RNA-binding protein DUS16 plays an essential role in primary miRNA processing in the unicellular alga Chlamydomonas reinhardtii

Significance

MicroRNAs are important regulators of gene expression in unicellular and multicellular eukaryotes. They are generally embedded in stem–loops of precursor transcripts and are excised by the dsRNA-specific nuclease DICER with the assistance of dsRNA-binding proteins. In animals and plants, proteins harboring two or three dsRNA-binding domains (dsRBDs) are involved in microRNA (miRNA) biogenesis. In contrast, we found that the Dull slicer-16 (DUS16) protein, which contains a single dsRBD and also an ssRNA-binding domain, is involved in miRNA biogenesis in the unicellular green alga Chlamydomonas. This finding sheds light on a molecular mechanism of miRNA biogenesis in unicellular organisms that may be similar to that in a common ancestor of animals and plants.

Abstract

Canonical microRNAs (miRNAs) are embedded in duplexed stem–loops in long precursor transcripts and are excised by sequential cleavage by DICER nuclease(s). In this miRNA biogenesis pathway, dsRNA-binding proteins play important roles in animals and plants by assisting DICER. However, these RNA-binding proteins are poorly characterized in unicellular organisms. Here we report that a unique RNA-binding protein, Dull slicer-16 (DUS16), plays an essential role in processing of primary-miRNA (pri-miRNA) transcripts in the unicellular green alga Chlamydomonas reinhardtii. In animals and plants, dsRNA-binding proteins involved in miRNA biogenesis harbor two or three dsRNA-binding domains (dsRBDs), whereas DUS16 contains one dsRBD and also an ssRNA-binding domain (RRM). The null mutant of DUS16 showed a drastic reduction in most miRNA species. Production of these miRNAs was complemented by expression of full-length DUS16, but the expression of RRM- or dsRBD-truncated DUS16 did not restore miRNA production. Furthermore, DUS16 is predominantly localized to the nucleus and associated with nascent (unspliced form) pri-miRNAs and the DICER-LIKE 3 protein. These results suggest that DUS16 recognizes pri-miRNA transcripts cotranscriptionally and promotes their processing into mature miRNAs as a component of a microprocessor complex. We propose that DUS16 is an essential factor for miRNA production in Chlamydomonas and, because DUS16 is functionally similar to the dsRNA-binding proteins involved in miRNA biogenesis in animals and land plants, our report provides insight into this mechanism in unicellular eukaryotes.