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Translation of 5' leaders is pervasive in genes resistant to eIF2 repression.

Andreev DE, O'Connor PB, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV - Elife (2015)

Bottom Line: However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response.Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition.Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products.

View Article: PubMed Central - PubMed

Affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

ABSTRACT
Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eukaryotic initiation factor 2 (eIF2). However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated upstream open reading frame (uORF) that represses translation of the main coding ORF under normal conditions. Site-specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products.

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Analysis of 5’ leader and upstream open reading frame (uORF)features in the resistant mRNAs.(A) WebLogo representation of information content withintranslation initiation sequences (from position −4 to position+3) for uORF starts in the resistant mRNAs. (B)Comparison of frequencies of various translation initiation sequences(−4 to +3) for annotated ORFs (x axis) andAUG present in 5' leaders (y axis). Translationinitiation sequences of uORFs in the resistant mRNAs are shown in blue.(C) Scatter plot representing relationship betweentranslation response (y axis) and the length of5′ leaders (x axis). (D)Relationship between translational response (y axis) andfree energy of potential RNA secondary structures within the first 240 ntof 5′ leaders (x axis).DOI:http://dx.doi.org/10.7554/eLife.03971.013
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fig3s1: Analysis of 5’ leader and upstream open reading frame (uORF)features in the resistant mRNAs.(A) WebLogo representation of information content withintranslation initiation sequences (from position −4 to position+3) for uORF starts in the resistant mRNAs. (B)Comparison of frequencies of various translation initiation sequences(−4 to +3) for annotated ORFs (x axis) andAUG present in 5' leaders (y axis). Translationinitiation sequences of uORFs in the resistant mRNAs are shown in blue.(C) Scatter plot representing relationship betweentranslation response (y axis) and the length of5′ leaders (x axis). (D)Relationship between translational response (y axis) andfree energy of potential RNA secondary structures within the first 240 ntof 5′ leaders (x axis).DOI:http://dx.doi.org/10.7554/eLife.03971.013

Mentions: We also compared various sequence features of 5′ leaders and uORFs between theresistant mRNAs and the remaining expressed mRNAs. We explored the nucleotide (nt)context surrounding uORF start codons (mostly AUG but also CUG) in resistant mRNAsbut found no evidence for selection for a particular context (Figure 3—figure supplement 1A); the frequency ofindividual heptameric initiation sequences (−3 to +4) is equallyvariable across uORFs of resistant and non-resistant mRNAs as well as at annotatedstarts of CDS (Figure 3—figure supplement1B). We found that the average 5′ leader length of resistant mRNAsis longer (378.5 nt) than that of other mRNAs (169.0 nt), but there is significantvariation within both distributions (Figure3—figure supplement 1C). We also found that 5′ leaders ofresistant mRNAs have lower potential for RNA secondary structure formation within thefirst 240 nt based on free energy estimates of potential structures predicted withRNAfold (Lorenz et al., 2011). Yet, thedifference is small and RNA secondary structure potential does not correlate wellwith resistance (Figure 3—figure supplement1D).


Translation of 5' leaders is pervasive in genes resistant to eIF2 repression.

Andreev DE, O'Connor PB, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV - Elife (2015)

Analysis of 5’ leader and upstream open reading frame (uORF)features in the resistant mRNAs.(A) WebLogo representation of information content withintranslation initiation sequences (from position −4 to position+3) for uORF starts in the resistant mRNAs. (B)Comparison of frequencies of various translation initiation sequences(−4 to +3) for annotated ORFs (x axis) andAUG present in 5' leaders (y axis). Translationinitiation sequences of uORFs in the resistant mRNAs are shown in blue.(C) Scatter plot representing relationship betweentranslation response (y axis) and the length of5′ leaders (x axis). (D)Relationship between translational response (y axis) andfree energy of potential RNA secondary structures within the first 240 ntof 5′ leaders (x axis).DOI:http://dx.doi.org/10.7554/eLife.03971.013
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4383229&req=5

fig3s1: Analysis of 5’ leader and upstream open reading frame (uORF)features in the resistant mRNAs.(A) WebLogo representation of information content withintranslation initiation sequences (from position −4 to position+3) for uORF starts in the resistant mRNAs. (B)Comparison of frequencies of various translation initiation sequences(−4 to +3) for annotated ORFs (x axis) andAUG present in 5' leaders (y axis). Translationinitiation sequences of uORFs in the resistant mRNAs are shown in blue.(C) Scatter plot representing relationship betweentranslation response (y axis) and the length of5′ leaders (x axis). (D)Relationship between translational response (y axis) andfree energy of potential RNA secondary structures within the first 240 ntof 5′ leaders (x axis).DOI:http://dx.doi.org/10.7554/eLife.03971.013
Mentions: We also compared various sequence features of 5′ leaders and uORFs between theresistant mRNAs and the remaining expressed mRNAs. We explored the nucleotide (nt)context surrounding uORF start codons (mostly AUG but also CUG) in resistant mRNAsbut found no evidence for selection for a particular context (Figure 3—figure supplement 1A); the frequency ofindividual heptameric initiation sequences (−3 to +4) is equallyvariable across uORFs of resistant and non-resistant mRNAs as well as at annotatedstarts of CDS (Figure 3—figure supplement1B). We found that the average 5′ leader length of resistant mRNAsis longer (378.5 nt) than that of other mRNAs (169.0 nt), but there is significantvariation within both distributions (Figure3—figure supplement 1C). We also found that 5′ leaders ofresistant mRNAs have lower potential for RNA secondary structure formation within thefirst 240 nt based on free energy estimates of potential structures predicted withRNAfold (Lorenz et al., 2011). Yet, thedifference is small and RNA secondary structure potential does not correlate wellwith resistance (Figure 3—figure supplement1D).

Bottom Line: However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response.Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition.Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products.

View Article: PubMed Central - PubMed

Affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

ABSTRACT
Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eukaryotic initiation factor 2 (eIF2). However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated upstream open reading frame (uORF) that represses translation of the main coding ORF under normal conditions. Site-specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products.

Show MeSH
Related in: MedlinePlus