Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation

Abstract

Rhizobial infection and root nodule formation in legumes require recognition of signal molecules produced by the bacteria and their hosts. Here, we show that rhizobial transfer RNA (tRNA)-derived small RNA fragments (tRFs) are signal molecules that modulate host nodulation. Three families of rhizobial tRFs were confirmed to regulate host genes associated with nodule initiation and development through hijacking the host RNA-interference machinery that involves ARGONAUTE 1. Silencing individual tRFs with the use of short tandem target mimics or by overexpressing their targets represses root hair curling and nodule formation, whereas repressing these targets with artificial microRNAs identical to the respective tRFs or mutating these targets with CRISPR-Cas9 promotes nodulation. Our findings thus uncover a bacterial small RNA–mediated mechanism for prokaryote-eukaryote interaction and may pave the way for enhancing nodulation efficiency in legumes.

tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model

“…S3A and Fig. S3B), corresponding to the previously reported size of tRF-3a and tRF-3b [35,39,44,57,58]. The small tRF-3s (< 30 nucleotides) derived from tRNA Ala , tRNA Val , tRNA Gln , tRNA Gly , tRNA Leu , tRNA Cys , tRNA Tyr , tRNA Thr and tRNA Ser contribute to most of the tRF-3 reads ( Fig.…”

“…The 18-22 nucleotide long tRF-3s could regulate placenta function or embryo development through protein translation control or/and gene expression regulation. Some tRF-3s can associate with Argonaute proteins and repress mRNA and protein expression by recognizing target mRNAs with complementarity to the tRF-3 sequence [35,39,57,58]. This microRNA-like action could be an important mechanism by which the tRF-3s altered in response to MIA may regulate gene expression in the maternal-fetal interface, or in other fetal or maternal tissues, if transported to the latter.…”

“…3' fragments from mature tRNA containing 3' CCA sequence are another important groups of tRFs that have previously been shown to have various functions. The short 3' fragments are also named tRF-3s, usually have length of 18 or 22 nucleotides and like microRNAs can repress genes by interacting with target mRNAs along with Argonaute and GW182 proteins [39,57,58]. They could also regulate protein translation [40] or inhibit retrotransposon activity [44].…”

Different Genetic Sources Contribute to the Small RNA Population in the Arbuscular Mycorrhizal Fungus Gigaspora margarita

“…This phenomenon, known as cross-kingdom RNAi, occurs in several pathogenic and parasitic interactions (Weiberg et al, 2013;Mayoral et al, 2014;Zhang et al, 2016;Shahid et al, 2018;Chow et al, 2019;Cui et al, 2019) where it can function as an attack or a defense strategy. Interestingly, it was also recently described in the legume-rhizobium symbiosis where bacterial transfer RNA (tRNA)-derived small RNA fragments are signal molecules that modulate host gene expression and nodule formation (Ren et al, 2019). It has been proposed that sRNAs can also be exchanged between the partners of the arbuscular mycorrhizal (AM) symbiosis (Huang et al, 2019), a very ancient mutualistic association established between the roots of most plants and the obligate biotrophic fungi belonging to Glomeromycotina (Mucoromycota phylum; Spatafora et al, 2016), known as arbuscular mycorrhizal fungi (AMF) .…”

Plant Small RNA Species Direct Gene Silencing in Pathogenic Bacteria as well as Disease Protection

“…In addition, a very recent report provides evidence that rhizobial tRNA-derived sRNAs can silence legume symbiotic genes 13 . However, whether plant sRNAs can in turn directly reprogram gene expression in plant-associated bacteria remains unknown.…”