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Global mRNA selection mechanisms for translation initiation.

Costello J, Castelli LM, Rowe W, Kershaw CJ, Talavera D, Mohammad-Qureshi SS, Sims PF, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP - Genome Biol. (2015)

Bottom Line: Components of the closed loop complex are highly relevant for many mRNAs, but some heavily translated mRNAs interact poorly with this machinery.Therefore, alternative, possibly Pab1p-dependent mechanisms likely exist to load ribosomes effectively onto mRNAs.Finally, these studies identify and characterize a complex self-regulatory circuit for the yeast 4E-BPs.

View Article: PubMed Central - PubMed

ABSTRACT

Background: The selection and regulation of individual mRNAs for translation initiation from a competing pool of mRNA are poorly understood processes. The closed loop complex, comprising eIF4E, eIF4G and PABP, and its regulation by 4E-BPs are perceived to be key players. Using RIP-seq, we aimed to evaluate the role in gene regulation of the closed loop complex and 4E-BP regulation across the entire yeast transcriptome.

Results: We find that there are distinct populations of mRNAs with coherent properties: one mRNA pool contains many ribosomal protein mRNAs and is enriched specifically with all of the closed loop translation initiation components. This class likely represents mRNAs that rely heavily on the closed loop complex for protein synthesis. Other heavily translated mRNAs are apparently under-represented with most closed loop components except Pab1p. Combined with data showing a close correlation between Pab1p interaction and levels of translation, these data suggest that Pab1p is important for the translation of these mRNAs in a closed loop independent manner. We also identify a translational regulatory mechanism for the 4E-BPs; these appear to self-regulate by inhibiting translation initiation of their own mRNAs.

Conclusions: Overall, we show that mRNA selection for translation initiation is not as uniformly regimented as previously anticipated. Components of the closed loop complex are highly relevant for many mRNAs, but some heavily translated mRNAs interact poorly with this machinery. Therefore, alternative, possibly Pab1p-dependent mechanisms likely exist to load ribosomes effectively onto mRNAs. Finally, these studies identify and characterize a complex self-regulatory circuit for the yeast 4E-BPs.

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Functional analysis of proteins encoded by the transcript clusters. (A) Gene Ontology (GO) terms that are significantly over-represented (red) or under-represented (blue) for transcripts that are present within the four clusters defined in Figure 4. Only the GO terms that show significant differences (via a Fisher test comparing that cluster with the rest of the genome; FDR <0.01) for at least one cluster and also had differences between the clusters (Chi-square test; FDR <0.01) are depicted. The color scale represents the statistical significance of GO term enrichment or under-enrichment as measured by log10FDR. For convenience the GO term enrichment log10FDR values have been multiplied by -1. (B,C) Box and whisker plots, as in Figure 2, detailing the variation in ribosome occupancy [42] and protein abundance according to the PaxDb database [49] for the transcripts enriched with the closed loop components and 4E-BPs. A Wilcoxon rank test between pairwise transcripts sets revealed a significant difference (P < 1 × 10-7) in all cases for both plots; the only exception being between group I and group III for ribosomal occupancy, which was significant at P < 0.03.
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Fig6: Functional analysis of proteins encoded by the transcript clusters. (A) Gene Ontology (GO) terms that are significantly over-represented (red) or under-represented (blue) for transcripts that are present within the four clusters defined in Figure 4. Only the GO terms that show significant differences (via a Fisher test comparing that cluster with the rest of the genome; FDR <0.01) for at least one cluster and also had differences between the clusters (Chi-square test; FDR <0.01) are depicted. The color scale represents the statistical significance of GO term enrichment or under-enrichment as measured by log10FDR. For convenience the GO term enrichment log10FDR values have been multiplied by -1. (B,C) Box and whisker plots, as in Figure 2, detailing the variation in ribosome occupancy [42] and protein abundance according to the PaxDb database [49] for the transcripts enriched with the closed loop components and 4E-BPs. A Wilcoxon rank test between pairwise transcripts sets revealed a significant difference (P < 1 × 10-7) in all cases for both plots; the only exception being between group I and group III for ribosomal occupancy, which was significant at P < 0.03.

Mentions: To further decipher the functional role of the closed loop components in translation initiation in yeast, we examined the groups of mRNAs derived from the heatmap for trends and patterns in terms of gene function. Initially we focussed on group III, as this group exhibits the clearest pattern of association with closed loop complex components. We found that the group III mRNAs exhibit high ribosome occupancy and their protein products are, on average, highly abundant (Figure 6B,C). This is consistent with closed loop complex-dependent translation initiation acting as an efficient route for the production of highly abundant, stable proteins. A functional analysis of the mRNAs present within this group lends further weight to this idea, as it demonstrates a very substantial enrichment in mRNAs for ribosomal proteins (Figure 6A); 115 of the 395 genes in group III encode ribosomal proteins. The fact that the mRNAs for the ribosomal proteins are heavily enriched with the closed loop machinery provides an interesting parallel with the situation in mammalian cells where many of the mRNAs encoding ribosomal proteins display discrete regulatory patterns by virtue of a 5’ terminal oligopyrimidine (TOP) motif [47]. No such cis-acting sequences are obvious in either the yeast ribosomal protein mRNAs or across the group III mRNA set (data not shown); however, it seems likely that such elements must dictate the very high level of association that we observe with the closed loop complex components. The parallels between the group III mRNA properties and those of mammalian TOP mRNAs run deeper. For instance, TOP mRNAs are especially sensitive to regulation by mammalian target of rapamycin (mTOR), and recent evidence suggests this occurs via the 4E-BP1 translation repressor [48]. The specific regulation of the TOP mRNAs in this manner suggests that these mRNAs are highly sensitive to cap complex and possibly closed loop complex inhibition [48]. Therefore, the specific enrichment of ribosomal protein mRNAs with components of the yeast closed loop complex highlights the possibility that a parallel mechanism could exist in yeast.Figure 6


Global mRNA selection mechanisms for translation initiation.

Costello J, Castelli LM, Rowe W, Kershaw CJ, Talavera D, Mohammad-Qureshi SS, Sims PF, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP - Genome Biol. (2015)

Functional analysis of proteins encoded by the transcript clusters. (A) Gene Ontology (GO) terms that are significantly over-represented (red) or under-represented (blue) for transcripts that are present within the four clusters defined in Figure 4. Only the GO terms that show significant differences (via a Fisher test comparing that cluster with the rest of the genome; FDR <0.01) for at least one cluster and also had differences between the clusters (Chi-square test; FDR <0.01) are depicted. The color scale represents the statistical significance of GO term enrichment or under-enrichment as measured by log10FDR. For convenience the GO term enrichment log10FDR values have been multiplied by -1. (B,C) Box and whisker plots, as in Figure 2, detailing the variation in ribosome occupancy [42] and protein abundance according to the PaxDb database [49] for the transcripts enriched with the closed loop components and 4E-BPs. A Wilcoxon rank test between pairwise transcripts sets revealed a significant difference (P < 1 × 10-7) in all cases for both plots; the only exception being between group I and group III for ribosomal occupancy, which was significant at P < 0.03.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4302535&req=5

Fig6: Functional analysis of proteins encoded by the transcript clusters. (A) Gene Ontology (GO) terms that are significantly over-represented (red) or under-represented (blue) for transcripts that are present within the four clusters defined in Figure 4. Only the GO terms that show significant differences (via a Fisher test comparing that cluster with the rest of the genome; FDR <0.01) for at least one cluster and also had differences between the clusters (Chi-square test; FDR <0.01) are depicted. The color scale represents the statistical significance of GO term enrichment or under-enrichment as measured by log10FDR. For convenience the GO term enrichment log10FDR values have been multiplied by -1. (B,C) Box and whisker plots, as in Figure 2, detailing the variation in ribosome occupancy [42] and protein abundance according to the PaxDb database [49] for the transcripts enriched with the closed loop components and 4E-BPs. A Wilcoxon rank test between pairwise transcripts sets revealed a significant difference (P < 1 × 10-7) in all cases for both plots; the only exception being between group I and group III for ribosomal occupancy, which was significant at P < 0.03.
Mentions: To further decipher the functional role of the closed loop components in translation initiation in yeast, we examined the groups of mRNAs derived from the heatmap for trends and patterns in terms of gene function. Initially we focussed on group III, as this group exhibits the clearest pattern of association with closed loop complex components. We found that the group III mRNAs exhibit high ribosome occupancy and their protein products are, on average, highly abundant (Figure 6B,C). This is consistent with closed loop complex-dependent translation initiation acting as an efficient route for the production of highly abundant, stable proteins. A functional analysis of the mRNAs present within this group lends further weight to this idea, as it demonstrates a very substantial enrichment in mRNAs for ribosomal proteins (Figure 6A); 115 of the 395 genes in group III encode ribosomal proteins. The fact that the mRNAs for the ribosomal proteins are heavily enriched with the closed loop machinery provides an interesting parallel with the situation in mammalian cells where many of the mRNAs encoding ribosomal proteins display discrete regulatory patterns by virtue of a 5’ terminal oligopyrimidine (TOP) motif [47]. No such cis-acting sequences are obvious in either the yeast ribosomal protein mRNAs or across the group III mRNA set (data not shown); however, it seems likely that such elements must dictate the very high level of association that we observe with the closed loop complex components. The parallels between the group III mRNA properties and those of mammalian TOP mRNAs run deeper. For instance, TOP mRNAs are especially sensitive to regulation by mammalian target of rapamycin (mTOR), and recent evidence suggests this occurs via the 4E-BP1 translation repressor [48]. The specific regulation of the TOP mRNAs in this manner suggests that these mRNAs are highly sensitive to cap complex and possibly closed loop complex inhibition [48]. Therefore, the specific enrichment of ribosomal protein mRNAs with components of the yeast closed loop complex highlights the possibility that a parallel mechanism could exist in yeast.Figure 6

Bottom Line: Components of the closed loop complex are highly relevant for many mRNAs, but some heavily translated mRNAs interact poorly with this machinery.Therefore, alternative, possibly Pab1p-dependent mechanisms likely exist to load ribosomes effectively onto mRNAs.Finally, these studies identify and characterize a complex self-regulatory circuit for the yeast 4E-BPs.

View Article: PubMed Central - PubMed

ABSTRACT

Background: The selection and regulation of individual mRNAs for translation initiation from a competing pool of mRNA are poorly understood processes. The closed loop complex, comprising eIF4E, eIF4G and PABP, and its regulation by 4E-BPs are perceived to be key players. Using RIP-seq, we aimed to evaluate the role in gene regulation of the closed loop complex and 4E-BP regulation across the entire yeast transcriptome.

Results: We find that there are distinct populations of mRNAs with coherent properties: one mRNA pool contains many ribosomal protein mRNAs and is enriched specifically with all of the closed loop translation initiation components. This class likely represents mRNAs that rely heavily on the closed loop complex for protein synthesis. Other heavily translated mRNAs are apparently under-represented with most closed loop components except Pab1p. Combined with data showing a close correlation between Pab1p interaction and levels of translation, these data suggest that Pab1p is important for the translation of these mRNAs in a closed loop independent manner. We also identify a translational regulatory mechanism for the 4E-BPs; these appear to self-regulate by inhibiting translation initiation of their own mRNAs.

Conclusions: Overall, we show that mRNA selection for translation initiation is not as uniformly regimented as previously anticipated. Components of the closed loop complex are highly relevant for many mRNAs, but some heavily translated mRNAs interact poorly with this machinery. Therefore, alternative, possibly Pab1p-dependent mechanisms likely exist to load ribosomes effectively onto mRNAs. Finally, these studies identify and characterize a complex self-regulatory circuit for the yeast 4E-BPs.

Show MeSH