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Leiva LE, Zegarra V, Bange G, Ibba M. At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria. Microbiol Mol Biol Rev 2023; 87:e0004422. [PMID: 36853029 PMCID: PMC10029340 DOI: 10.1128/mmbr.00044-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
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Affiliation(s)
- Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Victor Zegarra
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
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2
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The alarmones (p)ppGpp directly regulate translation initiation during entry into quiescence. Proc Natl Acad Sci U S A 2020; 117:15565-15572. [PMID: 32576694 DOI: 10.1073/pnas.1920013117] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many bacteria exist in a state of metabolic quiescence where energy consumption must be minimized so as to maximize available resources over a potentially extended period of time. As protein synthesis is the most energy intensive metabolic process in a bacterial cell, it would be an appropriate target for down-regulation during the transition from growth to quiescence. We observe that when Bacillus subtilis exits rapid growth, a subpopulation of cells emerges with very low protein synthetic activity. This phenotypic heterogeneity requires the production of the nucleotides (p)ppGpp, which we show are sufficient to inhibit protein synthesis in vivo. We then show that one of these molecules, ppGpp, inhibits protein synthesis by preventing the allosteric activation of the essential GTPase Initiation Factor 2 (IF2) during translation initiation. Finally, we demonstrate that the observed attenuation of protein synthesis during the entry into quiescence is a consequence of the direct interaction of (p)ppGpp and IF2.
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Sajish M, Kalayil S, Verma SK, Nandicoori VK, Prakash B. The significance of EXDD and RXKD motif conservation in Rel proteins. J Biol Chem 2009; 284:9115-23. [PMID: 19201753 PMCID: PMC2666561 DOI: 10.1074/jbc.m807187200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Monofunctional and bifunctional classes of Rel proteins catalyze
pyrophosphoryl transfer from ATP to 3′-OH of GTP/GDP to synthesize
(p)ppGpp, which is essential for normal microbial physiology and survival.
Bifunctional proteins additionally catalyze the hydrolysis of (p)ppGpp. We
have earlier demonstrated that although both catalyze identical the (p)ppGpp
synthesis reaction, they exhibit a differential response to Mg2+
due to a unique charge reversal in the synthesis domain; an RXKD
motif in the synthesis domain of bifunctional protein is substituted by an
EXDD motif in that of the monofunctional proteins. Here, we show that
these motifs also determine substrate specificities (GTP/GDP), cooperativity,
and regulation of catalytic activities at the N-terminal region through the
C-terminal region. Most importantly, a mutant bifunctional Rel carrying an
EXDD instigates a novel catalytic reaction, resulting in the
synthesis of pGpp by an independent hydrolysis of the
5′Pα-O-Pβ bond of GTP/GDP or (p)ppGpp.
Further experiments with RelA from Escherichia coli wherein
EXDD is naturally present also revealed the presence of pGpp, albeit
at low levels. This work brings out the biological significance of
RXKD/EXDD motif conservation in Rel proteins and reveals an
additional catalytic activity for the monofunctional proteins, prompting an
extensive investigation for the possible existence and role of pGpp in the
biological system.
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Affiliation(s)
- Mathew Sajish
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
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4
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Scorer CA, Carrier MJ, Rosenberger RF. Amino acid misincorporation during high-level expression of mouse epidermal growth factor in Escherichia coli. Nucleic Acids Res 1991; 19:3511-6. [PMID: 1852602 PMCID: PMC328373 DOI: 10.1093/nar/19.13.3511] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To determine whether the high-level expression of foreign proteins in Escherichia coli can lead to frequent translational errors, we analyzed amino acid misincorporation in mouse epidermal growth factor (mEGF) produced as a TrpE fusion protein. The mEGF DNA does not encode phenylalanine and determining the phenylalanine content of the purified protein will measure missense errors. Using this approach, we found an error frequency of about 1 in 40 for codons differing by a single base from those for phenylalanine. This is at least ten times higher than the error rate found for normal E. coli protein synthesis and may be due to limiting supply of charged tRNAs and GTP, brought about by the high-level production of the heterologous protein. The unexpectedly high error rate has implications for the clinical use of E. coli-derived therapeutic proteins.
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Affiliation(s)
- C A Scorer
- Genetics Division, National Institute for Medical Research, London, UK
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5
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Varenne S, Baty D, Verheij H, Shire D, Lazdunski C. The maximum rate of gene expression is dependent on the downstream context of unfavourable codons. Biochimie 1989; 71:1221-9. [PMID: 2517483 DOI: 10.1016/0300-9084(89)90027-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Presented here is an experimental demonstration of our theoretical predictions on the role of the downstream context of unfavourable codons in a gene on its expression level. Six non clustered AGG codons were inserted in the chloramphenicol acetyltransferase (cat) gene of E. coli and the expression of this modified gene (cat4) was compared with that of a cat gene in which four clustered AGG codons were inserted (cat2 gene). As predicted, the rate of production of the corresponding CAT4 and CAT2 proteins is equal as long as the rate of transcription of the gene does not exceed a given limit. When this limit is exceeded, production of CAT4 continues to increase, whereas CAT2 production decreases dramatically. Various consequences and possible applications of this downstream context effect are discussed.
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Affiliation(s)
- S Varenne
- CNRS, Centre de Biochimie et de Biologie Moléculaire, Marseille, France
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6
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Spanjaard RA, van Duin J. Translation of the sequence AGG-AGG yields 50% ribosomal frameshift. Proc Natl Acad Sci U S A 1988; 85:7967-71. [PMID: 3186700 PMCID: PMC282334 DOI: 10.1073/pnas.85.21.7967] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We have inserted the sequence 5'-AAG-GAGGU-3', which is complementary to the 3' terminus of Escherichia coli 16S rRNA, in a reading frame and analyzed its effect on the accuracy and overall rate of translation in vivo. Translation over the sequence yields a 50% ribosomal frameshift if the reading phase is A-AGG-AGG-U. The other two possible frames do not give shifts. The introduction of a UAA stop codon before (UAA-AGG-AGG-U) but not after (A-AGG-AGG-UAA) the AGG codons abolishes the frameshift. The change in the reading phase occurs exclusively to the +1 direction. Efficient frameshifting is also induced by the sequence A-AGA-AGA-U. The arginine codons AGG and AGA are read by minor tRNA. Suppression of frameshifting takes place when a gene for minor tRNA(Arg) is introduced on a multicopy plasmid. We suggest that frameshifting during translation of the A-AGG-AGG-U sequence is due to the erroneous decoding of the tandem AGG codons and arises by depletion of tRNA(Arg). The complementarity of tandem AGG codons to the 3' terminus of 16S rRNA is a coincidence and apparently not related to the shift. Replacing the AGG-AGG sequence by the optimal arginine codons CGU-CGU does not increase the overall rate of translation.
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Affiliation(s)
- R A Spanjaard
- Department of Biochemistry, Leiden University, The Netherlands
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8
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Williams MG, Rogers P. Expression of arg genes of Escherichia coli during arginine limitation dependent upon stringent control of translation. J Bacteriol 1987; 169:1644-50. [PMID: 2435708 PMCID: PMC211994 DOI: 10.1128/jb.169.4.1644-1650.1987] [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: 12/31/2022] Open
Abstract
The transcription and translation of operons for arginine biosynthetic enzymes after arginine removal (arginine down shift) were studied in relA and relA+ strains of Escherichia coli. After arginine down shift, derepression of synthesis of the arginine biosynthetic enzymes ornithine carbamoyltransferase (argF) and argininosuccinate lyase (argH) began at about 15 min in relA+ cells but was delayed in relA cells for more than 2 h. However, both relA+ and relA cells accumulated high levels of argCBH mRNA, as shown by dot blot hybridization, after arginine down shift. After 15 min of arginine limitation, the proportion of ribosome-bound argCBH mRNA was equivalent in both relA+ and relA cells. During the 15 min after the arginine down shift, relA+ cells produced a significant burst of argF and argH enzyme synthesis when arginine was added back to the culture, whereas relA cells did not produce this burst of enzyme synthesis. The relA cells regained the ability to produce a burst of argF and argH enzyme synthesis when alpha-methylglucose-induced glucose starvation was combined with arginine limitation. Significant guanosine 5'-diphosphate 3'-diphosphate accumulated in relA cells under this condition. Our results support the view that during periods of severe amino acid limitation guanosine 5'-diphosphate 3'-diphosphate acts in some way to ensure the translation of argCBH mRNA.
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Bouadloun F, Srichaiyo T, Isaksson LA, Björk GR. Influence of modification next to the anticodon in tRNA on codon context sensitivity of translational suppression and accuracy. J Bacteriol 1986; 166:1022-7. [PMID: 3086285 PMCID: PMC215227 DOI: 10.1128/jb.166.3.1022-1027.1986] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Effects on translation in vivo by modification deficiencies for 2-methylthio-N6-isopentenyladenosine (ms2i6A) (Escherichia coli) or 2-methylthio-N6-(4-hydroxyisopentenyl)adenosine (ms2io6A) (Salmonella typhimurium) in tRNA were studied in mutant strains. These hypermodified nucleosides are present on the 3' side of the anticodon (position 37) in tRNA reading codons starting with uridine. In E. coli, translational error caused by tRNA was strongly reduced in the case of third-position misreading of a tryptophan codon (UGG) in a particular codon context but was not affected in the case of first-position misreading of an arginine codon (CGU) in another codon context. Misreading of UGA nonsense codons at two different positions was codon context dependent. The efficiencies of some tRNA nonsense suppressors were decreased in a tRNA-dependent manner. Suppressor tRNA which lacks ms2i6A-ms2io6A becomes more sensitive to codon context. Our results therefore indicate that, besides improving translational efficiency, ms2i6A37 and ms2io6A37 modifications in tRNA are also involved in decreasing the intrinsic codon reading context sensitivity of tRNA. Possible consequences for regulation of gene expression are discussed.
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10
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Dix DB, Thompson RC. Elongation factor Tu.guanosine 3'-diphosphate 5'-diphosphate complex increases the fidelity of proofreading in protein biosynthesis: mechanism for reducing translational errors introduced by amino acid starvation. Proc Natl Acad Sci U S A 1986; 83:2027-31. [PMID: 3515344 PMCID: PMC323223 DOI: 10.1073/pnas.83.7.2027] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Complexes of elongation factor Tu (EF-Tu) with guanosine 3'-diphosphate 5'-diphosphate (ppGpp) bind to ribosomes where they slow the incorporation of aminoacyl-tRNAs into protein by inhibiting both the binding of aminoacyl-tRNA.EF-Tu.GTP ternary complexes and the formation of peptide bonds. The latter action increases the time available for aminoacyl-tRNA rejection by the ribosome and, therefore, increases the effectiveness of proofreading. Synthesis of ppGpp and the formation of EF-Tu.ppGpp occur in vivo in response to amino acid starvation. Our finding, therefore, suggests an explanation for the otherwise puzzling observation that amino acid starvation has, at most, a moderate effect on the fidelity of protein synthesis in wild-type Escherichia coli. We suggest that an EF-Tu.ppGpp-induced increase in the effectiveness of proofreading buffers the overall translational fidelity of these cells against amino acid starvation-induced errors in initial selection of aminoacyl-tRNA ternary complexes.
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11
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Khazaie K, Buchanan JH, Rosenberger RF. The accuracy of Q beta RNA translation. 1. Errors during the synthesis of Q beta proteins by intact Escherichia coli cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 144:485-9. [PMID: 6386472 DOI: 10.1111/j.1432-1033.1984.tb08491.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The fidelity of Q beta RNA translation by intact Escherichia coli cells has been studied. After infection, host protein synthesis was eliminated by adding rifampicin and the radioactive, phage-specified, proteins separated by one or two-dimensional gel electrophoresis. Labelled histidine and tryptophan were incorporated into the phage coat protein, whose message does not specify these amino acids, at a frequency of 0.09-0.13 per molecule. Errors leading to a change in the pI of the coat protein occurred at a rate of 0.05 per molecule, while the coat protein UGA stop codon was misread 6.5% of the time. These error rates are similar to data in some recent publications but much higher than the canonical 3-4 X 10(-4). They further provide a reference point in vivo to which the translation of the same message by E. coli extracts can be compared.
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12
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Rojas AM, Ehrenberg M, Andersson SG, Kurland CG. ppGpp inhibition of elongation factors Tu, G and Ts during polypeptide synthesis. MOLECULAR & GENERAL GENETICS : MGG 1984; 197:36-45. [PMID: 6392824 DOI: 10.1007/bf00327920] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The inhibition of elongation factors G, Tu and Ts by ppGpp was studied in vitro in a translation system with missense frequency and elongation rate similar to those in vivo. ppGpp inhibits EF-G with KI = 6 X 10(-5) M. When ppGpp is in twofold excess over GTP and EF-G is the rate-limiting component, the elongation rate is reduced twofold by ppGpp. EF-Tu is inhibited with KI = 7 X 10(-7) M in the absence of EF-Ts. When EF-Ts is added, the binding of ppGpp to EF-Tu becomes successively weaker. 1/KI depends linearly on 1/[Ts] and the intercept at the abscissa gives KI = 4 X 10(-5) M. This reflects the binding of ppGpp to the binary TuTs complex. The slope reveals that the binding of EF-Ts to the TuMS binary complex is strong (10(-6) M). ppGpp may thus inhibit the cycling of EF-Tu indirectly by the removal of the free EF-Ts by its adsorption to TuMS, as well as directly by simple binding to Tu. EF-Tu inhibition by ppGpp can be fully reversed by high levels of aminoacyl-tRNA only in the presence of EF-Ts and at low ribosomal activity. Our in vitro observations have been extrapolated to in vivo conditions with conclusions as follows: Under strong amino acid starvation ppGpp in twofold excess over GTP cannot reduce significantly the elongation rate of ribosomes and thereby restore the errors to their normal levels as in the stringent response. Under weak starvation, in contrast, a significant rate reduction can be achieved by the trapping of EF-Ts in complex with TuppGpp.
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13
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Abstract
Basal-level misreading of asparagine codons was examined in a number of Escherichia coli strains. Lysine substitutions were measured by quantitating the amount of charge heterogeneity in MS2 coat protein. In most strains the heterogeneity was consistent with misreading of AAU codons at a frequency of 3-6 X 10(-3). Strains with streptomycin resistance mutations (rpsL) have reduced levels of misreading. There is no significant difference in the frequency of basal-level errors in stringent (relA+) and relaxed (relA) strains, even during starvation for amino acids unrelated to the substitution being studied.
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14
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Andrieux E, Robert E, Cozzone AJ. Erroneous synthesis of ribosomal proteins in amino acid starved E. coli. Biochem Biophys Res Commun 1984; 118:246-53. [PMID: 6365097 DOI: 10.1016/0006-291x(84)91093-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The effect of amino acid starvation on the accuracy of translation of ribosomal proteins was analyzed in a stringent (relA+)/relaxed (relA) pair of E. coli strains. The degree of misreading was estimated from the amount of cysteine erroneously incorporated into individual proteins during arginine starvation of bacteria. Illegitimate incorporation of cysteine was found to occur to a significant extent in several proteins from both the small and the large subunits of ribosomes, in either type of strain.
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15
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Kurland CG, Ehrenberg M. Optimization of translation accuracy. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1984; 31:191-219. [PMID: 6397771 DOI: 10.1016/s0079-6603(08)60378-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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The elongation factor Tu from Escherichia coli, aminoacyl-tRNA, and guanosine tetraphosphate form a ternary complex which is bound by programmed ribosomes. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)43845-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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17
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Abraham AK, Pihl A. Effect of protein synthesis inhibitors on the fidelity of translation in eukaryotic systems. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 741:197-203. [PMID: 6652088 DOI: 10.1016/0167-4781(83)90059-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Factors influencing the accuracy of poly(U)-directed poly(Phe) synthesis in a wheat germ and in a reticulocyte system were studied. Addition of preformed phenylalanyl-tRNA, as well as increasing the ratio of poly(U) to ribosomes, significantly enhanced the poly(Phe) synthesis and concurrently reduced the misincorporation of leucine. The protein synthesis inhibitors cycloheximide, abrin and ricin had little or no effect on the misreading when the system was supplemented with 100 microM phenylalanyl-tRNA, but they reduced the relatively high error rate observed when the poly(U) system was not supplemented with the cognate substrate. Raising the incubation temperature enhanced the accuracy to the same extent whether or not ricin was present i.e., at widely different rates of elongation. The results show that the translational accuracy is not linked to the elongation rate as such. Translational inhibitors affect the fidelity by influencing the kinetics of the system. In systems containing limiting concentrations of cognate substrate, translational inhibitors will cause an increase in the limiting aminoacyl-tRNA species and thereby increase fidelity.
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18
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Dix DB, Thompson RC, Mackow ER, Chang FN. Effect of ppGpp on the accuracy of protein biosynthesis. Arch Biochem Biophys 1983; 223:319-24. [PMID: 6344795 DOI: 10.1016/0003-9861(83)90597-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The maintenance of accuracy in protein biosynthesis in amino acid-starved rel+ strains of Escherichia coli has been attributed to an effect of ppGpp on the accuracy of aa-tRNA selection by the ribosome. It has been determined that concentrations of ppGpp characteristic of those found in amino acid-starved cells have no effect on the rate of reaction of poly(U)-programmed ribosomes with either the cognate (Phe) or the near-cognate (Leu2) ternary complexes. Neither the rate of GTP hydrolysis, which signals selection of the ternary complex, nor the rate of peptide formation, which signals the acceptance of the aa-tRNA after proofreading, is affected by the nucleotide. The results indicate that the effect of ppGpp in maintaining the accuracy of protein biosynthesis in cells starved for an amino acid is not due to a direct effect on the rate constants for substrate selection by the ribosome.
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19
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Abstract
Some frameshift mutations are strongly suppressed by limitation for particular aminoacyl-tRNA species. Here, we show that ribosome frameshifting at a specific tryptophan codon during Trp-tRNA limitation accounts for suppression of a group of downstream frameshift alleles in the rIIB gene of bacteriophage T4. Genetic and physiological observations strongly suggest that ribosome frameshifting at this position depends on the binding of a noncognate (leucine) tRNA.
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20
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Goldman E. Effect of rate-limiting elongation on bacteriophage MS2 RNA-directed protein synthesis in extracts of Escherichia coli. J Mol Biol 1982; 158:619-36. [PMID: 6750139 DOI: 10.1016/0022-2836(82)90252-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Gallant J, Erlich H, Weiss R, Palmer L, Nyari L. Nonsense suppression in aminoacyl-t-RNA limited cells. MOLECULAR & GENERAL GENETICS : MGG 1982; 186:221-7. [PMID: 6180282 DOI: 10.1007/bf00331853] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A number of nonsense alleles of lacZ exhibit phenotypic suppression (as much as a sixteen-fold increase in leakiness) during partial limitation for certain aminoacyl-tRNA species in relA mutant cells. Each responsive allele has its individual pattern of response to limitation for one or more amino acids or aminoacyl-tRNA's. The phenotypic suppression occurs only during limitation, and ceases once limitation is reversed. Suppression is much reduced by the presence of the relA+ allele or an allele of rpsL which restricts ribosomal ambiguity. In one case, the suppressed product has been identified by radioimmune assay and gel electrophoresis, and is a full-length lacZ protomer. Mechanisms are discussed whereby aberrations of translation at codons calling for an aminoacyl-tRNA species in short supply might lead to readthrough of a nearby nonsense codon.
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22
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Wagner EG, Ehrenberg M, Kurland CG. Kinetic suppression of translational errors by (p)ppGpp. MOLECULAR & GENERAL GENETICS : MGG 1982; 185:269-74. [PMID: 7045583 DOI: 10.1007/bf00330797] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The effect of (p)ppGpp on the accuracy of translation was studied in vitro using a poly(U)-programmed poly(Phe)-synthesizing system operating at incorporation rates and missense error frequencies close to the values obtained in vivo. Simulation of a relaxed phenotype in vitro was accomplished by limitation of the cognate aminoacyl-tRNA synthetase, while the noncognate aminoacyl-tRNA synthetase was included at saturating concentrations. This protocol yielded a Phe-tRNA-starved steady state system displaying the expected decrease in Phe polymerization rates accompanied by a drastic increase in relative Leu misincorporation errors. The use of purified enzymes permitted us to assay for the effects of the individual nucleotides ppGpp and ppGpp as well as their potential targets, the elongation factors Tu and G, upon the missense error rates. Our results support the conclusion that ppGpp reduces misincorporation in a starved in vitro system by preferentially inhibiting EF-Tu. The details of the proposed mechanism and their relevance to an in vivo situation are discussed.
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23
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Wagner EG, Jelenc PC, Ehrenberg M, Kurland CG. Rate of elongation of polyphenylalanine in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 122:193-7. [PMID: 7037399 DOI: 10.1111/j.1432-1033.1982.tb05866.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Ribosomes purified from Escherichia coli were preincubated with AcPhe-tRNA and poly(U). Then purified components necessary for polypeptide synthesis were added. Incubation of the complete system led to a burst of elongation which lasted for nearly 10 s. During the initial burst approximately 10% of the ribosomes participated in the elongation of poly(Phe) at an average rate per ribosome close to eight peptide bonds/s. The missense error rate with leucine was 4 x 10(-4) during the burst. Accordingly, the preincubated elongation system functions at a rate, as well as an accuracy, close to those of protein synthesis in vivo.
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24
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Pingoud A, Block W. The elongation factor Tu . guanosine tetraphosphate complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 116:631-4. [PMID: 7021151 DOI: 10.1111/j.1432-1033.1981.tb05382.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The elongation factor Tu (EF-Tu) isolated from Escherichia coli cells that have undergone the stringent response is predominantly complexed with guanosine 5'-diphosphate 3'-diphosphate. This complex can be separated by anion-exchange chromatography from Ef-Tu . GDP. Unlike EF-Tu complexed with guanosine 5'-triphosphate 3'-diphosphate, the complex with guanosine 5'-diphosphate 3'-diphosphate cannot form a ternary complex with aminoacyl-tRNAs as can be shown directly by hydrolysis protection experiments.
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