Abstract
RNA interference (RNAi) is a biological process in which small RNAs regulate gene silencing at the transcriptional or posttranscriptional level. The trigger for gene silencing is double-stranded RNA generated from an endogenous genomic locus or a foreign source, such as a transgene or virus. In addition to regulating endogenous gene expression, RNAi provides the mechanistic basis for small RNA-mediated communication between plant hosts and interacting pathogenic microbes, known as cross-kingdom RNAi. Two core protein components, Argonaute (AGO) and Dicer (DCL), are central to the RNAi machinery of eukaryotes. Plants encode for several copies of AGO and DCL genes; in Arabidopsis thaliana, the AGO protein family contains 10 members, and the DCL family contains four. Little is known about the conservation and specific roles of these proteins in monocotyledonous plants, which account for the most important food staples. Here, we utilized in silico tools to investigate the structure and related functions of AGO and DCL proteins from the model grass Brachypodium distachyon. Based on the presence of characteristic domains, 16 BdAGO- and 6 BdDCL-predicted proteins were identified. Phylogenetic analysis showed that both protein families were expanded in Brachypodium as compared with Arabidopsis. For BdDCL proteins, both plant species contain a single copy of DCL1 and DCL4; however, Brachypodium contains two copies each of DCL2 and DCL3. Members of the BdAGO family were placed in all three functional clades of AGO proteins previously described in Arabidopsis. The greatest expansion occurred in the AtAGO1/5/10 clade, which contains nine BdAGOs (BdAGO5/6/7/9/10/11/12/15/16). The catalytic tetrad of the AGO P-element-induced wimpy testis domain (PIWI), which is required for endonuclease activity, is conserved in most BdAGOs, with the exception of BdAGO1, which lacks the last D/H residue. Three-dimensional modeling of BdAGO proteins using tertiary structure prediction software supported the phylogenetic classification. We also predicted a provisional interactome network for BdAGOs, their localization within the cell, and organ/tissue-specific expression. Exploring the specifics of RNAi machinery proteins in a model grass species can serve as a proxy for agronomically important cereals such as barley and wheat, where the development of RNAi-based plant protection strategies is of great interest.
Highlights
RNA interference (RNAi) is a regulatory mechanism utilized by most eukaryotes for endogenous gene silencing and protection against mobile repetitive sequences, transposons, and viruses (Fire et al, 1998; Wilson and Doudna, 2013)
The naming convention is similar to that used by Mirzaei et al (2014) for 16 AGO proteins identified by primary transcripts in the B. distachyon Bd21 v3.1 annotation (The International Brachypodium Initiative, 2010)
We investigated the phylogenetic relationships, domain, structure conservation, and predicted redundancy of AGO and DCL proteins in the model grass plant B. distachyon
Summary
RNA interference (RNAi) is a regulatory mechanism utilized by most eukaryotes for endogenous gene silencing and protection against mobile repetitive sequences, transposons, and viruses (Fire et al, 1998; Wilson and Doudna, 2013). Selection of the target for silencing is governed by sequence complementarity between a single-stranded small RNA (sRNA) and the target RNA. Delivery of artificial dsRNA through transgene expression [host-induced gene silencing (HIGS)] or exogenous application [spray-induced gene silencing (SIGS)] was proven effective against fungal pathogens (Nowara et al, 2010; Koch et al, 2013; Koch et al, 2016; Wang et al, 2016), nematodes (Dutta et al, 2015), insects (Coleman et al, 2014; Abdellatef et al, 2015; Head et al, 2017), and parasitic plants (Tomilov et al, 2008; for review, see Andrade and Hunter, 2016; Cai et al, 2018). A recent discovery revealed that RNAi is involved in natural cross-kingdom RNA communication (ckRNAi), where sRNA molecules function as mediators that are exchanged bidirectionally between a host plant and a microbial pathogen to silence their target transcripts and impact the outcome of the plant–pathogen interaction (Weiberg et al, 2013; Zhang et al, 2016; Wang et al, 2017a; Wang et al, 2017b)
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