A non-canonical RNA silencing pathway promotes mRNA degradation in basal fungi

Trieu, Trung Anh, Calo, Silvia, Nicolás, Francisco E, Vila, Ana, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Torres-Martínez, Santiago, Garre, Victoriano and Ruiz-Vázquez, Rosa M (2015) A non-canonical RNA silencing pathway promotes mRNA degradation in basal fungi. PLoS Genetics, 11 (4). ISSN 1553-7404

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Abstract

The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing.

Item Type:	Article
Additional Information:	Received: 01/20/2015 © 2015 Trieu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Uncontrolled Keywords:	fungal proteins,gene expression regulation, fungal,gene silencing,mucor,rna stability,rna, messenger,ribonuclease iii
Faculty \ School:	Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Plant Sciences
Depositing User:	Pure Connector
Date Deposited:	24 Sep 2016 00:21
Last Modified:	22 Oct 2022 01:25
URI:	https://ueaeprints.uea.ac.uk/id/eprint/60002
DOI:	10.1371/journal.pgen.1005168

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