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Jeon H, Choi E, Hwang J. Identification and characterization of VapBC toxin-antitoxin system in Bosea sp. PAMC 26642 isolated from Arctic lichens. RNA (NEW YORK, N.Y.) 2021; 27:1374-1389. [PMID: 34429367 PMCID: PMC8522696 DOI: 10.1261/rna.078786.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Toxin-antitoxin (TA) systems are genetic modules composed of a toxin interfering with cellular processes and its cognate antitoxin, which counteracts the activity of the toxin. TA modules are widespread in bacterial and archaeal genomes. It has been suggested that TA modules participate in the adaptation of prokaryotes to unfavorable conditions. The Bosea sp. PAMC 26642 used in this study was isolated from the Arctic lichen Stereocaulon sp. There are 12 putative type II TA loci in the genome of Bosea sp. PAMC 26642. Of these, nine functional TA systems have been shown to be toxic in Escherichia coli The toxin inhibits growth, but this inhibition is reversed when the cognate antitoxin genes are coexpressed, indicating that these putative TA loci were bona fide TA modules. Only the BoVapC1 (AXW83_01405) toxin, a homolog of VapC, showed growth inhibition specific to low temperatures, which was recovered by the coexpression of BoVapB1 (AXW83_01400). Microscopic observation and growth monitoring revealed that the BoVapC1 toxin had bacteriostatic effects on the growth of E. coli and induced morphological changes. Quantitative real time polymerase chain reaction and northern blotting analyses showed that the BoVapC1 toxin had a ribonuclease activity on the initiator tRNAfMet, implying that degradation of tRNAfMet might trigger growth arrest in E. coli Furthermore, the BoVapBC1 system was found to contribute to survival against prolonged exposure at 4°C. This is the first study to identify the function of TA systems in cold adaptation.
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Affiliation(s)
- Hyerin Jeon
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Eunsil Choi
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan 46241, Republic of Korea
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2
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Brandi A, Giangrossi M, Paoloni S, Spurio R, Giuliodori AM, Pon CL, Gualerzi CO. Transcriptional and post-transcriptional events trigger de novo infB expression in cold stressed Escherichia coli. Nucleic Acids Res 2019; 47:4638-4651. [PMID: 30916329 PMCID: PMC6511841 DOI: 10.1093/nar/gkz187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/07/2019] [Accepted: 03/22/2019] [Indexed: 11/13/2022] Open
Abstract
After a 37 to 10°C temperature downshift the level of translation initiation factor IF2, like that of IF1 and IF3, increases at least 3-fold with respect to the ribosomes. To clarify the mechanisms and conditions leading to cold-stress induction of infB expression, the consequences of this temperature shift on infB (IF2) transcription, infB mRNA stability and translation were analysed. The Escherichia coli gene encoding IF2 is part of the metY-nusA-infB operon that contains three known promoters (P-1, P0 and P2) in addition to two promoters P3 and P4 identified in this study, the latter committed to the synthesis of a monocistronic mRNA encoding exclusively IF2. The results obtained indicate that the increased level of IF2 following cold stress depends on three mechanisms: (i) activation of all the promoters of the operon, P-1 being the most cold-responsive, as a likely consequence of the reduction of the ppGpp level that follows cold stress; (ii) a large increase in infB mRNA half-life and (iii) the cold-shock induced translational bias that ensures efficient translation of infB mRNA by the translational apparatus of cold shocked cells. A comparison of the mechanisms responsible for the cold shock induction of the three initiation factors is also presented.
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Affiliation(s)
- Anna Brandi
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Mara Giangrossi
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Silvia Paoloni
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Roberto Spurio
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Anna M Giuliodori
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Cynthia L Pon
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Claudio O Gualerzi
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
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3
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Lalanne JB, Taggart JC, Guo MS, Herzel L, Schieler A, Li GW. Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry. Cell 2018; 173:749-761.e38. [PMID: 29606352 PMCID: PMC5978003 DOI: 10.1016/j.cell.2018.03.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/24/2017] [Accepted: 03/01/2018] [Indexed: 12/01/2022]
Abstract
Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. However, it remains unexplored whether the relative abundance of co-regulated proteins requires precise tuning. Here, we present large-scale analyses of protein stoichiometry and corresponding regulatory strategies for 21 pathways and 67-224 operons in divergent bacteria separated by 0.6-2 billion years. Using end-enriched RNA-sequencing (Rend-seq) with single-nucleotide resolution, we found that many bacterial gene clusters encoding conserved pathways have undergone massive divergence in transcript abundance and architectures via remodeling of internal promoters and terminators. Remarkably, these evolutionary changes are compensated post-transcriptionally to maintain preferred stoichiometry of protein synthesis rates. Even more strikingly, in eukaryotic budding yeast, functionally analogous proteins that arose independently from bacterial counterparts also evolved to convergent in-pathway expression. The broad requirement for exact protein stoichiometries despite regulatory divergence provides an unexpected principle for building biological pathways both in nature and for synthetic activities.
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Affiliation(s)
- Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James C Taggart
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monica S Guo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lydia Herzel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ariel Schieler
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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4
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Shetty S, Bhattacharyya S, Varshney U. Is the cellular initiation of translation an exclusive property of the initiator tRNAs? RNA Biol 2016; 12:675-80. [PMID: 25996503 DOI: 10.1080/15476286.2015.1043507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Translation of mRNAs is the primary function of the ribosomal machinery. Although cells allow for a certain level of translational errors/mistranslation (which may well be a strategic need), maintenance of the fidelity of translation is vital for the cellular function and fitness. The P-site bound initiator tRNA selects the start codon in an mRNA and specifies the reading frame. A direct P-site binding of the initiator tRNA is a function of its special structural features, ribosomal elements, and the initiation factors. A highly conserved feature of the 3 consecutive G:C base pairs (3 GC pairs) in the anticodon stem of the initiator tRNAs is vital in directing it to the P-site. Mutations in the 3 GC pairs diminish/abolish initiation under normal physiological conditions. Using molecular genetics approaches, we have identified conditions that allow initiation with the mutant tRNAs in Escherichia coli. During our studies, we have uncovered a novel phenomenon of in vivo initiation by elongator tRNAs. Here, we recapitulate how the cellular abundance of the initiator tRNA, and nucleoside modifications in rRNA are connected with the tRNA selection in the P-site. We then discuss our recent finding of how a conserved feature in the mRNA, the Shine-Dalgarno sequence, influences tRNA selection in the P-site.
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Affiliation(s)
- Sunil Shetty
- a Department of Microbiology and Cell Biology; Indian Institute of Science ; Bangalore , India
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5
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Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Nat Struct Mol Biol 2011; 18:1043-51. [PMID: 21857664 PMCID: PMC3167956 DOI: 10.1038/nsmb.2098] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 06/14/2011] [Indexed: 01/27/2023]
Abstract
Translocation of transfer RNAs (tRNAs) through the ribosome during protein synthesis involves large-scale structural rearrangements of the ribosome and the ribosome-bound tRNAs that are accompanied by extensive and dynamic remodeling of tRNA-ribosome interactions. The contributions that rearranging individual tRNA-ribosome interactions make to directing tRNA movements during translocation, however, remain largely unknown. To address this question, we have used single-molecule fluorescence resonance energy transfer to characterize the dynamics of ribosomal pre-translocation (PRE) complex analogs carrying either wild-type or systematically mutagenized tRNAs. Our data reveal how specific tRNA-ribosome interactions regulate the rate with which the PRE complex rearranges into a critical, on-pathway translocation intermediate and how these interactions control the stability of the resulting configuration. More interestingly, our results suggest that the conformational flexibility of the tRNA molecule itself plays a crucial role in directing the structural dynamics of the PRE complex during translocation.
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Bylund GO, Nord S, Lövgren JM, Wikström PM. Alterations in the β flap and β' dock domains of the RNA polymerase abolish NusA-mediated feedback regulation of the metY-nusA-infB operon. J Bacteriol 2011; 193:4113-22. [PMID: 21685293 PMCID: PMC3147696 DOI: 10.1128/jb.00196-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 06/04/2011] [Indexed: 11/20/2022] Open
Abstract
The RimM protein in Escherichia coli is important for the in vivo maturation of 30S ribosomal subunits and a ΔrimM mutant grows poorly due to assembly and translational defects. These deficiencies are suppressed partially by mutations that increase the synthesis of another assembly protein, RbfA, encoded by the metY-nusA-infB operon. Among these suppressors are mutations in nusA that impair the NusA-mediated negative-feedback regulation at internal intrinsic transcriptional terminators of the metY-nusA-infB operon. We describe here the isolation of two new mutations, one in rpoB and one in rpoC (encoding the β and β' subunits of the RNA polymerase, respectively), that increase the synthesis of RbfA by preventing NusA from stimulating termination at the internal intrinsic transcriptional terminators of the metY-nusA-infB operon. The rpoB2063 mutation changed the isoleucine in position 905 of the β flap-tip helix to a serine, while the rpoC2064 mutation duplicated positions 415 to 416 (valine-isoleucine) at the base of the β' dock domain. These findings support previously published in vitro results, which have suggested that the β flap-tip helix and β' dock domain at either side of the RNA exit tunnel mediate the binding to NusA during transcriptional pausing and termination.
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Affiliation(s)
| | | | | | - P. Mikael Wikström
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
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7
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Nord S, Bylund GO, Lövgren JM, Wikström PM. The RimP Protein Is Important for Maturation of the 30S Ribosomal Subunit. J Mol Biol 2009; 386:742-53. [DOI: 10.1016/j.jmb.2008.12.076] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 12/18/2008] [Accepted: 12/29/2008] [Indexed: 01/21/2023]
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8
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Improvement of NADPH-dependent bioconversion by transcriptome-based molecular breeding. Appl Environ Microbiol 2007; 73:7657-63. [PMID: 17921263 DOI: 10.1128/aem.01754-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptome data for a xylitol-producing recombinant Escherichia coli were obtained and used to tune up its productivity. Structural genes of NADPH-dependent D-xylose reductase and D-xylose permease were inserted into an Escherichia coli chromosome to construct a recombinant strain producing xylitol from D-xylose for use as a model system for NADPH-dependent bioconversion. Transcriptome analysis of xylitol-producing and nonproducing conditions for the recombinant revealed that xylitol production down-regulated 56 genes. These genes were then selected as candidate factors for suppression of the NADPH supply and were disrupted to validate their functions. Of the gene disruptants, that resulting from the deletion of yhbC showed the best bioconversion rate. Also, the deletion accelerated cell growth during log phase. The features of the mutant could be maintained in jar fermenter-scale production of xylitol. Thus, our novel molecular host strain breeding method using transcriptome analysis was fully effective and could be applied to improving various industrial strains.
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9
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Olejnik J, Gite S, Mamaev S, Rothschild KJ. N-terminal labeling of proteins using initiator tRNA. Methods 2005; 36:252-60. [PMID: 16076451 DOI: 10.1016/j.ymeth.2005.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Accepted: 04/28/2005] [Indexed: 11/25/2022] Open
Abstract
Methodology based on tRNA mediated protein engineering is described for the introduction of fluorophores and other labels at the N-terminus of proteins produced in cell-free translation systems. One method for low-level (trace) N-terminal labeling is based on the use of an Escherichia coli initiator tRNA(fMet) misaminoacylated with methionine modified at the alpha-amino group. In addition to the normal formyl group, the protein translational machinery incorporates the fluorophore BODIPY-FL and the affinity tag biotin at an N-terminal end of the nascent protein. A second method for higher N-terminal labeling uses a chemically aminoacylated amber initiator suppressor tRNA and a DNA template which contains a complementary amber (UAG) codon instead of the normal initiation (AUG) codon. This more versatile approach is demonstrated using a variety of N-terminal markers including fluorescein, biotin, PC-biotin, and a novel dual marker conjugate (Biotin/BODIPY-FL).
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Affiliation(s)
- Jerzy Olejnik
- AmberGen, 1106 Commonwealth Avenue, Boston, MA 02215, USA
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10
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Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU. Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev 2005; 69:101-23. [PMID: 15755955 PMCID: PMC1082788 DOI: 10.1128/mmbr.69.1.101-123.2005] [Citation(s) in RCA: 418] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Valuable information on translation initiation is available from biochemical data and recently solved structures. We present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. The first section describes the ribosomal features relevant to the initiation process. Subsequent sections describe the structure, function, and interactions of the mRNA, the initiator tRNA, and the initiation factors IF1, IF2, and IF3. Finally, we provide an overview of mechanisms of regulation of the translation initiation event. Translation occurs on ribonucleoprotein complexes called ribosomes. The ribosome is composed of a large subunit and a small subunit that hold the activities of peptidyltransfer and decode the triplet code of the mRNA, respectively. Translation initiation is promoted by IF1, IF2, and IF3, which mediate base pairing of the initiator tRNA anticodon to the mRNA initiation codon located in the ribosomal P-site. The mechanism of translation initiation differs for canonical and leaderless mRNAs, since the latter is dependent on the relative level of the initiation factors. Regulation of translation occurs primarily in the initiation phase. Secondary structures at the mRNA ribosomal binding site (RBS) inhibit translation initiation. The accessibility of the RBS is regulated by temperature and binding of small metabolites, proteins, or antisense RNAs. The future challenge is to obtain atomic-resolution structures of complete initiation complexes in order to understand the mechanism of translation initiation in molecular detail.
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Affiliation(s)
- Brian Søgaard Laursen
- Department of Molecular Biology, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus C, Denmark
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11
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Mamaev S, Olejnik J, Olejnik EK, Rothschild KJ. Cell-free N-terminal protein labeling using initiator suppressor tRNA. Anal Biochem 2004; 326:25-32. [PMID: 14769332 DOI: 10.1016/j.ab.2003.11.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Indexed: 11/17/2022]
Abstract
A highly efficient method for the introduction of fluorophores and other markers at the N terminus of proteins produced in a cell-free extract has been developed. The method utilizes an amber (CUA) initiator suppressor tRNA chemically aminoacylated with a fluorophore-amino acid conjugate which is introduced into an Escherichia coli S30 cell-free translation system. The DNA template contains a complementary amber (UAG) codon instead of the normal initiation (AUG) codon. Using this approach, the fluorophore BODIPY-F1 (4,4-difluoro-5,7-dimethyl-4-bora-3a,4a- diaza-s-indacene-3-propionic acid) has been incorporated at the N terminus of several model proteins. The specific labeling achieved (27-67%) using this approach is much higher than that of wild-type tRNAs. Several potential biophysical and biotechnological applications of this new technology are described.
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Affiliation(s)
- Sergey Mamaev
- AmberGen, Inc., 1106 Commonwealth Avenue, Boston, MA 02215, USA
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12
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Krin E, Laurent-Winter C, Bertin PN, Danchin A, Kolb A. Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12. J Bacteriol 2003; 185:3139-46. [PMID: 12730174 PMCID: PMC154083 DOI: 10.1128/jb.185.10.3139-3146.2003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cAMP-catabolite activator protein (CAP) complex is a pleiotropic regulator that regulates a vast number of Escherichia coli genes, including those involved in carbon metabolism. We identified two new targets of this complex: argG, which encodes the arginosuccinate synthase involved in the arginine biosynthetic pathway, and metY, which encodes one of the two methionine tRNA initiators, tRNAf2Met. The cAMP-CAP complex activates argG transcription and inhibits metY transcription from the same DNA position. We also show that ArgR, the specific repressor of the arginine biosynthetic pathway, together with its arginine cofactor, acts on the regulation of metY mediated by CAP. The regulation of the two divergent promoters is thus simultaneously controlled not only by the cAMP-CAP complex, a global regulator, but also by a specific regulator of arginine metabolism, suggesting a previously unsuspected link between carbon metabolism and translation initiation.
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Affiliation(s)
- Evelyne Krin
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France.
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13
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Bylund GO, Lövgren JM, Wikström PM. Characterization of mutations in the metY-nusA-infB operon that suppress the slow growth of a DeltarimM mutant. J Bacteriol 2001; 183:6095-106. [PMID: 11567010 PMCID: PMC99689 DOI: 10.1128/jb.183.20.6095-6106.2001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RimM protein in Escherichia coli is associated with free 30S ribosomal subunits but not with 70S ribosomes. A DeltarimM mutant shows a sevenfold-reduced growth rate and a reduced translational efficiency, probably as a result of aberrant assembly of the ribosomal 30S subunits. The slow growth and translational deficiency can be partially suppressed by increased synthesis of the ribosome binding factor RbfA. Here, we have identified 14 chromosomal suppressor mutations that increase the growth rate of a DeltarimM mutant by increasing the expression of rbfA. Nine of these mutations were in the nusA gene, which is located upstream from rbfA in the metY-nusA-infB operon; three mutations deleted the transcriptional terminator between infB and rbfA; one was an insertion of IS2 in infB, creating a new promoter for rbfA; and one was a duplication, placing a second copy of rbfA downstream from a promoter for the yhbM gene. Two of the nusA mutations were identical, while another mutation (nusA98) was identical to a previously isolated mutation, nusA11, shown to decrease termination of transcription. The different nusA mutations were found to increase the expression of rbfA by increasing the read-through of two internal transcriptional terminators located just downstream from the metY gene and that of the internal terminator preceding rbfA. Induced expression of the nusA(+) gene from a plasmid in a nusA(+) strain decreased the read-through of the two terminators just downstream from metY, demonstrating that one target for a previously proposed NusA-mediated feedback regulation of the metY-nusA-infB operon expression is these terminators. All of the nusA mutations produced temperature-sensitive phenotypes of rimM(+) strains. The nusA gene has previously been shown to be essential at 42 degrees C and below 32 degrees C. Here, we show that nusA is also essential at 37 degrees C.
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Affiliation(s)
- G O Bylund
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
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14
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Bae W, Xia B, Inouye M, Severinov K. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc Natl Acad Sci U S A 2000; 97:7784-9. [PMID: 10884409 PMCID: PMC16622 DOI: 10.1073/pnas.97.14.7784] [Citation(s) in RCA: 281] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone, which is thought to facilitate translation at low temperature by destabilizing mRNA structures. Here we demonstrate that CspA, as well as homologous RNA chaperones CspE and CspC, are transcription antiterminators. In vitro, the addition of physiological concentrations of recombinant CspA, CspE, or CspC decreased transcription termination at several intrinsic terminators and also decreased transcription pausing. In vivo, overexpression of cloned CspC and CspE at 37 degrees C was sufficient to induce transcription of the metY-rpsO operon genes nusA, infB, rbfA, and pnp located downstream of multiple transcription terminators. Similar induction of downstream metY-rpsO operon genes was observed at cold shock, a condition to which the cell responds by massive overproduction of CspA. The products of nusA, infB, rbfA, and pnp-NusA, IF2, RbfA, and PNP-are known to be induced at cold shock. We propose that the cold-shock induction of nusA, infB, rbfA, and pnp occurs through transcription antitermination, which is mediated by CspA and other cold shock-induced Csp proteins.
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Affiliation(s)
- W Bae
- Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA
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15
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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16
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Vasanthakrishna M, Rumpal N, Varshney U. Organization and copy number of initiator tRNA genes in slow- and fast-growing mycobacteria. J Biosci 1998. [DOI: 10.1007/bf02703001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Vasanthakrishna M, Kumar NV, Varshney U. Characterization of the initiator tRNA gene locus and identification of a strong promoter from Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 11):3591-3598. [PMID: 9387237 DOI: 10.1099/00221287-143-11-3591] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An initiator tRNA gene, metA, and a closely linked fragment of a second initiator-tRNA-like sequence, metB, from Mycobacterium tuberculosis H37Ra have been cloned and characterized. The promoter region of metA shows the presence of conserved sequence elements, TAGCCT and TTGGCG, with resemblance to -10 and -35 promoter regions. The deduced sequence of the mature tRNA contains the three unique features of the eubacterial initiator tRNAs represented by (i) a C:U mismatch at position 1:72, (ii) three consecutive base pairs, 29-31G:C39-41 in the anticodon stem, and (iii) a purine:pyrimidine (A:U) base pair at position 11:24 in the dihydrouridine stem. A putative hairpin structure consisting of an 11 bp stem and a three-base loop found in the 3' flanking region is followed by a stretch of T residues and may serve as a transcription terminator. Analysis of the expression of metA and of its promoter using chloramphenicol acetyltransferase fusion constructs in Mycobacterium smegmatis shows that metA is a functional gene driven by a strong promoter. Furthermore, the overexpressed transcripts are fully processed and formylated in vivo. The metB clone shows the presence of sequences corresponding to those downstream of position 30 of the tRNA. However, the CCA sequence at the 3' end has been mutated to CCG. Interestingly, the 3' flanking sequences of both the genes are rich in GCT repeats. The metB locus also harbours a repeat element, IS6110. A method to prepare total RNA from mycobacteria (under acidic conditions) to analyse in vivo status of tRNAs is described.
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MESH Headings
- Acylation
- Anticodon/genetics
- Base Sequence
- Cloning, Molecular
- Conserved Sequence/genetics
- Genes, Bacterial/genetics
- Molecular Sequence Data
- Mycobacterium/genetics
- Mycobacterium tuberculosis/genetics
- Nucleic Acid Conformation
- Promoter Regions, Genetic/genetics
- RNA, Bacterial/analysis
- RNA, Messenger/analysis
- RNA, Transfer, Met/analysis
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- Recombinant Fusion Proteins
- Repetitive Sequences, Nucleic Acid/genetics
- Restriction Mapping
- Sequence Analysis, DNA
- Transcription, Genetic/genetics
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Affiliation(s)
- M Vasanthakrishna
- Centre for Genetic Engineering, Indian Institute of Science, Bangalore 560 012, India
| | - N Vinay Kumar
- Centre for Genetic Engineering, Indian Institute of Science, Bangalore 560 012, India
| | - U Varshney
- Centre for Genetic Engineering, Indian Institute of Science, Bangalore 560 012, India
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18
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Meinnel T, Blanquet S. Maturation of pre-tRNA(fMet) by Escherichia coli RNase P is specified by a guanosine of the 5'-flanking sequence. J Biol Chem 1995; 270:15908-14. [PMID: 7797595 DOI: 10.1074/jbc.270.26.15908] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The C+1/A+72 base pair at the top of the acceptor stem of Escherichia coli tRNA(fMet) accounts for several of the specialized roles of this tRNA in translation initiation. According to the rules of RNA substrate recognition by RNase P, the C+1/A+72 pair is likely to disfavor the 5'-maturation of pre-tRNA(fMet). Indeed, in contrast to other E. coli tRNA species, tRNA(fMet) was not properly matured when overproduced from a multicopy expression vector. Half of the recovered tRNA(fMet) retained an extension at the 5' side. Such a defect of tRNA(fMet) processing could be cured by changing bases C+1 and A+72 by a Watson-Crick base pair or by non-paired bases, provided one of them was a G. It could also be compensated by either (i) over-expression of RNase P or (ii) introduction within the plasmid of one out of the three 5'-flanking sequences naturally occurring in the four E. coli tRNA(fMet) genes. The effect of these flanking sequences on the maturation of tRNA(fMet) could be accounted for by the presence of a G located 2 bases upstream from C+1. Notably, this G is the only residue that is conserved in the 5'-flanking sequences of all four E. coli tRNA(fMet) genes.
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Affiliation(s)
- T Meinnel
- Laboratoire de Biochimie, CNRS, Ecole Polytechnique, Palaiseau, France
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19
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Dammel CS, Noller HF. Suppression of a cold-sensitive mutation in 16S rRNA by overexpression of a novel ribosome-binding factor, RbfA. Genes Dev 1995; 9:626-37. [PMID: 7535280 DOI: 10.1101/gad.9.5.626] [Citation(s) in RCA: 137] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A novel 15-kDa protein, RbfA, has been identified by virtue of its ability to act as a high copy suppressor of a previously characterized dominant cold-sensitive mutation (C23U) in 16S rRNA. RbfA is found associated with free 30S ribosomal subunits, but not with 70S ribosomes or polysomes, and is essential for maximal cell growth, particularly at low temperatures. Cells lacking RbfA in a wild-type rRNA background exhibit a cold-sensitive phenotype that is strikingly similar to that of the cold-sensitive C23U rRNA mutant. The observed patterns of allele specificity of suppression and synthetic lethality in cells containing an RbfA knockout in combination with various 16S rRNA mutations suggests that RbfA interacts with the 5'-terminal helix region of 16S rRNA, possibly during a late step of 30S maturation.
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Affiliation(s)
- C S Dammel
- Department of Biology, University of California at Santa Cruz 95064
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20
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Affiliation(s)
- U L RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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21
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Rowley KB, Clements DE, Mandel M, Humphreys T, Patil SS. Multiple copies of a DNA sequence from Pseudomonas syringae pathovar phaseolicola abolish thermoregulation of phaseolotoxin production. Mol Microbiol 1993; 8:625-35. [PMID: 8326870 DOI: 10.1111/j.1365-2958.1993.tb01606.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Phaseolotoxin, a phytotoxin of Pseudomonas syringae pv. phaseolicola, is produced at 18 degrees C but not at 28 degrees C. Here we report that a fragment (24.4 kb) cloned from the wild-type strain, which does not harbour a gene(s) involved in phaseolotoxin biosynthesis, abolishes this thermoregulation in the wild type and suppresses a Tox- mutant at both temperatures. A subclone harbouring a 485 bp fragment contains motifs that are characteristic of DNA-binding sites. In mobility shift assays we have detected a protein(s) from the wild-type and the mutant strains, grown at appropriate temperatures, that specifically binds to the fragment containing the DNA-binding motifs. We propose that the binding protein is a repressor which is 'titrated' by this fragment when it is present in the cell on a multiple copy plasmid, thus allowing expression of phaseolotoxin genes.
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Affiliation(s)
- K B Rowley
- Department of Plant Pathology, University of Hawaii, Honolulu 96822
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22
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Shazand K, Tucker J, Grunberg-Manago M, Rabinowitz JC, Leighton T. Similar organization of the nusA-infB operon in Bacillus subtilis and Escherichia coli. J Bacteriol 1993; 175:2880-7. [PMID: 8491709 PMCID: PMC204605 DOI: 10.1128/jb.175.10.2880-2887.1993] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We reported previously the cloning and sequence of the Bacillus subtilis infB gene which encodes the essential IF2 factor required for initiation of translation (K. Shazand, J. Tucker, R. Chiang, K. Stansmore, H. U. Sperling-Petersen, M. Grunberg-Manago, J. C. Rabinowitz, and T. Leighton, J. Bacteriol. 172:2675-2687, 1990). The location of the 5' border of the infB operon was investigated by using integrative plasmids carrying various DNA fragments from the region upstream of the infB gene. The lethal effect of disruption of the infB transcriptional unit could be suppressed when the integrated plasmid introduced the spac promoter upstream of the infB operon and transformants were selected in conditions of induction of spac expression. Such an integrated plasmid was used as a starting point to clone the promoter of the infB operon. Primer extension mapping suggests that a single sigma A-type promoter controls transcription of the infB operon. The sequence of a 5,760-bp region encompassing the infB gene was determined. The infB operon is located immediately downstream of the polC gene and comprises seven open reading frames, four of which appear to be the homologs of genes present in the same order in the Escherichia coli infB operon, including nusA. The striking similarity between the E. coli and B. subtilis infB operons suggests that the function of each gene pair is conserved and that the B. subtilis NusA homolog, which is 124 residues shorter than its E. coli counterpart, could play a role similar to its role in E. coli.
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Affiliation(s)
- K Shazand
- Institut de Biologie Physico-Chimique, Paris, France
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23
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Abstract
An updated compilation of 300 E. coli mRNA promoter sequences is presented. For each sequence the most recent relevant paper was checked, to verify the location of the transcriptional start position as identified experimentally. We comment on the reliability of the sequence databanks and analyze the conservation of known promoter features in the current compilation. This database is available by E-mail.
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Affiliation(s)
- S Lisser
- Department of Molecular Genetics, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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24
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Dyson MR, Mandal N, RajBhandary UL. Relationship between the structure and function of Escherichia coli initiator tRNA. Biochimie 1993; 75:1051-60. [PMID: 7515283 DOI: 10.1016/0300-9084(93)90004-c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Through functional studies of mutant tRNAs, we have identified sequence and/or structural features important for specifying the many distinctive properties of E coli initiator tRNA. Many of the mutant tRNAs contain an anticodon sequence change from CAU-->CUA and are now substrates for E coli glutaminyl-tRNA synthetase (GlnRS). We describe here the effect of further mutating the discriminator base 73 and nucleotide 72 at the end of the acceptor stem on: i) recognition of the mutant tRNAs by E coli GlnRS; ii) recognition by E coli methionyl-tRNA transformylase; and iii) activity of the mutant tRNAs in initiation in E coli. For GlnRS recognition, our results are, in general, consistent with interactions found in the crystal structure of the E coli GlnRS-glutamine tRNA complex. The results also support our previous conclusion that formylation of initiator tRNA is important for its function in initiation.
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MESH Headings
- Acyltransferases/chemistry
- Acyltransferases/genetics
- Acyltransferases/metabolism
- Amino Acyl-tRNA Synthetases/chemistry
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/metabolism
- Base Sequence
- Binding Sites
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Hydroxymethyl and Formyl Transferases
- Immunoblotting
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Met
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- M R Dyson
- Institute of Cell and Molecular Biology, University of Edinburgh, UK
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25
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Hanafusa T, Saito K, Tominaga A, Enomoto M. Nucleotide sequence and regulated expression of the Salmonella fljA gene encoding a repressor of the phase 1 flagellin gene. MOLECULAR & GENERAL GENETICS : MGG 1993; 236:260-6. [PMID: 8437573 DOI: 10.1007/bf00277121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The nucleotide sequence of Salmonella abortus-equi fljA, which together with the phase 2 flagellin gene constitutes the fljBA operon and encodes the repressor for the phase 1 flagellin gene fliC, was determined. The repressor was predicted to be a basic protein consisting of 179 amino acid residues (M(r) = 20419 Da) encoded by ORFII. This was confirmed by the fact that host fliC is repressed by plasmid-encoded ORFII, which indeed expresses a 20 kDa product as determined by urea SDS-polyacrylamide gel electrophoresis. An amino acid sequence capable of forming a helix-turn-helix type of structure was predicted in the C-terminal region of FljA. A rho-independent intercistronic terminator was detected between fljB and fljA. Chloramphenicol acetyltransferase (CAT) assays of fusions indicated that the terminator is capable of reducing expression of fljA to the level of a few percent, relative to fljB in broth cultures and to 1% in M9 glycerol cultures.
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Affiliation(s)
- T Hanafusa
- Department of Biology, Faculty of Science, Okayama University, Japan
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26
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Mandal N, RajBhandary UL. Escherichia coli B lacks one of the two initiator tRNA species present in E. coli K-12. J Bacteriol 1992; 174:7827-30. [PMID: 1447149 PMCID: PMC207499 DOI: 10.1128/jb.174.23.7827-7830.1992] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We show that the metY locus which specifies tRNA(2fMet) in Escherichia coli K-12 specifies tRNA(1fMet) in E. coli B. This conclusion is based on results of Southern blot analysis of E. coli B and K-12 DNAs and on polymerase chain reaction amplification, cloning, and sequencing of an approximately 200-bp region of DNA corresponding to the metY loci of E. coli B and E. coli K-12. We also show that the metY locus of E. coli B is transcriptionally active. E. coli strains transformed with the multicopy plasmid vector pUC19 carrying the metY locus of E. coli B overproduce tRNA(1fMet) in E. coli B and E. coli K-12 in contrast to strains transformed with pUC19 carrying the corresponding locus from E. coli K-12, which overproduce tRNA(2fMet).
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Affiliation(s)
- N Mandal
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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27
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Qoronfleh MW, Debouck C, Keller J. Identification and characterization of novel low-temperature-inducible promoters of Escherichia coli. J Bacteriol 1992; 174:7902-9. [PMID: 1334067 PMCID: PMC207524 DOI: 10.1128/jb.174.24.7902-7909.1992] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli promoters that are more active at low temperature (15 to 20 degrees C) than at 37 degrees C were identified by using the transposon Tn5-lac to generate promoter fusions expressing beta-galactosidase (beta-Gal). Tn5-lac insertions that resulted in low-temperature-regulated beta-Gal expression were isolated by selecting kanamycin-resistant mutants capable of growth on lactose minimal medium at 15 degrees C but which grew poorly at 37 degrees C on this medium. Seven independent mutants were selected for further studies. In one such strain, designated WQ11, a temperature shift from 37 degrees C to either 20 or 15 degrees C resulted in a 15- to 24-fold induction of beta-Gal expression. Extended growth at 20 or 15 degrees C resulted in 36- to 42-fold-higher beta-Gal expression over that of cells grown at 37 degrees C. Treatment of WQ11 with streptomycin, reported to induce a response similar to heat shock, failed to induce beta-Gal expression. In contrast, treatment with either chloramphenicol or tetracycline, which mimics a cold shock response, resulted in a fourfold induction of beta-Gal expression in strain WQ11. Hfr genetic mapping studies complemented by physical mapping indicated that in at least three mutants (WQ3, WQ6, and WQ11), Tn5-lac insertions mapped at unique sites where no known cold shock genes have been reported. The Tn5-lac insertions of these mutants mapped to 81, 12, and 34 min on the E. coli chromosome, respectively. The cold-inducible promoters from two of the mutants (WQ3 and WQ11) were cloned and sequenced, and their temperature regulation was examined. Comparison of the nucleotide sequences of these two promoters with the regulatory elements of other known cold shock genes identified the sequence CCAAT as a putative conserved motif.
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Affiliation(s)
- M W Qoronfleh
- Department of Biological Process Sciences, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406
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28
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Dallas WS, Gowen JE, Ray PH, Cox MJ, Dev IK. Cloning, sequencing, and enhanced expression of the dihydropteroate synthase gene of Escherichia coli MC4100. J Bacteriol 1992; 174:5961-70. [PMID: 1522070 PMCID: PMC207134 DOI: 10.1128/jb.174.18.5961-5970.1992] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Escherichia coli gene coding for dihydropteroate synthase (DHPS) has been cloned and sequenced. The protein has 282 amino acids and a compositional molecular mass of 30,314 daltons. Increased expression of the enzyme was realized by using a T7 expression system. The enzyme was purified and crystallized. A temperature-sensitive mutant was isolated and found to express a DHPS with a lower specific activity and lower affinities for para-aminobenzoic acid and sulfathiazole. The allele had a point mutation that changed a phenylalanine codon to a leucine codon, and the mutation was in a codon that is conserved among published DHPS sequences.
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Affiliation(s)
- W S Dallas
- Department of Molecular Genetics and Microbiology, Burroughs Wellcome Co., Research Triangle Park, North Carolina 27709
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29
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Scholzen T, Arndt E. The alpha-operon equivalent genome region in the extreme halophilic archaebacterium Haloarcula (Halobacterium) marismortui. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)49814-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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30
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Abstract
The Escherichia coli argU gene encodes the rare arginine tRNA, tRNA(UCUArg), which decodes the similarly rare AGA codons. The argU promoter is, with two exceptions, a typical, strongly expressed stable RNA gene promoter which is stimulated by an upstream activator sequence. Unlike other tRNA operons, however, argU expression is severely inhibited by sequences downstream of the transcription start point. In vivo, nucleotides +2 to +45 inhibited expression by 25- to 100-fold when measured by fusion of argU promoter regions to the chloramphenicol acetyltransferase reporter gene or by quantitative primer extension analysis. In vitro, linearized argU promoter fragments on which the argU region ended at +1 supported 5- to 10-fold-more transcription than when the argU region ended at +45. This difference in degree of inhibition between in vivo and in vitro conditions suggests that several factors, some of which could be absent in vitro, might limit expression in vivo. Alternatively, one mechanism might limit expression both in vivo and in vitro but function more efficiently in vivo. A second difference from strongly expressed stable RNA promoters is the fact the argU gene is relatively insensitive to growth rate regulation, at least when assayed on a multicopy plasmid.
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Affiliation(s)
- P Saxena
- Department of Microbiology, University of Texas, Austin 78712-1095
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31
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Krömer W, Arndt E. Halobacterial S9 operon. Three ribosomal protein genes are cotranscribed with genes encoding a tRNA(Leu), the enolase, and a putative membrane protein in the archaebacterium Haloarcula (Halobacterium) marismortui. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54267-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Cummings H, Sands J, Foreman P, Fraser J, Hershey J. Structure and expression of the infA operon encoding translational initiation factor IF1. Transcriptional control by growth rate. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)55327-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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33
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Granston AE, Thompson DL, Friedman DI. Identification of a second promoter for the metY-nusA-infB operon of Escherichia coli. J Bacteriol 1990; 172:2336-42. [PMID: 1692017 PMCID: PMC208867 DOI: 10.1128/jb.172.5.2336-2342.1990] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The metY-nusA-infB operon of Escherichia coli encodes functions involved in both transcription and translation. Previous studies have identified a single promoter, P0, that directs transcription of the entire operon. We have identified a second promoter, P-1, that also is positioned to transcribe the complete operon. P-1 is located 50 base pairs upstream of and oriented in the same direction as P0. Sequences associated with P-1 have features suggestive of regulatory elements. P-1 differs from any previously described naturally occurring E. coli promoter by having -35 and -10 sequences that perfectly match the procaryotic promoter consensus hexamer sequences, although the spacing between the two elements is 1 base pair more than optimal. We demonstrate that P-1 is active in vivo.
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Affiliation(s)
- A E Granston
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109
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34
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Morel-Deville F, Vachon G, Sacerdot C, Cozzone AJ, Grunberg-Manago M, Cenatiempo Y. Characterization of the translational start site for IF2 beta, a short form of Escherichia coli initiation factor IF2. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 188:605-14. [PMID: 2110058 DOI: 10.1111/j.1432-1033.1990.tb15441.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The gene for initiation factor IF2, infB, represents one of the few examples in Escherichia coli of genes encoding two protein products in vivo. In a previous work, our group showed that both forms of IF2 (alpha and beta) are closely related and may arise from two independent translational events on infB mRNA. Unambiguous mapping and rigorous determination of the nature of the initiation triplet for IF2 beta, the smaller form of IF2, is critical for future mutagenesis of this codon, required for investigating the biological importance of both IF2 alpha and IF2 beta. Three types of experiments were carried out. First, a 77-bp deletion was created at the beginning of the structural gene leading to premature termination of IF2 alpha synthesis. Under these conditions, IF2 beta is still formed. Second, various Bal31 digests of infB containing the 77-bp deletion were fused to lacZ. Any synthesis of a fused protein with beta-galactosidase activity should reflect the occurrence of an initiation event on the messenger corresponding to this DNA segment. It was consequently possible to locate the IF2 beta initiation site within an 18-base region containing an in-phase GUG codon. Third, to avoid any artefactual reinitiation event possibly occurring under our experimental conditions, we fused to lacZ an infB fragment devoid of IF2 alpha start sequences but containing genetic information for this 18-base region. A hybrid protein with beta-galactosidase activity was synthesized. Moreover, its NH2-terminal amino acid sequence coincided with that of IF2 beta, demonstrating that GUG, located 471 bases downstream from the IF2 alpha external start codon, is the internal start codon for the shorter form of IF2.
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Affiliation(s)
- F Morel-Deville
- Laboratoire de Biologie Moléculaire, Université de Lyon I, Villeurbanne, France
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35
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Abstract
We show that the amber termination codon UAG can initiate protein synthesis in Escherichia coli. We mutated the initiation codon AUG of the chloramphenicol acetyltransferase (CAT) gene to UAG (CATam1) and translated mRNA derived from the mutant CAT gene in E. coli S-30 extracts. A full-length CAT polypeptide was synthesized in the presence of tRNA(fMetCUA), a mutant E. coli initiator tRNA which has a change in the anticodon sequence from CAU to CUA. Addition of purified E. coli glutaminyl-tRNA synthetase substantially stimulated synthesis of the CAT polypeptide. Thus, initiation of protein synthesis with UAG and tRNA(fMetCUA) most likely occurs with glutamine and not methionine. The UAG codon also initiates protein synthesis in vivo. To eliminate a weak secondary site of initiation from AUC, the fifth codon, we further mutagenized the CATam1 gene at codons 2 (GAG----GAC) and 5 (AUC----ACC). Transformation of E. coli with the resultant CATam1.2.5 gene yielded transformants that synthesized CAT polypeptide and were resistant to chloramphenicol only when they were also transformed with the mutant tRNA(fMetCUA) gene. Immunoblot analyses and assays for CAT enzyme activity in extracts from transformed cells indicate that initiation from UAG is efficient, 60-70% of that obtained from AUG. Initiation of protein synthesis from UAG using a mutant initiator tRNA allows tightly regulated expression of specific genes. This may be generally useful for overproduction in E. coli and other eubacteria of proteins which are toxic to these cells.
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36
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Sands JF, Regnier P, Cummings HS, Grunberg-Manago M, Hershey JW. The existence of two genes between infB and rpsO in the Escherichia coli genome: DNA sequencing and S1 nuclease mapping. Nucleic Acids Res 1988; 16:10803-16. [PMID: 2849753 PMCID: PMC338940 DOI: 10.1093/nar/16.22.10803] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A number of genes encoding proteins involved in transcription and translation are clustered between 68 and 69 minutes on the Escherichia coli genome map and are transcribed clockwise as two operons: the metY operon, containing metY, P15A, nusA, infB; and about a kilobase further downstream, the rpsO and pnp operon. The DNA sequence between infB and rpsO was determined and two open reading frames were detected which code for proteins of 15,200 (P15B) and 35,091 (P35) daltons. Maxicell analysis showed a relatively strong expression of P15B whereas P35 was synthesized more weakly. An overlap of the termination codon of P15B and the initiator codon for P35 suggests that translation of P15B and P35 may be coupled. S1 nuclease mapping of in vivo transcripts between infB and rpsO provided no evidence for major promoters but detected a moderately efficient rho-independent terminator between infB and P15B. The results indicate that P15B and P35 are expressed as part of the metY operon, but that some transcriptional read through into the rpsO operon also occurs, thereby, functionally linking the expression of these two complex systems.
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Affiliation(s)
- J F Sands
- Department of Biological Chemistry, School of Medicine, University of California, Davis 95616
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37
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Seong BL, RajBhandary UL. Mutants of Escherichia coli formylmethionine tRNA: a single base change enables initiator tRNA to act as an elongator in vitro. Proc Natl Acad Sci U S A 1987; 84:8859-63. [PMID: 3321059 PMCID: PMC299650 DOI: 10.1073/pnas.84.24.8859] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We show that the absence of a Watson-Crick base pair at the end of the amino acid acceptor stem, which is a hallmark of all prokaryotic initiator tRNAs, is one of the key features that prevents them from acting as an elongator in protein synthesis. We generated mutants of Escherichia coli formylmethionine tRNA that have a base pair at the end of the acceptor stem. The mutants generated were C1----T1, which had a U.A base pair, A72----G72, which had a C.G base pair, and the C1A72----T1G72 double mutant, which lacked the base pair. After aminoacylation, the activity of these and other mutant initiator methionyl-tRNAs (Met-tRNAs) in elongation were assayed in a MS2 RNA-directed E. coli protein-synthesizing system and in binding to the elongation factor Tu (EF-Tu). Unlike wild-type initiator tRNA or the T1G72 double mutant, the T1 and G72 mutant Met-tRNAs were active in elongation, the G72 mutant being more active than the T1 mutant. The T1 and G72 mutant Met-tRNAs also formed a ternary complex with elongation factor EF-Tu.GTP, and their relative affinities for EF-Tu.GTP paralleled their activities in elongation. Combination of the T1 or G72 mutation with mutations in the GGG.CCC sequence conserved in the anticodon stem of initiator tRNAs led to a further increase in the activities of these mutant tRNAs in elongation such that one of these mutants was now almost as good an elongator as E. coli elongator methionine tRNA.
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Affiliation(s)
- B L Seong
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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38
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Sands JF, Cummings HS, Sacerdot C, Dondon L, Grunberg-Manago M, Hershey JW. Cloning and mapping of infA, the gene for protein synthesis initiation factor IF1. Nucleic Acids Res 1987; 15:5157-68. [PMID: 3037488 PMCID: PMC305953 DOI: 10.1093/nar/15.13.5157] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The gene for translation initiation factor IF1, infA, has been identified by using two synthetic oligonucleotides to screen a Charon 30 library of Escherichia coli DNA. A recombinant lambda phage, C1921, was purified from a plaque positive for both probes. A 2.8 kb BglII fragment and a 2.0 kb HindIII fragment isolated from C1921 were subcloned into the BamHI and HindIII sites of pBR322 to yield pTB7 and pTH2 respectively. Synthesis of IF1 in maxicells transformed with pTB7 or pTH2 indicates the presence of inf A in both inserts. This was confirmed by DNA sequencing: a region was found that codes for a 8,119 dalton protein with an amino acid sequence corresponding to IF1. The chromosomal location of inf A was determined by mapping the closely linked beta-lactamase gene (Ampr) in pTB7 and pTH2. pTB7 and pTH2 were transformed into polA Hfr hosts, and integration of the plasmid by homologous recombination near inf A was selected on the basis of ampicillin resistance. The site of integration was confirmed by Southern blot analysis of restriction nuclease digested wild type and transformed genomic DNA. The Ampr marker (and therefore inf A) was mapped to about 20 minutes by Hfr interrupted matings and P1 transduction experiments. The structure and regulation of the inf A operon currently are being investigated.
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39
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Abstract
We have compiled and analyzed 263 promoters with known transcriptional start points for E. coli genes. Promoter elements (-35 hexamer, -10 hexamer, and spacing between these regions) were aligned by a program which selects the arrangement consistent with the start point and statistically most homologous to a reference list of promoters. The initial reference list was that of Hawley and McClure (Nucl. Acids Res. 11, 2237-2255, 1983). Alignment of the complete list was used for reference until successive analyses did not alter the structure of the list. In the final compilation, all bases in the -35 (TTGACA) and -10 (TATAAT) hexamers were highly conserved, 92% of promoters had inter-region spacing of 17 +/- 1 bp, and 75% of the uniquely defined start points initiated 7 +/- 1 bases downstream of the -10 region. The consensus sequence of promoters with inter-region spacing of 16, 17 or 18 bp did not differ. This compilation and analysis should be useful for studies of promoter structure and function and for programs which identify potential promoter sequences.
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40
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McMurry LM, Levy SB. Tn5 insertion in the polynucleotide phosphorylase (pnp) gene in Escherichia coli increases susceptibility to antibiotics. J Bacteriol 1987; 169:1321-4. [PMID: 3029034 PMCID: PMC211937 DOI: 10.1128/jb.169.3.1321-1324.1987] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A Tn5 insertional mutation on the Escherichia coli chromosome which caused a severalfold increase in susceptibility to structurally and functionally diverse antibiotics was found to map within the gene for polynucleotide phosphorylase (pnp) and to inactivate this enzyme, which is involved in RNA breakdown. The mutation also decreased the growth rate 10 to 25% and increased the rate of tetracycline uptake about 30%. The hypersensitivity due to the insertion was only partially complemented by a cloned pnp gene.
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41
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Ishihama A, Honda A, Nagasawa-Fujimori H, Glass RE, Maekawa T, Imamoto F. Multivalent regulation of the nusA operon of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1987; 206:185-91. [PMID: 3035333 DOI: 10.1007/bf00333573] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The rate of synthesis and intracellular content of the NusA protein, a transcription termination factor, were determined for wild-type and nusA and/or nusB mutants of Escherichia coli. Both the rate and content of NusA in wild-type strains were similar to that of the RNA polymerase sigma subunit, a transcription initiation factor, on a molar basis, and about 30%-40% the levels of RNA polymerase beta beta' subunits. At the stationary phase of cell growth, the values increased in parallel for both transcription factors up to approximately the level of the beta beta' subunits. In nus mutants, the rate of synthesis and the content of the sigma subunit were significantly increased. These observations together suggest that the two transcription factors are coordinately regulated.
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42
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Promoter selectivity of Escherichia coli RNA polymerase. Purification and properties of holoenzyme containing the heat-shock sigma subunit. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(19)75718-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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43
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Cenatiempo Y, Deville F, Brot N, Weissbach H. In vitro expression of the Escherichia coli nusA-infB operon. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(19)75902-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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44
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Seong BL, RajBhandary UL. Escherichia coli formylmethionine tRNA: mutations in GGGCCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop. Proc Natl Acad Sci U S A 1987; 84:334-8. [PMID: 3540960 PMCID: PMC304201 DOI: 10.1073/pnas.84.2.334] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We have generated mutants of Escherichia coli formylmethionine initiator tRNA in which one, two, and all three G X C base pairs in the GGGCCC sequence in the anticodon stem are changed to those found in E. coli elongator methionine tRNA. Overproduction of the mutant tRNAs using M13 recombinants as an expression vector and development of a one-step purification scheme allowed us to purify, characterize, and analyze the function of the mutant tRNAs. After aminoacylation and formylation, the function of mutant formylmethionyl tRNAs was analyzed in an MS2 RNA-directed in vitro protein-synthesizing system, in AUG-dependent ribosomal P site binding, and in initiation factor binding. The mutant tRNAs show progressive loss of activity in initiation, the mutant with all three G X C base pairs substituted being the least active. The mutations affect binding to the ribosomal P site. None of the mutations affects binding to initiation factor 2. We also show that there is a progressive increase in accessibility of phosphodiester bonds in the anticodon loop of the three mutants to S1 nuclease, such that the cleavage pattern of the mutant with all three G X C base-pair changes resembles that of elongator tRNAs. These results are consistent with the notion that the contiguous G X C base pairs in the anticodon stem of initiator tRNAs impart on the anticodon loop a unique conformation, which may be important in targeting the initiator tRNA to the ribosomal P site during initiation of protein synthesis.
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45
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King TC, Sirdeskmukh R, Schlessinger D. Nucleolytic processing of ribonucleic acid transcripts in procaryotes. Microbiol Rev 1986; 50:428-51. [PMID: 2432388 PMCID: PMC373081 DOI: 10.1128/mr.50.4.428-451.1986] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
MESH Headings
- Bacteria/genetics
- Bacteria/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribonucleases/metabolism
- Transcription, Genetic
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46
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Kersten H. [Adaptation of cell metabolism to environmental changes: regulation of gene expression of transfer RNA and unusual nucleic acid building-blocks]. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1986; 73:593-604. [PMID: 3785431 DOI: 10.1007/bf00368770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In the living cell transfer ribonucleic acids (tRNAs) serve for the transfer of information from genes to proteins. In this article evidence will be presented showing that changes of particular tRNA modifications cause alterations in gene expression, when an organism is exposed to a metabolic stress, e.g. limitation of oxygen or nutrients. tRNA modifications seem to be important to adapt cells to environmental changes. These mechanisms of adaptation are considered to have developed as survival strategies in microorganisms especially when oxygen accumulated in the atmosphere.
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47
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Nomura T, Fujita N, Ishihama A. Promoter selectivity of Escherichia coli RNA polymerase: alteration by fMet-tRNAfMet. Nucleic Acids Res 1986; 14:6857-70. [PMID: 3532031 PMCID: PMC311704 DOI: 10.1093/nar/14.17.6857] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
An in vitro mixed transcription system was employed to examine the possible alteration of the promoter selectivity of Escherichia coli RNA polymerase by specific tRNAs. Transcription in vitro was inhibited by most of the tRNAs examined, although the extent of the inhibition differed with the tRNA species. The inhibition by tRNAs was due to competition with DNA for binding RNA polymerase. This inhibitory effect remained after charging of the tRNAs with amino acids. The charging of tRNAfMet with fMet, but not with Met, abolished its inhibitory effect, and instead gave a stimulatory effect on the transcription from some promoters. These observations suggest that fMet-tRNAfMet plays a specific regulatory role in the coupling of transcription to translation.
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48
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Glass RE, Jones ST, Nene V, Nomura T, Fujita N, Ishihama A. Genetic studies on the beta subunit of Escherichia coli RNA polymerase. VIII. Localisation of a region involved in promoter selectivity. MOLECULAR & GENERAL GENETICS : MGG 1986; 203:487-91. [PMID: 3528751 DOI: 10.1007/bf00422074] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have previously isolated an E. coli derivative carrying a small internal deletion (delta(rpoB)1570-1) of the beta structural gene. This RNA polymerase deletion mutant has no noticeable phenotype other than a slightly increased generation time in minimal medium. The deletion, which removes about 165 bp, has been localised to between codons 965 and 1,083, indicating it excises part of a tandem repeat structure present in the C-terminal region of beta. Analysis in vitro of purified RNA polymerase from the deletion mutant indicates that this enzyme has an altered promoter selectivity. These observations allow localisation of a site on the beta polypeptide of E. coli RNA polymerase involved in transcriptional initiation.
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49
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Structure and organization of the transfer ribonucleic acid genes of Escherichia coli K-12. Microbiol Rev 1985; 49:379-97. [PMID: 2419743 PMCID: PMC373044 DOI: 10.1128/mr.49.4.379-397.1985] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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50
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Caillet J, Plumbridge JA, Springer M. Evidence that pheV, a gene for tRNAPhe of E. coli is transcribed from tandem promoters. Nucleic Acids Res 1985; 13:3699-710. [PMID: 3892481 PMCID: PMC341267 DOI: 10.1093/nar/13.10.3699] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A DNA fragment of 487 bp containing a gene for tRNAPhe has been sequenced. Although the tRNAPhe sequence is identical to that of pheU (which maps at 94.5 min) the surrounding sequences are quite different. This sequence is thus that of a second gene for tRNAPhe (which we shall call pheV). In vitro transcription experiments and S1 mapping in vivo show the existence of two promoters separated by about 60 nucleotides. The second transcript starts only 3 nucleotides 5' from the tRNAPhe structural sequence. A DNA sequence characteristic of a rho-independent terminator is located 30 nucleotides 3' of the end of the structural gene and is shown to function efficiently in vitro.
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