Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants

Abstract

The manuscript by Alves et al. entitled "Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants" describes the identification and characterization of tRNAderived sRNA fragments in plants. By combining bioinformatic analysis and genetic and molecular approaches, we show that tRF biogenesis does not rely on canonical microRNA/siRNA processing machinery (i.e., independent of DICER-LIKE proteins). Moreover, we provide evidences that the Arabidopsis S-like Ribonuclease 1 (RNS1) might be involved in the biogenesis of tRFs. Detailed analyses showed that plant tRFs are sorted into different types of ARGONAUTE proteins and that they have potential target candidate genes. Our work advances the understanding of the tRF biology in plants by providing evidences that plant and animal tRFs shared common features and raising the hypothesis that an interplay between tRFs and other sRNAs might be important to fine-tune gene expression and protein biosynthesis in plant cells. Small RNA (sRNA) fragments derived from tRNAs (3'-loop, 5'-loop, anti-codon loop), named tRFs, have been reported in several organisms, including humans and plants. Although they may interfere with gene expression, their biogenesis and biological functions in plants remain poorly understood. Here, we capitalized on small RNA sequencing data from distinct species such as Arabidopsis thaliana, Oryza sativa, and Physcomitrella patens to examine the diversity of plant tRFs and provide insight into their properties. In silico analyzes of 19 to 25-nt tRFs derived from 5' (tRF-5s) and 3'CCA (tRF-3s) tRNA loops in these three evolutionary distant species showed that they are conserved and their abundance did not correlate with the number of genomic copies of the parental tRNAs. Moreover, tRF-5 is the most abundant variant in all three species. In silico and in vivo expression analyses unraveled differential accumulation of tRFs in Arabidopsis tissues/organs, suggesting that they are not byproducts of tRNA degradation. We also verified that the biogenesis of most Arabidopsis 19-25 nt tRF-5s and tRF-3s is not primarily dependent on DICER-LIKE proteins, though they seem to be associated with ARGONAUTE proteins and have few potential targets. Finally, we provide evidence that Arabidopsis ribonuclease RNS1 might be involved in the processing and/or degradation of tRFs. Our data support the notion that an interplay between tRFs and other sRNAs might be important to fine tune gene expression and protein biosynthesis in plant cells.

tRNA Derived smallRNAs: smallRNAs Repertoire Has Yet to Be Decoded in Plants

“…Coordinated regulatory activities and interaction networks of these smallRNAs classes have been previously shown to play a key role in understanding the plant functional and developmental genomics (Rubio-Somoza and Weigel, 2011; Meng et al, 2011; Li and Zhang, 2016). With the rapid development in the next generation sequencing technologies and miRNAs moving to the single cell miRNAs transcriptome (Faridani et al, 2016), a new class of smallRNAs, tRNA derived smallRNAs (Hsieh et al, 2009), which have been explored widely in animals have now recently started gaining substantial importance in plant genomics with recent evidences showing their canonical interactions with AGO1 and TE like microRNAs (Alves et al, 2017; Martinez et al, 2017). …”

“…Alongside, this class of smallRNAs has been shown to be involved in translation repression in Cucurbita maxima where phloem specific tRNAs fragments have been shown to interfere with ribosomal activity and represses translation (Zhang et al, 2009). Interestingly, recent comparative analysis revealed hints toward the biogenesis of these tRNA derived smallRNAs independent of DICER-like proteins (Alves et al, 2017), however, reduced abundance of tRNA derived smallRNAs has been observed in dcl1 double mutants (Martinez et al, 2017). Using both dcl1 and ago1 single mutants, specific reduction of the tRNAs derived smallRNAs was observed as compared to miRNAs, which concludes the involvement of AGO1 in tRNA derived smallRNAs biogenesis pathway (Martinez et al, 2017).…”

“…In plants, however, the detection and possible association of tRNA derived smallRNAs (Nowacka et al, 2013) is still lacking with only few reports indicating the roles of tRNAs derived smallRNAs in tissues, embryogenic callus (Chen et al, 2011), phloem (Zhang et al, 2009) and recently in pollens (Martinez et al, 2017). tRNA derived smallRNAs classification and nomenclature in plants have been correlated with 5′, 3′ and CCA proximities and have been length classified as 19–25 nt (Loss-Morais et al, 2013; Alves et al, 2017). Taking into account the length variations in correlation with abundance, so far observed length variations were found to be between 19 and 25 nt, while majority of them belonging to 5′ 19-nt and has been seen conserved across dicot ( Arabidopsis thaliana -Gly UCC ), Zea mays (C4 species) and evolutionary conserved moss ( Physcomitrella patens ) (Alves et al, 2017; Martinez et al, 2017) except monocot ( Oryza sativa - Ala AGC ), where 25-nt abundance was seen as the most dominant length of these smallRNAs (Chen et al, 2011).…”

“…tRNA derived smallRNAs classification and nomenclature in plants have been correlated with 5′, 3′ and CCA proximities and have been length classified as 19–25 nt (Loss-Morais et al, 2013; Alves et al, 2017). Taking into account the length variations in correlation with abundance, so far observed length variations were found to be between 19 and 25 nt, while majority of them belonging to 5′ 19-nt and has been seen conserved across dicot ( Arabidopsis thaliana -Gly UCC ), Zea mays (C4 species) and evolutionary conserved moss ( Physcomitrella patens ) (Alves et al, 2017; Martinez et al, 2017) except monocot ( Oryza sativa - Ala AGC ), where 25-nt abundance was seen as the most dominant length of these smallRNAs (Chen et al, 2011). Previously observed correlation of length and corresponding abundances of tRNA derived smallRNAs are also supported by recent observations of Martinez et al (2017), which highlighted the abundance of the 19-nt tRNAs derived smallRNAs as a part of the 5′ tRNA processing in pollens of Arabidopsis thaliana .…”

“…However, across polyploids such as Triticum aestivum , abundance of 21-nt with most of them originating from Val CAC has been observed (Wang Y. et al, 2016). Despite being conserved in patterns of distribution across monocots and dicots, Oryza sativa AGO reveals high abundance of specific Arg CCT and Arg TCG tRNA derived 19-nt smallRNAs as compared to the Ala AGC (Alves et al, 2017). Difference in these patterns of length abundances might be due to species ploidy or due to the cleavage asymmetry and role of anticodon loop required for tRNA processing (Wang Y. et al, 2016).…”