RNA degradation is among the most fundamental processes that occur in living cells. The continuous decay of RNA molecules is associated not only with nucleotide turnover, but also with transcript maturation and quality control. The efficiency of RNA decay is ensured by a broad spectrum of both specific and non-specific ribonucleases. Some of these ribonucleases participate mainly in processing primary transcripts and in RNA quality control. Others preferentially digest mature, functional RNAs to yield a variety of molecules that together constitute the RNA degradome. Recently, it has become increasingly clear that the composition of the cellular RNA degradome can be modulated by numerous endogenous and exogenous factors (e.g. by stress). In addition, instead of being hydrolyzed to single nucleotides, some intermediates of RNA degradation can accumulate and function as signalling molecules or participate in mechanisms that control gene expression. Thus, RNA degradation appears to be not only a process that contributes to the maintenance of cellular homeostasis but also an underestimated source of regulatory molecules.

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.

An ability to form symbiotic associations with rhizobia and to utilize atmospheric nitrogen makes legumes ecologically successful. High iron content in legume grains, partially relocated from root nodules, is another-nutritional-advantage of this group of plants. The ferritin complex is the major cell iron storage and detoxification unit and has been recognized as a marker of many stress-induced responses. The possible participation of ferritin in nodule formation and functioning was investigated here. Correlation of increased accumulation of both ferritin polypeptide and mRNA with actual in situ localization of ferritin allowed ferritin synthesis in the developing, indeterminate-type root nodules to be related to differentiating bacteroid tissue. This kind of tissue, in contrast to the determinate-type nodules, is present in lupin nodules at almost all stages of their development. Interestingly, it was found that, in this type of nodule, senescence starting in the decaying zones induces ferritin accumulation in younger, still active, tissues. Based on the presented data, and in correlation with previous results, some aspects of the regulation of expression of lupin ferritin genes are also discussed.

We identified three genes coding for ferritins in the legume plant – yellow lupine (LlFer1, LlFer2, LlFer3). Proteins coded by these genes have a typical ‘plant’ structure, and precursors of their functional subunits are probably targeted to plastids. Despite very high amino acid sequence identity of mature polypeptides (86–90%), their genes are differentially induced by iron and the ‘stress‐related’ hormone abscisic acid (ABA). In tissues of lupine plants grown in hydroponics, the transcription of all three classes was induced by both iron and ABA with different kinetics. However, in homogenous lupine cell suspension, the accumulation of all classes of ferritin messages was also induced with iron, whereas only one gene (LlFer2 class) was transcribed in response to ABA. Moreover, the activity of LlFer3 gene was repressed by ABA, but up‐regulated by light. During the development of symbiotic interactions of lupine plants with the bacteria Bradyrhizobium lupini, only two out of three ferritin genes were active –LlFer2 and LlFer3. Increased accumulation of ferritin RNAs and polypeptide(s) correlated with late developmental stages of root nodules, suggesting the involvement of two types of ferritin subunits in the protection against senescence‐related iron release. The phylogenetic analysis of ferritin amino acid sequences is in agreement with classical systematics. However, because of clear grouping of some legume ferritins outside all other legume sequences, a possibility of a more diverse character of ferritins in this family should also be considered.