Abstract

Along with the well-studied microRNA (miRNA) and small interfering RNA (siRNA) is a new class of transfer RNA-derived small RNA (tsRNA), which has recently been detected in multiple organisms and is implicated in gene regulation. However, while miRNAs and siRNAs are known to repress gene expression through sequence-specific RNA cleavage or translational repression, how tsRNAs regulate gene expression remains unclear. Here we report the identification and functional characterization of tsRNAs in the oomycete pathogen Phytophthora sojae. We show that multiple tRNAs are processed into abundant tsRNAs, which accumulate in a similar developmental stage-specific manner and are negatively correlated with the expression of predicted target genes. Degradome sequencing and 5′ RLM RACE experiments indicate tsRNAs can trigger degradation of target transcripts. Transient expression assays using GUS sensor constructs confirmed the requirement of sequence complementarity in tsRNA-mediated RNA degradation in P. sojae. Our results show that the tsRNA are a class of functional endogenous sRNAs and suggest that tsRNA regulate gene expression through inducing sequence-specific degradation of target RNAs in oomycetes.

Highlights

  • Small non-protein-coding RNAs play important roles in transcriptional and posttranscriptional gene regulation in eukaryotic organisms

  • TsRNA is an Endogenous sRNA in Oomycete Pathogen Phytophthora sojae

  • High throughput sequencing led to the identification of a total of 41 candidate transfer RNA-derived small RNA (tsRNA) derived from 26 tRNAs (Figure 1A and Supplemental Table S1)

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Summary

Introduction

Small non-protein-coding RNAs (sRNAs) play important roles in transcriptional and posttranscriptional gene regulation in eukaryotic organisms. Animal and plant sRNAs, microRNA (miRNA) and small interfering RNA (siRNA), have been identified and extensively studied over the last 15 years (Carthew and Sontheimer, 2009). A third class of sRNAs, the Piwiinteracting RNA (piRNA), was identified in animal germlines (Girard et al, 2006; Lau et al, 2006). All these sRNAs employ sequence-specific targeting mechanisms (Carthew and Sontheimer, 2009; Thomson and Lin, 2009). In the human parasite euglenoid trypanosomes, Trypanosoma cruzi, tsRNAs accumulated in cytoplasmic granules (Garcia-Silva et al, 2010). A diversity of protein factors have been implicated in tsRNA processing in different organisms, including the RNase T2 family protein Rny1p in yeast (2009), RNase A superfamily protein angiogenin (Fu et al, 2009), RNase III family protein Dicer (Babiarz et al, 2008; Cole et al, 2009), Argonaute (AGO) family proteins (Haussecker et al, 2010), Piwi family proteins Twi (Couvillion et al, 2010), and Hiwi (Keam et al, 2014), and DNA methyltransferase enzyme Dnmt in mammals (Schaefer et al, 2010)

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