Transfer RNA Derived Small RNAs Targeting Defense Responsive Genes Are Induced during Phytophthora capsici Infection in Black Pepper (Piper nigrum L.)

Abstract

Small RNAs derived from transfer RNAs were recently assigned as potential gene regulatory candidates for various stress responses in eukaryotes. In this study, we report on the cloning and identification of tRNA derived small RNAs from black pepper plants in response to the infection of the quick wilt pathogen, Phytophthora capsici. 5′tRFs cloned from black pepper were validated as highly expressed during P. capsici infection. A high-throughput systematic analysis of the small RNAome (sRNAome) revealed the predominance of 5′tRFs in the infected leaf and root. The abundance of 5′tRFs in the sRNAome and the defense responsive genes as their potential targets indicated their regulatory role during stress response in black pepper. The 5′AlaCGC tRF mediated cleavage was experimentally mapped at the tRF binding sites on the mRNA targets of Non-expresser of pathogenesis related protein (NPR1), which was down-regulated during pathogen infection. Comparative sRNAome further demonstrated sequence conservation of 5′Ala tRFs across the angiosperm plant groups, and many important genes in the defense response were identified in silico as their potential targets. Our findings uncovered the diversity, differential expression and stress responsive functional role of tRNA-derived small RNAs during Phytophthora infection in black pepper.

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

“…7). AGO4 is localized in the nucleus and associates predominantly with 24 nt small RNAs having 5′ terminal A in order to mediate DNA methylation in transposons and a few coding loci (Mi et al 2008;Li et al 2008). tRF-3 Leu CAA (5′-AAGAGGGCG TGGGTTCAAACCCCA) is 24 nt in length and it is associated with AGO4 (~28 RPM; data not shown).…”

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

“…Asha and Soniya (2016) demonstrated the involvement of the tRNAs derived smallRNAs in regulating the expression patterns of defense related genes during Phytophthora capsici infection in Black Pepper ( Piper nigrum L.). Interestingly the dominance of 5′ tRNA derived smallRNAs was found among the observed tRNAs population, which supports that in plants the major class of these smallRNAs is represented by 5′ tRNAs (Alves et al, 2017; Martinez et al, 2017).…”

Transgenerational Response to Heat Stress in the Form of Differential Expression of Noncoding RNA Fragments in Brassica rapa Plants

“…Type of tRNA or tRF Transgenerational response (this study) Somatic response No. of reads mapping to tRNAs tRNA Asp Upregulated Heat-induced in B. rapa (Byeon et al, 2018) Upregulated by P-deficiency in Arabidopsis (Hsieh et al, 2009) Induced by salt and osmotic stress in Physcomitrella patens (Arya et al, 2016) Enriched Enriched in unpollinated ovules in heat-stressed B. rapa (Byeon et al, 2018) Enriched by heat and drought in wheat Enriched by salt in Arabidopsis (Loss-Morais et al, 2013) Enriched by infection of black pepper with Phytophthora capsici (Asha and Soniya, 2016) tRF Ala(UGC) Enriched Enriched in unpollinated ovules in heat-stressed B. rapa (Byeon et al, 2018) Underrepresented in apical meristem and endosperm of heat-stressed B. rapa (Byeon et al, 2018) tRF Arg(UCG) Enriched Under-represented Enriched by heat/drought in wheat ) Enriched by P-deficiency in barley (Hackenberg et al, 2013) tRF Val(CAC) Enriched Enriched by heat/drought in wheat ; Enriched by infection of black pepper with Phytophthora capsici (Asha and Soniya, 2016) SD. The asterisks show a significant (p < 0.05) difference between parental and progeny plants.…”