Mistranslational errors associated with the rare arginine codon CGG in Escherichia coli

McNulty, Dean E.; Claffee, Brett A; Huddleston, Michael J.; Kane, James F.

doi:10.1016/s1046-5928(02)00610-1

Cited by 104 publications

(61 citation statements)

References 18 publications

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“…Because we detected no differences in transcription error rates between these different growth conditions, we reason that this variation manifests during translation and is most likely caused by tRNA scarcity during stationary phase (6,55,56). Although decreases in ribonucleotide concentration also occur during stationary phase (57), this has little effect on the overall fidelity of gene expression.…”

Section: Discussionmentioning

confidence: 72%

Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles

Traverse

Ochman

2016

Proc. Natl. Acad. Sci. U.S.A.

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Errors that occur during transcription have received much less attention than the mutations that occur in DNA because transcription errors are not heritable and usually result in a very limited number of altered proteins. However, transcription error rates are typically several orders of magnitude higher than the mutation rate. Also, individual transcripts can be translated multiple times, so a single error can have substantial effects on the pool of proteins. Transcription errors can also contribute to cellular noise, thereby influencing cell survival under stressful conditions, such as starvation or antibiotic stress. Implementing a method that captures transcription errors genome-wide, we measured the rates and spectra of transcription errors in Escherichia coli and in endosymbionts for which mutation and/or substitution rates are greatly elevated over those of E. coli. Under all tested conditions, across all species, and even for different categories of RNA sequences (mRNA and rRNAs), there were no significant differences in rates of transcription errors, which ranged from 2.3 × 10−5 per nucleotide in mRNA of the endosymbiont Buchnera aphidicola to 5.2 × 10−5 per nucleotide in rRNA of the endosymbiont Carsonella ruddii. The similarity of transcription error rates in these bacterial endosymbionts to that in E. coli (4.63 × 10−5 per nucleotide) is all the more surprising given that genomic erosion has resulted in the loss of transcription fidelity factors in both Buchnera and Carsonella.

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Section: Discussionmentioning

confidence: 72%

Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles

Traverse

Ochman

2016

Proc. Natl. Acad. Sci. U.S.A.

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“…23,40,41 Unlike PFS, the incidental frameshift does not require the presence of both of the slippery sequence and the stimulatory structure. Instead, it is driven by specific mRNA structure features such as rare codons [44][45][46][47][48] or mononucleotide repeat of 6 to 9 guanine nucleotides (termed G-string). 31,42,[49][50][51][52] The efficiency of incidental frameshift is usually low (i.e., <5%) although the efficiency of frame shifts at hungry codons can reach as high as 50%.…”

Section: Discussionmentioning

confidence: 99%

“…[44][45][46][47][48] Recently, an example of out-of-frame expression as a result of DNA sequence rearrangement was reported in IgG produced in CHO. 18 To our knowledge, this study represents the first example of a pure frameshift variant observed in recombinant proteins expressed in a mammalian cell line, CHO in this case.…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of a -1 reading frameshift in the heavy chain constant region of an IgG1 recombinant monoclonal antibody produced in CHO cells

Lian

Wang

2015

mAbs

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Frameshifts lead to complete alteration of the intended amino acid sequences, and therefore may affect the biological activities of protein therapeutics and pose potential immunogenicity risks. We report here the identification and characterization of a novel -1 frameshift variant in a recombinant IgG1 therapeutic monoclonal antibody (mAb) produced in Chinese hamster ovary cells during the cell line selection studies. The variant was initially observed as an atypical post-monomer fragment peak in size exclusion chromatography. Characterization of the fragment peak using intact and reduced liquid chromatographymass spectrometry (LC-MS) analyses determined that the fragment consisted of a normal light chain disulfide-linked to an aberrant 26 kDa fragment that could not be assigned to any HC fragment even after considering common modifications. Further analysis using LC-MS/MS peptide mapping revealed that the aberrant fragment contained the expected HC amino acid sequence (1-232) followed by a 20-mer novel sequence corresponding to expression of heavy chain DNA sequence in the -1 reading frame. Examination of the DNA sequence around the frameshift initiation site revealed that a mononucleotide repeat GGGGGG located in the IgG1 HC constant region was most likely the structural root cause of the frameshift. Rapid identification of the frameshift allowed us to avoid use of a problematic cell line containing the frameshift as the production cell line. The frameshift reported here may be observed in other mAb products and the hypothesis-driven analytical approaches employed here may be valuable for rapid identification and characterization of frameshift variants in other recombinant proteins.

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“…Codon bias extremes represented by the DsRed2 gene and rickettsial genomes may have disrupted translation of DsRed2 mRNA in R. monacensis due to low levels of appropriate tRNAs. Studies of E. coli showed that rare codons (frequencies of 1% or less) could cause amino acid misincorporation, frameshifts, and premature termination (28,29,33), especially when clustered or near the 5Ј end of mRNA (24,28). Considering only the 59 more restrictively defined very rare rickettsial codons (Table 3) in the DsRed2 gene, 16 occur as doublets, 9 occur as triplets, 4 occur as a quadruplet, and 17 occur within the first 200 nucleotides.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Fluorescent Protein Expression in Transformants ofRickettsia monacensis, an Obligate Intracellular Tick Symbiont

Baldridge

Burkhardt

Herron

et al. 2005

Appl Environ Microbiol

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Mistranslational errors associated with the rare arginine codon CGG in Escherichia coli

Cited by 104 publications

References 18 publications

Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles

Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles

Identification and characterization of a -1 reading frameshift in the heavy chain constant region of an IgG1 recombinant monoclonal antibody produced in CHO cells

Analysis of Fluorescent Protein Expression in Transformants ofRickettsia monacensis, an Obligate Intracellular Tick Symbiont

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