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Irastortza-Olaziregi M, Amster-Choder O. RNA localization in prokaryotes: Where, when, how, and why. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1615. [PMID: 32851805 DOI: 10.1002/wrna.1615] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/27/2022]
Abstract
Only recently has it been recognized that the transcriptome of bacteria and archaea can be spatiotemporally regulated. All types of prokaryotic transcripts-rRNAs, tRNAs, mRNAs, and regulatory RNAs-may acquire specific localization and these patterns can be temporally regulated. In some cases bacterial RNAs reside in the vicinity of the transcription site, but in many others, transcripts show distinct localizations to the cytoplasm, the inner membrane, or the pole of rod-shaped species. This localization, which often overlaps with that of the encoded proteins, can be achieved either in a translation-dependent or translation-independent fashion. The latter implies that RNAs carry sequence-level features that determine their final localization with the aid of RNA-targeting factors. Localization of transcripts regulates their posttranscriptional fate by affecting their degradation and processing, translation efficiency, sRNA-mediated regulation, and/or propensity to undergo RNA modifications. By facilitating complex assembly and liquid-liquid phase separation, RNA localization is not only a consequence but also a driver of subcellular spatiotemporal complexity. We foresee that in the coming years the study of RNA localization in prokaryotes will produce important novel insights regarding the fundamental understanding of membrane-less subcellular organization and lead to practical outputs with biotechnological and therapeutic implications. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Abstract
Spatial organization is a hallmark of all living systems. Even bacteria, the smallest forms of cellular life, display defined shapes and complex internal organization, showcasing a highly structured genome, cytoskeletal filaments, localized scaffolding structures, dynamic spatial patterns, active transport, and occasionally, intracellular organelles. Spatial order is required for faithful and efficient cellular replication and offers a powerful means for the development of unique biological properties. Here, we discuss organizational features of bacterial cells and highlight how bacteria have evolved diverse spatial mechanisms to overcome challenges cells face as self-replicating entities.
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Chen H, Shiroguchi K, Ge H, Xie XS. Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol Syst Biol 2015; 11:781. [PMID: 25583150 PMCID: PMC4332155 DOI: 10.15252/msb.20145794] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An essential part of gene expression is the coordination of RNA synthesis and degradation, which occurs in the same cellular compartment in bacteria. Here, we report a genome-wide RNA degradation study in Escherichia coli using RNA-seq, and present evidence that the stereotypical exponential RNA decay curve obtained using initiation inhibitor, rifampicin, consists of two phases: residual RNA synthesis, a delay in the interruption of steady state that is dependent on distance relative to the mRNA's 5′ end, and the exponential decay. This gives a more accurate RNA lifetime and RNA polymerase elongation rate simultaneously genome-wide. Transcripts typically have a single RNA decay constant along all positions, which is distinct between different operons, indicating that RNA stability is unlikely determined by local sequences. These measurements allowed us to establish a model for RNA processing involving co-transcriptional degradation, providing quantitative description of the macromolecular coordination in gene expression in bacteria on a system-wide level.
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Affiliation(s)
- Huiyi Chen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Katsuyuki Shiroguchi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hao Ge
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Science Peking University, Beijing, China Beijing International Center for Mathematical Research (BICMR) Peking University, Beijing, China
| | - Xiaoliang Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA Biodynamic Optical Imaging Center (BIOPIC), School of Life Science Peking University, Beijing, China
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Evguenieva-Hackenberg E, Klug G. New aspects of RNA processing in prokaryotes. Curr Opin Microbiol 2011; 14:587-92. [DOI: 10.1016/j.mib.2011.07.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 07/15/2011] [Accepted: 07/23/2011] [Indexed: 10/17/2022]
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Dreyfus M. Killer and protective ribosomes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:423-66. [PMID: 19215779 DOI: 10.1016/s0079-6603(08)00811-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In prokaryotes, translation influences mRNA decay. The breakdown of most Escherichia coli mRNAs is initiated by RNase E, a 5'-dependent endonuclease. Some mRNAs are protected by ribosomes even if these are located far upstream of cleavage sites ("protection at a distance"), whereas others require direct shielding of these sites. I argue that these situations reflect different modes of interaction of RNase E with mRNAs. Protection at a distance is most impressive in Bacilli, where ribosomes can protect kilobases of unstable downstream sequences. I propose that this protection reflects the role in mRNA decay of RNase J1, a 5'-->3' exonuclease with no E. coli equivalent. Finally, recent years have shown that besides their protective role, ribosomes can also cleave their mRNA under circumstances that cause ribosome stalling. The endonuclease associated with this "killing" activity, which has a eukaryotic counterpart ("no-go decay"), is not characterized; it may be borne by the distressed ribosome itself.
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Abstract
Fusion proteins are commonly used as a source of antigen for producing antibodies and in many cases can be useful for biochemical analyses. This unit describes two widely used expression systems for producing large amounts of proteins in E. coli. One system expresses lacZ fusions using the pUR series of vectors and the other expresses trpE fusions using the pATH vectors. The gene of interest is first subcloned into either a pUR or pATH vector in the correct reading frame. The correct transformant is selected, grown, and then induced with either IPTG or IAA. Sonication of cells in the presence of protease inhibitors is used to prepare extracts containing both types of fusion proteins, as well as other types of proteins overexpressed in E. coli. The extracts are checked for the presence of fusion protein on an SDS-polyacrylamide gel.
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Affiliation(s)
- T Hoey
- University of California, Berkeley, California, USA
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8
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Schimke RT. Control of enzyme levels in mammalian tissues. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 37:135-87. [PMID: 4570065 DOI: 10.1002/9780470122822.ch3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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9
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Yanofsky C. Advancing our knowledge in biochemistry, genetics, and microbiology through studies on tryptophan metabolism. Annu Rev Biochem 2002; 70:1-37. [PMID: 11395401 DOI: 10.1146/annurev.biochem.70.1.1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
I was fortunate to practice science during the last half of the previous century, when many basic biological and biochemical concepts could be experimentally addressed for the first time. My introduction to research involved isolating and identifying intermediates in the niacin biosynthetic pathway. These studies were followed by investigations focused on determining the properties of genes and enzymes essential to metabolism and examining how they were alterable by mutation. The most challenging problem I initially attacked was establishing the colinear relationship between gene and protein. Subsequent research emphasized identification and characterization of regulatory mechanisms that microorganisms use to control gene expression. An elaborate regulatory strategy, transcription attenuation, was discovered that is often based on selection between alternative RNA structures. Throughout my career I enjoyed the excitement of solving basic scientific problems. Most rewarding, however, was the feeling that I was helping young scientists experience the pleasure of performing creative research.
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Affiliation(s)
- C Yanofsky
- Department of Biological Sciences, Stanford University, Stanford, California 94305, USA.
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Wagner LA, Gesteland RF, Dayhuff TJ, Weiss RB. An efficient Shine-Dalgarno sequence but not translation is necessary for lacZ mRNA stability in Escherichia coli. J Bacteriol 1994; 176:1683-8. [PMID: 7510674 PMCID: PMC205255 DOI: 10.1128/jb.176.6.1683-1688.1994] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The 5' ends of many bacterial transcripts are important in determining mRNA stability. A series of Shine-Dalgarno (SD) sequence changes showed that the complementarity of the SD sequence to the anti-SD sequence of 16S rRNA correlates with lacZ mRNA stability in Escherichia coli. Several initiation codon changes showed that an efficient initiation codon is not necessary to maintain lacZ mRNA stability. A stop codon in the 10th codon of lacZ increased mRNA stability. Therefore, ribosomal binding via the SD sequence but not translation of the coding region is necessary to maintain lacZ mRNA stability.
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Affiliation(s)
- L A Wagner
- Department of Human Genetics, University of Utah, Salt Lake City 84132
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11
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Bouvet P, Belasco JG. Control of RNase E-mediated RNA degradation by 5'-terminal base pairing in E. coli. Nature 1992; 360:488-91. [PMID: 1280335 DOI: 10.1038/360488a0] [Citation(s) in RCA: 189] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Despite the variety of messenger RNA half-lives in bacteria (0.5-30 min in Escherichia coli) and their importance in controlling gene expression, their molecular basis remains obscure. The lifetime of an entire mRNA molecule can be determined by features near its 5' end, but no 5' exoribonuclease has been identified in any prokaryotic organism. A mutation that inactivates E. coli RNase E also increases the average lifetime of bulk E. coli mRNA and of many individual messages, suggesting that cleavage by this endonuclease may be the rate-determining step in the degradation of most mRNAs in E. coli. We have investigated the substrate preference of RNase E in E. coli by using variants of RNA I, a small untranslated RNA whose swift degradation in vivo is initiated by RNase E cleavage at an internal site. We report here that RNase E has an unprecedented substrate specificity for an endoribonuclease, as it preferentially cleaves RNAs that have several unpaired nucleotides at the 5' end. The sensitivity of RNase E to 5'-terminal base pairing may explain how determinants near the 5' end can control rates of mRNA decay in bacteria.
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Affiliation(s)
- P Bouvet
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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Koerner TJ, Hill JE, Myers AM, Tzagoloff A. High-expression vectors with multiple cloning sites for construction of trpE fusion genes: pATH vectors. Methods Enzymol 1991; 194:477-90. [PMID: 2005804 DOI: 10.1016/0076-6879(91)94036-c] [Citation(s) in RCA: 302] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Emory SA, Belasco JG. The ompA 5' untranslated RNA segment functions in Escherichia coli as a growth-rate-regulated mRNA stabilizer whose activity is unrelated to translational efficiency. J Bacteriol 1990; 172:4472-81. [PMID: 1695894 PMCID: PMC213277 DOI: 10.1128/jb.172.8.4472-4481.1990] [Citation(s) in RCA: 155] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The 5' untranslated region (UTR) of the long-lived Escherichia coli ompA message can function in vivo as an mRNA stabilizer. Substitution of this ompA mRNA segment for the corresponding segment of the labile bla gene transcripts prolongs their lifetime by a factor of 6. We show here that the function of this ompA mRNA stabilizer requires the presence of a 115-nucleotide ompA RNA segment that lies upstream of the ribosome-binding site. Although deletion of this segment reduced the half-life of the ompA transcript by a factor of 5, its absence had almost no effect on the translational efficiency of ompA mRNA. Like the ompA transcript, but unlike bla mRNA, hybrid ompA-bla messages containing the complete ompA 5' UTR were significantly less stable under conditions of slow bacterial growth. We conclude that the stabilizing activity of the ompA 5' UTR is growth rate regulated and that the mechanism of mRNA stabilization by this RNA segment is not related to the spacing between translating ribosomes.
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Affiliation(s)
- S A Emory
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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14
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Ray JM, Yanofsky C, Bauerle R. Mutational analysis of the catalytic and feedback sites of the tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase of Escherichia coli. J Bacteriol 1988; 170:5500-6. [PMID: 2903857 PMCID: PMC211643 DOI: 10.1128/jb.170.12.5500-5506.1988] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The nucleotide sequence of aroH, the structural gene for the tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase [DAHPS(Trp)], is presented, and the deduced amino acid sequence of AroH is compared with that of the tyrosine-sensitive (AroF) and phenylalanine-sensitive (AroG) DAHPS isoenzymes. The high degree of sequence similarity among the three isoenzymes strongly indicates that they have a common evolutionary origin. In vitro chemical mutagenesis of the cloned aroH gene was used to identify residues and regions of the polypeptide essential for catalytic activity and for tryptophan feedback regulation. Missense mutations leading either to loss of catalytic activity or to feedback resistance were found interspersed throughout the polypeptide, suggesting overlapping catalytic and regulatory sites in DAHPS(Trp). We conclude that the specificity of feedback regulation of the isoenzymes was probably acquired by the duplication and divergent evolution of an ancestral gene, rather than by domain recruitment.
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Affiliation(s)
- J M Ray
- Department of Biology and Molecular Biology Institute, University of Virginia, Charlottesville 22901
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15
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Duvall EJ, Lovett PS. Chloramphenicol induces translation of the mRNA for a chloramphenicol-resistance gene in Bacillus subtilis. Proc Natl Acad Sci U S A 1986; 83:3939-43. [PMID: 3086871 PMCID: PMC323640 DOI: 10.1073/pnas.83.11.3939] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
cat-86 is a plasmid gene specifying chloramphenicol-inducible chloramphenicol acetyltransferase activity in Bacillus subtilis. Inducibility has been suggested to result primarily from activation of the translation of cat-86 mRNA by subinhibitory levels of chloramphenicol. To directly test the involvement of transcription in cat-86 induction, the gene was transcriptionally activated with a strong promoter, resulting in the synthesis of relatively high levels of cat-86 mRNA in uninduced cells. When RNA synthesis was blocked with rifampin (100 micrograms/ml), de novo inducibility of cat-86 by chloramphenicol could be demonstrated for more than 30 min. These results indicate that concurrent transcription is not essential for cat-86 induction. Accordingly, cat-86 is one of only a few inducible bacterial genes in which the primary form of regulation is at the translational level. This form of regulation may apply to other cat genes of Gram-positive origin whose expression is also inducible by chloramphenicol.
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16
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French S, Martin K, Patterson T, Bauerle R, Miller OL. Electron microscopic visualization of trp operon expression in Salmonella typhimurium. Proc Natl Acad Sci U S A 1985; 82:4638-42. [PMID: 3895222 PMCID: PMC390441 DOI: 10.1073/pnas.82.14.4638] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Transcriptional activity of plasmids carrying wild-type and mutant trp operons was visualized in cell lysates of Salmonella typhimurium. Plasmid and transcription-unit sizes varied with the size of the cloned operon. Following 3-(3-indolyl)acrylic acid derepression, all operons of a particular type exhibited the same high level of transcriptional activity. An estimated 11-14 transcripts must be initiated each minute to maintain the 190-base-pair spacing of RNA polymerases observed on the promoter-proximal half of the wild-type trp operon. A decline in RNA polymerase density was observed on promoter-distal portions of cloned trp operons, which may be attributable to premature transcription termination accompanying translation inhibition due to indolylacrylic acid's interference with normal tryptophanyl-tRNA synthetase activity.
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17
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Cannistraro VJ, Kennell D. Evidence that the 5' end of lac mRNA starts to decay as soon as it is synthesized. J Bacteriol 1985; 161:820-2. [PMID: 3918023 PMCID: PMC214966 DOI: 10.1128/jb.161.2.820-822.1985] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
By monitoring the decay of the first 16% of the beta-galactosidase message, we showed that the 5' end started to decay before the 3' end was completed and at a rate equivalent to that of the whole molecule. Thus, decay was neither from 3' to 5' nor from random internal fragmentation but rather proceeded in a net 5' to 3' direction.
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18
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Belasco JG, Beatty JT, Adams CW, von Gabain A, Cohen SN. Differential expression of photosynthesis genes in R. capsulata results from segmental differences in stability within the polycistronic rxcA transcript. Cell 1985; 40:171-81. [PMID: 2981627 DOI: 10.1016/0092-8674(85)90320-4] [Citation(s) in RCA: 256] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We report that the light-harvesting and reaction center genes in the rxcA locus of R. capsulata are contained within a single operon and that their differential expression results predominantly from marked segmental differences in stability within the polycistronic rxcA transcript. The 3' portion of this transcript is rapidly degraded to give rise to either of two slowly decaying mRNA remnants, both of which encode only the light-harvesting polypeptides. The greater stability of these remnants accounts for nearly all of the difference between the concentrations of the light-harvesting and reaction center proteins. The unstable 3' portion of the transcript is delimited by two alternative stem-and-loop structures, which apparently act as barriers to 3' exoribonucleases and thereby protect the upstream RNA segment. When a DNA fragment containing the rxcA locus was fused to a plasmid promoter and transcribed in E. coli, the long precursor transcript was processed to two short messages of greater stability, as in R. capsulata.
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19
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von Gabain A, Belasco JG, Schottel JL, Chang AC, Cohen SN. Decay of mRNA in Escherichia coli: investigation of the fate of specific segments of transcripts. Proc Natl Acad Sci U S A 1983; 80:653-7. [PMID: 6187001 PMCID: PMC393437 DOI: 10.1073/pnas.80.3.653] [Citation(s) in RCA: 300] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
An assay was developed to investigate the fate of specific segments of beta-lactamase (bla) and ompA gene transcripts in Escherichia coli. DNA probes cloned in bacteriophage M13 were treated with an endonuclease capable of cleaving single-stranded DNA, the fragments produced were annealed with total cellular RNA, and the resulting RNA . DNA hybrids were subjected to S1 nuclease treatment and gel fractionation. By using this assay, direct evidence was obtained for 3'-to-5' directionality in the decay of the long-lived mRNA encoded by the ompA gene, and no preferential stability was observed for translated versus untranslated mRNA segments. In the case of bla mRNA, initial cleavage of the full-length transcript was rate limiting, and no decay intermediates were detected. No difference in degradation rate was seen for bla transcripts having variant 3' or 5' termini.
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20
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Lim LW, Kennell D. Evidence for random endonucleolytic cleavages between messages in decay of Escherichia coli trp mRNA. J Mol Biol 1980; 141:227-33. [PMID: 6160252 DOI: 10.1016/0022-2836(80)90388-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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21
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Lim LW, Kennell D. Models for decay of Escherichia coli lac messenger RNA and evidence for inactivating cleavages between its messages. J Mol Biol 1979; 135:369-90. [PMID: 94103 DOI: 10.1016/0022-2836(79)90442-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Kano Y, Nakamura H, Somerville RL, Imamoto F. Decay rates of Escherichia coli trp messenger RNA molecules lacking the normal 5'-terminal sequences. MOLECULAR & GENERAL GENETICS : MGG 1979; 176:379-84. [PMID: 392239 DOI: 10.1007/bf00333101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Berman ML, Beckwith J. Fusions of the lac operon to the transfer RNA gene tyrT of Escherichia coli. J Mol Biol 1979; 130:285-301. [PMID: 381675 DOI: 10.1016/0022-2836(79)90542-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Kano Y, Imamoto F. Evidence for endonucleolytic cleavage at the 5'-proximal segment of the trp messenger RNA in Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1979; 172:25-30. [PMID: 377022 DOI: 10.1007/bf00276211] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 5'-proximal trp leader RNA segment (about 5S) decays at 2 to 3 times slower rates than the distal trp mRNA sequence. This has been demonstrated by employing the deletion mutants which lack a large portion of the structural genes but retain the promoter-proximal region of the trp operon. Relative stability of the leader RNA is not merely due to the presence of an untranslatable region in the segment; the internal untranslatable segment of trp mRNA downstream from the nonsense alteration site of a double mutant trpAD28.trpE9758 decays as fast as the normal trp mRNA sequence. These results suggest that the trp mRNA is endonucleolytically cleaved to yield the small 5'-proximal leader RNA segment before the distal mRNA decays and that the leader RNA sequence is not subject to usual mode of mRNA decay in the 5' to 3' direction.
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25
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Sens D, Natter W, Garvin RT, James E. Transcription of the argF and argI genes of the arginine biosynthetic regulon of Escherichia coli K12, performed in vitro. MOLECULAR & GENERAL GENETICS : MGG 1977; 155:7-18. [PMID: 337119 DOI: 10.1007/bf00268555] [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 cell-free transcription of the argF and argI genes of the arginine biosynthetic regions is described using an S-30 system capable of coupled in vitro transcription-translation. Template DNA isolated from two independently isolated arginine transducing phages was used in this work. Steady state mRNA synthesis was observed which was attributed to RNAase degradation. Regulation of argF mRNA synthesis, directed by the argF gene carried on the specialized transducing phage phi80dargF is effected to the extent of at least 95% by the arginine holorepressor at the transcriptional stage and at least 80% of the regulation of the expression of the argI gene is mediated at the transcriptional stage. Evidence is presented which indicates that the arginine holorepressor prevents RNA polymerase from binding to the arginine promoter and suggests that the operator and promoter sites may overlap.
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Schlessinger D, Jacobs KA, Gupta RS, Kano Y, Imamoto F. Decay of individual Escherichia coli trp messenger RNA molecules is sequentially ordered. J Mol Biol 1977; 110:421-39. [PMID: 321792 DOI: 10.1016/s0022-2836(77)80107-1] [Citation(s) in RCA: 28] [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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27
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Karam J, McCulley C, Leach M. Genetic control of mRNA decay in T4 phage-infected Escherichia coli. Virology 1977; 76:685-700. [PMID: 320754 DOI: 10.1016/0042-6822(77)90251-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Fernandez L, Singh UN. Studies on the stability of ribosomal protein messenger RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 454:79-85. [PMID: 791371 DOI: 10.1016/0005-2787(76)90356-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Morse DE, Morse AN. Dual-control of the tryptophan operon is mediated by both tryptophanyl-tRNA synthetase and the repressor. J Mol Biol 1976; 103:209-26. [PMID: 781267 DOI: 10.1016/0022-2836(76)90310-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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30
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Datta AK, Niyogi SK. Biochemistry and physiology of bacterial ribonucleases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1976; 17:271-308. [PMID: 6997 DOI: 10.1016/s0079-6603(08)60073-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Gupta RS, Schlessinger D. Coupling of rates of transcription, translation, and messenger ribonucleic acid degradation in streptomycin-dependent mutants of Escherichia coli. J Bacteriol 1976; 125:84-93. [PMID: 1107319 PMCID: PMC233338 DOI: 10.1128/jb.125.1.84-93.1976] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The growth rates of streptomycin-dependent mutants varied in proportion to the level of streptomycin supplied; growth also varied characteristically from one dependent strain to another at a given streptomycin concentration. When cells growing at different rates (over a threefold range) were treated with rifampin, direct proportionality was observed for three parameters: (i) the rates of shutoff of transcription of total ribonucleic acid (RNA) and ribosomal RNA, as measured by pulse labeling at later times; (ii) the translation time for molecules of beta-galactosidase; and (iii) the rate of chemical degradation of messenger RNA. In contrast, the rate of functional inactivation of both total and beta-galactosidase messenger RNA was about the same at all growth rates. None of the variations of growth or other parameters were observed in an otherwise isogenic streptomycin-resistant strain treated with streptomycin. Since the mutational change in strd mutants and the site of action of streptomycin are in the 30S ribosomal subunits, it is suggested that the rate of ribosome function is set by the dependent lesion (and the level of streptomycin). One possibility is that the other correlated effects are mechanistically "coupled" to ribosome function, but the apparent coupling could also be an indirect result of differential effects of streptomycin on variables such as ribosomal miscoding and nucleotide pool size. However, since the rate of functional inactivation of messenger RNA is constant even when the RNA is broken down two- to fourfold more slowly, translation yield tends to be proportional to the growth rate of the dependent strains.
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Levy CC, Schmukler M, Frank JJ, Karpetsky TP, Jewett PB, Hieter PA, LeGendre SM, Dorr RG. Possible role for poly(A) as an inhibitor of endonuclease activity in eukaryotic cells. Nature 1975; 256:340-2. [PMID: 1143339 DOI: 10.1038/256340a0] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Yamamoto T, Imamoto F. Differential stability of trp messenger RNA synthesized originating at the trp promoter and pL promoter of lambda trp phage. J Mol Biol 1975; 92:289-304. [PMID: 1142425 DOI: 10.1016/0022-2836(75)90228-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Cremer K, Schlessinger D. Ca2+ Ions Inhibit Messenger Ribonucleic Acid Degradation, but Permit Messenger Ribonucleic Acid Transcription and Translation in Deoxyribonucleic Acid-coupled Systems from Escherichia coli. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42380-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Wice M, Kennell D. Letter: Decay of messenger RNA from the tryptophan operon of Escherichia coli as a function of growth temperature. J Mol Biol 1974; 84:649-52. [PMID: 4601393 DOI: 10.1016/0022-2836(74)90123-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Blundell M, Kennell D. Evidence for endonucleolytic attack in decay of lac messenger RNA in Escherichia coli. J Mol Biol 1974; 83:143-61. [PMID: 4595422 DOI: 10.1016/0022-2836(74)90385-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Hamkalo BA, Miller OL. Fine structure of active genes in prokaryotes and eukaryotes. BASIC LIFE SCIENCES 1974; 3:1-14. [PMID: 4595838 DOI: 10.1007/978-1-4613-4529-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Mangiarotti G, Turco E. Ribonuclease activity in Escherichia coli polyribosomes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 38:507-15. [PMID: 4359138 DOI: 10.1111/j.1432-1033.1973.tb03086.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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McGeoch D, McGeoch J, Morse D. Synthesis of tryptophan operon RNA in a cell-free system. NATURE: NEW BIOLOGY 1973; 245:137-40. [PMID: 4582893 DOI: 10.1038/newbio245137a0] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Hiraga S, Yanofsky C. Inhibition of the progress of transcription on the tryptophan operon of Escherichia coli. J Mol Biol 1973; 79:339-49. [PMID: 4586412 DOI: 10.1016/0022-2836(73)90010-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Shimizu Y, Shimizu N, Hayashi M. In vitro repression of transcription of the tryptophan operon by trp repressor. Proc Natl Acad Sci U S A 1973; 70:1990-4. [PMID: 4579009 PMCID: PMC433649 DOI: 10.1073/pnas.70.7.1990] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The in vitro repression of transcription of the tryptophan operon by the trp repressor from Escherichia coli was studied. By measuring the inhibitory effect for trp-specific RNA synthesis in an in vitro transcription system directed by DNA of trp-transducing phage, we have detected and concentrated a trp repressor in an eluate of a Phi80 ptED native DNA-cellulose column. The repression of transcription of trp operon required the addition of L-tryptophan in the system, and when several tryptophan analogues were added, the repression or derepression was similar to that observed in vivo. The repressor fraction was separated from the majority of tryptophanyl-tRNA synthetase activity by Bio-gel P60 column chromatography.
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Apirion D. Degradation of RNA in Escherichia coli. A hypothesis. MOLECULAR & GENERAL GENETICS : MGG 1973; 122:313-22. [PMID: 4577538 DOI: 10.1007/bf00269431] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Cohen PT, Yaniv M, Yanofsky C. Nucleotide sequences from messenger RNA transcribed from the operator-proximal portion of the tryptophan operon of Escherichia coli. J Mol Biol 1973; 74:163-77. [PMID: 4347739 DOI: 10.1016/0022-2836(73)90105-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Kennell D, Bicknell I. Decay of messenger ribonucleic acid from the lactose operon of Escherichia coli as a function of growth temperature. J Mol Biol 1973; 74:21-31. [PMID: 4581286 DOI: 10.1016/0022-2836(73)90351-3] [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: 01/11/2023]
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