Abstract
The unicellular alga Chlamydomonas reinhardtii contains many types of small RNAs (sRNAs) but the biological role(s) of bona fide microRNAs (miRNAs) remains unclear. To address their possible function(s) in responses to nutrient availability, we examined miRNA expression in cells cultured under different trophic conditions (mixotrophic in the presence of acetate or photoautotrophic in the presence or absence of nitrogen). We also reanalyzed miRNA expression data in Chlamydomonas subject to sulfur or phosphate deprivation. Several miRNAs were differentially expressed under the various trophic conditions. However, in transcriptome analyses, the majority of their predicted targets did not show expected changes in transcript abundance, suggesting that they are not subject to miRNA-mediated RNA degradation. Mutant strains, defective in sRNAs or in ARGONAUTE3 (a key component of sRNA-mediated gene silencing), did not display major phenotypic defects when grown under multiple nutritional regimes. Additionally, Chlamydomonas miRNAs were not conserved, even in algae of the closely related Volvocaceae family, and many showed features resembling those of recently evolved, species-specific miRNAs in the genus Arabidopsis. Our results suggest that, in C. reinhardtii, miRNAs might be subject to relatively fast evolution and have only a minor, largely modulatory role in gene regulation under diverse trophic states.
Highlights
MicroRNAs are short RNA molecules (~20–24 nt in length) that generally function as negative regulators of gene expression, by binding complementary sequences in target transcripts and leading to translation repression and/ or mRNA degradation[1,2,3,4,5,6]
In order to characterize the possible roles of miRNAs in C. reinhardtii, in response to nutrient availability, we investigated changes in miRNA populations and their putative targets in Chlamydomonas cells grown under mixotrophic conditions and under photoautotrophic conditions with or without a source of nitrogen
Comparison of AGO3-associated sRNA populations from Chlamydomonas cells grown under various trophic conditions revealed that some miRNAs are differentially expressed in response to nutritional changes, but none of the identified miRNAs appears to be strictly condition specific (Table S1A)
Summary
MicroRNAs are short RNA molecules (~20–24 nt in length) that generally function as negative regulators of gene expression, by binding complementary sequences in target transcripts and leading to translation repression and/ or mRNA degradation[1,2,3,4,5,6]. This generation of novel miRNA genes from random sequences may account for the large number of miRNAs corresponding uniquely to A. thaliana or A. lyrata (~13% of their total miRNA populations) despite their relatively recent evolutionary divergence[24, 26] These species-specific miRNAs appear to be lowly expressed, whereas miRNAs conserved among plant species generally show higher expression levels[25, 26]. Subsets of differentially expressed miRNAs were identified under the various trophic conditions but very few of their predicted targets displayed expected changes in transcript abundance (assuming regulation by miRNA-triggered RNA degradation) or coded for proteins involved in direct responses to nutrient deficiency. The RNAi defective mutants displayed slight phenotypic defects, suggesting that miRNAs might not play an essential role in endogenous gene regulation under the conditions examined
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