A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa)

Abstract

BackgroundNon-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific importance in biological research. Several studies in recent years have reported a small number of non-coding small RNAs that map to chloroplast genomes. However, it remains uncertain whether small RNAs are generated from chloroplast genome and how they respond to environmental stress, such as high temperature. Chinese cabbage is an important vegetable crop, and heat stress usually causes great losses in yields and quality. Under heat stress, the leaves become etiolated due to the disruption and disassembly of chloroplasts. In an attempt to determine the heat-responsive small RNAs in chloroplast genome of Chinese cabbage, we carried out deep sequencing, using heat-treated samples, and analysed the proportion of small RNAs that were matched to chloroplast genome.ResultsDeep sequencing provided evidence that a novel subset of small RNAs were derived from the chloroplast genome of Chinese cabbage. The chloroplast small RNAs (csRNAs) include those derived from mRNA, rRNA, tRNA and intergenic RNA. The rRNA-derived csRNAs were preferentially located at the 3'-ends of the rRNAs, while the tRNA-derived csRNAs were mainly located at 5'-termini of the tRNAs. After heat treatment, the abundance of csRNAs decreased in seedlings, except those of 24 nt in length. The novel heat-responsive csRNAs and their locations in the chloroplast were verified by Northern blotting. The regulation of some csRNAs to the putative target genes were identified by real-time PCR. Our results reveal that high temperature suppresses the production of some csRNAs, which have potential roles in transcriptional or post-transcriptional regulation.ConclusionsIn addition to nucleus, the chloroplast is another important organelle that generates a number of small RNAs. Many members of csRNA families are highly sensitive to heat stress. Some csRNAs respond to heat stress by silencing target genes. We suggest that proper temperature is important for production of chloroplast small RNAs, which are associated with plant resistance to abiotic stress.

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

“…This is in agreement with the presence of numerous tRFs deriving from plastid tRNAs in Brassica napa (8). These tRFs are formed by cleavage in positions very similar to those found for nuclear tRFs.…”

A Comprehensive Expression Profile of MicroRNAs and Other Classes of Non-Coding Small RNAs in Barley Under Phosphorous-Deficient and -Sufficient Conditions

“…Many chloroplast-derived sRNAs (csRNAs) have recently been identified. 32–34 We took advantage of the available barley chloroplast genome sequence to distinguish between sRNAs derived from the chloroplast and nuclear genomes in barley and found that about one-fourth of sRNAs were derived from the chloroplast genome in both P-deficient and P-sufficient shoots (Table 1). In contrast to sRNAs derived from the nuclear genome, csRNAs were highly redundant in both P treatments.…”

Identification of miRNAs and their targets using high-throughput sequencing and degradome analysis in cytoplasmic male-sterile and its maintainer fertile lines of Brassica juncea

“…Interestingly, some new candidate miRNAs were observed to be organelle-derived miRNAs (Additional file 1: Table S10), which suggested that these miRNAs were derived by alternative biogenesis pathways, not via Dicer proteins. Indeed, sRNAs can be generated from organelles including chloroplasts and mitochondria in animals, plants, fungi and humans [33-36]. New candidate miRNAs are considered to be young miRNAs that have evolved recently, and are often expressed at a lower level than conserved miRNAs, as reported from Arabidopsis and Triticum [37,38].…”