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The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25.

ABSTRACT: RNA-binding proteins (RBP) are critical regulators of gene expression. Recent studies have uncovered hundreds of mRNA-binding proteins that do not contain annotated RNA-binding domains and have well-established roles in other cellular processes. Investigation of these nonconventional RBPs is critical for revealing novel RNA-binding domains and may disclose connections between RNA regulation and other aspects of cell biology. The endosomal sorting complex required for transport II (ESCRT-II) is a nonconventional RNA-binding complex that has a canonical role in multivesicular body formation. ESCRT-II was identified previously as an RNA-binding complex in Drosophila oocytes, but whether its RNA-binding properties extend beyond Drosophila is unknown. In this study, we found that the RNA-binding properties of ESCRT-II are conserved in Xenopus eggs, where ESCRT-II interacted with hundreds of mRNAs. Using a UV cross-linking approach, we demonstrated that ESCRT-II binds directly to RNA through its subunit, Vps25. UV cross-linking and immunoprecipitation (CLIP)-Seq revealed that Vps25 specifically recognizes a polypurine (i.e. GA-rich) motif in RNA. Using purified components, we could reconstitute the selective Vps25-mediated binding of the polypurine motif in vitro Our results provide insight into the mechanism by which ESCRT-II selectively binds to mRNA and also suggest an unexpected link between endosome biology and RNA regulation.

SUBMITTER: Emerman AB

PROVIDER: S-EPMC6093225 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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The RNA-binding complex ESCRT-II in <i>Xenopus laevis</i> eggs recognizes purine-rich sequences through its subunit, Vps25.

Emerman Amy B AB Blower Michael D MD

The Journal of biological chemistry 20180614 32

RNA-binding proteins (RBP) are critical regulators of gene expression. Recent studies have uncovered hundreds of mRNA-binding proteins that do not contain annotated RNA-binding domains and have well-established roles in other cellular processes. Investigation of these nonconventional RBPs is critical for revealing novel RNA-binding domains and may disclose connections between RNA regulation and other aspects of cell biology. The endosomal sorting complex required for transport II (ESCRT-II) is a ...[more]

PMID: 29903915

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Project description:BackgroundVps25p is the product of yeast gene VPS25 and is found in an endosomal sorting complex required for transport (ESCRT)-II, along with Vps22p and Vps36p. This complex is essential for sorting of ubiquitinated biosynthetic and endosomal cargoes into endosomes.ResultsWe found that VPS25 is a highly conserved and widely expressed eukaryotic gene, with single orthologs in chromalveolate, excavate, amoebozoan, plant, fungal and metazoan species. Two paralogs were found in Trichomonas vaginalis. An ortholog was strikingly absent from the Encephalitozoon cuniculi genome. Intron positions were analyzed in VPS25 from 36 species. We found evidence for five ancestral VPS25 introns, intron loss, and single instances of intron gain (a Paramecium species) and intron slippage (Theileria species). Processed pseudogenes were identified in four mammalian genomes, with a notable absence in the mouse genome. Two retropseudogenes were found in the chimpanzee genome, one more recently inserted, and one evolving from a common primate ancestor. The amino acid sequences of 119 Vps25 orthologs are aligned, compared with the known secondary structure of yeast Vps25p, and used to carry out phylogenetic analysis. Residues in two amino-terminal PPXY motifs (motif I and II), involved in dimerization of Vps25p and interaction with Vps22p and Vps36p, were closely, but not absolutely conserved. Specifically, motif I was absent in Vps25 homologs of chromalveolates, euglenozoa, and diplomonads. A highly conserved carboxy-terminal lysine was identified, which suggests Vps25 is ubiquitinated. Arginine-83 of yeast Vps25p involved in Vps22p interaction was highly, but not absolutely, conserved. Human tissue expression analysis showed universal expression.ConclusionWe have identified 119 orthologs of yeast Vps25p. Expression of mammalian VPS25 in a wide range of tissues, and the presence in a broad range of eukaryotic species, indicates a basic role in eukaryotic cell function. Intron splice site positions were highly conserved across all major eukaryotic species, suggesting an ancestral origin. Amino acid sequence analysis showed the consensus for the amino-terminal proline-rich motifs is P- [WP]-X-[YF] for motif I (when present) and P-P-[FYL]-[FY] for motif II, and that Vps25 may be ubiquitinated.

Dataset Information

The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25.

Publications

The RNA-binding complex ESCRT-II in <i>Xenopus laevis</i> eggs recognizes purine-rich sequences through its subunit, Vps25.

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