect the role of an RNase in any spirochete. We demonstrate that an RNase III mutant is viable but has altered processing of rRNA.
Collapse
MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Borrelia burgdorferi/enzymology
- Borrelia burgdorferi/genetics
- Borrelia burgdorferi/metabolism
- Humans
- Lyme Disease/microbiology
- Operon
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Ribonuclease III/genetics
- Ribonuclease III/metabolism
Collapse
Affiliation(s)
- Melissa L Anacker
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Richard D LeCoultre
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Meghan Lybecker
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Department of Biology, University of Colorado, Colorado Springs, Colorado, USA
| | - D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana, USA
| |
Collapse
|
2
|
Incarnato D, Morandi E, Anselmi F, Simon LM, Basile G, Oliviero S. In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding. Nucleic Acids Res 2017; 45:9716-9725. [PMID: 28934475 PMCID: PMC5766169 DOI: 10.1093/nar/gkx617] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 01/07/2023] Open
Abstract
Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates' secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5'-halves of long-range helices get sequestered into transient non-native interactions until their 3' counterparts have been transcribed. Together our work provides the first transcriptome-scale overview of RNA cotranscriptional folding in a living organism.
Collapse
Affiliation(s)
- Danny Incarnato
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina, 13, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy
| | - Edoardo Morandi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina, 13, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy
| | - Francesca Anselmi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina, 13, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy
| | - Lisa M. Simon
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina, 13, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy
| | - Giulia Basile
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina, 13, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina, 13, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy
| |
Collapse
|
3
|
Jin DJ, Cagliero C, Zhou YN. Role of RNA polymerase and transcription in the organization of the bacterial nucleoid. Chem Rev 2013; 113:8662-82. [PMID: 23941620 PMCID: PMC3830623 DOI: 10.1021/cr4001429] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ding Jun Jin
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
| | - Cedric Cagliero
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
| | - Yan Ning Zhou
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
| |
Collapse
|
4
|
Ohniwa RL, Ushijima Y, Saito S, Morikawa K. Proteomic analyses of nucleoid-associated proteins in Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus. PLoS One 2011; 6:e19172. [PMID: 21541338 PMCID: PMC3082553 DOI: 10.1371/journal.pone.0019172] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 03/29/2011] [Indexed: 11/18/2022] Open
Abstract
Background The bacterial nucleoid contains several hundred kinds of nucleoid-associated proteins (NAPs), which play critical roles in genome functions such as transcription and replication. Several NAPs, such as Hu and H-NS in Escherichia coli, have so far been identified. Methodology/Principal Findings Log- and stationary-phase cells of E. coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus were lysed in spermidine solutions. Nucleoids were collected by sucrose gradient centrifugation, and their protein constituents analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Over 200 proteins were identified in each species. Envelope and soluble protein fractions were also identified. By using these data sets, we obtained lists of contaminant-subtracted proteins enriched in the nucleoid fractions (csNAP lists). The lists do not cover all of the NAPs, but included Hu regardless of the growth phases and species. In addition, the csNAP lists of each species suggested that the bacterial nucleoid is equipped with the species-specific set of global regulators, oxidation-reduction enzymes, and fatty acid synthases. This implies bacteria individually developed nucleoid associated proteins toward obtaining similar characteristics. Conclusions/Significance Ours is the first study to reveal hundreds of NAPs in the bacterial nucleoid, and the obtained data set enabled us to overview some important features of the nucleoid. Several implications obtained from the present proteomic study may make it a landmark for the future functional and evolutionary study of the bacterial nucleoid.
Collapse
Affiliation(s)
- Ryosuke L Ohniwa
- Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan.
| | | | | | | |
Collapse
|
5
|
Hirschbein L, Guillen N. Characterization, assay, and use of isolated bacterial nucleoids. METHODS OF BIOCHEMICAL ANALYSIS 2006; 28:297-328. [PMID: 6178944 DOI: 10.1002/9780470110485.ch7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
6
|
Abstract
The transcription systems of chloroplasts and bacteria share different properties. The genetic material of chloroplasts is organized in the same way as bacterial nucleoids. The regulatory DNA sequences for transcription have a strong homology with their E. coli counterparts and some regulatory mechanisms could be conserved. The RNA polymerase subunits and some transcription factors also share similarities with prokaryotes. However, the chloroplast core-enzyme seems to be synthesized in the cytoplasm from nuclear encoded messages.
Collapse
|
7
|
Szeberényi J, Roy MK, Apirion D. 7 S RNA: a single site substrate for the RNA processing enzyme ribonuclease E of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 740:282-90. [PMID: 6347257 DOI: 10.1016/0167-4781(83)90137-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
7 S RNA accumulates at non-permissive temperatures in an RNAase E strain containing the recombinant plasmid pJR3 delta which carries a single 5 S rRNA gene and expression sequences. 7 S RNA is a processing intermediate that contains the complete sequence of 5 S rRNA as well as a stem-and-loop structure encoded by the terminator of rrnD. 7 S RNA can be processed in vitro by RNAase E. Structural analysis of the products (5 S rRNA and the stem) of in vitro processing of 7 S RNA revealed that the cleavage site of RNAase E in 7 S RNA is 3 nucleotides downstream from the 3' end of the mature 5 S rRNA. The cleavage generates 3'-hydroxyl and 5'-phosphate termini.
Collapse
|
8
|
|
9
|
|
10
|
Hartley MR, Head C. The synthesis of chloroplast high-molecular-weight ribosomal ribonucleic acid in spinach. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 96:301-9. [PMID: 456375 DOI: 10.1111/j.1432-1033.1979.tb13041.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Illuminated suspensions of chloroplasts isolated from young spinach leaves show incorporation of [3H]uridine into several species of RNA. One such RNA species of Mr 2.7 x 10(6) shows sequence homology with both the chloroplast 23-S rRNA (Mr = 1.05 x 10(6)) and 16-S rRNA (Mr = 0.56 x 10(6)), as judged by DNA/RNA competition hybridization. Leaves labelled in vivo with [32P]orthophosphate in the presence of chloramphenicol accumulate labelled RNAs of Mr 1.28 x 10(6), 0.71/0.75 x 10(6) and 0.47 x 10(6). The 1.28 x 10(6)-Mr RNA shows 80.5% sequence homology with the 1.05 x 10(6)-Mr rRNA and the 0.71/0.75 x 10(6)-Mr RNA mixture shows 76% sequence homology with the 0.56 x 10(6)-Mr rRNA. We conclude that the pathway of rRNA maturation in spinach chloroplasts is similar to that of Escherichia coli.
Collapse
|
11
|
Hofmann S, Miller OL. Visualization of ribosomal ribonucleic acid synthesis in a ribonuclease III-Deficient strain of Escherichia coli. J Bacteriol 1977; 132:718-22. [PMID: 334750 PMCID: PMC221915 DOI: 10.1128/jb.132.2.718-722.1977] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transmission electron microscopy was used to examine active ribosomal ribonucleic acid (rRNA) genes in two strains of Escherichia coli: N2077, deficient in the enzyme responsible for proper cleavage of the 16S sequence from the elongating nascent rRNA transcript; and N2076, functional in ribonuclease (RNase) III activity, yet otherwise isogenic to N2077. In the strain with wild-type RNase III, double gradients corresponding to a pattern of 16S-cleavage-23S transcription were observed. However, the RNase III-deficient strain exhibited a single ribosomal gradient of approximately the same length as the combined 16S-23S gradients of the wild-type strain. When the rRNA genes were somewhat loosely packed with RNA polymerases, a few of the nascent chains in the ribosomal matrixes of the RNase III-deficient strain were cleaved, but most appeared to be unprocessed. The completed, uncleaved transcripts originating from these gradients are believed to be 30S rRNA molecules recently characterized by biochemical probes.
Collapse
|
12
|
Hahn WE, Pettijohn DE, Van Ness J. One strand equivalent of the Escherichia coli genome is transcribed: complexity and abundance classes of mRNA. Science 1977; 197:582-5. [PMID: 327551 DOI: 10.1126/science.327551] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA-RNA hybridization experiments show that essentially all of the genomic information is transcribed. High, intermediate, and rare abundance classes of messenger RNA (mRNA) are present, and their estimated complexities are equal to about 240, 1300, and 700 average-sized mRNA species, respectively. The high abundance mRNA species are present, an average, two to three copies per cell and constitute about 95 percent of the mRNA mass. Intermediate abundance mRNA species are present, on average, about once per 35 cells. The relative abundance and complexity of these mRNA classes correspond well with previous respective measurements on protein. Rare RNA species are thought to represent maximally repressed genes. Analysis of RNA synthesized in vitro by isolated nucleoids (chromosomes) suggests that sense and nonsense sequences are extensively interspersed on a given strand of the DNA.
Collapse
|
13
|
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
|
14
|
Muto A. Control of ribosomal RNA synthesis in Escherichia coli. II. Ribosomal RNA synthesis in isolated nucleoids. MOLECULAR & GENERAL GENETICS : MGG 1977; 152:153-9. [PMID: 327272 DOI: 10.1007/bf00268812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effect of amino acid-starvation on the transcription in vitro of overall RNA and ribosomal RNA was investigated using nucleoids prepared from the exponentially growing and the amino acid-starved cells of rel+ and rel- strains of Escherichia coli. In this system, the synthesis of RNA is exclusively due to elongation of the chains which have been initiated in vivo. The amounts of overall and ribosomal RNA synthesized per unit of DNA in the nucleoids were analyzed for each preparation. The following observations have been made. (1) The total RNA synthesis per unit of DNA in the nucleoids from the amino acid-starved rel+ and rel- cells was not significantly different from each other. (2) The preferential ribosomal RNA synthesis occurred in the nucleoids from the growing cells; the ribosomal RNA synthesis was restricted in the nucleoids from the starved rel+ cells, while no restriction was observed in the nucleoids from the starved rel- cells. The results suggest that the ribosomal RNA synthesis is regulated at the initiation or less likely elongation level of the transcription. (3) A ribosomal RNA of a discrete size of about 30S was synthesized in the nucleoids. No mature ribosomal RNA species was produced in this system. The 30S RNA is probably a primary transcript of ribosomal RNA genes containing 23S, 16S and 5S mature ribosomal RNA sequences.
Collapse
|
15
|
Ishii S, Imamoto F. In vitro transcription of the tryptophan operon in isolated bacterial nucleoids. MOLECULAR & GENERAL GENETICS : MGG 1976; 148:295-305. [PMID: 796665 DOI: 10.1007/bf00332904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In vitro transcription of the trp operon in isolated nucleoids from Escherichia coli was studied. RNA synthesis in this system occurred primarily as a continuation of transcription which had been initiated in vivo; little or no initiation of new RNA chains was observed. Transcription of the trp operon in nucleoids by endogenous RNA polymerase procedded efficiently and ceases sequentially in the order of the gene sequence within the operon. Under these conditions, no appreciable exonuccleolytic digestion of nascent 3H-RNA was found, though some endonucleolytic cleavage was generally seen. Little or no incorporation of 14C-leucine into polypeptides was observed, inspite of tha fact that considerable number of ribosomes and nascent RNA chains were found attached to the isolated nucleoids. The synthesis of trp mRNA continued in the presence of chloramphenicol or fusidic acid, or under conditions where the rebosomal translocation factor G was inactivated. From these and other kinetic studies of trp mRNA synthesis in nucleoids obtained from nonsense strong polar mutants of the trp operon, it was shown that transcription in nucleoids was not connected functionally with transloational processes and thus unable to exhibit polarity effected by a nonsense mutation or by general translational blockage. In studies employing nucleoids from nonsense strong polar mutants of the trp operon, it was demonstrated that RNA polymerase are scantily distributed over the region downstream from the nonsense mutation site of the operon, thereby supporting a notion that in vivo transcription is eventually terminated near the nonsense mutation.
Collapse
|
16
|
Abstract
Recent studies of the structure of the bacterial nucleoid are reviewed. In the past 4 to 5 years results of electron microscopic and physical-chemical investigations of the isolated bacterial nucleoids have greatly advanced our understanding of this comparatively simple chromosome. Evidence for both long-range and short-range conformational organization of the packaged DNA has emerged, and preliminary characterization of the molecular interactions organizing this structure has been accomplished.
Collapse
|
17
|
Yuki A. Detection of ribonucleic acids which are larger than 30S precursor ribosomal RNA in RNase III deficient E. coli cells. MOLECULAR & GENERAL GENETICS : MGG 1976; 144:141-50. [PMID: 775288 DOI: 10.1007/bf02428102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
1. New high molecular weight RNA species have been found in an RNase III deficient mutant of E. coli. These RNA's were very minor but stable components of the cells, and their molecular weights, which range from 3-5.5 million daltons, are higher than that of 30S precursor ribosomal RNA. In these respects these RNAs are similar to the 2.5 M RNA reported previously (Yuki and Wittmann, 1974). 2. A method to analyse minor RNA components is described. A linear relationship between logarithms of molecular weights and logarithms of distance moved in 1.5-7.5% polyacrylamide concentration gradient gels is also described in this report. 3. DNA species whose molecular weights ranged from 1.8 to 5.5 million daltons and also a species of 8 million daltons are described. two techniques commonly used to identify RNA, viz. DNase treatment and labeling with radioactive uridine, are discussed in connection with these DNAs. 4. The determination of the molecular weight of 30S precursor ribosomal RNA is discussed and it is suggested that this RNA is heterogenous, consisting of two species of molecular weight 1.8 million daltons and 2.0 million daltons, respectively.
Collapse
|
18
|
Hecht RM, Pettijohn DE. Studies of DNA bound RNA molecules isolated from nucleoids of Escherichia coli. Nucleic Acids Res 1976; 3:767-88. [PMID: 775442 PMCID: PMC342939 DOI: 10.1093/nar/3.3.767] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Methods are developed for studying RNA molecules bound directly to DNA in bacterial nucleoids. It is found that among the 1000-3000 nascent RNA chains that normally are attached to the DNA via their associated RNA polymerase molecules, 74 +/- 14 chains per nucleoid can be bound differently. These chains unlike the other nascent RNAs remained bound to the DNA after the chromosome was deproteinized and sheared. Sensitive assays using radioactive labels detected no RNA polymerase involved in the RNA-DNA linkage. The linkage was stable at low temperatures, but the RNA separated from the DNA at high temperature. The bound RNA molecules were heterodisperse (weight average length 1200 bases). Pulse-chase experiments and studies of the fate of these RNA molecules in rifampicin treated cells demonstrated that they are nascent RNAs, degraded or released from the DNA in vivo with kinetics similar to that of the total nascent RNA. Hybridization analyses showed that the chains are composed at least in part of nascent rRNA and known mRNA molecules. Some, but not more than 5% of the bound chains, contained sequences of about 300 nucleotides in length, bound to the DNA in an RNase resistant form.
Collapse
|
19
|
Herzfeld F, Kiper M. The reconstitution of Anacystis nidulans DNA-dependent RNA polymerase from its isolated subunits. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 62:189-92. [PMID: 814000 DOI: 10.1111/j.1432-1033.1976.tb10112.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The DNA-dependent RNA polymerase of the blud-green alga Anacystis nidulans was reconstituted from its isolated subunits in the absence of urea. Applying this technique the kinetics and the subunit requirements of the reconstitution process were analyzed. The results reveal differences with respect to the reconstitution of Escherichia coli polymerase. Reconstitution proceeds much more slowly in the case of the A. nidulans enzyme. Reconstitution here is absolutely dependent on the presence of the subunit sigma. On the other hand, the largest of the subunits of Mr=190000 can be fully substituted by a specific degradation product of this subunit of Mr=175000. Heterologous reconstitution between subunits of E. coli and A. nidulans polymerase does not result in active enzyme hybrids, showing a divergent evolution of the structure of this enzyme in these procaryotic organisms.
Collapse
|
20
|
Drlica K, Worcel A. Conformational transitions in the Escherichia coli chromosome: analysis by viscometry and sedimentation. J Mol Biol 1975; 98:393-411. [PMID: 1104870 DOI: 10.1016/s0022-2836(75)80126-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
21
|
|
22
|
Giorno R, Hecht RM, Pettijohn D. Analysis by isopycnic centrifugation of isolated nucleoids of Escherichia coli. Nucleic Acids Res 1975; 2:1559-67. [PMID: 1101227 PMCID: PMC343523 DOI: 10.1093/nar/2.9.1559] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The isolated, formaldehyde-fixed nucleoid of E. coli has been analyzed by isopycnic centrifugation in CsCl density gradients. The membrane-free nucleoid bands at a density of 1.69 +/- 0.02 g/cm3. The membrane-associated nucleoid bands at a density of 1.46 +/- 0.02 g/cm3. Both species sediment to equilibrium as nearly monodisperse bands in CsCl, suggesting that the nucleoid components of DNA, RNA and protein are present in relatively constant ratios. These ratios are constant regardless of the position of the nucleoids in the heterogeneous sedimentation profile of a preparative sucrose gradient. The fixed nucleoids remain condensed during isopycnic centrifugation and there is no detectable loss of RNA from the nucleoid.
Collapse
|
23
|
Giorno R, Stamato T, Lydersen B, Pettijohn D. Transcription in vitro of DNA in isolated bacterial nucleoids. J Mol Biol 1975; 96:217-37. [PMID: 1100843 DOI: 10.1016/0022-2836(75)90344-7] [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: 12/25/2022]
|
24
|
The 30 S ribosomal precursor RNA from Escherichia coli. A primary transcript containing 23 S, 16 S, and 5 S sequences. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41228-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
25
|
Duncan MJ, Gorini L. A ribonucleoprotein precursor of both the 30S and 50S ribosomal sunbunits of Escherichia coli. Proc Natl Acad Sci U S A 1975; 72:1533-7. [PMID: 1093184 PMCID: PMC432571 DOI: 10.1073/pnas.72.4.1533] [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: 12/25/2022] Open
Abstract
A ribonucleoprotein particle (46S) has been isolated from [3H]uridine pulse-labeled cultures of E. Coli AB301/105. Evidence from pulse chase experiments and from protein analysis suggested that this particle may give rise to both the 30S and 50S ribosomal subunits. Direct deproteinization of the particle yielded 30S RNA, while deproteinization after treatment with a crude RNase III preparation yielded products similar to 23S and 16S RNA. This result is consistent with the idea that the 46S ribonucleoprotein is the in vivo counterpart of 30S RNA, which is the in vitro product obtained after phenol extraction.
Collapse
|
26
|
Muto A. Preferential ribosomal RNA synthesis in the lysate of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1975; 138:1-10. [PMID: 1102922 DOI: 10.1007/bf00268822] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The RNA synthesis in non-viscous lysates containing the intact folded chromosome and cytoplasm fractions prepared from Escherichia coli has been examined in vitro. The RNA synthesis not only by chain extension but also by new chain initiation occurs in this system. While the RNA synthesis by chain extension takes place on the chromosome fraction alone (Pettijohn et al., 1970), an addition of the cytoplasm fraction is necessary for the synthesis by new chain initiations (de novo synthesis). Analyses of the in vitro synthesized RNA by hybridization-competition and by sucrose gradient centrifugation show that 16S and 23S ribosomal RNAs account for about 40% of the total RNA products. The cytoplasm fraction is required for the de novo synthesis of ribosomal RNA at high relative rate. Guanosine tetraphosphate (ppGpp) does not specifically inhibit ribosomal RNA synthesis in this system.
Collapse
|
27
|
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
|
28
|
|
29
|
Dean JR, Sykes J. The role of ribonuclease II in the maturation of precursor 16S ribosomal ribonucleic acid in Escherichia coli. Biochem J 1974; 140:443-50. [PMID: 4614796 PMCID: PMC1168021 DOI: 10.1042/bj1400443] [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: 01/11/2023]
Abstract
The suggested involvement of ribonuclease II in the maturation of rRNA has been examined directly by determining the activity of the enzyme and the amount of p16S rRNA in cell-free extracts from Escherichia coli A19 and its temperature-sensitive derivative N464 grown under experimental conditions designed to vary the amounts of enzyme and precursor independently. In strain A19 the enzyme showed maximum activity in circumstances where the amount of p16S rRNA was normal (e.g. exponential-phase cells) or raised eight times (e.g. during inhibition of growth by methionine starvation of the relaxed auxotroph or by chloramphenicol or puromycin treatment). In strain N464 at the non-permissive temperature the ribonuclease II activity may be decreased by 50% without effect upon the amount of p16S rRNA, whereas in methionine starvation of this strain the enzyme activity is at a maximum and the p16S rRNA is eight times that in exponential-phase cells. These observations are discussed in relation to the previously implied role of ribonuclease II in the maturation of rRNA within ribosome precursors.
Collapse
|
30
|
Chamberlin MJ. 10. Bacterial DNA-Dependent RNA Polymerase. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s1874-6047(08)60142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
|
31
|
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]
|
32
|
Dunn JJ, Studier FW. T7 early RNAs and Escherichia coli ribosomal RNAs are cut from large precursor RNAs in vivo by ribonuclease 3. Proc Natl Acad Sci U S A 1973; 70:3296-3300. [PMID: 4587248 PMCID: PMC427223 DOI: 10.1073/pnas.70.12.3296] [Citation(s) in RCA: 274] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The early region of T7 DNA is transcribed as a single unit in a Ribonuclease III-deficient E. coli strain to produce large molecules essentially identical to those produced in vitro by E. coli RNA polymerase. As with the in vitro RNAs, these molecules are cut by purified RNase III in vitro to produce the messenger RNAs normally observed in vivo. Thus, the normal pathway for producing the T7 early messenger RNAs in vivo appears to involve endonucleolytic cleavage by RNase III. The uninfected RNase III-deficient strain contains several RNAs not observed in the parent strain. Patterns of labeling in vivo suggest that the largest of these RNAs, about 1.8 x 10(6) daltons, may be a precursor to the 16S and 23S ribosomal RNAs. When this large molecule is treated in vitro with purified RNase III, molecules the size of precursor 16S and 23S ribosomal RNAs are released; hybridization competition experiments also indicate that the 1.8 x 10(6) dalton RNA does indeed represent ribosomal RNA. Thus, RNase III cleavage seems to be part of the normal pathway for producing at least the 16S and 23S ribosomal RNAs in vivo. Several smaller molecules are also released from the 1.8 x 10(6) dalton RNA by RNase III, but it is not yet established whether any of these contain 5S RNA sequences.
Collapse
MESH Headings
- Centrifugation, Density Gradient
- Coliphages/metabolism
- DNA, Bacterial/metabolism
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/enzymology
- Molecular Weight
- Nucleic Acid Hybridization
- Phosphorus Radioisotopes
- RNA, Bacterial/analysis
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/metabolism
- RNA, Ribosomal/analysis
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/metabolism
- RNA, Viral/analysis
- RNA, Viral/biosynthesis
- Ribonucleases/metabolism
- Ribonucleotides/metabolism
- Transcription, Genetic
Collapse
|
33
|
Abstract
Chloroplasts isolated from young spinach leaves incorporate [(3)H]uridine into RNA. This incorporation shows an absolute requirement for light and does not occur in lysed chloroplasts. Fractionation by polyacrylamide-gel electrophoresis of the RNA synthesized in vitro reveals a major discrete product of molecular weight 2.7x10(6) and two minor products of molecular weight 1.2x10(6) and 0.47x10(6). These discrete products are super-imposed on a background of polydisperse RNA. The incorporation of (32)P(i) into chloroplast rRNA species (mol.wt. 1.05x10(6) and 0.56x10(6)) in excised spinach leaves proceeds after a distinct lag period compared with the incorporation into cytoplasmic rRNA species (mol.wt. 1.34x10(6) and 0.7x10(6)). Incorporation of (32)P(i) into chloroplast RNA species of molecular weight 2.7x10(6), 1.2x10(6), 0.65x10(6) and 0.47x10(6) proceeds without such a time-lag. The kinetics of labelling of the individual RNA components is consistent with the rapidly labelled RNA species of molecular weight 1.2x10(6) and 0.65x10(6) being precursors to the more slowly labelled rRNA species of molecular weight 1.05x10(6) and 0.56x10(6) respectively.
Collapse
|
34
|
Pace NR, Pato ML, McKibbin J, Radcliffe CW. Precursors of 5 S ribosomal RNA in Bacillus subtilis. J Mol Biol 1973; 75:619-31. [PMID: 4200018 DOI: 10.1016/0022-2836(73)90296-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
35
|
Osenholts M, Yankofsky SA, Segal E. Ribosomal RNA cistron topography in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 308:88-100. [PMID: 4353004 DOI: 10.1016/0005-2787(73)90125-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
36
|
Jarry B, Rosset R. Localization of some 5s RNA cistrons on Escherichia coli chromosome. MOLECULAR & GENERAL GENETICS : MGG 1973; 121:151-62. [PMID: 4571522 DOI: 10.1007/bf00277529] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
37
|
Rüger W. Die Transkription der genetischen Information und ihre Regulation durch Proteinfaktoren. Angew Chem Int Ed Engl 1972. [DOI: 10.1002/ange.19720842002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
38
|
Rüger W. Transcription of genetic information and its regulation by protein factors. Angew Chem Int Ed Engl 1972; 11:883-93. [PMID: 4628292 DOI: 10.1002/anie.197208831] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
39
|
Winsten JA, Huang PC. Ribosomal RNA synthesis in vitro: a protein-DNA complex from Bacillus subtilis active in initiation of transcription. Proc Natl Acad Sci U S A 1972; 69:1387-91. [PMID: 4624758 PMCID: PMC426708 DOI: 10.1073/pnas.69.6.1387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A protein-DNA transcription complex, isolated from logarithmic-phase cells of Bacillus subtilis, is active in the initiation of new rounds of RNA synthesis in vitro. Transcription directed by the endogenous DNA of the complex is sensitive to inhibitors of initiation. In addition, the effect of addition of a competing template indicates that RNA polymerase in the complex is bound to endogenous DNA in a dissociable, preinitiation state. Hybridization-competition analysis of the RNA product obtained from the in vitro reaction indicates that it is greatly enriched for ribosomal RNA sequences. This initiating complex should be useful for the study of regulation of expression of ribosomal RNA genes.
Collapse
|
40
|
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]
|
41
|
Stamato TD, Pettijohn DE. Regulation of ribosomal RNA synthesis in stringent bacteria. NATURE: NEW BIOLOGY 1971; 234:99-102. [PMID: 4943521 DOI: 10.1038/newbio234099a0] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
42
|
Transcriptional organization of the ribosomal RNA cistrons in Escherichia coli. Proc Natl Acad Sci U S A 1971; 68:1786-90. [PMID: 4942914 PMCID: PMC389293 DOI: 10.1073/pnas.68.8.1786] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The data presented support the hypothesis that 16S, 23S, and 5S ribosomal RNAs of Escherichia coli are transcribed in vivo from transcriptional units consisting of single cistrons for these species arranged in the order 16S-23S-5S, with transcription beginning at the 16S end.
Collapse
|
43
|
Abstract
The mode of biosynthesis of the 16S and 23S ribosomal ribonucleic acids (rRNA) was studied in Bacillus subtilis 168thy(-). Three criteria were used to define the characteristics of the rRNA species: (i) the time required at 37 degrees C to synthesize 16S and 23S rRNA chains de novo in growing cultures; (ii) the degree of reactivity of the 3'-terminal groups of the rRNA molecules with periodate and [carbonyl-(14)C]isonicotinic acid hydrazide; and (iii) the reactivity of the 5'-terminal regions of the rRNA molecules with the bacterial exonuclease purified by Riley (1969). The 16S and 23S chains of B. subtilis were synthesized at rates of 22+/-2 and 21+/-2 nucleotides added/s. The periodate-[(14)C]isonicotinic acid hydrazide and the exonuclease techniques for estimating apparent chain lengths of RNA indicated that the chain length of the 23S rRNA was 1.8 times that of the 16S fraction. The apparent chain lengths of each rRNA species were: 16S rRNA, 1650+/-50 nucleotide residues; 23S rRNA, 3050+/-90 nucleotide residues. It appears that, the 16S and 23S rRNA molecules in B. subtilis are synthesized in the expected manner, by simple polymerization of the final products on independent cistrons.
Collapse
|
44
|
|
45
|
Stonington OG, Pettijohn DE. The folded genome of Escherichia coli isolated in a protein-DNA-RNA complex. Proc Natl Acad Sci U S A 1971; 68:6-9. [PMID: 4924971 PMCID: PMC391088 DOI: 10.1073/pnas.68.1.6] [Citation(s) in RCA: 190] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The DNA of Escherichia coli has been isolated in a compact structure containing small amounts of protein and RNA and having a sedimentation coefficient of approximately 3200 S. The molecular weight of the DNA in the complex is very large (probably higher than 10(9)); the protein is predominantly core RNA polymerase; the RNA is chiefly nascent messenger and ribosomal chains. Solutions containing the complex have low viscosities; this plus its sedimentation rate suggest that the DNA is in a tightly folded conformation. The DNA unfolds after exposure to RNase or heat; this indicates that an RNA component of the complex is involved in stabilizing the structure.
Collapse
|