Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions

Abstract

It is becoming increasingly evident that the RNA degradome is a crucial component of the total cellular RNA pool. Here, we present an analysis of the medium-sized RNAs (midi RNAs) that form in Arabidopsis thaliana. Our analyses revealed that the midi RNA fraction contained mostly 20–70-nt-long fragments derived from various RNA species, including tRNA, rRNA, mRNA and snRNA. The majority of these fragments could be classified as stable RNA degradation intermediates (RNA degradants). Using two dimensional polyacrylamide gel electrophoresis, we demonstrated that high copy number RNA (hcn RNA) degradants appear in plant cells not only during stress, as it was earlier suggested. They are continuously produced also under physiological conditions. The data collected indicated that the accumulation pattern of the hcn RNA degradants is organ-specific and can be affected by various endogenous and exogenous factors. In addition, we demonstrated that selected degradants efficiently inhibit translation in vitro. Thus, the results of our studies suggest that hcn RNA degradants are likely to be involved in the regulation of gene expression in plants.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-013-0079-3) contains supplementary material, which is available to authorized users.

Slicing tRNAs to boost functional ncRNA diversity

“…52 Notably, stress granules have still been observed even in the case YB-1 was removed by RNAi, thus leaving many mechanistic questions still unanswered how 5′ tRNA halves are involved in translation control. Similar inhibitory effects of 5′ tRNA halves on translation were recently observed in the plant Arabidopsis thaliana, 27 but with some notable differences: (1) diverse tRNA pieces, including tRNA halves, have been observed independent of stress and, (2) the inhibitory effect of the 5′ tRNA halves on in vitro translation did not correlate with the number of consecutive guanine residues at the 5′ end as proposed by Anderson et al Furthermore, it was demonstrated that the human tRNA halves (Ala/Cys), which repressed translation initiation in rabbit reticulocyte lysate, 52 showed no inhibitory effect in wheat germ extract. This either hints to species specificity or to missing cofactors that determine the inhibitory potential.…”

“…The generated 3′ tRFs seem to be the result of global tRNA cleavage, induced by different stress stimuli (e.g., encystation, serum deprivation, cold stress, and heat shock). 82 tRFs of aberrant size and yet unknown function have also been detected in other studies, including 3′ quarters of tRNAs 27 and "mid"-fragments. 83 While most of the so far identified tRFs derive from mature tRNAs (with the exception of 3′U tRFs), Hanada et al recently reported on novel tRFs originating from aberrant pre-tRNA splicing.…”

“…It is important to note that the targeted tRNAs are typically fully matured tRNA transcripts, carrying an entire set of nucleoside modifications, lacking introns, and have processed 5′ and 3′ termini, often including the 3′ CCA sequences. 27,28 The trigger for tRNA cleavage is in the majority of cases nutritional, biological, or physicochemical stress, although tRNA halves have also been observed under unstressed conditions. 27,29 Furthermore, the extent of cleavage depends on the nature of stress.…”

“…27,28 The trigger for tRNA cleavage is in the majority of cases nutritional, biological, or physicochemical stress, although tRNA halves have also been observed under unstressed conditions. 27,29 Furthermore, the extent of cleavage depends on the nature of stress. 30 For example, in Tetrahymena thermophila tRNA halves production has been detected under cold shock, but not during heat shock.…”

“…Therefore, a generation of 5′ tRFs can occur at any point of tRNA processing, given that RNase P has already removed the 5′ leader of the pre-tRNA. Importantly, since many studies report on mixed populations of tRFs and tRNA halves, 27,47,54 it cannot be excluded that tRFs are produced from 5′ tRNA halves by 3′ exonuclease chew-back (Fig. 1).…”