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Jeanneau S, Jacques PÉ, Lafontaine DA. Investigating the role of RNA structures in transcriptional pausing using in vitro assays and in silico analyses. RNA Biol 2022; 19:916-927. [PMID: 35833713 PMCID: PMC9291695 DOI: 10.1080/15476286.2022.2096794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Transcriptional pausing occurs across the bacterial genome but the importance of this mechanism is still poorly understood. Only few pauses were observed during the previous decades, leaving an important gap in understanding transcription mechanisms. Using the well-known Escherichia coli hisL and trpL pause sites as models, we describe here the relation of pause sites with upstream RNA structures suspected to stabilize pausing. We find that the transcription factor NusA influences the pause half-life at leuL, pheL and thrL pause sites. Using a mutagenesis approach, we observe that transcriptional pausing is affected in all tested pause sites, suggesting that the upstream RNA sequence is important for transcriptional pausing. Compensatory mutations assessing the presence of RNA hairpins did not yield clear conclusions, indicating that complex RNA structures or transcriptional features may be playing a role in pausing. Moreover, using a bioinformatic approach, we explored the relation between a DNA consensus sequence important for pausing and putative hairpins among thousands of pause sites in E. coli. We identified 2125 sites presenting hairpin-dependent transcriptional pausing without consensus sequence, suggesting that this mechanism is widespread across E. coli. This study paves the way to understand the role of RNA structures in transcriptional pausing.
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Affiliation(s)
- Simon Jeanneau
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Pierre-Étienne Jacques
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec, Canada.,Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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Aubee JI, Olu M, Thompson KM. The i6A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation. RNA (NEW YORK, N.Y.) 2016; 22:729-742. [PMID: 26979278 PMCID: PMC4836647 DOI: 10.1261/rna.053165.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
The translation of rpoS(σ(S)), the general stress/stationary phase sigma factor, is tightly regulated at the post-transcriptional level by several factors via mechanisms that are not clearly defined. One of these factors is MiaA, the enzyme necessary for the first step in theN(6)-isopentyl-2-thiomethyl adenosinemethyl adenosine 37 (ms(2)i(6)A37) tRNA modification. We tested the hypothesis that an elevated UUX-Leucine/total leucine codon ratio can be used to identify transcripts whose translation would be sensitive to loss of the MiaA-dependent modification. We identified iraPas another candidate MiaA-sensitive gene, based on the UUX-Leucine/total leucine codon ratio. AniraP-lacZ fusion was significantly decreased in the abse nce of MiaA, consistent with our predictive model. To determine the role of MiaA in UUX-Leucine decoding in rpoS and iraP, we measured β-galactosidase-specific activity of miaA(-)rpo Sandira P translational fusions upon overexpression of leucine tRNAs. We observed suppression of the MiaA effect on rpoS, and notira P, via overexpression of tRNA(LeuX)but not tRNA(LeuZ) We also tested the hypothesis that the MiaA requirement for rpoS and iraP translation is due to decoding of UUX-Leucine codons within the rpoS and iraP transcripts, respectively. We observed a partial suppression of the MiaA requirement for rpoS and iraP translational fusions containing one or both UUX-Leucine codons removed. Taken together, this suggests that MiaA is necessary for rpoS and iraP translation through proper decoding of UUX-Leucine codons and that rpoS and iraP mRNAs are both modification tunable transcripts (MoTTs) via the presence of the modification.
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Affiliation(s)
- Joseph I Aubee
- Department of Microbiology, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Morenike Olu
- Department of Microbiology, College of Medicine, Howard University, Washington, DC 20059, USA Department of Biology, Howard University, Washington, DC 20059, USA
| | - Karl M Thompson
- Department of Microbiology, College of Medicine, Howard University, Washington, DC 20059, USA
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3
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Regulation of transcription by unnatural amino acids. Nat Biotechnol 2011; 29:164-8. [DOI: 10.1038/nbt.1741] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/01/2010] [Indexed: 11/09/2022]
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Benítez-Páez A, Villarroya M, Douthwaite S, Gabaldón T, Armengod ME. YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA (NEW YORK, N.Y.) 2010; 16:2131-43. [PMID: 20855540 PMCID: PMC2957053 DOI: 10.1261/rna.2245910] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 08/18/2010] [Indexed: 05/25/2023]
Abstract
Transfer RNAs are the most densely modified nucleic acid molecules in living cells. In Escherichia coli, more than 30 nucleoside modifications have been characterized, ranging from methylations and pseudouridylations to more complex additions that require multiple enzymatic steps. Most of the modifying enzymes have been identified, although a few notable exceptions include the 2'-O-methyltransferase(s) that methylate the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Here, we have used a comparative genomics approach to uncover candidate E. coli genes for the missing enzyme(s). Transfer RNAs from null mutants for candidate genes were analyzed by mass spectrometry and revealed that inactivation of yibK leads to loss of 2'-O-methylation at position 34 in both tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Loss of YibK methylation reduces the efficiency of codon-wobble base interaction, as demonstrated in an amber suppressor supP system. Inactivation of yibK had no detectable effect on steady-state growth rate, although a distinct disadvantage was noted in multiple-round, mixed-population growth experiments, suggesting that the ability to recover from the stationary phase was impaired. Methylation is restored in vivo by complementing with a recombinant copy of yibK. Despite being one of the smallest characterized α/β knot proteins, YibK independently catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide; YibK recognition of this target requires a pyridine at position 34 and N⁶-(isopentenyl)-2-methylthioadenosine at position 37. YibK is one of the last remaining E. coli tRNA modification enzymes to be identified and is now renamed TrmL.
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Affiliation(s)
- Alfonso Benítez-Páez
- Laboratorio de Genética Molecular, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
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Večerek B, Moll I, Bläsi U. Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding. EMBO J 2007; 26:965-75. [PMID: 17268550 PMCID: PMC1852835 DOI: 10.1038/sj.emboj.7601553] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 12/18/2006] [Indexed: 11/08/2022] Open
Abstract
The Fe2+-dependent Fur protein serves as a negative regulator of iron uptake in bacteria. As only metallo-Fur acts as an autogeneous repressor, Fe2+scarcity would direct fur expression when continued supply is not obviously required. We show that in Escherichia coli post-transcriptional regulatory mechanisms ensure that Fur synthesis remains steady in iron limitation. Our studies revealed that fur translation is coupled to that of an upstream open reading frame (uof), translation of which is downregulated by the non-coding RNA (ncRNA) RyhB. As RyhB transcription is negatively controlled by metallo-Fur, iron depletion creates a negative feedback loop. RyhB-mediated regulation of uof-fur provides the first example for indirect translational regulation by a trans-encoded ncRNA. In addition, we present evidence for an iron-responsive decoding mechanism of the uof-fur entity. It could serve as a backup mechanism of the RyhB circuitry, and represents the first link between iron availability and synthesis of an iron-containing protein.
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Affiliation(s)
- Branislav Večerek
- Department of Microbiology and Immunobiology, Max F Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Isabella Moll
- Department of Microbiology and Immunobiology, Max F Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology and Immunobiology, Max F Perutz Laboratories, University of Vienna, Vienna, Austria
- Department of Microbiology and Immunobiology, Max F Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/4, Vienna 1030, Austria. Tel.: +43 1 4277 54609; Fax: +43 1 4277 9546; E-mail:
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Paulus M, Haslbeck M, Watzele M. RNA stem-loop enhanced expression of previously non-expressible genes. Nucleic Acids Res 2004; 32:e78. [PMID: 15163763 PMCID: PMC419630 DOI: 10.1093/nar/gnh076] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The key step in bacterial translation is formation of the pre-initiation complex. This requires initial contacts between mRNA, fMet-tRNA and the 30S subunit of the ribosome, steps that limit the initiation of translation. Here we report a method for improving translational initiation, which allows expression of several previously non-expressible genes. This method has potential applications in heterologous protein synthesis and high-throughput expression systems. We introduced a synthetic RNA stem-loop (stem length, 7 bp; DeltaG(0) = -9.9 kcal/mol) in front of various gene sequences. In each case, the stem-loop was inserted 15 nt downstream from the start codon. Insertion of the stem-loop allowed in vitro expression of five previously non-expressible genes and enhanced the expression of all other genes investigated. Analysis of the RNA structure proved that the stem-loop was formed in vitro, and demonstrated that stabilization of the ribosome binding site is due to stem-loop introduction. By theoretical RNA structure analysis we showed that the inserted RNA stem-loop suppresses long-range interactions between the translation initiation domain and gene-specific mRNA sequences. Thus the inserted RNA stem-loop supports the formation of a separate translational initiation domain, which is more accessible to ribosome binding.
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Affiliation(s)
- Michael Paulus
- Roche Diagnostics, Nonnenwald 2, D-82377 Penzberg, Germany
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Vitreschak AG, Lyubetskaya EV, Shirshin MA, Gelfand MS, Lyubetsky VA. Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09555.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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8
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Knezevic I, Bachem S, Sickmann A, Meyer HE, Stülke J, Hengstenberg W. Regulation of the glucose-specific phosphotransferase system (PTS) of Staphylococcus carnosus by the antiterminator protein GlcT. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 9):2333-2342. [PMID: 10974121 DOI: 10.1099/00221287-146-9-2333] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ptsG operon of Staphylococcus carnosus consists of two adjacent genes, glcA and glcB, encoding glucose- and glucoside-specific enzymes II, respectively, the sugar permeases of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). The expression of the ptsG operon is glucose-inducible. Putative RAT (ribonucleic antiterminator) and terminator sequences localized in the promoter region of glcA suggest regulation via antitermination. The glcT gene was cloned and the putative antiterminator protein GlcT was purified. Activity of this protein was demonstrated in vivo in Escherichia coli and Bacillus subtilis. In vitro studies led to the assumption that phosphoenolpyruvate-dependent phosphorylation of residue His105 via the general PTS components enzyme I and HPr facilitates dimerization of GlcT and consequently activation. Because of the high similarity of the two ptsG-RAT sequences of B. subtilis and S. carnosus, in vivo studies were performed in B. subtilis. These indicated that GlcT of S. carnosus is able to recognize ptsG-RAT sequences of B. subtilis and to cause antitermination. The specific interaction between B. subtilis ptsG-RAT and S. carnosus GlcT demonstrated by surface plasmon resonance suggests that only the dimer of GlcT binds to the RAT sequence. HPr-dependent phosphorylation of GlcT facilitates dimer formation and may be a control device for the proper function of the general PTS components enzyme I and HPr necessary for glucose uptake and phosphorylation by the corresponding enzyme II.
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Affiliation(s)
- Igor Knezevic
- AG Physiologie der Mikroorganismen, Ruhr-Universität Bochum, ND 06/744, Universitätsstr. 150, D-44780 Bochum, Germany1
| | - Steffi Bachem
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Biochemie und Genetik der Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany2
| | - Albert Sickmann
- Institut für Immunologie, Abteilung Proteinstrukturlabor, MA 2/143, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany3
| | - Helmut E Meyer
- Institut für Immunologie, Abteilung Proteinstrukturlabor, MA 2/143, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany3
| | - Jörg Stülke
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Biochemie und Genetik der Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany2
| | - Wolfgang Hengstenberg
- AG Physiologie der Mikroorganismen, Ruhr-Universität Bochum, ND 06/744, Universitätsstr. 150, D-44780 Bochum, Germany1
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9
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Moore JA, Mathis JR, Poulter CD. Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: pre-steady-state kinetic studies. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1479:166-74. [PMID: 11004538 DOI: 10.1016/s0167-4838(00)00031-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase (DMAPP-tRNA transferase) catalyzes the first step in the biosynthesis of the hypermodified A37 residue in tRNAs that read codons beginning with uridine. The mechanism of the enzyme-catalyzed reaction was studied by isotope trapping, pre-steady-state rapid quench, and single turnover experiments. Isotope trapping indicated that the enzyme.tRNA complex is catalytically competent, whereas the enzyme.DMAPP complex is not. The results are consistent with an ordered sequential mechanism for substrate binding where tRNA binds first. The association and dissociation rate constants for the enzyme.tRNA binary complex are 1. 15+/-0.33x10(7) M(-1) s(-1) and 0.06+/-0.01 s(-1), respectively. Addition of DMAPP gives an enzyme.tRNA.DMAPP ternary complex in rapid equilibrium with the binary complex and DMAPP. Rapid quench studies yielded a linear profile (k(cat)=0.36+/-0.01 s(-1)) with no evidence for buildup of enzyme-bound product. Product release from DMAPP-tRNA transferase is therefore not rate-limiting. The Michaelis constant for tRNA and the equilibrium dissociation constant for DMAPP calculated from the individual rate constants determined here are consistent with values obtained from a steady-state kinetic analysis.
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Affiliation(s)
- J A Moore
- Department of Chemistry, University of Utah, Salt Lake City 84112, USA
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10
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Zažímalová E, Kamínek M, Březinová A, Motyka V. Control of cytokinin biosynthesis and metabolism. BIOCHEMISTRY AND MOLECULAR BIOLOGY OF PLANT HORMONES 1999. [DOI: 10.1016/s0167-7306(08)60486-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Leung HC, Chen Y, Winkler ME. Regulation of substrate recognition by the MiaA tRNA prenyltransferase modification enzyme of Escherichia coli K-12. J Biol Chem 1997; 272:13073-83. [PMID: 9148919 DOI: 10.1074/jbc.272.20.13073] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We purified polyhistidine (His6)-tagged and native Escherichia coli MiaA tRNA prenyltransferase, which uses dimethylallyl diphosphate (DMAPP) to isopentenylate A residues adjacent to the anticodons of most tRNA species that read codons starting with U residues. Kinetic and binding studies of purified MiaA were performed with several substrates, including synthetic wild-type tRNAPhe, the anticodon stem-loop (ACSLPhe) of tRNAPhe, and bulk tRNA isolated from a miaA mutant. Gel filtration shift and steady-state kinetic determinations showed that affinity-purified MiaA had the same properties as native MiaA and was completely active for tRNAPhe binding. MiaA had a Kmapp (tRNA substrates) approximately 3 nM, which is orders of magnitude lower than that of other purified tRNA modification enzymes, a Kmapp (DMAPP) = 632 nM, and a kcatapp = 0.44 s-1. MiaA activity was minimally affected by other modifications or nonsubstrate tRNA species present in bulk tRNA isolated from a miaA mutant. MiaA modified ACSLPhe with a kcatapp/Kmapp substrate specificity about 17-fold lower than that for intact tRNAPhe, mostly due to a decrease in apparent substrate binding affinity. Quantitative Western immunoblotting showed that MiaA is an abundant protein in exponentially growing bacteria (660 monomers per cell; 1.0 microM concentration) and is present in a catalytic excess. However, MiaA activity was strongly competitively inhibited for DMAPP by ATP and ADP (Kiapp = 0.06 microM), suggesting that MiaA activity is inhibited substantially in vivo and that DMAPP may bind to a conserved P-loop motif in this class of prenyltransferases. Band shift, filter binding, and gel filtration shift experiments support a model in which MiaA tRNA substrates are recognized by binding tightly to MiaA multimers possibly in a positively cooperative way (Kdapp approximately 0.07 microM).
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Affiliation(s)
- H C Leung
- Department of Microbiology and Molecular Genetics, University of Texas Houston Medical School, Houston, Texas 77030-1501, USA
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12
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Tavormina PL, Landick R, Gross CA. Isolation, purification, and in vitro characterization of recessive-lethal-mutant RNA polymerases from Escherichia coli. J Bacteriol 1996; 178:5263-71. [PMID: 8752347 PMCID: PMC178326 DOI: 10.1128/jb.178.17.5263-5271.1996] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The beta subunit of prokaryotic RNA polymerase shares significant sequence similarity with its eukaryotic and archaeal counterparts across most of the protein. Nine segments of particularly high similarity have been identified and are termed segments A through I. We have isolated severely defective Escherichia coli RNA polymerase mutants, most of which are unable to support bacterial growth. The majority of the substitutions affect residues in one of the conserved segments of beta, including invariant residues in segments D (amino acids 548 to 577), E (amino acids 660 to 678), and I (amino acids 1198 to 1296). In addition, recessive-lethal mutations that affect residues highly conserved only among prokaryotes were identified. They include a substitution in the extreme amino terminus of beta, a region in which no substitutions have previously been identified, and one rpoB mutation that truncates the polypeptide without abolishing minimal polymerase function in vitro. To examine the recessive-lethal alleles in vitro, we devised a novel method to remove nonmutant enzyme from RNA polymerase preparations by affinity tagging the chromosomal rpoB gene. In vitro examination of a subset of purified recessive-lethal RNA polymerases revealed that several substitutions, including all of those altering conserved residues in segment I, severely decrease transcript elongation and increase termination. We discuss the insights these mutants lend to a structure-function analysis of RNA polymerase.
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Affiliation(s)
- P L Tavormina
- Department of Bacteriology, University of Wisconsin--Madison 53706, USA
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13
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Irwin B, Heck JD, Hatfield GW. Codon pair utilization biases influence translational elongation step times. J Biol Chem 1995; 270:22801-6. [PMID: 7559409 DOI: 10.1074/jbc.270.39.22801] [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] Open
Abstract
Two independent assays capable of measuring the relative in vivo translational step times across a selected codon pair in a growing polypeptide in the bacterium Escherichia coli have been employed to demonstrate that codon pairs observed in protein coding sequences more frequently than predicted (over-represented codon pairs) are translated slower than pairs observed less frequently than expected (under-represented codon pairs). These results are consistent with the findings that translational step times are influenced by codon context and that these context effects are related to the compatabilities of adjacent tRNA isoacceptor molecules on the surface of a translating ribosome. These results also support our previous suggestion that the frequency of one codon next to another has co-evolved with the structure and abundance of tRNA isoacceptors in order to control the rates of translational step times without imposing additional constraints on amino acid sequences or protein structures.
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Affiliation(s)
- B Irwin
- Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine 92717, USA
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Björk GR. Genetic dissection of synthesis and function of modified nucleosides in bacterial transfer RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1995; 50:263-338. [PMID: 7538683 DOI: 10.1016/s0079-6603(08)60817-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- G R Björk
- Department of Microbiology, Umeå University, Sweden
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15
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Vanet A, Plumbridge JA, Guérin MF, Alix JH. Ribosomal protein methylation in Escherichia coli: the gene prmA, encoding the ribosomal protein L11 methyltransferase, is dispensable. Mol Microbiol 1994; 14:947-58. [PMID: 7715456 DOI: 10.1111/j.1365-2958.1994.tb01330.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The prmA gene, located at 72 min on the Escherichia coli chromosome, is the genetic determinant of ribosomal protein L11-methyltransferase activity. Mutations at this locus, prmA1 and prmA3, result in a severely undermethylated form of L11. No effect, other than the lack of methyl groups on L11, has been ascribed to these mutations. DNA sequence analysis of the mutant alleles prmA1 and prmA3 detected point mutations near the C-terminus of the protein and plasmids overproducing the wild-type and the two mutant proteins have been constructed. The wild-type PrmA protein could be crosslinked to its radiolabelled substrate, S-adenosyl-L-methionine (SAM), by u.v. irradiation indicating that it is the gene for the methyltransferase rather than a regulatory protein. One of the mutant proteins, PrmA3, was also weakly crosslinked to SAM. Both mutant enzymes when expressed from the overproducing plasmids were capable of catalysing the incorporation of 3H-labelled methyl groups from SAM to L11 in vitro. This confirmed the observation that the mutant proteins possess significant residual activity which could account for their lack of growth phenotype. However, a strain carrying an in vitro-constructed null mutation of the prmA gene, transferred to the E. coli chromosome by homologous recombination, was perfectly viable.
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Affiliation(s)
- A Vanet
- Institut de Biologie Physico-Chimique, URA1139 CNRS, Paris, France
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16
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Yanofsky C, Horn V. Role of regulatory features of the trp operon of Escherichia coli in mediating a response to a nutritional shift. J Bacteriol 1994; 176:6245-54. [PMID: 7928995 PMCID: PMC196965 DOI: 10.1128/jb.176.20.6245-6254.1994] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Physiological studies were performed under nutritional stress and nonstress conditions to assess the relative importance of the various regulatory mechanisms that Escherichia coli can use to alter its rate of tryptophan synthesis. Mutants were examined in which the trp repressor was inactive, transcription termination at the trp attenuator was altered, transcription initiation at the trp promoter was reduced, or feedback inhibition of anthranilate synthase was abolished. Strains were examined in media with and without tryptophan, phenylalanine and tyrosine, or acid-hydrolyzed casein and following shifts from one medium to another. Growth rates and anthranilate synthase levels were measured. In media lacking tryptophan, each of the mutants showed relief of repression and/or attenuation and maintained a near-normal growth rate. Following a shift from a medium containing tryptophan to a tryptophan-free medium containing phenylalanine and tyrosine or acid-hydrolyzed casein, mutants with abnormally low trp enzyme levels exhibited an appreciable growth lag before resuming growth. The wild-type strain displayed termination relief only under one extreme shift condition, upon transfer from a minimal medium containing tryptophan to minimal medium with only phenylalanine and tyrosine. A promoter down-mutant had difficulty adjusting to a shift from high tryptophan to low tryptophan levels in a medium containing acid-hydrolyzed casein. In all media tested, anthranilate synthase levels were lower in a feedback-resistant mutant than in the wild type. These studies demonstrate the capacity of E. coli to adjust its rate of tryptophan synthesis to maintain rapid growth following a shift to stressful nutritional conditions.
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Affiliation(s)
- C Yanofsky
- Department of Biological Sciences, Stanford University, California 94305-5020
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Feng G, Lee D, Wang D, Chan C, Landick R. GreA-induced transcript cleavage in transcription complexes containing Escherichia coli RNA polymerase is controlled by multiple factors, including nascent transcript location and structure. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31788-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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18
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Persson BC, Esberg B, Olafsson O, Björk GR. Synthesis and function of isopentenyl adenosine derivatives in tRNA. Biochimie 1994; 76:1152-60. [PMID: 7748950 DOI: 10.1016/0300-9084(94)90044-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Isopentenyl adenosine derivatives can be found next to the anticodon (position 37) in tRNA from both the Bacteria and Eucarya domains. These modified nucleosides improve the efficiency of tRNA in translation, can increase and decrease translational fidelity, and make the tRNA less codon context sensitive. In bacteria the synthesis of isopentenyl adenosine derivatives seems to be linked to iron metabolism and central metabolic pathways.
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Affiliation(s)
- B C Persson
- Department of Microbiology, Umeå University, Sweden
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Heery DM, Dunican LK. Cloning of the trp gene cluster from a tryptophan-hyperproducing strain of Corynebacterium glutamicum: identification of a mutation in the trp leader sequence. Appl Environ Microbiol 1993; 59:791-9. [PMID: 7683184 PMCID: PMC202191 DOI: 10.1128/aem.59.3.791-799.1993] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Corynebacterium glutamicum ATCC 21850 produces up to 5 g of extracellular L-tryptophan per liter in broth culture and displays resistance to several synthetic analogs of aromatic amino acids. Here we report the cloning of the tryptophan biosynthesis (trp) gene cluster of this strain on a 14.5-kb BamHI fragment. Subcloning and complementation of Escherichia coli trp auxotrophs revealed that as in Brevibacterium lactofermentum, the C. glutamicum trp genes are clustered in an operon in the order trpE, trpD, trpC, trpB, trpA. The cloned fragment also confers increased resistance to the analogs 5-methyltryptophan and 6-fluorotryptophan on E. coli. The sequence of the ATCC 21850 trpE gene revealed no significant changes when compared to the trpE sequence of a wild-type strain reported previously. However, analysis of the promoter-regulatory region revealed a nonsense (TGG-to-TGA) mutation in the third of three tandem Trp codons present within a trp leader gene. Polymerase chain reaction amplification and sequencing of the corresponding region confirmed the absence of this mutation in the wild-type strain. RNA secondary-structure predictions and sequence similarities to the E. coli trp attenuator suggest that this mutation results in a constitutive antitermination response.
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Affiliation(s)
- D M Heery
- Department of Microbiology, University College, Galway, Ireland
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Abstract
A 50-nucleotide (nt) untranslated region (coding gap sequence) that interrupts the amino acid coding sequence in T4 gene 60, plus an additional 5 nt upstream and another 3 nt downstream from the gap sequence, shows unusual folding patterns according to RNA structure prediction. A predicted highly stable and significant hairpin structure in the 5' half of the gap sequence and a plausible tertiary structural element computed in the 3' part of the gap sequence seem significant by statistical tests on the wild-type (wt) sequence. This feature is absent in insertion, deletion and substitution variants of the gap sequence, in which template activities are markedly lower than that of the wt. The proposed feature is consistent with currently available data showing that the translational bypass of the coding gap is correlated with a stop codon involved in a stem-loop structure folded in the gap sequence. We suggest that the role of this segment in 'ribosomal bypass' of a portion of the mRNA sequence is a property of its special folded structure.
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Affiliation(s)
- Le Shu-Yun
- Laboratory of Mathematical Biology, Division of Cancer Biology and Diagnosis Centers, National Cancer Institute, NIH, Frederick, MD 21702, USA
- Correspondence to: Dr. S.-Y. Le, Laboratory of Mathematical Biol., DCBDC, NCI, NIH, Bldg. 469, Rm. 151, Frederick, MD 21702, USA. Tel. (301)846-5576; Fax (301)846-5598.
| | - Chen Jih-Hsiang
- Biomedical Supercomputing Center, Program Resources Inc., DynCorp, NCI/FCRDC, Frederick, MD 21702, USA. Tel. (301)846-5773
| | - Jacob V. Maizel
- Laboratory of Mathematical Biology, Division of Cancer Biology and Diagnosis Centers, National Cancer Institute, NIH, Frederick, MD 21702, USA
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Zalatan F, Platt T. Effects of decreased cytosine content on rho interaction with the rho-dependent terminator trp t' in Escherichia coli. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41744-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Gavini N, Pulakat L. Role of translation of the pheA leader peptide coding region in attenuation regulation of the Escherichia coli pheA gene. J Bacteriol 1991; 173:4904-7. [PMID: 1856183 PMCID: PMC208172 DOI: 10.1128/jb.173.15.4904-4907.1991] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In Escherichia coli, the expression of the pheA gene is regulated by attenuation of transcription. To study the molecular details of pheA attenuation, we introduced mutations in the pheA leader peptide coding region and analyzed their effects by using pheA promoter-lacZ gene transcription fusions (pheAp-lacZ). Mutations in the ribosome-binding site (pheAe1213) or in the translation initiation codon (pheAe24) of the pheA leader peptide coding region resulted in superattenuation of pheA expression. However, the presence of a stop codon upstream to the tandem phenylalanine codons (pheAe3334) led to an increase in the basal-level expression of pheA. This increase was further enhanced in the presence of prfA release factor mutant. The level of pheA expression in all three mutants was the same when cells were starved for phenylalanine. These results demonstrate that efficient translation of the pheA leader peptide coding region and the position of the ribosome on the leader transcript play decisive roles in the attenuation regulation of pheA.
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Affiliation(s)
- N Gavini
- Russell Grimwade School of Biochemistry, University of Melbourne, Parkville, Victoria, Australia
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Chen JW, Harms E, Umbarger HE. Mutations replacing the leucine codons or altering the length of the amino acid-coding portion of the ilvGMEDA leader region of Escherichia coli. J Bacteriol 1991; 173:2341-53. [PMID: 2007556 PMCID: PMC207787 DOI: 10.1128/jb.173.7.2341-2353.1991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The specificity of regulation by attenuation of the ilvGMEDA operon of Escherichia coli was examined by making alterations in the peptide-coding portion of the leader region. The effects of the alterations on attenuation control were monitored by operon fusions with the lacZ or cat gene. Substitution of the tandem leucine codons with arginine codons did not result in arginine control of attenuation even though the altered leader transcripts contained three consecutive arginine codons. Substitution of the single leucine codon with a proline codon at position 10 of the putative peptide, which had been shown to be important in the regulation of the Serratia marcescens ilv operon, did not result in control of attenuation by proline. Since the formation of neither proline nor arginine biosynthetic enzymes is regulated by attenuation control, the effect of tandem phenylalanine codons in place of the tandem leucine codons was examined and found not to result in control by phenylalanine supply. The latter failure may have been due to a configuration in the secondary structure of the protector stem of the leader transcript different from that of the wild-type transcript. The results of the study favored the idea that the lead ribosome does not initiate translation of the leader transcript until after the RNA polymerase has reached the pause site (117 bases into the leader region).
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Affiliation(s)
- J W Chen
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
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