The accumulation of chloroplast small RNAs in unicellular alga Chlamydomonas reinhardtii is affected by nitrogen deprivation

Small RNAs generated from the chloroplast genome may play a role in gene regulation. Given that chloroplast function is affected by nitrogen deprivation, there is yet an attempt to link chloroplast small RNAs to this stress condition. This study aims to determine the response of chloroplast small RNAs under nitrogen deprivation and their putative mode of action. A comparative transcriptomic approach was carried out to analyze the differential accumulation of chloroplast small RNAs from Chlamydomonas reinhardtii cells grown in nitrogen-deprived versus nitrogen-based medium. A total of 101 chloroplast small RNA candidates were successfully annotated. Growth in nitrogen-deprived medium revealed 17 significantly upregulated and 12 downregulated chloroplast small RNAs. These chloroplast small RNAs originated from different genomic locations such as untranslated, intergenic or antisense regions as well as the ends of tRNA and rRNA genes. The differentially accumulated csRNAs from 3-untranslated regions were all upregulated. In contrast, the csRNAs from the ends of tRNA and rRNA genes were all downregulated during nitrogen deprivation. Fluctuations of the chloroplast small RNA levels indicated their importance in the chloroplasts during changes in nitrogen levels. The primary sequences of three selected chloroplast small RNA were found to be conserved in the chloroplast genomes of a few microalgae, again reflecting their functional importance. The findings from this study provided new insights into the involvement of non-coding RNAs in chloroplast during metabolic stress.