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Alternative 3' UTRs act as scaffolds to regulate membrane protein localization.

Berkovits BD, Mayr C - Nature (2015)

Bottom Line: This facilitates interaction of SET with the newly translated cytoplasmic domains of CD47 and results in subsequent translocation of CD47 to the plasma membrane via activated RAC1 (ref. 5).Thus, ApA contributes to the functional diversity of the proteome without changing the amino acid sequence. 3' UTR-dependent protein localization has the potential to be a widespread trafficking mechanism for membrane proteins because HuR binds to thousands of mRNAs, and we show that the long 3' UTRs of CD44, ITGA1 and TNFRSF13C, which are bound by HuR, increase surface protein expression compared to their corresponding short 3' UTRs.We propose that during translation the scaffold function of 3' UTRs facilitates binding of proteins to nascent proteins to direct their transport or function--and this role of 3' UTRs can be regulated by ApA.

View Article: PubMed Central - PubMed

Affiliation: Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, New York 10065, USA.

ABSTRACT
About half of human genes use alternative cleavage and polyadenylation (ApA) to generate messenger RNA transcripts that differ in the length of their 3' untranslated regions (3' UTRs) while producing the same protein. Here we show in human cell lines that alternative 3' UTRs differentially regulate the localization of membrane proteins. The long 3' UTR of CD47 enables efficient cell surface expression of CD47 protein, whereas the short 3' UTR primarily localizes CD47 protein to the endoplasmic reticulum. CD47 protein localization occurs post-translationally and independently of RNA localization. In our model of 3' UTR-dependent protein localization, the long 3' UTR of CD47 acts as a scaffold to recruit a protein complex containing the RNA-binding protein HuR (also known as ELAVL1) and SET to the site of translation. This facilitates interaction of SET with the newly translated cytoplasmic domains of CD47 and results in subsequent translocation of CD47 to the plasma membrane via activated RAC1 (ref. 5). We also show that CD47 protein has different functions depending on whether it was generated by the short or long 3' UTR isoforms. Thus, ApA contributes to the functional diversity of the proteome without changing the amino acid sequence. 3' UTR-dependent protein localization has the potential to be a widespread trafficking mechanism for membrane proteins because HuR binds to thousands of mRNAs, and we show that the long 3' UTRs of CD44, ITGA1 and TNFRSF13C, which are bound by HuR, increase surface protein expression compared to their corresponding short 3' UTRs. We propose that during translation the scaffold function of 3' UTRs facilitates binding of proteins to nascent proteins to direct their transport or function--and this role of 3' UTRs can be regulated by ApA.

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All tested UDPL candidates have potential SET-binding sites in their cytoplasmic domainsShown are the amino acid sequences of the TMDs and cytoplasmic domains of the membrane proteins studied. The TMDs are shown in green and the positively charged amino acids in the cytoplasmic domains, indicating potential SET-binding sites, are shown in red.
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Figure 13: All tested UDPL candidates have potential SET-binding sites in their cytoplasmic domainsShown are the amino acid sequences of the TMDs and cytoplasmic domains of the membrane proteins studied. The TMDs are shown in green and the positively charged amino acids in the cytoplasmic domains, indicating potential SET-binding sites, are shown in red.

Mentions: We propose that UDPL is a widespread mechanism for surface expression of membrane proteins. All currently known components of the pathway (HuR, SET and RAC1) are ubiquitously and highly expressed (Extended Data Fig. 8a) 3. UDPL requires the presence of HuR-binding sites in the 3'UTR and SET-binding sites in the cytoplasmic domains of membrane proteins (Extended Data Figs 3, 4 and 9). All candidates tested so far that met both requirements used UDPL for surface expression (Figs 1f–h, 2d, 4b and Extended Data Figs 2g, 7c). HuR-binding sites are highly abundant as HuR binds to thousands of mRNAs6–9, with a third of them being membrane proteins (Extended Data Fig. 8b). Although the SET-binding motif is currently unknown, we (Fig. 3d, e and Extended Data Fig. 6) and others have shown that SET binds to positively charged amino acids in histone tails or cytoplasmic domains of membrane proteins 18,27. According to the positive-inside rule for integral membrane proteins, the cytoplasmic domains of membrane proteins are enriched in positively charged amino acids for topological reasons 28. Therefore, potential SET-BS in cytoplasmic domains of membrane proteins are very widespread.


Alternative 3' UTRs act as scaffolds to regulate membrane protein localization.

Berkovits BD, Mayr C - Nature (2015)

All tested UDPL candidates have potential SET-binding sites in their cytoplasmic domainsShown are the amino acid sequences of the TMDs and cytoplasmic domains of the membrane proteins studied. The TMDs are shown in green and the positively charged amino acids in the cytoplasmic domains, indicating potential SET-binding sites, are shown in red.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4697748&req=5

Figure 13: All tested UDPL candidates have potential SET-binding sites in their cytoplasmic domainsShown are the amino acid sequences of the TMDs and cytoplasmic domains of the membrane proteins studied. The TMDs are shown in green and the positively charged amino acids in the cytoplasmic domains, indicating potential SET-binding sites, are shown in red.
Mentions: We propose that UDPL is a widespread mechanism for surface expression of membrane proteins. All currently known components of the pathway (HuR, SET and RAC1) are ubiquitously and highly expressed (Extended Data Fig. 8a) 3. UDPL requires the presence of HuR-binding sites in the 3'UTR and SET-binding sites in the cytoplasmic domains of membrane proteins (Extended Data Figs 3, 4 and 9). All candidates tested so far that met both requirements used UDPL for surface expression (Figs 1f–h, 2d, 4b and Extended Data Figs 2g, 7c). HuR-binding sites are highly abundant as HuR binds to thousands of mRNAs6–9, with a third of them being membrane proteins (Extended Data Fig. 8b). Although the SET-binding motif is currently unknown, we (Fig. 3d, e and Extended Data Fig. 6) and others have shown that SET binds to positively charged amino acids in histone tails or cytoplasmic domains of membrane proteins 18,27. According to the positive-inside rule for integral membrane proteins, the cytoplasmic domains of membrane proteins are enriched in positively charged amino acids for topological reasons 28. Therefore, potential SET-BS in cytoplasmic domains of membrane proteins are very widespread.

Bottom Line: This facilitates interaction of SET with the newly translated cytoplasmic domains of CD47 and results in subsequent translocation of CD47 to the plasma membrane via activated RAC1 (ref. 5).Thus, ApA contributes to the functional diversity of the proteome without changing the amino acid sequence. 3' UTR-dependent protein localization has the potential to be a widespread trafficking mechanism for membrane proteins because HuR binds to thousands of mRNAs, and we show that the long 3' UTRs of CD44, ITGA1 and TNFRSF13C, which are bound by HuR, increase surface protein expression compared to their corresponding short 3' UTRs.We propose that during translation the scaffold function of 3' UTRs facilitates binding of proteins to nascent proteins to direct their transport or function--and this role of 3' UTRs can be regulated by ApA.

View Article: PubMed Central - PubMed

Affiliation: Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, New York 10065, USA.

ABSTRACT
About half of human genes use alternative cleavage and polyadenylation (ApA) to generate messenger RNA transcripts that differ in the length of their 3' untranslated regions (3' UTRs) while producing the same protein. Here we show in human cell lines that alternative 3' UTRs differentially regulate the localization of membrane proteins. The long 3' UTR of CD47 enables efficient cell surface expression of CD47 protein, whereas the short 3' UTR primarily localizes CD47 protein to the endoplasmic reticulum. CD47 protein localization occurs post-translationally and independently of RNA localization. In our model of 3' UTR-dependent protein localization, the long 3' UTR of CD47 acts as a scaffold to recruit a protein complex containing the RNA-binding protein HuR (also known as ELAVL1) and SET to the site of translation. This facilitates interaction of SET with the newly translated cytoplasmic domains of CD47 and results in subsequent translocation of CD47 to the plasma membrane via activated RAC1 (ref. 5). We also show that CD47 protein has different functions depending on whether it was generated by the short or long 3' UTR isoforms. Thus, ApA contributes to the functional diversity of the proteome without changing the amino acid sequence. 3' UTR-dependent protein localization has the potential to be a widespread trafficking mechanism for membrane proteins because HuR binds to thousands of mRNAs, and we show that the long 3' UTRs of CD44, ITGA1 and TNFRSF13C, which are bound by HuR, increase surface protein expression compared to their corresponding short 3' UTRs. We propose that during translation the scaffold function of 3' UTRs facilitates binding of proteins to nascent proteins to direct their transport or function--and this role of 3' UTRs can be regulated by ApA.

Show MeSH
Related in: MedlinePlus