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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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Multiple alignments of codon sequences from 100 vertebrate genomesaligned to the region of conserved MIEF1 upstream open reading frame(uORF) in three different frames.See Figure 2—figure supplement1 for the explanation of the colour scheme used for thealignment visualization.DOI:http://dx.doi.org/10.7554/eLife.03971.010
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fig2s2: Multiple alignments of codon sequences from 100 vertebrate genomesaligned to the region of conserved MIEF1 upstream open reading frame(uORF) in three different frames.See Figure 2—figure supplement1 for the explanation of the colour scheme used for thealignment visualization.DOI:http://dx.doi.org/10.7554/eLife.03971.010

Mentions: Although they did not pass our stringent criteria for a resistant gene, othercandidates which we identified (based on the gene function and their profiles) areAZIN1 (TE Z-score 2.76) and MIEF1 (TE Z-score2.88). AZIN1 encodes an inhibitor of ODC1 (ornithinedecarboxylase) antizymes. Antizymes are proteins that target ODC1 for degradation,and AZIN1 is highly similar to ODC1 but lacks ornithine decarboxylation enzymaticactivity. This makes it a competitive inhibitor of antizymes (Murakami et al., 1988). It has been shown that an uORFinitiated with a non-cognate AUU codon mediates sensitivity of AZIN1mRNA translation to polyamine levels (Ivanov etal., 2008). MIEF1, mitochondrial elongation factor 1, isanother candidate bicistronic mRNA that we have identified (the other isSLC35A4). Similar to SLC35A4, we observedevidence of protein coding evolution within its uORF (Figure 2—figure supplement 2). Its translation is alsosupported by multiple ribo-seq datasets available in GWIPS-viz (Michel et al., 2014), see Figure 2—figure supplement 3B. Examination of the sequence encodedby its uORF revealed that it contains a conserved domain that belongs to a PFAMfamily Complex 1 protein (LYR family), ID PF05347.


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)

Multiple alignments of codon sequences from 100 vertebrate genomesaligned to the region of conserved MIEF1 upstream open reading frame(uORF) in three different frames.See Figure 2—figure supplement1 for the explanation of the colour scheme used for thealignment visualization.DOI:http://dx.doi.org/10.7554/eLife.03971.010
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383229&req=5

fig2s2: Multiple alignments of codon sequences from 100 vertebrate genomesaligned to the region of conserved MIEF1 upstream open reading frame(uORF) in three different frames.See Figure 2—figure supplement1 for the explanation of the colour scheme used for thealignment visualization.DOI:http://dx.doi.org/10.7554/eLife.03971.010
Mentions: Although they did not pass our stringent criteria for a resistant gene, othercandidates which we identified (based on the gene function and their profiles) areAZIN1 (TE Z-score 2.76) and MIEF1 (TE Z-score2.88). AZIN1 encodes an inhibitor of ODC1 (ornithinedecarboxylase) antizymes. Antizymes are proteins that target ODC1 for degradation,and AZIN1 is highly similar to ODC1 but lacks ornithine decarboxylation enzymaticactivity. This makes it a competitive inhibitor of antizymes (Murakami et al., 1988). It has been shown that an uORFinitiated with a non-cognate AUU codon mediates sensitivity of AZIN1mRNA translation to polyamine levels (Ivanov etal., 2008). MIEF1, mitochondrial elongation factor 1, isanother candidate bicistronic mRNA that we have identified (the other isSLC35A4). Similar to SLC35A4, we observedevidence of protein coding evolution within its uORF (Figure 2—figure supplement 2). Its translation is alsosupported by multiple ribo-seq datasets available in GWIPS-viz (Michel et al., 2014), see Figure 2—figure supplement 3B. Examination of the sequence encodedby its uORF revealed that it contains a conserved domain that belongs to a PFAMfamily Complex 1 protein (LYR family), ID PF05347.

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