Small RNA-guided gene silencing pathways in Chlamydomonas

H. Cerutti, F. Ibrahim, A. Casas-Mollano, E. J. Kim, J. Becker, X. Ma, and E. Balassa

Biological Sciences and Plant Science Initiative, University of Nebraska, Lincoln, NE 68588, USA

RNA interference (RNAi) is an evolutionarily conserved process that operates by a variety of molecular mechanisms. In multicellular eukaryotes, the core components of RNA-mediated silencing have significantly expanded and diversified resulting in partly distinct pathways for the epigenetic control of genomic parasites and the regulation of gene expression. The unicellular alga C. reinhardtii also shows extensive duplication of Dicer and Argonaute proteins (three copies of each). Two of these polypeptides, DICER-LIKE1 (DCL1) and ARGONAUTE1 (AGO1), appear to be uniquely involved in a siRNA-mediated pathway for the silencing of transposable elements. DCL1 and AGO1 are encoded by adjacent, divergently transcribed genes and their expression is also regulated post-transcriptionally by spliceosome components such as MUT6. However, Chlamydomonas also relies on a DCL1-independent, transcriptional silencing mechanism(s) for the maintenance of transposon repression. We speculate that multiple, partly independent epigenetic mechanisms may allow a more effective control of transposon mobilization over a wider range of environmental conditions. Another RNAi component, AGO3, appears to be involved in a microRNA-mediated pathway(s) that may regulate endogenous gene expression. Interestingly, miRNA biogenesis in Chlamydomonas has mechanistic similarities to that in higher eukaryotes, including the involvement of an Exportin-5 homolog. The steady-state levels of miRNAs are also affected by a noncanonical poly(A) polymerase (MUT68) and the RRP6 exosome subunit. We hypothesize that MUT68 and the RRP6 exosome subunit may be part of a quality control mechanism to eliminate aberrant or damaged small RNAs associated with the RNA induced silencing complex. Our findings suggest that functional diversification of RNAi components has occurred in Chlamydomonas but the biological role(s) of different RNAi pathways remains largely uncharacterized.

e-mail address of presenting author: hcerutti1@unl.edu