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Codon and amino acid content are associated with mRNA stability in mammalian cells

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Forrest, Megan E., Pinkard, Otis, Martin, Sophie, Sweet, Thomas J., Hanson, Gavin, Coller, Jeff·2020·PLOS ONE
DOI 10.1371/journal.pone.0228730PMC PMC7018022
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Abstract

Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in the cell and is a major control point for modulating gene expression. In yeast and other model organisms, codon identity is a powerful determinant of transcript stability, contributing broadly to impact half-lives. General principles governing mRNA stability are poorly understood in mammalian systems. Importantly, however, the degradation machinery is highly conserved, thus it seems logical that mammalian transcript half-lives would also be strongly influenced by coding determinants. Herein we characterize the contribution of coding sequence towards mRNA decay in human and Chinese Hamster Ovary cells. In agreement with previous studies, we observed that synonymous codon usage impacts mRNA stability in mammalian cells. Surprisingly, however, we also observe that the amino acid content of a gene is an additional determinant correlating with transcript stability. The impact of codon and amino acid identity on mRNA decay appears to be associated with underlying tRNA and intracellular amino acid concentrations. Accordingly, genes of similar physiological function appear to coordinate their mRNA stabilities in part through codon and amino acid content. Together, these results raise the possibility that intracellular tRNA and amino acid levels interplay to mediate coupling between translational elongation and mRNA degradation rate in mammals.

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Fig 1 Synonymous codon content modulates mRNA stability in human cells. (A) Schematic diagram of single-gene mRNA decay reporter constructs. Tet-off promoter = minimal CMV promoter coupled to tetracycline-inducible Tet Advanced transactivator binding site for transcription shutoff. Black bar indicates Northern blot asymmetric PCR probe position. (B) (top) Northern blot analysis of steady-state Firefly luciferase mRNA levels and U6 snRNA loading control for Firefly luciferase reporters with indicated optimal codon content in HEK293 Tet-off cells. (bottom) Quantitation of northern blot signal. Error bars represent standard error of three replicates. Relative mRNA level vs. % optimal codons R = 0.75, p = 0.008 (Pearson correlation test). (C) mRNA decay analysis by northern blot for Firefly luciferase reporter constructs with indicated optimal codon content in HEK293 Tet-Off cells. Timepoints represent time elapsed after shutoff of transcription with doxycycline. t½ = half-life (min) ± standard error (n = 3). 32% optimal vs. 83% optimal difference in means = 130 min; p = 0.002 (two-tailed t-test). (D) mRNA decay analysis by northern blot for MECP2 reporter constructs with indicated optimal codon content in HEK293 Tet-Off cells. Timepoints represent time elapsed after shutoff of transcription with doxycycline. t½ = half-life (min) ± standard error (n = 3). 34% optimal vs. 93% optimal difference in means = 100 min; p = 0.01 (two-tailed t-test). (E) mRNA decay analysis by northern blot for CFTR Δ5F08 endogenous sequence (53.7% optimal codons) and maximally optimized sequence (78.1% optimal codons) reporter constructs. Timepoints represent time elapsed after shutoff of transcription with doxycycline. t½ = half-life (min). See also S1 Fig for northern blot loading controls, S1 Table for northern probe sequences and reporter ORF sequences, and S2 Table for tAI and CSC values.
Fig 1 Synonymous codon content modulates mRNA stability in human cells. (A) Schematic diagram of single-gene mRNA decay reporter constructs. Tet-off promoter = minimal CMV promoter coupled to tetracycline-inducible Tet Advanced transactivator binding site for transcription shutoff. Black bar indicates Northern blot asymmetric PCR probe position. (B) (top) Northern blot analysis of steady-state Firefly luciferase mRNA levels and U6 snRNA loading control for Firefly luciferase reporters with indicated optimal codon content in HEK293 Tet-off cells. (bottom) Quantitation of northern blot signal. Error bars represent standard error of three replicates. Relative mRNA level vs. % optimal codons R = 0.75, p = 0.008 (Pearson correlation test). (C) mRNA decay analysis by northern blot for Firefly luciferase reporter constructs with indicated optimal codon content in HEK293 Tet-Off cells. Timepoints represent time elapsed after shutoff of transcription with doxycycline. t½ = half-life (min) ± standard error (n = 3). 32% optimal vs. 83% optimal difference in means = 130 min; p = 0.002 (two-tailed t-test). (D) mRNA decay analysis by northern blot for MECP2 reporter constructs with indicated optimal codon content in HEK293 Tet-Off cells. Timepoints represent time elapsed after shutoff of transcription with doxycycline. t½ = half-life (min) ± standard error (n = 3). 34% optimal vs. 93% optimal difference in means = 100 min; p = 0.01 (two-tailed t-test). (E) mRNA decay analysis by northern blot for CFTR Δ5F08 endogenous sequence (53.7% optimal codons) and maximally optimized sequence (78.1% optimal codons) reporter constructs. Timepoints represent time elapsed after shutoff of transcription with doxycycline. t½ = half-life (min). See also S1 Fig for northern blot loading controls, S1 Table for northern probe sequences and reporter ORF sequences, and S2 Table for tAI and CSC values.CC BY · PubMed Central
Fig 2 Specific codons are globally associated with mRNA stability in mammalian cells. (A) Plot of codon stability coefficients (CSC) for endogenous HeLa mRNAs (n = 11,800). Blue represents significantly stabilizing codons; red represents significantly destabilizing codons (Pearson correlation test; p < 0.01). Dotted lines indicate cutoff for genome-wide significance level (p < 5 x 10−8). Error bars indicate confidence interval about Pearson R estimate. (B-D) Plots of CSCs grouped by amino acid as calculated for (B) In-frame ORF sequences (F0), (C) ORF sequences frame-shifted by one nucleotide (F+1), and (D) ORF sequences frame-shifted by two nucleotides (F+2). Colors indicate 3’-nucleotide identity (GC3 = G or C at 3’-position, purple; AT3 = A or T at 3’-position, gray). P-values indicate results of Welch’s two-tailed t-test for difference in mean CSC between GC3 and AT3 codons. (E) Plot of codon stability coefficients (CSC) for endogenous CHO mRNAs (n = 6,855). Blue represents significantly stabilizing codons; red represents significantly destabilizing codons (Pearson correlation test; p < 0.01). Dotted lines indicate cutoff for genome-wide significance level (p < 5 x 10−8). Error bars indicate confidence interval about Pearson R estimate. See also S2 Table for CSC values and statistical data and S3 Table for half-life data and coding sequence sources.
Fig 2 Specific codons are globally associated with mRNA stability in mammalian cells. (A) Plot of codon stability coefficients (CSC) for endogenous HeLa mRNAs (n = 11,800). Blue represents significantly stabilizing codons; red represents significantly destabilizing codons (Pearson correlation test; p < 0.01). Dotted lines indicate cutoff for genome-wide significance level (p < 5 x 10−8). Error bars indicate confidence interval about Pearson R estimate. (B-D) Plots of CSCs grouped by amino acid as calculated for (B) In-frame ORF sequences (F0), (C) ORF sequences frame-shifted by one nucleotide (F+1), and (D) ORF sequences frame-shifted by two nucleotides (F+2). Colors indicate 3’-nucleotide identity (GC3 = G or C at 3’-position, purple; AT3 = A or T at 3’-position, gray). P-values indicate results of Welch’s two-tailed t-test for difference in mean CSC between GC3 and AT3 codons. (E) Plot of codon stability coefficients (CSC) for endogenous CHO mRNAs (n = 6,855). Blue represents significantly stabilizing codons; red represents significantly destabilizing codons (Pearson correlation test; p < 0.01). Dotted lines indicate cutoff for genome-wide significance level (p < 5 x 10−8). Error bars indicate confidence interval about Pearson R estimate. See also S2 Table for CSC values and statistical data and S3 Table for half-life data and coding sequence sources.CC BY · PubMed Central
Fig 3 Specific amino acids are globally associated with mRNA stability in mammalian cells. (A) Plot of amino acid stabilization coefficients (AASC) for endogenous HeLa mRNAs (n = 11,800). Blue represents significantly stabilizing amino acids; red represents significantly destabilizing amino acids (Pearson correlation test; p < 0.001). Dotted lines indicate cutoff for genome-wide significance level (p < 5 x 10−8). Error bars indicate confidence interval about Pearson R estimate. (B) Plot of amino acid stabilization coefficients (AASC) for endogenous CHO mRNAs (n = 6,855). Blue represents significantly stabilizing amino acids; red represents significantly destabilizing amino acids (Pearson correlation test; p < 0.001). Dotted lines indicate cutoff for genome-wide significance level (p < 5 x 10−8). Error bars indicate confidence interval about Pearson R estimate. (C) Boxplots of HeLa mRNA half-life distributions binned by valine frequency. Number of transcripts in bin is indicated above each boxplot. Overall difference in means p < 2.2 x 10−16 (Kruskal-Wallis test). (D) Boxplots of HeLa mRNA half-life distributions binned by serine frequency. Number of transcripts in bin is indicated above each boxplot. Overall difference in means p < 2.2 x 10−16 (Kruskal-Wallis test). (E) Boxplots of HeLa mRNA half-life distributions comparing transcripts containing homopolymeric repeats of the four most highly destabilizing amino acids (S, H, Q, and C) vs. transcripts containing the four most highly stabilizing amino acids (V, I, Y, and A) as defined by AASC (Fig 3A); p = 1.1 x 10−5 (Wilcoxon test). (F) Schematic diagram of amino acid stretch insertion reporter constructs for single-gene mRNA decay analysis. Tet-off promoter = minimal CMV promoter coupled to tetracycline-responsive Tet Advanced transactivator binding site for transcription shutoff. Black bar indicates Northern blot asymmetric PCR probe position. (G) Transcription shutoff/northern mRNA decay analysis of amino acid stretch insertion reporter constructs with indicated insertions in HEK293 Tet-off cells. Timepoints represent time elapsed after shutoff of transcription shutoff doxycycline. t½ = half-life (min) ± standard error (n = 4). CRIP1 + SH vs. VI difference in means = 127 min; p = 0.01 (two-tailed t-test). LSM8 + SH vs. VI difference in means = 96 min; p = 0.007 (two-tailed t-test). SPTSSA + SH vs. VI difference in means = 145 min; p = 0.02 (two-tailed t-test). See also S2 Fig for northern blot loading controls, S1 Table for northern probe sequences and reporter ORF sequences, S2 Table for AASC values and statistical data, S3 Table for half-life data and coding sequence sources, and S4 Table for homopolymeric amino acid repeat half-life data.
Fig 3 Specific amino acids are globally associated with mRNA stability in mammalian cells. (A) Plot of amino acid stabilization coefficients (AASC) for endogenous HeLa mRNAs (n = 11,800). Blue represents significantly stabilizing amino acids; red represents significantly destabilizing amino acids (Pearson correlation test; p < 0.001). Dotted lines indicate cutoff for genome-wide significance level (p < 5 x 10−8). Error bars indicate confidence interval about Pearson R estimate. (B) Plot of amino acid stabilization coefficients (AASC) for endogenous CHO mRNAs (n = 6,855). Blue represents significantly stabilizing amino acids; red represents significantly destabilizing amino acids (Pearson correlation test; p < 0.001). Dotted lines indicate cutoff for genome-wide significance level (p < 5 x 10−8). Error bars indicate confidence interval about Pearson R estimate. (C) Boxplots of HeLa mRNA half-life distributions binned by valine frequency. Number of transcripts in bin is indicated above each boxplot. Overall difference in means p < 2.2 x 10−16 (Kruskal-Wallis test). (D) Boxplots of HeLa mRNA half-life distributions binned by serine frequency. Number of transcripts in bin is indicated above each boxplot. Overall difference in means p < 2.2 x 10−16 (Kruskal-Wallis test). (E) Boxplots of HeLa mRNA half-life distributions comparing transcripts containing homopolymeric repeats of the four most highly destabilizing amino acids (S, H, Q, and C) vs. transcripts containing the four most highly stabilizing amino acids (V, I, Y, and A) as defined by AASC (Fig 3A); p = 1.1 x 10−5 (Wilcoxon test). (F) Schematic diagram of amino acid stretch insertion reporter constructs for single-gene mRNA decay analysis. Tet-off promoter = minimal CMV promoter coupled to tetracycline-responsive Tet Advanced transactivator binding site for transcription shutoff. Black bar indicates Northern blot asymmetric PCR probe position. (G) Transcription shutoff/northern mRNA decay analysis of amino acid stretch insertion reporter constructs with indicated insertions in HEK293 Tet-off cells. Timepoints represent time elapsed after shutoff of transcription shutoff doxycycline. t½ = half-life (min) ± standard error (n = 4). CRIP1 + SH vs. VI difference in means = 127 min; p = 0.01 (two-tailed t-test). LSM8 + SH vs. VI difference in means = 96 min; p = 0.007 (two-tailed t-test). SPTSSA + SH vs. VI difference in means = 145 min; p = 0.02 (two-tailed t-test). See also S2 Fig for northern blot loading controls, S1 Table for northern probe sequences and reporter ORF sequences, S2 Table for AASC values and statistical data, S3 Table for half-life data and coding sequence sources, and S4 Table for homopolymeric amino acid repeat half-life data.CC BY · PubMed Central
Fig 4 Codon-specific effects on stability are associated with tRNA and amino acid levels. (A) Plot of tRNA adaptive indices (tAI) representing relative tRNA levels calculated from tRNA sequencing data in HeLa cells. Purple represents optimal codons, defined by tAI > median (0.1478). Green represents non-optimal codons, defined by tAI < median. Errorbars indicate standard deviation of three replicates. (B) Plot of HeLa tAI vs. HeLa CSC for all 61 codons. Purple represents optimal codons; green represents non-optimal codons (defined in Fig 4A). Red dotted line indicates linear regression trendline. rho (ρ) = 0.14, p = 0.29 (Spearman correlation test). (C) Boxplots comparing distribution of HeLa CSCs for optimal and non-optimal codons as defined in Fig 4A; p = 0.37 (Wilcoxon test). (D) Plot of relative free amino acid concentrations (versus glycine) determined from HeLa cell lysates. Errorbars indicate standard deviation of two replicates. (E) Plot of HeLa relative free amino acid concentration vs. HeLa CSC for all codons except those encoding Cys and Glu (n = 57). Red line indicates linear regression trendline. rho (ρ) = 0.079, p = 0.56 (Spearman correlation test). (F) Plot of HeLa tAI vs. HeLa CSC for all 61 codons. Blue dotted line indicates linear regression trendline. Gray indicates codons encoding amino acids with mild-moderate effect on stability; magenta indicates codons encoding amino acids with extreme effects on stability (AASC > 0.10 or < -0.10 and p < 1.0 x 10−30). Overall rho (ρ) = 0.14, p = 0.29 (Spearman correlation test). (G) Plot of HeLa tAI vs. HeLa CSC for the 42 codons encoding amino acids with mild-moderate effect on stability. Blue dotted line indicates linear regression trendline. rho (ρ) = 0.48, p = 0.0015 (Spearman correlation test). (H) Plot of HeLa relative intracellular amino acid concentration vs. HeLa CSC for the 19 codons encoding amino acids with extreme effects on stability as defined in Fig 4F. Blue dotted line indicates linear regression trendline. rho (ρ) = 0.43, p = 0.064 (Spearman correlation test). See also S2 Table for CSC, tAI, and free amino acid concentration values and statistical data.
Fig 4 Codon-specific effects on stability are associated with tRNA and amino acid levels. (A) Plot of tRNA adaptive indices (tAI) representing relative tRNA levels calculated from tRNA sequencing data in HeLa cells. Purple represents optimal codons, defined by tAI > median (0.1478). Green represents non-optimal codons, defined by tAI < median. Errorbars indicate standard deviation of three replicates. (B) Plot of HeLa tAI vs. HeLa CSC for all 61 codons. Purple represents optimal codons; green represents non-optimal codons (defined in Fig 4A). Red dotted line indicates linear regression trendline. rho (ρ) = 0.14, p = 0.29 (Spearman correlation test). (C) Boxplots comparing distribution of HeLa CSCs for optimal and non-optimal codons as defined in Fig 4A; p = 0.37 (Wilcoxon test). (D) Plot of relative free amino acid concentrations (versus glycine) determined from HeLa cell lysates. Errorbars indicate standard deviation of two replicates. (E) Plot of HeLa relative free amino acid concentration vs. HeLa CSC for all codons except those encoding Cys and Glu (n = 57). Red line indicates linear regression trendline. rho (ρ) = 0.079, p = 0.56 (Spearman correlation test). (F) Plot of HeLa tAI vs. HeLa CSC for all 61 codons. Blue dotted line indicates linear regression trendline. Gray indicates codons encoding amino acids with mild-moderate effect on stability; magenta indicates codons encoding amino acids with extreme effects on stability (AASC > 0.10 or < -0.10 and p < 1.0 x 10−30). Overall rho (ρ) = 0.14, p = 0.29 (Spearman correlation test). (G) Plot of HeLa tAI vs. HeLa CSC for the 42 codons encoding amino acids with mild-moderate effect on stability. Blue dotted line indicates linear regression trendline. rho (ρ) = 0.48, p = 0.0015 (Spearman correlation test). (H) Plot of HeLa relative intracellular amino acid concentration vs. HeLa CSC for the 19 codons encoding amino acids with extreme effects on stability as defined in Fig 4F. Blue dotted line indicates linear regression trendline. rho (ρ) = 0.43, p = 0.064 (Spearman correlation test). See also S2 Table for CSC, tAI, and free amino acid concentration values and statistical data.CC BY · PubMed Central
Fig 5 Codon and amino acid content are associated with observed differences in mRNA stability among functionally related genes. (A) Boxplots comparing endogenous HeLa mRNA half-life distributions for indicated gene groups. Overall difference in means among all groups p < 2.2 x 10−16 (Kruskal-Wallis test). (B) Boxplots comparing transcript average codon stability coefficient (CSC) distributions for indicated gene groups. Overall half-life vs. transcript average CSC R = 0.5413; p < 2.2 x 10−16 (Pearson correlation test). (C) Boxplots comparing transcript average amino acid stabilization coefficient (AASC) distributions for indicated gene groups. Overall half-life vs. transcript average AASC R = 0.4626; p < 2.2 x 10−16 (Pearson correlation test). (D) Boxplots directly comparing transcript average CSC distributions for human cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red) using HeLa CSC values; p = 1.1 x 10−12 (Wilcoxon test). (E) Boxplots directly comparing transcript average AASC distributions for human cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red) using HeLa AASC values; p = 2.1 x 10−6 (Wilcoxon test). (F) Boxplots directly comparing amino acid frequency distributions for indicated stabilizing (V, I) and destabilizing (H, S) amino acids (defined by HeLa AASC) for human cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red). P-values indicate results of Wilcoxon test of difference in means for each amino acid. (G) Boxplots directly comparing transcript average CSC distributions for S. cerevisiae cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red) using S. cerevisiae CSC values; p < 2.2 x 10−16 (Wilcoxon test). (H) Boxplots directly comparing transcript average AASC distributions for S. cerevisiae cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red) using S. cerevisiae AASC values; p < 2.2 x 10−16 (Wilcoxon test). (I) Boxplots directly comparing amino acid frequency distributions for indicated stabilizing (A, G) and destabilizing (L, R) amino acids (defined by S. cerevisiae AASC) for S. cerevisiae cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red). P-values indicate results of Wilcoxon test of difference in means for each amino acid. See also S2 Table for CSC and AASC values and S5 Table for gene group designations, half-life data, and average CSC/AASC values for HeLa and S. cerevisiae.
Fig 5 Codon and amino acid content are associated with observed differences in mRNA stability among functionally related genes. (A) Boxplots comparing endogenous HeLa mRNA half-life distributions for indicated gene groups. Overall difference in means among all groups p < 2.2 x 10−16 (Kruskal-Wallis test). (B) Boxplots comparing transcript average codon stability coefficient (CSC) distributions for indicated gene groups. Overall half-life vs. transcript average CSC R = 0.5413; p < 2.2 x 10−16 (Pearson correlation test). (C) Boxplots comparing transcript average amino acid stabilization coefficient (AASC) distributions for indicated gene groups. Overall half-life vs. transcript average AASC R = 0.4626; p < 2.2 x 10−16 (Pearson correlation test). (D) Boxplots directly comparing transcript average CSC distributions for human cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red) using HeLa CSC values; p = 1.1 x 10−12 (Wilcoxon test). (E) Boxplots directly comparing transcript average AASC distributions for human cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red) using HeLa AASC values; p = 2.1 x 10−6 (Wilcoxon test). (F) Boxplots directly comparing amino acid frequency distributions for indicated stabilizing (V, I) and destabilizing (H, S) amino acids (defined by HeLa AASC) for human cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red). P-values indicate results of Wilcoxon test of difference in means for each amino acid. (G) Boxplots directly comparing transcript average CSC distributions for S. cerevisiae cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red) using S. cerevisiae CSC values; p < 2.2 x 10−16 (Wilcoxon test). (H) Boxplots directly comparing transcript average AASC distributions for S. cerevisiae cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red) using S. cerevisiae AASC values; p < 2.2 x 10−16 (Wilcoxon test). (I) Boxplots directly comparing amino acid frequency distributions for indicated stabilizing (A, G) and destabilizing (L, R) amino acids (defined by S. cerevisiae AASC) for S. cerevisiae cytoplasmic ribosomal proteins (blue) and mitochondrial ribosomal proteins (red). P-values indicate results of Wilcoxon test of difference in means for each amino acid. See also S2 Table for CSC and AASC values and S5 Table for gene group designations, half-life data, and average CSC/AASC values for HeLa and S. cerevisiae.CC BY · PubMed Central
Fig 6 Codon and amino acid-based effects on mRNA stability differ between mammals and yeast. (A) Plot of codon stability coefficients (CSC) grouped by encoded amino acid for endogenous HeLa mRNAs. Purple indicates optimal codons; green indicates non-optimal codons (defined by tRNA sequencing-based tRNA adaptive indices in Fig 4A). Amino acids with exclusively stabilizing (CSC > 0) or destabilizing (CSC < 0) synonymous codons are indicated by bolded magenta letters (n = 11). (B) Plot of codon stability coefficients (CSC) grouped by encoded amino acid for S. cerevisiae (budding yeast) mRNAs [28]. Amino acids with exclusively stabilizing (CSC > 0) or destabilizing (CSC < 0) synonymous codons are indicated by bolded magenta letters (n = 1). Purple indicates optimal codons; green indicates non-optimal codons (defined by tRNA adaptive indices in [28]). (C) Phylogenetic tree diagram showing qualitative evolutionary relationships between the 8 species presented in Fig 6A-G and S6A and S6B Fig, generated using the Interactive Tree of Life (iTOL) online tool [98]. (D-G) Plots of codon stability coefficients (CSC) grouped by encoded amino acid for (D) Mus musculus (embryonic stem cells), (E) Schizosaccharomyces pombe (fission yeast), (F) Cricetulus griseus (Chinese hamster ovary cells), and (G) Trypanosoma brucei (bloodstream lifecycle stage). Magenta indicates amino acids encoded exclusively by stabilizing (CSC > 0) or destabilizing (CSC < 0) synonymous codons. See also S2 Table for CSC values and S3 Table for half-life data sources.
Fig 6 Codon and amino acid-based effects on mRNA stability differ between mammals and yeast. (A) Plot of codon stability coefficients (CSC) grouped by encoded amino acid for endogenous HeLa mRNAs. Purple indicates optimal codons; green indicates non-optimal codons (defined by tRNA sequencing-based tRNA adaptive indices in Fig 4A). Amino acids with exclusively stabilizing (CSC > 0) or destabilizing (CSC < 0) synonymous codons are indicated by bolded magenta letters (n = 11). (B) Plot of codon stability coefficients (CSC) grouped by encoded amino acid for S. cerevisiae (budding yeast) mRNAs [28]. Amino acids with exclusively stabilizing (CSC > 0) or destabilizing (CSC < 0) synonymous codons are indicated by bolded magenta letters (n = 1). Purple indicates optimal codons; green indicates non-optimal codons (defined by tRNA adaptive indices in [28]). (C) Phylogenetic tree diagram showing qualitative evolutionary relationships between the 8 species presented in Fig 6A-G and S6A and S6B Fig, generated using the Interactive Tree of Life (iTOL) online tool [98]. (D-G) Plots of codon stability coefficients (CSC) grouped by encoded amino acid for (D) Mus musculus (embryonic stem cells), (E) Schizosaccharomyces pombe (fission yeast), (F) Cricetulus griseus (Chinese hamster ovary cells), and (G) Trypanosoma brucei (bloodstream lifecycle stage). Magenta indicates amino acids encoded exclusively by stabilizing (CSC > 0) or destabilizing (CSC < 0) synonymous codons. See also S2 Table for CSC values and S3 Table for half-life data sources.CC BY · PubMed Central
Fig 7 Model of coordinated codon and amino acid-based effects on mRNA stability in mammalian cells. Model of coordinate effects of codon and amino acid content on mRNA stability in mammalian cells. In this model, the stability of a given mRNA ORF sequence is related to functional cognate tRNA availability, which is in turn influenced by upstream amino acid concentrations. Stable mRNAs contain high proportions of codons with relatively high functional tRNA availability and are translated quickly. In contrast, mRNAs containing high proportions of codons with low tRNA availability are translated more slowly and targeted for decay via unknown protein effectors, which ultimately recruit decapping/deadenylation factors.
Fig 7 Model of coordinated codon and amino acid-based effects on mRNA stability in mammalian cells. Model of coordinate effects of codon and amino acid content on mRNA stability in mammalian cells. In this model, the stability of a given mRNA ORF sequence is related to functional cognate tRNA availability, which is in turn influenced by upstream amino acid concentrations. Stable mRNAs contain high proportions of codons with relatively high functional tRNA availability and are translated quickly. In contrast, mRNAs containing high proportions of codons with low tRNA availability are translated more slowly and targeted for decay via unknown protein effectors, which ultimately recruit decapping/deadenylation factors.CC BY · PubMed Central

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Metadata

Authors
Forrest, M. E., Pinkard, O., Martin, S., Sweet, T. J., Hanson, G., & Coller, J.
Affiliations
Case Western Reserve University (US)
Corresponding author
Coller, Jeff
ORCID
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2020-02-13
Volume
15
Issue
2
Pages
e0228730
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0228730
PMC
PMC7018022
OpenAlex
W3006243445
Cited by
116
References
104
Citations by year
2026: 15 · 2025: 23 · 2024: 25 · 2023: 15 · 2022: 12 · 2021: 15 · 2020: 9
FWCI
4.14
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Funders
  • National Institutes of Health (GM125086)
  • National Institute of General Medical Sciences (GM118018, T32GM136570)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords
mRNA stability, mRNA degradation, codon usage, synonymous codons, amino acid content, transcript half-life, translation elongation, gene expression regulation, mammalian cells, CHO cells
MeSH terms
Amino Acids, Animals, Codon, Cricetulus, Half-Life, Cricetinae, HeLa Cells, Humans, RNA, Messenger, RNA, Transfer, Open Reading Frames, CHO Cells, RNA Stability

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