Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas

Abstract

Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including three AGOs and three DICER-like (DCL) proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, these >26 nt sRNAs are derived from moderately repetitive genomic clusters and their biogenesis is DICER-independent. Interestingly, the sequences generating these >26-nt sRNAs have been conserved and amplified in several Chlamydomonas species. Moreover, expression of these longer sRNAs increases substantially under nitrogen or sulfur deprivation, concurrently with the downregulation of predicted target transcripts. We hypothesize that the transposon-like sequences from which >26-nt sRNAs are produced might have been ancestrally targeted for silencing by the RNAi machinery but, during evolution, certain sRNAs might have fortuitously acquired endogenous target genes and become integrated into gene regulatory networks.

Novel long small RNAs (lsRNAs) are evolutionary conserved in plants and differentially expressed during epitype inducing conditions in Norway spruce embryos

“…In plants, a speci c class of 23-27 nt long miRNAs was previously reported inArabidopsis thaliana (Gozmanova et al, 2017). Similarly, 27-30 nt sRNAs are present in unicellular eukaryotes (Lee and Collins, 2006), green algae (Li et al, 2023) and pathogenic fungi (Wang et al, 2016;Jia et al, 2017).…”

A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis

“…Examples of functional specialization include the monocot‐specific DCL5, which evolved from the duplication of an ancient DCL3 from a eudicot ancestor (Ono et al ., 2018) and that is involved in the cell‐type specific production of 24‐nt sRNAs that participate in temperature‐dependent fertility (Teng et al ., 2020). Another example is the preferential loading of unusually long sRNAs (> 26 nt) into AGO1 in the unicellular alga Chlamydomonas reinhardtii (Li et al ., 2023).…”

The small RNA family gets bigger: AGO1-bound noncanonical sRNAs are upregulated under nutrient deprivation in Chlamydomonas

“…In new work, Li et al (2023) show that AGO1 in C. reinhardtii preferentially binds sRNAs longer than >26 nt and that the expression of these sRNAs is induced under sulfur and nitrogen deprivation. The upregulation of these sRNAs coincides with the downregulation of expression of genes sharing sequence similarity, indicating a potential role of these sRNAs in nutrient stress response.…”

“…Location of genomic loci encoding AGO1-associated >26 nt sRNAs on Chlamydomonas chromosomes (bottom left) and immunoblot analyses of small RNAs isolated from the indicated strains and detected with probes specific for the most abundant >26 nt sRNAs (bottom right). Adapted from Li et al (2023 , Figures 2, 3, and 4).…”