Adjacent effect on suppression efficiency

Yahata, Hiroko; Ocada, Yoshiko; Tsugita, Akira

doi:10.1007/bf00340380

Cited by 48 publications

(3 citation statements)

References 10 publications

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“…In our case, a read-through of the termination signal might be occurring similar to that reported in bacteriophage Q/3 or X (Horiuchi et al, 1971;Yates et al, 1971), several filamentous phages (Engelberg-Kulka et al, 1979), and Mul and Ms viral RNAs (Philipson et al, 1978). Considerable evidence for a role of sequences near the 3' end of the termination signal in the suppression of a termination codon has also accumulated in prokaryotes (Sasler, 1969;Yahata et al, 1970;Bosi & Roth, 1980, Bosi, 1983Murgola et al, 1984).…”

Section: Chjhgohsupporting

confidence: 81%

Translation of the human C3b/C4b receptor mRNA in a cell-free system and by Xenopus oocytes

Kumar¹,

Farries²,

Swierkoz³

et al. 1989

Biochemistry

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The C3b/C4b complement receptor (CR1) is a large, single-chain integral membrane glycoprotein present on erythrocytes, leukocytes, glomerular podocytes, and splenic dendritic-reticular cells that mediates the binding of complement-coated particles and immune complexes. CR1 is unusual in that it is polymorphic in size with the four allelic variants having molecular weights of 190,000, 220,000, 250,000, and 280,000 (SDS-PAGE, reducing conditions). The in vitro translation of the common (Mr 220,000) allelic variant CR1 has been achieved by using mRNA in lysates of rabbit reticulocytes and in Xenopus oocytes. HL-60, a promyelocytic human leukemic cell line, was treated with DMSO to induce differentiation and synthesis of CR1. Poly(A+) RNA was purified from these cells by column chromatography on oligo(dT)-cellulose. In the rabbit reticulocyte system, no CR1 was detected unless the translation mixture was denatured. In the presence of methylmercuric hydroxide, the CR1 translation product, unlike most translation products, had the same molecular weight in gel electrophoresis as the high-mannose-containing pro-CR1 and was 15-20K larger than nonglycosylated CR1. This suggests that a cotranslational modification of CR1 structure occurs, probably involving a proteolytic cleavage event. When poly(A+) RNA was translated in Xenopus oocytes, CR1 could be detected by treatment of oocytes with anti-CR1 monoclonal antibody followed by fluorescein-conjugated goat anti-mouse IgG. CR1 was diffusely distributed but preferentially localized to the vegetal surface. The molecular weight of this product, identified in immunoprecipitates of lysates of [35S]methionine-labeled oocytes, was identical with that of CR1 of HL-60.

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Section: Chjhgohsupporting

confidence: 81%

Translation of the human C3b/C4b receptor mRNA in a cell-free system and by Xenopus oocytes

Kumar¹,

Farries²,

Swierkoz³

et al. 1989

Biochemistry

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“…RF1 determines the termination on UAA and UAG stop codons, RF2-on UAA and UGA stop codons (for review see [2,3]). It is known, that nucleotides surrounding the stop and the sense codons influence the efficiency of nonsense [4][5][6][7][8][9][10][11][12][13] or missense [ 14] suppression respectively. Experimental observations point to the effect of nucleotides 3' to the stop codon on nonsense suppression [7][8][9][11][12][13]].…”

Section: Introductionmentioning

confidence: 99%

Termination of translation in bacteria may be modulated via specific interaction between peptide chain release factor 2 and the last peptidyl-tRNA^Ser/Phe

Arkov¹,

Korolev²,

Kisselev³

1993

Nucl Acids Res

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The 5' context of 671 Escherichia coli stop codons UGA and UAA has been compared with the context of stop-like codons (UAC, UAU and CAA for UAA; UGG, UGC, UGU and CGA for UGA). We have observed highly significant deviations from the expected nucleotide distribution: adenine is over-represented whereas pyrimidines are under-represented in position -2 upstream from UAA. Uridine is over-represented in position -3 upstream from UGA. Lysine codons are preferable immediately prior to UAA. A complete set of codons for serine and the phenylalanine UUC codon are preferable immediately 5' to UGA. This non-random codon distribution before stop codons could be considered as a molecular device for modulation of translation termination. We have found that certain fragment of E. coli release factor 2 (RF2) (amino acids 93-114) is similar to the amino acid sequences of seryl-tRNA synthetase (positions 10-19 and 80-93) and of beta (small) subunit (positions 72-94) of phenylalanyl-tRNA synthetase from E. coli. Three-dimensional structure of E. coli seryl-tRNA synthetase is known [1]: Its N-terminus represents an antiparallel alpha-helical coiled-coil domain and contains a region homologous to RF2. On the basis of the above-mentioned results we assume that a specific interaction between RF2 and the last peptidyl-tRNA(Ser/Phe) occurs during polypeptide chain termination in prokaryotic ribosomes.

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“…Beyond variability due to system composition, the sequence context in which a nonsense codon appears also modulates the efficiency of natural nonsense suppression [ 13 , 14 ]. Direct measurement of sequence context effects in sense codon reading are also evident from single molecule experiments and ribosome profiling, but systems that provide simple read-outs for sense codon reading are not available [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair

Schwark

Schmitt

Fisk

2018

Genes

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Non-canonical amino acids (ncAAs) are finding increasing use in basic biochemical studies and biomedical applications. The efficiency of ncAA incorporation is highly variable, as a result of competing system composition and codon context effects. The relative quantitative contribution of the multiple factors affecting incorporation efficiency are largely unknown. This manuscript describes the use of green fluorescent protein (GFP) reporters to quantify the efficiency of amber codon reassignment using the Methanocaldococcus jannaschii orthogonal pair system, commonly employed for ncAA incorporation, and quantify the contribution of release factor 1 (RF1) to the overall efficiency of amino acid incorporation. The efficiencies of amber codon reassignments were quantified at eight positions in GFP and evaluated in multiple combinations. The quantitative contribution of RF1 competition to reassignment efficiency was evaluated through comparisons of amber codon suppression efficiencies in normal and genomically recoded Escherichia coli strains. Measured amber stop codon reassignment efficiencies for eight single stop codon GFP variants ranged from 51 to 117% in E. coli DH10B and 76 to 104% in the RF1 deleted E. coli C321.ΔA.exp. Evaluation of efficiency changes in specific sequence contexts in the presence and absence of RF1 suggested that RF1 specifically interacts with +4 Cs and that the RF1 interactions contributed approximately half of the observed sequence context-dependent variation in measured reassignment efficiency. Evaluation of multisite suppression efficiencies suggests that increasing demand for translation system components limits multisite incorporation in cells with competing RF1.

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Adjacent effect on suppression efficiency

Cited by 48 publications

References 10 publications

Translation of the human C3b/C4b receptor mRNA in a cell-free system and by Xenopus oocytes

Translation of the human C3b/C4b receptor mRNA in a cell-free system and by Xenopus oocytes

Termination of translation in bacteria may be modulated via specific interaction between peptide chain release factor 2 and the last peptidyl-tRNA^Ser/Phe

Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair

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Adjacent effect on suppression efficiency

Cited by 48 publications

References 10 publications

Translation of the human C3b/C4b receptor mRNA in a cell-free system and by Xenopus oocytes

Translation of the human C3b/C4b receptor mRNA in a cell-free system and by Xenopus oocytes

Termination of translation in bacteria may be modulated via specific interaction between peptide chain release factor 2 and the last peptidyl-tRNASer/Phe

Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair

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Termination of translation in bacteria may be modulated via specific interaction between peptide chain release factor 2 and the last peptidyl-tRNA^Ser/Phe